Value of the Application of CE-MRI Radiomics and Machine Learning in Preoperative Prediction of Sentinel Lymph Node Metastasis in Breast Cancer

Machine learning models for differential diagnosing HER2-low breast cancer: A radiomics approach

To develop machine learning models based on preoperative dynamic enhanced magnetic resonance imaging (DCE-MRI) radiomics and to explore their potential prognostic value in the differential diagnosis of human epidermal growth factor receptor 2 (HER2)-low from HER2-positive breast cancer (BC). A total of 233 patients with pathologically confirmed invasive breast cancer admitted to our hospital between January 2018 and December 2022 were included in this retrospective analysis. Of these, 103 cases were diagnosed as HER2-positive and 130 cases were HER2 low-expression BC. The Synthetic Minority Oversampling Technique is employed to address the class imbalance problem. Patients were randomly split into a training set (163 cases) and a validation set (70 cases) in a 7:3 ratio. Radiomics features from DCE-MRI second-phase imaging were extracted. Z-score normalization was used to standardize the radiomics features, and Pearson's correlation coefficient and recursive feature elimination were used to explore the significant features. Prediction models were constructed using 6 machine learning algorithms: logistic regression, random forest, support vector machine, AdaBoost, decision tree, and auto-encoder. Receiver operating characteristic curves were constructed, and predictive models were evaluated according to the area under the curve (AUC), accuracy, sensitivity, and specificity. In the training set, the AUC, accuracy, sensitivity, and specificity of all models were 1.000. However, in the validation set, the auto-encoder model's AUC, accuracy, sensitivity, and specificity were 0.994, 0.976, 0.972, and 0.978, respectively. The remaining models' AUC, accuracy, sensitivity, and specificity were 1.000. The DeLong test showed no statistically significant differences between the machine learning models in the training and validation sets (Z = 0, P = 1). Our study investigated the feasibility of using DCE-MRI-based radiomics features to predict HER2-low BC. Certain radiomics features showed associations with HER2-low BC and may have predictive value. Machine learning prediction models developed using these radiomics features could be beneficial for distinguishing between HER2-low and HER2-positive BC. These noninvasive preoperative models have the potential to assist in clinical decision-making for HER2-low breast cancer, thereby advancing personalized clinical precision.

Clinical applications of radiomics and deep learning in breast and lung cancer: A narrative literature review on current evidence and future perspectives

Radiomics, analysing quantitative features from medical imaging, has rapidly become an emerging field in translational oncology. Radiomics has been investigated in several neoplastic malignancies as it might allow for a non-invasive tumour characterization and for the identification of predictive and prognostic biomarkers. Over the last few years, evidence has been accumulating regarding potential clinical applications of machine learning in many crucial moments of cancer patients' history. However, the incorporation of radiomics in clinical decision-making process is still limited by low data reproducibility and study variability. Moreover, the need for prospective validations and standardizations is emerging. In this narrative review, we summarize current evidence regarding radiomic applications in high-incidence cancers (breast and lung) for screening, diagnosis, staging, treatment choice, response, and clinical outcome evaluation. We also discuss pro and cons of the radiomic approach, suggesting possible solutions to critical issues which might invalidate radiomics studies and propose future perspectives.

Machine learning-based CT radiomics enhances bladder cancer staging predictions: A comparative study of clinical, radiomics, and combined models

BACKGROUND

Predicting the accurate preoperative staging of bladder cancer (BLCA), which markedly affects treatment decisions and patient outcomes, using traditional clinical parameters is challenging. Nevertheless, emerging studies in radiomics, especially machine learning-based computed tomography (CT) image-based radiomics, hold promise in improving stage prediction accuracy in various tumors. However, the comparative performance and clinical utility of models for BLCA are under investigation.

PURPOSE

We aimed to investigate the application value of machine learning-based CT radiomics in preoperative staging prediction by comparing the performance of clinical, radiomics, and clinical-radiomics combined models.

