Dataset Information

LncRNAs classifier to accurately predict the recurrence of thymic epithelial tumors.

ABSTRACT: BACKGROUND:Long non-coding RNAs (lncRNAs), which have little or no ability to encode proteins, have attracted special attention due to their potential role in cancer disease. In this study we aimed to establish a lncRNAs classifier to improve the accuracy of recurrence prediction for thymic epithelial tumors (TETs). METHODS:TETs RNA sequencing (RNA-seq) data set and the matched clinicopathologic information were downloaded from the Cancer Genome Atlas. Using univariate Cox regression and least absolute shrinkage and selection operator (LASSO) analysis, we developed a lncRNAs classifier related to recurrence. Functional analysis was conducted to investigate the potential biological processes of the lncRNAs target genes. The independent prognostic factors were identified by Cox regression model. Additionally, predictive ability and clinical application of the lncRNAs classifier were assessed, and compared with the Masaoka staging by receiver operating characteristic (ROC) analysis and decision curve analysis (DCA). RESULTS:Four recurrence-free survival (RFS)-related lncRNAs were identified, and the classifier consisting of the identified four lncRNAs was able to effectively divide the patients into high and low risk subgroups, with an area under curve (AUC) of 0.796 (three-year RFS) and 0.788 (five-year RFS), respectively. Multivariate analysis indicated that the lncRNAs classifier was an independent recurrence risk factor. The AUC of the lncRNAs classifier in predicting RFS was significantly higher than the Masaoka staging system. Decision curve analysis further demonstrated that the lncRNAs classifier had a larger net benefit than the Masaoka staging system. CONCLUSIONS:A lncRNAs classifier for patients with TETs was an independent risk factor for RFS despite other clinicopathologic variables. It generated more accurate estimations of the recurrence probability when compared to the Masaoka staging system, but additional data is required before it can be used in clinical practice.

SUBMITTER: Su Y

PROVIDER: S-EPMC7327696 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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lncRNAs classifier to accurately predict the recurrence of thymic epithelial tumors.

Su Yongchao Y Chen Yongbing Y Tian Zuochun Z Lu Chuangang C Chen Liang L Ma Ximiao X

Thoracic cancer 20200506 7

<h4>Background</h4>Long non-coding RNAs (lncRNAs), which have little or no ability to encode proteins, have attracted special attention due to their potential role in cancer disease. In this study we aimed to establish a lncRNAs classifier to improve the accuracy of recurrence prediction for thymic epithelial tumors (TETs).<h4>Methods</h4>TETs RNA sequencing (RNA-seq) data set and the matched clinicopathologic information were downloaded from the Cancer Genome Atlas. Using univariate Cox regress ...[more]

PMID: 32374079

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Project description:Long non-coding RNAs (lncRNAs) which have little or no protein-coding capacity, due to their potential roles in the cancer disease, caught a particular interest. Our study aims to develop an lncRNAs-based classifier and a nomogram incorporating the lncRNAs classifier and clinicopathologic factors to help to improve the accuracy of recurrence prediction for head and neck squamous cell carcinoma (HNSCC) patients. The HNSCC lncRNAs profiling data and the corresponding clinicopathologic information were downloaded from TANRIC database and cBioPortal. Using univariable Cox regression and Least absolute shrinkage and selection operator (LASSO) analysis, we developed 15-lncRNAs-based classifier related to recurrence. On the basis of multivariable Cox regression analysis results, a nomogram integrating the genomic and clinicopathologic predictors was built. The predictive accuracy and discriminative ability of the inclusive nomogram were confirmed by calibration curve and a concordance index (C-index), and compared with TNM stage system by C-index, receiver operating characteristic (ROC) analysis. Decision curve analysis (DCA) was conducted to evaluate clinical value of our nomogram. Consequently, fifteen recurrence-free survival (RFS) -related lncRNAs were identified, and the classifier consisting of the established 15 lncRNAs could effectively divide patients into high-risk and low-risk subgroup. The prediction ability of the 15-lncRNAs-based classifier for predicting 3- year and 5-year RFS were 0.833 and 0.771. Independent factors derived from multivariable analysis to predict recurrence were number of positive LNs, margin status, mutation count and lncRNAs classifier, which were all embedded into the nomogram. The calibration curve for the recurrence probability showed that the predictions based on the nomogram were in good coincide with practical observations. The C-index of the nomogram was 0.76 (0.72-0.79), and the area under curve (AUC) of nomogram in predicting RFS was 0.809, which were significantly higher than traditional TNM stage and 15-lncRNAs-based classifier. Decision curve analysis further demonstrated that our nomogram had larger net benefit than TNM stage and 15-lncRNAs-based classifier. The results were confirmed externally. In summary, a visually inclusive nomogram for patients with HNSCC, comprising genomic and clinicopathologic variables, generates more accurate prediction of the recurrence probability when compared TNM stage alone, but more additional data remains needed before being used in clinical practice.

Project description:In the present study, we aimed to construct a radiomics model using contrast‑enhanced computed tomography (CT) to predict the pathological invasiveness of thymic epithelial tumors (TETs). We retrospectively reviewed the records of 179 consecutive patients (89 females) with histologically confirmed TETs from two hospitals. The 82 low‑ and 97 high‑risk TETs were assigned to training (90 tumors), internal validation (49 tumors) and external validation (40 tumors) cohorts. Radiomics features extracted from preoperative contrast‑enhanced chest CT were selected using least absolute shrinkage and selection operator logistic regression. Three prediction models were developed using multivariate logistic regression analysis. Their performance and clinical utility were assessed using receiver operating characteristic curves and the DeLong test, respectively. Eight radiomics features with non‑zero coefficients were used to develop a radiomics score, which significantly differed between low‑ and high‑risk TETs (P<0.001). The subjective finding, infiltration, was independently associated with high‑risk TETs. Prediction models based on infiltration alone, the radiomics signature alone, and both these parameters showed diagnostic accuracies of 72.2% [area under curve (AUC), 0.731; 95% confidence interval (CI): 0.627‑0.819; sensitivity, 85.7%; specificity, 60.4%], 88.9% (AUC, 0.944; 95% CI: 0.874‑0.981; sensitivity, 92.9%; specificity, 85.4%), and 90.0% (AUC, 0.953; 95% CI: 0.887‑0.987; sensitivity, 92.9%; specificity, 87.5%), respectively. Decision‑curve analysis showed that the combined model added more net benefit than the single‑parameter models. In conclusion, a radiomics signature based on contrast‑enhanced CT has the potential to differentiate between low‑ and high‑risk TETs. The model incorporating the radiomics signature and subjective finding may facilitate the individualized, preoperative prediction of the pathological invasiveness of TETs.

Dataset Information

LncRNAs classifier to accurately predict the recurrence of thymic epithelial tumors.

Publications

lncRNAs classifier to accurately predict the recurrence of thymic epithelial tumors.

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