A CT-Based Radiomics Nomogram Integrated With Clinic-Radiological Features for Preoperatively Predicting WHO/ISUP Grade of Clear Cell Renal Cell Carcinoma

Machine learning-based multiparametric MRI radiomics nomogram for predicting WHO/ISUP nuclear grading of clear cell renal cell carcinoma

Objective

To explore the effectiveness of a machine learning-based multiparametric MRI radiomics nomogram for predicting the WHO/ISUP nuclear grading of clear cell renal cell carcinoma (ccRCC) before surgery.

Methods

Data from 86 patients who underwent preoperative renal MRI scans (both plain and enhanced) and were confirmed to have ccRCC were retrospectively collected. Based on the 2016 WHO/ISUP grading standards, patients were divided into a low-grade group (Grade I and II) and a high-grade group (Grade III and IV), and randomly split into training and testing sets at a 7:3 ratio. Radiomics features were extracted from FS-T2WI, DWI, and CE-T1WI sequences. Optimal features were selected using the Mann-Whitney U test, Spearman correlation analysis, and the least absolute shrinkage and selection operator (LASSO). Five machine learning classifiers-logistic regression (LR), naive bayes (NB), k-nearest neighbors (KNN), adaptive boosting (AdaBoost), and multilayer perceptron (MLP)-were used to build models to predict ccRCC WHO/ISUP nuclear grading. The model with the highest area under the curve (AUC) in the testing set was chosen as the best radiomics model. Independent clinical risk factors were identified using univariate and multivariate logistic regression to create a clinical model, which was combined with radiomics score (rad-score) to develop a nomogram. The model's effectiveness was assessed using the receiver operating characteristic (ROC) curve, its calibration was evaluated using a calibration curve, and its clinical utility was analyzed using decision curve analysis.

Results

Six radiomics features were ultimately selected. The MLP classifier showed the highest diagnostic performance in the testing set (AUC=0.933). Corticomedullary enhancement level (P=0.020) and renal vein invasion (P=0.011) were identified as independent risk factors for predicting the WHO/ISUP nuclear classification and were included in the nomogram with the rad-score. The ROC curves indicated that the nomogram model had strong diagnostic performance, with AUC values of 0.964 in the training set and 0.933 in the testing set.

Conclusion

The machine learning-based multiparametric MRI radiomics nomogram provides a highly predictive, non-invasive tool for preoperative prediction of WHO/ISUP nuclear grading in patients with ccRCC.

Multiparameter computed tomography (CT) radiomics signature fusion-based model for the preoperative prediction of clear cell renal cell carcinoma nuclear grade: a multicenter development and external validation study

Background

The preoperative prediction of the pathological nuclear grade of clear cell renal cell carcinoma (CCRCC) is crucial for clinical decision making. However, radiomics features from one or two computed tomography (CT) phases are required to predict the CCRCC grade, which reduces the predictive performance and generalizability of this method. We aimed to develop and externally validate a multiparameter CT radiomics-based model for predicting the World Health Organization/International Society of Urological Pathology (WHO/ISUP) grade of CCRCC.

Methods

A total of 500 CCRCC patients at The First, Second, and Yongchuan Hospitals of Chongqing Medical University between January 2016 and May 2022 were retrospectively enrolled in this study. The patients were divided into the training set (n=268), internal testing set (n=115), and two external testing sets (testing set 1, n=62; testing set 2, n=55). Radiomics features were extracted from multi-phase CT images, and radiomics signatures (RSs) were created by least absolute shrinkage and selection operator (LASSO) regression. In addition, a clinical model was developed. A combined model was also established that integrated the RSs with the clinical factors, and was visualized via a nomogram. The performance of the established model was assessed using area under the curve (AUC) values, a calibration curve analysis, and a decision curve analysis (DCA).

