Identification of a Ubiquitin Related Genes Signature for Predicting Prognosis of Prostate Cancer

Background: Ubiquitin and ubiquitin-like (UB/UBL) conjugations are one of the most important post-translational modifications and involve in the occurrence of cancers. However, the biological function and clinical significance of ubiquitin related genes (URGs) in prostate cancer (PCa) are still unclear.Methods: The transcriptome data and clinicopathological data were downloaded from The Cancer Genome Atlas (TCGA), which was served as training cohort. The GSE21034 dataset was used to validate. The two datasets were removed batch effects and normalized using the “sva” R package. Univariate Cox, LASSO Cox, and multivariate Cox regression were performed to identify a URGs prognostic signature. Then Kaplan-Meier curve and receiver operating characteristic (ROC) curve analyses were used to evaluate the performance of the URGs signature. Thereafter, a nomogram was constructed and evaluated.Results: A six-URGs signature was established to predict biochemical recurrence (BCR) of PCa, which included ARIH2, FBXO6, GNB4, HECW2, LZTR1 and RNF185. Kaplan-Meier curve and ROC curve analyses revealed good performance of the prognostic signature in both training cohort and validation cohort. Univariate and multivariate Cox analyses showed the signature was an independent prognostic factor for BCR of PCa in training cohort. Then a nomogram based on the URGs signature and clinicopathological factors was established and showed an accurate prediction for prognosis in PCa.Conclusion: Our study established a URGs prognostic signature and constructed a nomogram to predict the BCR of PCa. This study could help with individualized treatment and identify PCa patients with high BCR risks.

Consolidation Tumor Ratio Combined With Pathological Features Could Predict Status of Lymph Nodes of Early-Stage Lung Adenocarcinoma

IntroductionStage IA lung adenocarcinoma manifested as part-solid nodules (PSNs), has attracted immense attention owing to its unique characteristics and the definition of its invasiveness remains unclear. We sought to develop a nomogram for predicting the status of lymph nodes of this kind of nodules.MethodsA total of 2,504 patients between September 2018 to October 2020 with part-solid nodules in our center were reviewed. Their histopathological features were extracted from paraffin sections, whereas frozen sections were reviewed to confirm the consistency of frozen sections and paraffin sections. Univariate and multivariate logistic regression analyses and Akaike information criterion (AIC) variable selection were performed to assess the risk factors of lymph node metastasis and construct the nomogram. The nomogram was subjected to bootstrap internal validation and external validation. The concordance index (C-index) was applied to evaluate the predictive accuracy and discriminative ability.ResultsWe enrolled 215 and 161 eligible patients in the training cohort and validation cohort, respectively. The sensitivity between frozen and paraffin sections on the presence of micropapillary/solid subtype was 78.4%. Multivariable analysis demonstrated that MVI, the presence of micropapillary/solid subtype, and CTR >0.61 were independently associated with lymph node metastasis (p < 0.01). Five risk factors were integrated into the nomogram. The nomogram demonstrated good accuracy in estimating the risk of lymph node metastasis, with a C-index of 0.945 (95% CI: 0.916–0.974) in the training cohort and a C-index of 0.975 (95% CI: 0.954–0.995) in the validation cohort. The model’s calibration was excellent in both cohorts.ConclusionThe nomogram established showed excellent discrimination and calibration and could predict the status of lymph nodes for patients with ≤3 cm PSNs. Also, this prediction model has the prediction potential before the end of surgery.

