Radiomics Assessment of the Tumor Immune Microenvironment to Predict Outcomes in Breast Cancer

Machine Learning Model for Predicting Axillary Lymph Node Metastasis in Clinically Node Positive Breast Cancer Based on Peritumoral Ultrasound Radiomics and SHAP Feature Analysis

OBJECTIVE

This study seeks to construct a machine learning model that merges clinical characteristics with ultrasound radiomic analysis-encompassing both the intratumoral and peritumoral-to predict the status of axillary lymph nodes in patients with early-stage breast cancer.

METHODS

The study employed retrospective methods, collecting clinical information, ultrasound data, and postoperative pathological results from 321 breast cancer patients (including 224 in the training group and 97 in the validation group). Through correlation analysis, univariate analysis, and Lasso regression analysis, independent risk factors related to axillary lymph node metastasis in breast cancer were identified from conventional ultrasound and immunohistochemical indicators, and a clinical feature model was constructed. Additionally, features were extracted from ultrasound images of the intratumoral and its 1-5 mm peritumoral to establish a radiomics feature formula. Furthermore, by combining clinical features and ultrasound radiomics features, six machine learning models (Logistic Regression, Decision Tree, Support Vector Machine, Extreme Gradient Boosting, Random Forest, and K-Nearest Neighbors) were compared for diagnostic efficacy, and constructing a joint prediction model based on the optimal ML algorithm. The use of Shapley Additive Explanations (SHAP) enhanced the visualization and interpretability of the model during the diagnostic process.

RESULTS

Among the 321 breast cancer patients, 121 had axillary lymph node metastasis, and 200 did not. The clinical feature model had an AUC of 0.779 and 0.777 in the training and validation groups, respectively. Radiomics model analysis showed that the model including the Intratumor +3 mm peritumor area had the best diagnostic performance, with AUCs of 0.847 and 0.844 in the training and validation groups, respectively. The joint prediction model based on the XGBoost algorithm reached AUCs of 0.917 and 0.905 in the training and validation groups, respectively. SHAP analysis indicated that the Rad Score had the highest weight in the prediction model, playing a significant role in predicting axillary lymph node metastasis in breast cancer.

CONCLUSION

The predictive model, which integrates clinical features and radiomic characteristics using the XGBoost algorithm, demonstrates significant diagnostic value for axillary lymph node metastasis in breast cancer. This model can provide significant references for preoperative surgical strategy selection and prognosis evaluation for breast cancer patients, helping to reduce postoperative complications and improve long-term survival rates. Additionally, the utilization of SHAP enhancing the global and local interpretability of the model.

Machine learning-based MRI radiomics for assessing the level of tumor infiltrating lymphocytes in oral tongue squamous cell carcinoma: a pilot study

BACKGROUND

To investigate the value of machine learning (ML)-based magnetic resonance imaging (MRI) radiomics in assessing tumor-infiltrating lymphocyte (TIL) levels in patients with oral tongue squamous cell carcinoma (OTSCC).

METHODS

The study included 68 patients with pathologically diagnosed OTSCC (30 with high TILs and 38 with low TILs) who underwent pretreatment MRI. Based on the regions of interest encompassing the entire tumor, a total of 750 radiomics features were extracted from T2-weighted (T2WI) and contrast-enhanced T1-weighted (ceT1WI) imaging. To reduce dimensionality, reproducibility analysis by two radiologists and collinearity analysis were performed. The top six features were selected from each sequence alone, as well as their combination, using the minimum-redundancy maximum-relevance algorithm. Random forest, logistic regression, and support vector machine models were used to predict TIL levels in OTSCC, and 10-fold cross-validation was employed to assess the performance of the classifiers.

RESULTS

Based on the features selected from each sequence alone, the ceT1WI models outperformed the T2WI models, with a maximum area under the curve (AUC) of 0.820 versus 0.754. When combining the two sequences, the optimal features consisted of one T2WI and five ceT1WI features, all of which exhibited significant differences between patients with low and high TILs (all P < 0.05). The logistic regression model constructed using these features demonstrated the best predictive performance, with an AUC of 0.846 and an accuracy of 80.9%.

CONCLUSIONS

ML-based T2WI and ceT1WI radiomics can serve as valuable tools for determining the level of TILs in patients with OTSCC.

Magnetic resonance imaging-based radiomics was used to evaluate the level of prognosis-related immune cell infiltration in breast cancer tumor microenvironment

PURPOSE

The tumor immune microenvironment is a valuable source of information for predicting prognosis in breast cancer (BRCA) patients. To identify immune cells associated with BRCA patient prognosis from the Cancer Genetic Atlas (TCGA), we established an MRI-based radiomics model for evaluating the degree of immune cell infiltration in breast cancer patients.

METHODS

CIBERSORT was utilized to evaluate the degree of infiltration of 22 immune cell types in breast cancer patients from the TCGA database, and both univariate and multivariate Cox regressions were employed to determine the prognostic significance of immune cell infiltration levels in BRCA patients. We identified independent prognostic factors for BRCA patients. Additionally, we obtained imaging features from the Cancer Imaging Archive (TCIA) database for 73 patients who underwent preoperative MRI procedures, and used the Least Absolute Shrinkage and Selection Operator (LASSO) to select the best imaging features for constructing an MRI-based radiomics model for evaluating immune cell infiltration levels in breast cancer patients.