Results

Among the four RSs and the clinical model, the RS-Triphasic had the best predictive performance with AUCs of 0.88 [95% confidence interval (CI): 0.85-0.91] and 0.84 (95% CI: 0.74-0.95) in the training and testing sets, respectively, and 0.82 (95% CI: 0.72-0.93) and 0.82 (95% CI: 0.71-0.93) in external testing sets 1 and 2. Integrating the RS-Triphasic, RS-corticomedullary phase (CMP), RS-nephrographic phase (NP), RS-non-contrast phase (NCP) with the clinical risk factors, a combined model was established with AUCs of 0.92 (95% CI: 0.89-0.94), 0.86 (95% CI: 0.76-0.95), 0.84 (95% CI: 0.73-0.95), and 0.82 (95% CI: 0.70-0.94) for the training, internal testing, and external testing sets 1 and 2, respectively. The DCA indicated that the nomogram had a greater overall net benefit than the clinical and radiomics models.

Conclusions

The multiparameter CT RS fusion-based model had high accuracy in differentiating between high- and low-grade CCRCC preoperatively. Thus, it has great potential as a useful tool for personalized treatment planning and clinical decision making for CCRCC patients.

Sub-regional Radiomics Analysis for Predicting Metastasis Risk in Clear Cell Renal Cell Carcinoma: A Multicenter Retrospective Study

RATIONALE AND OBJECTIVES

Clear cell renal cell carcinoma (ccRCC) is the most common malignant neoplasm affecting the kidney, exhibiting a dismal prognosis in metastatic instances. Elucidating the composition of ccRCC holds promise for the discovery of highly sensitive biomarkers. Our objective was to utilize habitat imaging techniques and integrate multimodal data to precisely predict the risk of metastasis, ultimately enabling early intervention and enhancing patient survival rates.

MATERIAL AND METHODS

A retrospective analysis was performed on a cohort of 263 patients with ccRCC from three hospitals between April 2013 and March 2021. Preoperative CT images, ultrasound images, and clinical data were comprehensively analyzed. Patients from two campuses of Qilu Hospital of Shandong University were assigned to the training dataset, while the third hospital served as the independent testing dataset. A robust consensus clustering method was used to classify the primary tumor space into distinct sub-regions (i.e., habitats) using contrast-enhanced CT images. Radiomic features were extracted from these tumor sub-regions and subsequently reduced to identify meaningful features for constructing a predictive model for ccRCC metastasis risk assessment. In addition, the potential value of radiomics in predicting ccRCC metastasis risk was explored by integrating ultrasound image features and clinical data to construct and compare alternative models.

RESULTS

In this study, we performed k-means clustering within the tumor region to generate three distinct tumor subregions. We quantified the Hounsfiled Unit (HU) value, volume fraction, and distribution of high- and low-risk groups in each subregion. Our investigation focused on 252 patients with Habitat1 + Habitat3 to assess the discriminative power of these two subregions. We then developed a risk prediction model for ccRCC metastasis risk classification based on radiomic features extracted from CT and ultrasound images, and clinical data. The Combined model and the CT_Habitat3 model showed AUC values of 0.935 [95%CI: 0.902-0.968] and 0.934 [95%CI: 0.902-0.966], respectively, in the training dataset, while in the independent testing dataset, they achieved AUC values of 0.891 [95%CI: 0.794-0.988] and 0.903 [95%CI: 0.819-0.987], respectively.

CONCLUSION

We have identified a non-invasive imaging predictor and the proposed sub-regional radiomics model can accurately predict the risk of metastasis in ccRCC. This predictive tool has potential for clinical application to refine individualized treatment strategies for patients with ccRCC.

Multimodal data integration using machine learning to predict the risk of clear cell renal cancer metastasis: a retrospective multicentre study

PURPOSE

To develop and validate a predictive combined model for metastasis in patients with clear cell renal cell carcinoma (ccRCC) by integrating multimodal data.

MATERIALS AND METHODS

In this retrospective study, the clinical and imaging data (CT and ultrasound) of patients with ccRCC confirmed by pathology from three tertiary hospitals in different regions were collected from January 2013 to January 2023. We developed three models, including a clinical model, a radiomics model, and a combined model. The performance of the model was determined based on its discriminative power and clinical utility. The evaluation indicators included area under the receiver operating characteristic curve (AUC) value, accuracy, sensitivity, specificity, negative predictive value, positive predictive value and decision curve analysis (DCA) curve.