Real-Time Elastography: A Web-Based Nomogram Improves the Preoperative Prediction of Central Lymph Node Metastasis in cN0 PTC

BackgroundGiven the difficulty of accurately determining the central lymph node metastasis (CLNM) status of patients with clinically node-negative (cN0) papillary thyroid carcinoma (PTC) before surgery, this study aims to combine real-time elastography (RTE) and conventional ultrasound (US) features with clinical features. The information is combined to construct and verify the nomogram to foresee the risk of CLNM in patients with cN0 PTC and to develop a network-based nomogram.MethodsFrom January 2018 to February 2020, 1,157 consecutive cases of cN0 PTC after thyroidectomy and central compartment neck dissection were retrospectively analyzed. The patients were indiscriminately allocated (2:1) to a training cohort (771 patients) and validation cohort (386 patients). Multivariate logistic regression analysis of US characteristics and clinical information in the training cohort was performed to screen for CLNM risk predictors. RTE data were included to construct prediction model 1 but were excluded when constructing model 2. DeLong’s test was used to select a forecast model with better receiver operator characteristic curve performance to establish a web-based nomogram. The clinical applicability, discrimination, and calibration of the preferable prediction model were assessed.ResultsMultivariate regression analysis showed that age, sex, tumor size, bilateral tumors, the number of tumor contacting surfaces, chronic lymphocytic thyroiditis, and RTE were risk predictors of CLNM in cN0 PTC patients, which constituted prediction model 1. Model 2 included the first six risk predictors. Comparison of the areas under the curves of the two models showed that model 1 had better prediction performance (training set 0.798 vs. 0.733, validation set 0.792 vs. 0.715, p < 0.001) and good discrimination and calibration. RTE contributed significantly to the performance of the prediction model. Decision curve analysis showed that patients could obtain good net benefits with the application of model 1.ConclusionA noninvasive web-based nomogram combining US characteristics and clinical risk factors was developed in the research. RTE could improve the prediction accuracy of the model. The dynamic nomogram has good performance in predicting the probability of CLNM in cN0 PTC patients.

Prediction of distant metastasis of spinal and pelvic osteosarcoma by constructing and validating nomogram:a retrospective study based on SEER database

Background:Spinal and pelvic osteosarcoma is a rare type of all osteosarcomas,and distant metastasis is an important factor for poor prognosis of this disease. There are no similar studies on prediction of distant metastasis of spinal and pelvic osteosarcoma. We aim to construct and validate a nomogram to predict the risk of distant metastasis of spinal and pelvic osteosarcoma.Methods:We collected the data on patients with spinal and pelvic osteosarcoma from the Surveillance, Epidemiology, and End Results(SEER) database retrospectively. The Kaplan-Meier curve was used to compare differences in survival time between patients with metastasis and non-metastasis. Total patients were randomly divided into training cohort and validation cohort. The risk factor of distant metastasis were identified via the least absolute shrinkage and selection operator(LASSO) regression and multivariate logistic analysis. The nomogram we constructed were validated internally and externally by C-index, calibration curves,receiver operating characteristic(ROC) curve and Decision curve analysis (DCA).Results:The Kaplan-Meier curve showed that the survival time of non-metastatic patients was longer than that of metastatic patients(P＜0.001).All patients(n=358) were divided into training cohort(n=269) and validation cohort(n=89).The LASSO regression selected five meaningful variables in the training cohort. The multivariate logistic regression analysis demonstrated that surgery(yes,OR=0.175, 95%CI=0.095-0.321,p=0.000) was the independent risk factors for distant metastasis of patients with spinal and pelvic osteosarcoma. The C-index and calibration curves showed the good agreement between the predicted results and the actual results. The area under the receiver operating characteristic curve(AUC) values were 0.748(95%CI=0.687-0.817) and 0.758(95%CI=0.631-0.868) in the training and validation cohorts respectively. The DCA showed that the nomogram has a good clinical usefulness and net benefit.Conclusion:No surgery is the independent risk factor of distant metastasis of spinal and pelvic osteosarcoma. The nomogram we constructed to predict the probability of distant metastasis of patients with spinal and pelvic osteosarcoma is reliable and effective by internal and external verification.

