Development and verification of a nomogram for prediction of recurrence-free survival in clear cell renal cell carcinoma

Prognostic significance of Naples prognostic score in operable renal cell carcinoma

Background

Naples prognostic score (NPS), a novel scoring system based on nutritional and inflammatory status, is associated with prognosis in several cancers. This study aimed to evaluate the prognostic significance of preoperative NPS in patients undergoing nephrectomy.

Patients and Methods

This study retrospectively analyzed patients with renal cell carcinoma (RCC) who underwent radical or partial nephrectomy between 2010 and 2013. The clinicopathological characteristics of patients stratified by preoperative NPS were compared. Survival analysis was performed using the Kaplan–Meier method and log-rank test. Univariate and multivariate Cox proportional hazards models were used to identify independent prognostic factors. Receiver operating characteristic curves were used to evaluate prediction efficiency.

Results

A total of 638 patients with operable RCC were included. The high-NPS group (NPS group 2) was significantly associated with older age (P < 0.001), larger tumor size (P < 0.001), worse pathological T stage (P < 0.001), positive lymph node pathology (P = 0.002), higher tumor grade (P < 0.001), and greater tumor necrosis (P < 0.001). Multivariable analysis demonstrated that the high-NPS subgroup had significantly worse overall survival (OS) [hazard ratio (HR): 2.25, 95% confidence interval (CI): 1.45–3.50, P < 0.001] and progression-free survival (PFS) (HR: 2.26, 95% CI: 1.48–3.44, P < 0.001). Among several preoperative scoring systems, NPS had the strongest discriminatory power for predicting OS and PFS.

Conclusion

Preoperative NPS can serve as a simple novel risk stratification tool to optimize the prognosis of patients with operable RCC. Further prospective and large-scale studies are needed to validate our findings.

A Simple Weaning Model Based on Interpretable Machine Learning Algorithm for Patients With Sepsis: A Research of MIMIC-IV and eICU Databases

Background

Invasive mechanical ventilation plays an important role in the prognosis of patients with sepsis. However, there are, currently, no tools specifically designed to assess weaning from invasive mechanical ventilation in patients with sepsis. The aim of our study was to develop a practical model to predict weaning in patients with sepsis.

Methods

We extracted patient information from the Medical Information Mart for Intensive Care Database-IV (MIMIC-IV) and the eICU Collaborative Research Database (eICU-CRD). Kaplan–Meier curves were plotted to compare the 28-day mortality between patients who successfully weaned and those who failed to wean. Subsequently, MIMIC-IV was divided into a training set and an internal verification set, and the eICU-CRD was designated as the external verification set. We selected the best model to simplify the internal and external validation sets based on the performance of the model.

Results

A total of 5020 and 7081 sepsis patients with invasive mechanical ventilation in MIMIC-IV and eICU-CRD were included, respectively. After matching, weaning was independently associated with 28-day mortality and length of ICU stay (p &lt; 0.001 and p = 0.002, respectively). After comparison, 35 clinical variables were extracted to build weaning models. XGBoost performed the best discrimination among the models in the internal and external validation sets (AUROC: 0.80 and 0.86, respectively). Finally, a simplified model was developed based on XGBoost, which included only four variables. The simplified model also had good predictive performance (AUROC:0.75 and 0.78 in internal and external validation sets, respectively) and was developed into a web-based tool for further review.

Conclusions

Weaning success is independently related to short-term mortality in patients with sepsis. The simplified model based on the XGBoost algorithm provides good predictive performance and great clinical applicablity for weaning, and a web-based tool was developed for better clinical application.

Profiles of overall survival-related gene expression-based risk signature and their prognostic implications in clear cell renal cell carcinoma

The present work aimed to evaluate the prognostic value of overall survival (OS)-related genes in clear cell renal cell carcinoma (ccRCC) and to develop a nomogram for clinical use. Transcriptome data from The Cancer Genome Atlas (TCGA) were collected to screen differentially expressed genes (DEGs) between ccRCC patients with OS > 5 years (149 patients) and those with <1 year (52 patients). In TCGA training set (265 patients), seven DEGs (cytochrome P450 family 3 subfamily A member 7 (CYP3A7), contactin-associated protein family member 5 (CNTNAP5), adenylate cyclase 2 (ADCY2), TOX high mobility group box family member 3 (TOX3), plasminogen (PLG), enamelin (ENAM), and collagen type VII α 1 chain (COL7A1)) were further selected to build a prognostic risk signature by the least absolute shrinkage and selection operator (LASSO) Cox regression model. Survival analysis confirmed that the OS in the high-risk group was dramatically shorter than their low-risk counterparts. Next, univariate and multivariate Cox regression revealed the seven genes-based risk score, age, and Tumor, lymph Node, and Metastasis staging system (TNM) stage were independent prognostic factors to OS, based on which a novel nomogram was constructed and validated in both TCGA validation set (265 patients) and the International Cancer Genome Consortium cohort (ICGC, 84 patients). A decent predictive performance of the nomogram was observed, the C-indices and corresponding 95% confidence intervals of TCGA training set, validation set, and ICGC cohort were 0.78 (0.74–0.82), 0.75 (0.70–0.80), and 0.70 (0.60–0.80), respectively. Moreover, the calibration plots of 3- and 5 years survival probability indicated favorable curve-fitting performance in the above three groups. In conclusion, the proposed seven genes signature-based nomogram is a promising and robust tool for predicting the OS of ccRCC, which may help tailor individualized therapeutic strategies.