METHODS

A retrospective cohort of 105 patients with initial BLCA was randomized into training (70%) and testing (30%) cohorts. Radiomics features were extracted from CT images using the optimal feature filter, followed by the application of the least absolute shrinkage and selection operator algorithm for optimum feature selection. Furthermore, machine learning algorithms were used to establish a radiomics model within the training cohort. Independent risk factors for muscle-invasive BLCA (MIBC) obtained by multivariate logistic regression (LR) analysis were separately used to construct a clinical model. For a clinical-radiomics fusion model, radiomics features were combined with clinical parameters. Performance was evaluated based on receiver operating characteristic curves, calibration curves, decision curve analysis (DCA), and standard performance metrics.

RESULTS

Patients exhibited a significantly higher age (p = 0.029), larger tumor size (p = 0.01), and an increased neutrophil-to-lymphocyte ratio (NLR; p = 0.045) in the MIBC group than in the NMIBC group. LR analysis revealed age (p = 0.026), tumor size (p = 0.007), and NLR (p = 0.019) as significant predictors for constructing the clinical model. In the testing cohort, the radiomics model, which used an Support Vector Machine classifier, achieved the highest area under the curve (AUC) value of 0.857. The clinical-radiomics model outperformed the remaining two models, with AUC values of 0.958 and 0.893 in the training and testing cohorts, respectively. DeLong's test indicated significant differences between the three models. Calibration curves showed good agreement, and DCA confirmed the superior clinical utility of the clinical-radiomics model.

CONCLUSIONS

Machine learning-based CT radiomics combined with clinical parameters was a promising approach in staging BLCA accurately, which outperformed the individual models. Integrating radiomics features with clinical information holds the potential to improve personalized treatment planning and patient outcomes in BLCA.

Performance evaluation of ML models for preoperative prediction of HER2-low BC based on CE-CBBCT radiomic features: A prospective study

To explore the value of machine learning (ML) models based on contrast-enhanced cone-beam breast computed tomography (CE-CBBCT) radiomics features for the preoperative prediction of human epidermal growth factor receptor 2 (HER2)-low expression breast cancer (BC). Fifty-six patients with HER2-negative invasive BC who underwent preoperative CE-CBBCT were prospectively analyzed. Patients were randomly divided into training and validation cohorts at approximately 7:3. A total of 1046 quantitative radiomic features were extracted from CE-CBBCT images and normalized using z-scores. The Pearson correlation coefficient and recursive feature elimination were used to identify the optimal features. Six ML models were constructed based on the selected features: linear discriminant analysis (LDA), random forest (RF), support vector machine (SVM), logistic regression (LR), AdaBoost (AB), and decision tree (DT). To evaluate the performance of these models, receiver operating characteristic curves and area under the curve (AUC) were used. Seven features were selected as the optimal features for constructing the ML models. In the training cohort, the AUC values for SVM, LDA, RF, LR, AB, and DT were 0.984, 0.981, 1.000, 0.970, 1.000, and 1.000, respectively. In the validation cohort, the AUC values for the SVM, LDA, RF, LR, AB, and DT were 0.859, 0.880, 0.781, 0.880, 0.750, and 0.713, respectively. Among all ML models, the LDA and LR models demonstrated the best performance. The DeLong test showed that there were no significant differences among the receiver operating characteristic curves in all ML models in the training cohort (P > .05); however, in the validation cohort, the DeLong test showed that the differences between the AUCs of LDA and RF, AB, and DT were statistically significant (P = .037, .003, .046). The AUCs of LR and RF, AB, and DT were statistically significant (P = .023, .005, .030). Nevertheless, no statistically significant differences were observed when compared to the other ML models. ML models based on CE-CBBCT radiomics features achieved excellent performance in the preoperative prediction of HER2-low BC and could potentially serve as an effective tool to assist in precise and personalized targeted therapy.

Deep Learning Radiomics of Preoperative Breast MRI for Prediction of Axillary Lymph Node Metastasis in Breast Cancer