A Web-Based Prediction Model for Cancer-Specific Survival of Elderly Patients With Early Hepatocellular Carcinoma: A Study Based on SEER Database

Background: Primary liver cancer is a common malignant tumor primarily represented by hepatocellular carcinoma (HCC). The number of elderly patients with early HCC is increasing, and older age is related to a worse prognosis. However, an accurate predictive model for the prognosis of these patients is still lacking.Methods: Data of eligible elderly patients with early HCC in Surveillance, Epidemiology, and End Results database from 2010 to 2016 were downloaded. Patients from 2010 to 2015 were randomly assigned to the training cohort (n = 1093) and validation cohort (n = 461). Patients' data in 2016 (n = 431) was used for external validation. Independent prognostic factors were obtained using univariate and multivariate analyses. Based on these factors, a cancer-specific survival (CSS) nomogram was constructed. The predictive performance and clinical practicability of our nomogram were validated. According to the risk scores of our nomogram, patients were divided into low-, intermediate-, and high-risk groups. A survival analysis was performed using Kaplan–Meier curves and log-rank tests.Results: Age, race, T stage, histological grade, surgery, radiotherapy, and chemotherapy were independent predictors for CSS and thus were included in our nomogram. In the training cohort and validation cohort, the concordance indices (C-indices) of our nomogram were 0.739 (95% CI: 0.714–0.764) and 0.756 (95% CI: 0.719–0.793), respectively. The 1-, 3-, and 5-year areas under receiver operating characteristic curves (AUCs) showed similar results. Calibration curves revealed high consistency between observations and predictions. In external validation cohort, C-index (0.802, 95%CI: 0.778–0.826) and calibration curves also revealed high consistency between observations and predictions. Compared with the TNM stage, nomogram-related decision curve analysis (DCA) curves indicated better clinical practicability. Kaplan–Meier curves revealed that CSS significantly differed among the three different risk groups. In addition, an online prediction tool for CSS was developed.Conclusions: A web-based prediction model for CSS of elderly patients with early HCC was constructed and validated, and it may be helpful for the prognostic evaluation, therapeutic strategy selection, and follow-up management of these patients.

A Predictive Model of Live Birth Based on Obesity and Metabolic Parameters in Patients With PCOS Undergoing Frozen-Thawed Embryo Transfer

AimsTo determine the clinical predictors of live birth in women with polycystic ovary syndrome (PCOS) undergoing frozen-thawed embryo transfer (F-ET), and to determine whether these parameters can be used to develop a clinical nomogram model capable of predicting live birth outcomes for these women.MethodsIn total, 1158 PCOS patients that were clinically pregnant following F-ET treatment were retrospectively enrolled in this study and randomly divided into the training cohort (n = 928) and the validation cohort (n = 230) at an 8:2 ratio. Relevant risk factors were selected via a logistic regression analysis approach based on the data from patients in the training cohort, and odds ratios (ORs) were calculated. A nomogram was constructed based on relevant risk factors, and its performance was assessed based on its calibration and discriminative ability.ResultsIn total, 20 variables were analyzed in the present study, of which five were found to be independently associated with the odds of live birth in univariate and multivariate logistic regression analyses, including advanced age, obesity, total cholesterol (TC), triglycerides (TG), and insulin resistance (IR). Having advanced age (OR:0.499, 95% confidence interval [CI]: 0.257 – 967), being obese (OR:0.506, 95% CI: 0.306 - 0.837), having higher TC levels (OR: 0.528, 95% CI: 0.423 - 0.660), having higher TG levels (OR: 0.585, 95% CI: 0.465 - 737), and exhibiting IR (OR:0.611, 95% CI: 0.416 - 0.896) were all independently associated with a reduced chance of achieving a live birth. A predictive nomogram incorporating these five variables was found to be well-calibrated and to exhibit good discriminatory capabilities, with an area under the curve (AUC) for the training group of 0.750 (95% CI, 0.709 - 0.788). In the independent validation cohort, this model also exhibited satisfactory goodness-of-fit and discriminative capabilities, with an AUC of 0.708 (95% CI, 0.615 - 0.781).ConclusionsThe nomogram developed in this study may be of value as a tool for predicting the odds of live birth for PCOS patients undergoing F-ET, and has the potential to improve the efficiency of pre-transfer management.