RESULTS

A total of 251 patients were evaluated. Patients (n = 166) from Shandong University Qilu Hospital (Jinan) were divided into the training cohort, of which 50 patients developed metastases; patients (n = 37) from Shandong University Qilu Hospital (Qingdao) were used as internal testing, of which 15 patients developed metastases; patients (n = 48) from Changzhou Second People's Hospital were used as external testing, of which 13 patients developed metastases. In the training set, the combined model showed the highest performance (AUC, 0.924) in predicting lymph node metastasis (LNM), while the clinical and radiomics models both had AUCs of 0.845 and 0.870, respectively. In the internal testing, the combined model had the highest performance (AUC, 0.877) for predicting LNM, while the AUCs of the clinical and radiomics models were 0.726 and 0.836, respectively. In the external testing, the combined model had the highest performance (AUC, 0.849) for predicting LNM, while the AUCs of the clinical and radiomics models were 0.708 and 0.804, respectively. The DCA curve showed that the combined model had a significant prediction probability in predicting the risk of LNM in ccRCC patients compared with the clinical model or the radiomics model.

CONCLUSION

The combined model was superior to the clinical and radiomics models in predicting LNM in ccRCC patients.

Radiogenomics uncovers an interplay between angiogenesis and clinical outcomes in bladder cancer

BACKGROUND

Precision medicine has become a promising clinical treatment strategy for various cancers, including bladder cancer, where angiogenesis plays a critical role in cancer progression. However, the relationship between angiogenesis, immune cell infiltration, clinical outcomes, chemotherapy, and targeted therapy remains unclear.

METHODS

We conducted a comprehensive evaluation of angiogenesis-related genes (ARGs) to identify their association with immune cell infiltration, transcription patterns, and clinical outcomes in bladder cancer. An ARG score was constructed to identify angiogenic subgroups in each sample and we evaluated their predictive performance for overall survival rate and treatment response. In addition, we optimized existing clinical detection protocols by performing image data processing.

RESULTS

Our study revealed the genomic-level mutant landscape and expression patterns of ARGs in bladder cancer specimens. Using analysis, we identified three molecular subgroups where ARG mutations correlated with patients' pathological features, clinical outcomes, and immune cell infiltration. To facilitate clinical applicability, we constructed a precise nomogram based on the ARG score, which significantly correlated with stem cell index and drug sensitivity. Finally, we proposed the radiogenomics model, which combines the precision of genomics with the convenience of radiomics.

CONCLUSION

Our study sheds light on the prognostic characteristics of ARGs in bladder cancer and provides insights into the tumor environment's characteristics to explore more effective immunotherapy strategies. The findings have significant implications for the development of personalized treatment approaches in bladder cancer and pave the way for future studies in this field.

A computed tomography urography-based machine learning model for predicting preoperative pathological grade of upper urinary tract urothelial carcinoma

OBJECTIVES

Development and validation of a computed tomography urography (CTU)-based machine learning (ML) model for prediction of preoperative pathology grade of upper urinary tract urothelial carcinoma (UTUC).

METHODS

A total of 140 patients with UTUC who underwent CTU examination from January 2017 to August 2023 were retrospectively enrolled. Tumor lesions on the unenhanced, medullary, and excretory periods of CTU were used to extract Features, respectively. Feature selection was screened by the Pearson and Spearman correlation analysis, least absolute shrinkage and selection operator algorithm, random forest (RF), support vector machine (SVM), and eXtreme Gradient Boosting (XGBoost). The logistic regression (LR) was used to screen for independent influencing factors of clinical baseline characteristics. Machine learning models based on different feature datasets were constructed and validated using algorithms such as LR, RF, SVM, and XGBoost. By computing the selected features, a radiomics score was generated, and a diverse feature dataset was constructed. Based on the training set, 16 ML models were created, and their performance was evaluated using the validation set for metrics including sensitivity, specificity, accuracy, area under the receiver operating characteristic curve (AUC), and others.

RESULTS

The training set consisted of 98 patients (mean age: 64.5 ± 10.5 years; 30 males), whereas the validation set consisted of 42 patients (mean age: 65.3 ± 9.78 years; 17 males). Hydronephrosis was the best independent influence factor (p < 0.05). The RF model had the best performance in predicting high-grade UTUC, with AUC of 0.914 (95% Confidence Interval [95%CI] 0.852-0.977) and 0.903 (95%CI 0.809-0.997) in the training set and validation set, and accuracy of 0.878 and 0.857, respectively.