The objective of this study is to develop a radiomic signature constructed from deep learning features and a nomogram for prediction of axillary lymph node metastasis (ALNM) in breast cancer patients. Preoperative magnetic resonance imaging data from 479 breast cancer patients with 488 lesions were studied. The included patients were divided into two cohorts by time (training/testing cohort, n = 366/122). Deep learning features were extracted from diffusion-weighted imaging-quantitatively measured apparent diffusion coefficient (DWI-ADC) imaging and dynamic contrast-enhanced MRI (DCE-MRI) by a pretrained neural network of DenseNet121. After the selection of both radiomic and clinicopathological features, deep learning signature and a nomogram were built for independent validation. Twenty-three deep learning features were automatically selected in the training cohort to establish the deep learning signature of ALNM. Three clinicopathological factors, including LN palpability (odds ratio (OR) = 6.04; 95% confidence interval (CI) = 3.06-12.54, P = 0.004), tumor size in MRI (OR = 1.45, 95% CI = 1.18-1.80, P = 0.104), and Ki-67 (OR = 1.01; 95% CI = 1.00-1.02, P = 0.099), were selected and combined with radiomic signature to build a combined nomogram. The nomogram showed excellent predictive ability for ALNM (AUC 0.80 and 0.71 in training and testing cohorts, respectively). The sensitivity, specificity, and accuracy were 65%, 80%, and 75%, respectively, in the testing cohort. MRI-based deep learning radiomics in patients with breast cancer could be used to predict ALNM, providing a noninvasive approach to structuring the treatment strategy.

Value of the application of computed tomography-based radiomics for preoperative prediction of unfavorable pathology in initial bladder cancer

OBJECTIVES

To construct and validate unfavorable pathology (UFP) prediction models for patients with the first diagnosis of bladder cancer (initial BLCA) and to compare the comprehensive predictive performance of these models.

MATERIALS AND METHODS

A total of 105 patients with initial BLCA were included and randomly enrolled into the training and testing cohorts in a 7:3 ratio. The clinical model was constructed using independent UFP-risk factors determined by multivariate logistic regression (LR) analysis in the training cohort. Radiomics features were extracted from manually segmented regions of interest in computed tomography (CT) images. The optimal CT-based radiomics features to predict UFP were determined by the optimal feature filter and the least absolute shrinkage and selection operator algorithm. The radiomics model consist with the optimal features was constructed by the best of the six machine learning filters. The clinic-radiomics model combined the clinical and radiomics models via LR. The area under the curve (AUC), accuracy, sensitivity, specificity, positive and negative predictive value, calibration curve and decision curve analysis were used to evaluate the predictive performance of the models.

RESULTS

Patients in the UFP group had a significantly older age (69.61 vs. 63.93 years, p = 0.034), lager tumor size (45.7% vs. 11.1%, p = 0.002) and higher neutrophil to lymphocyte ratio (NLR; 2.76 vs. 2.33, p = 0.017) than favorable pathologic group in the training cohort. Tumor size (OR, 6.02; 95% CI, 1.50-24.10; p = 0.011) and NLR (OR, 1.50; 95% CI, 1.05-2.16; p = 0.026) were identified as independent predictive factors for UFP, and the clinical model was constructed using these factors. The LR classifier with the best AUC (0.817, the testing cohorts) was used to construct the radiomics model based on the optimal radiomics features. Finally, the clinic-radiomics model was developed by combining the clinical and radiomics models using LR. After comparison, the clinic-radiomics model had the best performance in comprehensive predictive efficacy (accuracy = 0.750, AUC = 0.817, the testing cohorts) and clinical net benefit among UFP-prediction models, while the clinical model (accuracy = 0.625, AUC = 0.742, the testing cohorts) was the worst.

CONCLUSION

Our study demonstrates that the clinic-radiomics model exhibits the best predictive efficacy and clinical net benefit for predicting UFP in initial BLCA compared with the clinical and radiomics model. The integration of radiomics features significantly improves the comprehensive performance of the clinical model.

Development and validation of radiomics machine learning model based on contrast-enhanced computed tomography to predict axillary lymph node metastasis in breast cancer

Preoperative identification of axillary lymph node metastasis can play an important role in treatment selection strategy and prognosis evaluation. This study aimed to establish a clinical nomogram based on lymph node images to predict lymph node metastasis in breast cancer patients. A total of 193 patients with non-specific invasive breast cancer were divided into training (n = 135) and validation set (n = 58). Radiomics features were extracted from lymph node images instead of tumor region, and the least absolute shrinkage and selection operator logistic algorithm was used to select the extracted features and generate radiomics score. Then, the important clinical factors and radiomics score were integrated into a nomogram. A receiver operating characteristic curve was used to evaluate the nomogram, and the clinical benefit of using the nomogram was evaluated by decision curve analysis. We found that clinical N stage and radiomics score were independent clinical predictors. Besides, the nomogram accurately predicted axillary lymph node metastasis, yielding an area under the receiver operating characteristic curve of 0.95 (95% confidence interval 0.93-0.98) in the validation set, indicating satisfactory calibration. Decision curve analysis confirmed that the nomogram had higher clinical utility than clinical N stage or radiomics score alone. Overall, the nomogram based on radiomics features and clinical factors can help radiologists to predict axillary lymph node metastasis preoperatively and provide valuable information for individual treatment.