Prognostic Score-based Clinical Factors and Metabolism-related Biomarkers for Predicting the Progression of Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is a common malignant tumor representing more than 90% of primary liver cancer. This study aimed to identify metabolism-related biomarkers with prognostic value by developing the novel prognostic score (PS) model. Transcriptomic profiles derived from TCGA and EBIArray databases were analyzed to identify differentially expressed genes (DEGs) in HCC tumor samples compared with normal samples. The overlapped genes between DEGs and metabolism-related genes (crucial genes) were screened and functionally analyzed. A novel PS model was constructed to identify optimal signature genes. Cox regression analysis was performed to identify independent clinical factors related to prognosis. Nomogram model was constructed to estimate the predictability of clinical factors. Finally, protein expression of crucial genes was explored in different cancer tissues and cell types from the Human Protein Atlas (HPA). We screened a total of 305 overlapped genes (differentially expressed metabolism-related genes). These genes were mainly involved in "oxidation reduction," "steroid hormone biosynthesis," "fatty acid metabolic process," and "linoleic acid metabolism." Furthermore, we screened ten optimal DEGs (CYP2C9, CYP3A4, and TKT, among others) by using the PS model. Two clinical factors of pathologic stage (P < .001, HR: 1.512 [1.219-1.875]) and PS status (P <.001, HR: 2.259 [1.522-3.354]) were independent prognostic predictors by cox regression analysis. Nomogram model showed a high predicted probability of overall survival time, and the AUC value was 0.837. The expression status of 7 proteins was frequently altered in normal or differential tumor tissues, such as liver cancer and stomach cancer samples.We have identified several metabolism-related biomarkers for prognosis prediction of HCC based on the PS model. Two clinical factors were independent prognostic predictors of pathologic stage and PS status (high/low risk). The prognosis prediction model described in this study is a useful and stable method for novel biomarker identification.

Construction and validation of a seven-gene signature for predicting overall survival in patients with kidney renal clear cell carcinoma via an integrated bioinformatics analysis

Kidney renal clear cell carcinoma (KIRC) remains a significant challenge worldwide because of its poor prognosis and high mortality rate, and accurate prognostic gene signatures are urgently required for individual therapy. This study aimed to construct and validate a seven-gene signature for predicting overall survival (OS) in patients with KIRC. The mRNA expression profile and clinical data of patients with KIRC were obtained from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC). Prognosis-associated genes were identified, and a prognostic gene signature was constructed. Then, the prognostic efficiency of the gene signature was assessed. The results obtained using data from the TCGA were validated using those from the ICGC and other online databases. Gene set enrichment analyses (GSEA) were performed to explore potential molecular mechanisms. A seven-gene signature (PODXL, SLC16A12, ZIC2, ATP2B3, KRT75, C20orf141, and CHGA) was constructed, and it was found to be effective in classifying KIRC patients into high- and low-risk groups, with significantly different survival based on the TCGA and ICGC validation data set. Cox regression analysis revealed that the seven-gene signature had an independent prognostic value. Then, we established a nomogram, including the seven-gene signature, which had a significant clinical net benefit. Interestingly, the seven-gene signature had a good performance in distinguishing KIRC from normal tissues. GSEA revealed that several oncological signatures and GO terms were enriched. This study developed a novel seven-gene signature and nomogram for predicting the OS of patients with KIRC, which may be helpful for clinicians in establishing individualized treatments.

Development and verification of a nomogram for prediction of recurrence-free survival in clear cell renal cell carcinoma

Nowadays, gene expression profiling has been widely used in screening out prognostic biomarkers in numerous kinds of carcinoma. Our studies attempt to construct a clinical nomogram which combines risk gene signature and clinical features for individual recurrent risk assessment and offer personalized managements for clear cell renal cell carcinoma. A total of 580 differentially expressed genes (DEGs) were identified via microarray. Functional analysis revealed that DEGs are of fundamental importance in ccRCC progression and metastasis. In our study, 338 ccRCC patients were retrospectively analysed and a risk gene signature which composed of 5 genes was obtained from a LASSO Cox regression model. Further analysis revealed that identified risk gene signature could usefully distinguish the patients with poor prognosis in training cohort (hazard ratio [HR] = 3.554, 95% confidence interval [CI] 2.261‐7.472, P < .0001, n = 107). Moreover, the prognostic value of this gene‐signature was independent of clinical features (P = .002). The efficacy of risk gene signature was verified in both internal and external cohorts. The area under receiver operating characteristic curve of this signature was 0.770, 0.765 and 0.774 in the training, testing and external validation cohorts, respectively. Finally, a nomogram was developed for clinicians and did well in the calibration plots. This nomogram based on risk gene signature and clinical features might provide a practical way for recurrence prediction and facilitating personalized managements of ccRCC patients after surgery.