CONCLUSIONS

An ML model based on the RF algorithm exhibits excellent predictive performance, offering a non-invasive approach for predicting preoperative high-grade UTUC.

Collateral vessels on preoperative enhanced computed tomography for predicting pathological grade of clear cell renal cell carcinoma: A retrospective study

OBJECTIVES

To retrospectively evaluate the association between the presence of collateral vessels and grade of clear cell renal cell carcinoma (ccRCC) and whether the presence of collateral vessels could serve as a predictor to differentiate high- and low-grade ccRCC.

MATERIALS AND METHODS

From May 2018 to September 2022, a total of 160 ccRCC patients with pathological diagnosis were enrolled in this study. Patients were divided into a high-grade group and a low-grade group according to World Health Organization/International Society of Urological Pathology (WHO/ISUP) grading system. The significant variables were extracted based on the univariate analyses using Student t test, Mann-Whitney U test, Chi-square test or Fisher's exact test. Multivariate logistic regression analyses were performed to determine independent factors among extracted variables. We calculated the sensitivity, specificity and their 95% confidence intervals (CI) of collateral vessels for predicting high WHO/ISUP grade to quantify its predictive performance. Furthermore, to investigate the additional predictive contribution of collateral vessels, a primary model and a control model were constructed to predict WHO/ISUP grade. The primary model included all extracted significant variables and the control model included significant variables except collateral vessels.

RESULTS

The proportion of ccRCC patients with collateral vessels was significantly larger in high-grade ccRCC than those in low-grade ccRCC (87.5 % vs. 26.8 %, P < 0.001). Multivariate logistic regression analyses showed that the presence of collateral vessels was an independent predictor for high WHO/ISUP grade (P < 0.001). The sensitivity and specificity of the presence of collateral vessels for differentiating high- and low-grade ccRCC were 87.5 % (95 % CI 0.753-0.941) and 73.2 % (95 % CI 0.643-0.806) respectively. Including collateral vessels in predictive model improves predictive performance for WHO/ISUP grade, increasing the area under the curve (AUC) value from 0.889 to 0.914.

CONCLUSION

The presence of collateral vessels has high sensitivity and specificity for differentiating high- and low-grade ccRCC and can improve the predictive performance for high WHO/ISUP grade.

Multiphase CT radiomics nomogram for preoperatively predicting the WHO/ISUP nuclear grade of small (< 4 cm) clear cell renal cell carcinoma

BACKGROUND

Small (< 4 cm) clear cell renal cell carcinoma (ccRCC) is the most common type of small renal cancer and its prognosis is poor. However, conventional radiological characteristics obtained by computed tomography (CT) are not sufficient to predict the nuclear grade of small ccRCC before surgery.

METHODS

A total of 113 patients with histologically confirmed ccRCC were randomly assigned to the training set (n = 67) and the testing set (n = 46). The baseline and CT imaging data of the patients were evaluated statistically to develop a clinical model. A radiomics model was created, and the radiomics score (Rad-score) was calculated by extracting radiomics features from the CT images. Then, a clinical radiomics nomogram was developed using multivariate logistic regression analysis by combining the Rad-score and critical clinical characteristics. The receiver operating characteristic (ROC) curve was used to evaluate the discrimination of small ccRCC in both the training and testing sets.

RESULTS

The radiomics model was constructed using six features obtained from the CT images. The shape and relative enhancement value of the nephrographic phase (REV of the NP) were found to be independent risk factors in the clinical model. The area under the curve (AUC) values for the training and testing sets for the clinical radiomics nomogram were 0.940 and 0.902, respectively. Decision curve analysis (DCA) revealed that the radiomics nomogram model was a better predictor, with the highest degree of coincidence.

CONCLUSION

The CT-based radiomics nomogram has the potential to be a noninvasive and preoperative method for predicting the WHO/ISUP grade of small ccRCC.

Application of DCE-MRI radiomics signature analysis in differentiating molecular subtypes of luminal and non-luminal breast cancer

Background

The goal of this study was to develop and validate a radiomics signature based on dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) preoperatively differentiating luminal and non-luminal molecular subtypes in patients with invasive breast cancer.