Radiomics signatures based on contrast-enhanced CT for preoperative prediction of the Ki-67 proliferation state in gastrointestinal stromal tumors

PURPOSE

This study aimed to evaluate the Ki-67 proliferation state in patients with gastrointestinal stromal tumors (GISTs) using radiomics prediction signatures based on contrast-enhanced computed tomography (CE-CT).

MATERIALS AND METHODS

This single-center, retrospective study involved 103 patients (48 men and 55 women, mean age 61.1 ± 10.6 years) who had pathologically confirmed GISTs after curative resection, including 63 with low Ki-67 proliferation level (Ki-67 labeling index ≤ 6%) and 40 with high Ki-67 proliferation level (Ki-67 labeling index > 6%). Radiomics features of the delineated lesions were preoperatively extracted from three-phase CE-CT images, including the arterial, venous, and delayed phases. The most relevant features were selected to construct the radiomics signatures using a logistic regression algorithm. Significant demographic characteristics and semantic features on CT were selected to develop a nomogram along with the optimal radiomics feature. We calculated the sensitivity, specificity, accuracy, F1 score, and area under the receiver operating characteristic (ROC) curve to evaluate the predictive performance of radiomics signatures.

RESULTS

Ten quantitative radiomics features (two first-order and eight texture features) were selected to construct radiomics signatures. The radiomics signature based on the three-phase CE-CT images showed better predictive performance than that based on the single-phase CE-CT images, with an area under the curve (AUC) of 0.83 (95% CI 0.73-0.92) and F1 score of 82% in the training dataset and an AUC of 0.80 (95% CI 0.63-0.95) and F1 score of 75% in the testing dataset. The nomogram showed good calibration.

CONCLUSION

Radiomics signatures using CE-CT images are generalizable and could be used in clinical practice to determine the proliferation state of Ki-67 in GISTs.

Diagnostic performance of radiomics in predicting axillary lymph node metastasis in breast cancer: A systematic review and meta-analysis

BACKGROUND

This study aimed to perform a meta-analysis to evaluate the diagnostic performance of radiomics in predicting axillary lymph node metastasis (ALNM) and sentinel lymph node metastasis (SLNM) in breast cancer.

MATERIALS AND METHODS

Multiple electronic databases were systematically searched to identify relevant studies published before April 29, 2022: PubMed, Embase, Web of Science, Cochrane Library, China National Knowledge Infrastructure, and Wanfang Data. The quality of the included studies was assessed using the Quality Assessment of Diagnostic Accuracy Studies-2 tool. The overall diagnostic odds ratio (DOR), sensitivity, specificity, and area under the curve (AUC) were calculated to evaluate the diagnostic performance of radiomic features for lymph node metastasis (LNM) in patients with breast cancer. Spearman's correlation coefficient was determined to assess the threshold effect, and meta-regression and subgroup analyses were performed to explore the possible causes of heterogeneity.

RESULTS

A total of 30 studies with 5611 patients were included in the meta-analysis. Pooled estimates suggesting overall diagnostic accuracy of radiomics in detecting LNM were determined: DOR, 23 (95% CI, 16-33); sensitivity, 0.86 (95% CI, 0.82-0.88); specificity, 0.79 (95% CI, 0.73-0.84); and AUC, 0.90 (95% CI, 0.87-0.92). The meta-analysis showed significant heterogeneity between sensitivity and specificity across the included studies, with no evidence for a threshold effect. Meta-regression and subgroup analyses showed that combined clinical factors, modeling method, region, and imaging modality (magnetic resonance imaging [MRI], ultrasound, computed tomography [CT], and X-ray mammography [MMG]) contributed to the heterogeneity in the sensitivity analysis (P < 0.05). Furthermore, modeling methods, MRI, and MMG contributed to the heterogeneity in the specificity analysis (P < 0.05).