MRI-Based Random Survival Forest Model Improves the Prediction of Progression-Free Survival to Induction Chemotherapy plus Concurrent Chemoradiotherapy in Locoregionally Advanced Nasopharyngeal Carcinoma

BackgroundThe present study aimed to explore the application value of random survival forest (RSF) model and Cox model in predicting the progression-free survival (PFS) among patients with locoregionally advanced nasopharyngeal carcinoma (LANPC) after induction chemotherapy plus concurrent chemoradiotherapy (IC+CCRT).MethodsEligible LANPC patients underwent magnetic resonance imaging (MRI) scan before treatment were subjected to radiomics feature extraction. Radiomics and clinical features of patients in the training cohort were subjected to RSF analysis to predict PFS and were tested in the testing cohort. The performance of an RSF model with clinical and radiologic predictors was assessed with the area under the receiver operating characteristic (ROC) curve (AUC) and Delong test and compared with Cox models based on clinical and radiologic parameters. Further, the Kaplan-Meier method was used for risk stratification of patients.ResultsA total of 294 LANPC patients (206 in the training cohort; 88 in the testing cohort) were enrolled and underwent magnetic resonance imaging (MRI) scans before treatment. The AUC value of the clinical Cox model, radiomics Cox model, clinical + radiomics Cox model, and clinical + radiomics RSF model in predicting 3- and 5-year PFS for LANPC patients was [0.545 vs 0.648 vs 0.648 vs 0.899 (training cohort), and 0.566 vs 0.736 vs 0.73 vs 0.861 (testing cohort); 0.556 vs 0.604 vs 0.611 vs 0.897 (training cohort), and 0.591 vs 0.661 vs 0.676 vs 0.847 (testing cohort), respectively]. Delong test showed that the RSF model and the other three Cox models were statistically significant, and the RSF model markedly improved prediction performance (P<0.001). Additionally, the PFS of the high-risk group was lower than that of the low-risk group in the RSF model (P<0.001), while comparable in the Cox model (P>0.05).ConclusionThe RSF model may be a potential tool for prognostic prediction and risk stratification of LANPC patients.

Alpha-Fetoprotein Ratio Predicts Alpha-Fetoprotein Positive Hepatocellular Cancer Patient Prognosis after Hepatectomy

Background. This study was conducted to investigate the effect of alpha-fetoprotein (AFP) ratio on the prognosis of AFP-positive hepatocellular carcinoma (HCC) patients after hepatectomy. Methods. We retrospectively included 879 HCC patients with AFP-positive who underwent hepatectomy from February 2012 to October 2017 and randomly divided into training cohort and validation cohort. AFP ratio was equal to the AFP level within one week before hepatectomy to AFP level within 20-40 days after surgery. The end point of follow-up was disease-free survival (DFS) and overall survival (OS). Results. AFP ratio was not associated with clinical characteristics in training cohort and validation cohort. According to the X-tile software, the optimum cut-off point was 17.8 for AFP ratio. Significant differences between AFP ratio high and AFP ratio low were observed in DFS and OS in both cohort ( p < 0.05 ). Kaplan-Meier curves and receiver-operating curves were showed that AFP ratio was better than AFP level preoperation in predicting the prognosis of AFP-positive HCC patients after hepatectomy. The multivariate analysis demonstrated that AFP ratio was a significant independent risk factor for both OS and DFS in HCC patients with AFP-positive. Conclusions. AFP ratio might be a prognosis predictor for HCC patients with AFP-positive after hepatectomy.