Methods

One hundred and thirty-five invasive breast cancer patients with luminal (n = 78) and non-luminal (n = 57) molecular subtypes were divided into training set (n = 95) and testing set (n = 40) in a 7:3 ratio. Demographics and MRI radiological features were used to construct clinical risk factors. Radiomics signature was constructed by extracting radiomics features from the second phase of DCE-MRI images and radiomics score (rad-score) was calculated. Finally, the prediction performance was evaluated in terms of calibration, discrimination, and clinical usefulness.

Results

Multivariate logistic regression analysis showed that no clinical risk factors were independent predictors of luminal and non-luminal molecular subtypes in invasive breast cancer patients. Meanwhile, the radiomics signature showed good discrimination in the training set (AUC, 0.86; 95% CI, 0.78-0.93) and the testing set (AUC, 0.80; 95% CI, 0.65-0.95).

Conclusion

The DCE-MRI radiomics signature is a promising tool to discrimination luminal and non-luminal molecular subtypes in invasive breast cancer patients preoperatively and noninvasively.

Deep learning and radiomic feature-based blending ensemble classifier for malignancy risk prediction in cystic renal lesions

BACKGROUND

The rising prevalence of cystic renal lesions (CRLs) detected by computed tomography necessitates better identification of the malignant cystic renal neoplasms since a significant majority of CRLs are benign renal cysts. Using arterial phase CT scans combined with pathology diagnosis results, a fusion feature-based blending ensemble machine learning model was created to identify malignant renal neoplasms from cystic renal lesions (CRLs). Histopathology results were adopted as diagnosis standard. Pretrained 3D-ResNet50 network was selected for non-handcrafted features extraction and pyradiomics toolbox was selected for handcrafted features extraction. Tenfold cross validated least absolute shrinkage and selection operator regression methods were selected to identify the most discriminative candidate features in the development cohort. Feature's reproducibility was evaluated by intra-class correlation coefficients and inter-class correlation coefficients. Pearson correlation coefficients for normal distribution and Spearman's rank correlation coefficients for non-normal distribution were utilized to remove redundant features. After that, a blending ensemble machine learning model were developed in training cohort. Area under the receiver operator characteristic curve (AUC), accuracy score (ACC), and decision curve analysis (DCA) were employed to evaluate the performance of the final model in testing cohort.

RESULTS

The fusion feature-based machine learning algorithm demonstrated excellent diagnostic performance in external validation dataset (AUC = 0.934, ACC = 0.905). Net benefits presented by DCA are higher than Bosniak-2019 version classification for stratifying patients with CRL to the appropriate surgery procedure.

CONCLUSIONS

Fusion feature-based classifier accurately distinguished malignant and benign CRLs which outperformed the Bosniak-2019 version classification and illustrated improved clinical decision-making utility.

Clinical features combined with ultrasound-based radiomics nomogram for discrimination between benign and malignant lesions in ultrasound suspected supraclavicular lymphadenectasis

Background

Conventional ultrasound (CUS) is the first choice for discrimination benign and malignant lymphadenectasis in supraclavicular lymph nodes (SCLNs), which is important for the further treatment. Radiomics provide more comprehensive and richer information than radiographic images, which are imperceptible to human eyes.

Objective

This study aimed to explore the clinical value of CUS-based radiomics analysis in preoperative differentiation of malignant from benign lymphadenectasis in CUS suspected SCLNs.

Methods

The characteristics of CUS images of 189 SCLNs were retrospectively analyzed, including 139 pathologically confirmed benign SCLNs and 50 malignant SCLNs. The data were randomly divided (7:3) into a training set (n=131) and a validation set (n=58). A total of 744 radiomics features were extracted from CUS images, radiomics score (Rad-score) built were using least absolute shrinkage and selection operator (LASSO) logistic regression. Rad-score model, CUS model, radiomics-CUS (Rad-score + CUS) model, clinic-radiomics (Clin + Rad-score) model, and combined CUS-clinic-radiomics (Clin + CUS + Rad-score) model were built using logistic regression. Diagnostic accuracy was assessed by receiver operating characteristic (ROC) curve analysis.