CONCLUSION

Our results show that radiomics has good diagnostic performance in predicting ALNM and SLNM in breast cancer. Thus, we propose this approach as a clinical method for the preoperative identification of LNM.

A nomogram based on radiomics signature and deep-learning signature for preoperative prediction of axillary lymph node metastasis in breast cancer

PURPOSE

To develop a nomogram based on radiomics signature and deep-learning signature for predicting the axillary lymph node (ALN) metastasis in breast cancer.

METHODS

A total of 151 patients were assigned to a training cohort (n = 106) and a test cohort (n = 45) in this study. Radiomics features were extracted from DCE-MRI images, and deep-learning features were extracted by VGG-16 algorithm. Seven machine learning models were built using the selected features to evaluate the predictive value of radiomics or deep-learning features for the ALN metastasis in breast cancer. A nomogram was then constructed based on the multivariate logistic regression model incorporating radiomics signature, deep-learning signature, and clinical risk factors.

RESULTS

Five radiomics features and two deep-learning features were selected for machine learning model construction. In the test cohort, the AUC was above 0.80 for most of the radiomics models except DecisionTree and ExtraTrees. In addition, the K-nearest neighbor (KNN), XGBoost, and LightGBM models using deep-learning features had AUCs above 0.80 in the test cohort. The nomogram, which incorporated the radiomics signature, deep-learning signature, and MRI-reported LN status, showed good calibration and performance with the AUC of 0.90 (0.85-0.96) in the training cohort and 0.90 (0.80-0.99) in the test cohort. The DCA showed that the nomogram could offer more net benefit than radiomics signature or deep-learning signature.

CONCLUSIONS

Both radiomics and deep-learning features are diagnostic for predicting ALN metastasis in breast cancer. The nomogram incorporating radiomics and deep-learning signatures can achieve better prediction performance than every signature used alone.

Identification of an Epithelial-Mesenchymal Transition-Related Long Non-coding RNA Prognostic Signature to Determine the Prognosis and Drug Treatment of Hepatocellular Carcinoma Patients

Introduction

Hepatocellular carcinoma (HCC) is one of the most common malignant tumors with poor prognosis. Epithelial–mesenchymal transition (EMT) is crucial for cancer progression and metastasis. Thus, we aimed to construct an EMT-related lncRNA signature for predicting the prognosis of HCC patients.

Methods

Cox regression analysis and LASSO regression method were used to build an EMT-related lncRNAs risk signature based on TCGA database. Kaplan-Meier survival analysis was conducted to compare the overall survival (OS) in different risk groups. ROC curves and Cox proportional-hazards analysis were performed to evaluate the performance of the risk signature. RT-qPCR was conducted in HCC cell lines and tissue samples to detect the expression of some lncRNAs in this risk model. Furthermore, a nomogram involving the risk score and clinicopathological features was built and validated with calibration curves and ROC curves. In addition, we explored the association between risk signature and tumor immunity, somatic mutations status, and drugs sensitivity.

Results

Twelve EMT-related lncRNAs were obtained to construct the prognostic risk signature for patients with HCC. The Kaplan-Meier curve analysis revealed that patients in the high-risk group had worse overall survival (OS) than those in low-risk group. ROC curves and Cox regression analysis suggested the risk signature could predict HCC survival exactly and independently. The prognostic value of the risk model was confirmed in the testing and entire groups. We also found AC099850.3 and AC092171.2 were highly expressed in HCC cells and HCC tissues. The nomogram could accurately predict survival probability of HCC patients. Gene set enrichment analysis (GSEA) and gene ontology (GO) analysis showed that cancer-related pathways and cell division activity were enriched in high-risk group. The SNPs showed that the prevalence of TP53 mutations was significantly different between high- and low-risk groups; the TP53 mutations and the high TMB were both associated with a worse prognosis in patients with HCC. We also observed widely associations between risk signature and drugs sensitivity in HCC.

Conclusion

A novel EMT-related lncRNAs risk signature, including 12 lncRNAs, was established and identified in patients with HCC, which can accurately predict the prognosis of HCC patients and may be used to guide individualized treatment in the clinical practice.