Nomogram to Predict Intensive Care Following Gastrectomy for Gastric Cancer: A Useful Clinical Tool to Guide the Decision-Making of Intensive Care Unit Admission

BackgroundWe aimed to generate and validate a nomogram to predict patients most likely to require intensive care unit (ICU) admission following gastric cancer surgery to improve postoperative outcomes and optimize the allocation of medical resources.MethodsWe retrospectively analyzed 3,468 patients who underwent gastrectomy for gastric cancer from January 2009 to June 2018. Here, 70.0% of the patients were randomly assigned to the training cohort, and 30.0% were assigned to the validation cohort. Least absolute shrinkage and selection operator (LASSO) method was performed to screen out risk factors for ICU-specific care using the training cohort. Then, based on the results of LASSO regression analysis, multivariable logistic regression analysis was performed to establish the prediction nomogram. The calibration and discrimination of the nomogram were evaluated in the training cohort and validated in the validation cohort. Finally, the clinical usefulness was determined by decision curve analysis (DCA).ResultsAge, the American Society of Anesthesiologists (ASA) score, chronic pulmonary disease, heart disease, hypertension, combined organ resection, and preoperative and/or intraoperative blood transfusions were selected for the model. The concordance index (C-index) of the model was 0.843 in the training cohort and 0.831 in the validation cohort. The calibration curves of the ICU-specific care risk nomogram suggested great agreement in both training and validation cohorts. The DCA showed that the nomogram was clinically useful.ConclusionsAge, ASA score, chronic pulmonary disease, heart disease, hypertension, combined organ resection, and preoperative and/or intraoperative blood transfusions were identified as risk factors for ICU-specific care after gastric surgery. A clinically friendly model was generated to identify those most likely to require intensive care.

A combined risk model for the multi-encompassing identification of heterogeneities of prognoses, biological pathway variations and immune states for sepsis patients

Background Sepsis is a highly heterogeneous syndrome with stratified severity levels and immune states. Even in patients with similar clinical appearances, the underlying signal transduction pathways are significantly different. To identify the heterogeneities of sepsis from multiple angles, we aimed to establish a combined risk model including the molecular risk score for rapid mortality prediction, pathway risk score for the identification of biological pathway variations, and immunity risk score for guidance with immune-modulation therapy. Methods We systematically searched and screened the mRNA expression profiles of patients with sepsis in the Gene Expression Omnibus public database. The screened datasets were divided into a training cohort and a validation cohort. In the training cohort, authentic prognostic predictor characteristics (differentially expressed mRNAs, pathway activity variations and immune cells) were screened for model construction through bioinformatics analysis and univariate Cox regression, and a P value less than 0.05 of univariate Cox regression on 28-day mortality was set as the cut-off value. The combined risk model was finally established by the decision tree algorithm. In the validation cohort, the model performance was assessed and validated by C statistics and the area under the receiver operating characteristic curve (AUC). Additionally, the current models were further compared in clinical value with traditional indicators, including procalcitonin (PCT) and interleukin-8 (IL-8). Results Datasets from two sepsis cohort studies with a total of 585 consecutive sepsis patients admitted to two intensive care units were downloaded as the training cohort (n = 479) and external validation cohort (n = 106). In the training cohort, 15 molecules, 20 pathways and 4 immune cells were eventually enrolled in model construction. These prognostic factors mainly reflected hypoxia, cellular injury, metabolic disorders and immune dysregulation in sepsis patients. In the validation cohort, the AUCs of the molecular model, pathway model, immune model, and combined model were 0.81, 0.82, 0.62 and 0.873, respectively. The AUCs of the traditional biomarkers (PCT and IL-8) were 0.565 and 0.585, respectively. The survival analysis indicated that patients in the high-risk group identified by models in the current study had a poor prognosis (P < 0.05). The above results indicated that the models in this study are all superior to the traditional biomarkers for the predicting the prognosis of sepsis patients. Furthermore, the current study provides some therapeutic recommendations for patients with high risk scores identified by the three submodels. Conclusions In summary, the present study provides opportunities for bedside tests that could quantitatively and rapidly measure heterogeneous prognosis, underlying biological pathway variations and immune dysfunction in sepsis patients. Further therapeutic recommendations for patients with high risk scores could improve the therapeutic system for sepsis.