Results

A total of 20 radiomics features were selected from 744 radiomics features and calculated to construct Rad-score. The AUCs of Rad-score model, CUS model, Clin + Rad-score model, Rad-score + CUS model, and Clin + CUS + Rad-score model were 0.80, 0.72, 0.85, 0.83, 0.86 in the training set and 0.77, 0.80, 0.82, 0.81, 0.85 in the validation set. There was no statistical significance among the AUC of all models in the training and validation set. The calibration curve also indicated the good predictive performance of the proposed nomogram.

Conclusions

The Rad-score model, derived from supraclavicular ultrasound images, showed good predictive effect in differentiating benign from malignant lesions in patients with suspected supraclavicular lymphadenectasis.

Stratification of malignant renal neoplasms from cystic renal lesions using deep learning and radiomics features based on a stacking ensemble CT machine learning algorithm

Using nephrographic phase CT images combined with pathology diagnosis, we aim to develop and validate a fusion feature-based stacking ensemble machine learning model to distinguish malignant renal neoplasms from cystic renal lesions (CRLs). This retrospective research includes 166 individuals with CRLs for model training and 47 individuals with CRLs in another institution for model testing. Histopathology results are adopted as diagnosis criterion. Nephrographic phase CT scans are selected to build the fusion feature-based machine learning algorithms. The pretrained 3D-ResNet50 CNN model and radiomics methods are selected to extract deep features and radiomics features, respectively. Fivefold cross-validated least absolute shrinkage and selection operator (LASSO) regression methods are adopted to identify the most discriminative candidate features in the development cohort. Intraclass correlation coefficients and interclass correlation coefficients are employed to evaluate feature’s reproducibility. Pearson correlation coefficients for normal distribution features and Spearman’s rank correlation coefficients for non-normal distribution features are used to eliminate redundant features. After that, stacking ensemble machine learning models are developed in the training cohort. The area under the receiver operator characteristic curve (ROC), calibration curve, and decision curve analysis (DCA) are adopted in the testing cohort to evaluate the performance of each model. The stacking ensemble machine learning algorithm reached excellent diagnostic performance in the testing dataset. The calibration plot shows good stability when using the stacking ensemble model. Net benefits presented by DCA are higher than the Bosniak 2019 version classification when employing any machine learning algorithm. The fusion feature-based machine learning algorithm accurately distinguishes malignant renal neoplasms from CRLs, which outperformed the Bosniak 2019 version classification, and proves to be more applicable for clinical decision-making.

The potential value of cuprotosis (copper-induced cell death) in the therapy of clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) accounts for 75% of the total incidence of renal cancer, and every year the number of morbidity and mortality increases, posing a serious threat to public health. The current main treatment methods for kidney cancer include drug-targeted therapy and immunotherapy. Although there are many treatment options for kidney cancer, they all have limitations, including drug resistance, unsatisfied long-term benefits, and adverse effects. Therefore, it is crucial to identify more effective therapeutic targets. As a newly discovered mechanism of cell death, copper-induced cell death (cuprotosis) is closely related to changes in cell metabolism, particularly in copper metabolism. Current studies have shown that the key signaling pathway of cuprotosis, the FDX1 (Ferredoxin 1)-LIAS (Lipoic Acid Synthetase) axis, plays an important role in the regulation of cellular oxidative stress, which can directly affect cell survival via inducing or promoting cancer cell death. Therefore, we speculated that this regulatory cell death mechanism might serve as a potential therapeutic target for the clinical treatment of renal cancer. To test this, we first performed a pan-cancer analysis based on cuprotosis-related genomic and transcriptomic levels to reveal the expression of cuprotosis in cancer. Next, GSVA-clustering analysis was performed with data from the Cancer Genome Atlas (TCGA) cohort, and the cohort was divided into three clusters according to the gene enrichment levels of cuprotosis marker genes. In addition, we analyzed the potential of using cuprotosis in clinical treatment from multiple perspectives, including chemotherapeutic drug susceptibility test, immune target inhibition treatment responsiveness, and histone modification. Combining the results of multi-omics analysis, we focused on the feasibility of this novel regulatory cell death mechanism in ccRCC treatment and further constructed a prognostic model. Finally, we verified our results by integrating the patient's gene expression information and radiomics information. Our study provides new insights into the development and clinical application of targeting cuprotosis pathway.