RESULTS

According to the results of Cox regression analysis, M2 macrophages were identified as an independent prognostic factor for BRCA patients (HR = 32.288, 95% CI: 3.100-357.478). A total of nine significant features were selected to calculate the radiomics-based score. We established an intratumoral model with AUCs (95% CI) of 0.662 (0.495-0.802) and 0.678 (0.438-0.901) in the training and testing cohorts, respectively. Additionally, a peritumoral model was created with AUCs (95% CI) of 0.826 (0.710-0.924) and 0.752 (0.525-0.957), and a combined model was established with AUCs (95% CI) of 0.843 (0.723-0.938) and 0.744 (0.491-0.965). The peritumoral model demonstrated the highest diagnostic efficacy, with an accuracy, sensitivity, and specificity of 0.773, 0.727, and 0.818, respectively, in its testing cohort.

CONCLUSION

The MRI-based radiomics model has the potential to evaluate the degree of immune cell infiltration in breast cancer patients, offering a non-invasive imaging biomarker for assessing the tumor microenvironment in this disease.

Ultrasound-based radiomics nomogram for predicting axillary lymph node metastasis in early-stage breast cancer

PURPOSE

We aimed at assessing the predictive ability of ultrasound-based radiomics combined with clinical characteristics for axillary lymph node (ALN) status in early-stage breast cancer patients and to compare performance in different peritumoral regions.

MATERIALS AND METHODS

A total of 755 patients (527 in the primary cohort and 228 in the external validation cohort) were enrolled in this study. Ultrasound images for all patients were acquired and radiomics analysis performed for intratumoral and different peritumoral regions. The MRMR and LASSO regression analyses were performed on extracted features from the primary cohort to construct a radiomics signature formula combined with clinical characteristics. Pearson's coefficient and the variance inflation factor (VIF) were performed to check the correlation and the multicollinearity among the final predictors. The best performing model was selected to develop a nomogram, which was established by performing binary logistic regression and acquiring cut-off values based on the corresponding nomogram scores of the masses.

RESULTS

Among all the radiomics models, the "Mass + Margin3mm" model exhibited the best performance. The areas under the curves (AUC) of the nomogram in the primary and external validation cohorts were 0.906 (95% confidence intervals [CI] 0.882-0.930) and 0.922 (95% CI 0.894-0.960), respectively. They both showed good calibrations. The nomogram exhibited a good ability to discriminate between positive and negative lymph nodes (AUC: 0.853 (95% CI 0.816-0.889) in primary cohort, 0.870 (95% CI 0.818-0.922) in validation cohort), and between low-volume and high-volume lymph nodes (AUC: 0.832 (95% CI 0.781-0.884) in primary cohort, 0.911 (95% CI 0.858-0.964) in validation cohort).

CONCLUSIONS

The established nomogram is a prospective clinical prediction tool for non-invasive assessment of ALN status. It has the ability to enhance the accuracy of early-stage breast cancer treatment.

Development of a machine learning-based radiomics signature for estimating breast cancer TME phenotypes and predicting anti-PD-1/PD-L1 immunotherapy response

BACKGROUNDS

Since breast cancer patients respond diversely to immunotherapy, there is an urgent need to explore novel biomarkers to precisely predict clinical responses and enhance therapeutic efficacy. The purpose of our present research was to construct and independently validate a biomarker of tumor microenvironment (TME) phenotypes via a machine learning-based radiomics way. The interrelationship between the biomarker, TME phenotypes and recipients' clinical response was also revealed.

METHODS

In this retrospective multi-cohort investigation, five separate cohorts of breast cancer patients were recruited to measure breast cancer TME phenotypes via a radiomics signature, which was constructed and validated by integrating RNA-seq data with DCE-MRI images for predicting immunotherapy response. Initially, we constructed TME phenotypes using RNA-seq of 1089 breast cancer patients in the TCGA database. Then, parallel DCE-MRI images and RNA-seq of 94 breast cancer patients obtained from TCIA were applied to develop a radiomics-based TME phenotypes signature using random forest in machine learning. The repeatability of the radiomics signature was then validated in an internal validation set. Two additional independent external validation sets were analyzed to reassess this signature. The Immune phenotype cohort (n = 158) was divided based on CD8 cell infiltration into immune-inflamed and immune-desert phenotypes; these data were utilized to examine the relationship between the immune phenotypes and this signature. Finally, we utilized an Immunotherapy-treated cohort with 77 cases who received anti-PD-1/PD-L1 treatment to evaluate the predictive efficiency of this signature in terms of clinical outcomes.

RESULTS

The TME phenotypes of breast cancer were separated into two heterogeneous clusters: Cluster A, an "immune-inflamed" cluster, containing substantial innate and adaptive immune cell infiltration, and Cluster B, an "immune-desert" cluster, with modest TME cell infiltration. We constructed a radiomics signature for the TME phenotypes ([AUC] = 0.855; 95% CI 0.777-0.932; p < 0.05) and verified it in an internal validation set (0.844; 0.606-1; p < 0.05). In the known immune phenotypes cohort, the signature can identify either immune-inflamed or immune-desert tumor (0.814; 0.717-0.911; p < 0.05). In the Immunotherapy-treated cohort, patients with objective response had higher baseline radiomics scores than those with stable or progressing disease (p < 0.05); moreover, the radiomics signature achieved an AUC of 0.784 (0.643-0.926; p < 0.05) for predicting immunotherapy response.

CONCLUSIONS

Our imaging biomarker, a practicable radiomics signature, is beneficial for predicting the TME phenotypes and clinical response in anti-PD-1/PD-L1-treated breast cancer patients. It is particularly effective in identifying the "immune-desert" phenotype and may aid in its transformation into an "immune-inflamed" phenotype.

Adaptive Cancer Therapy in the Age of Generative Artificial Intelligence

Therapeutic resistance is a major challenge facing the design of effective cancer treatments. Adaptive cancer therapy is in principle the most viable approach to manage cancer's adaptive dynamics through drug combinations with dose timing and modulation. However, there are numerous open issues facing the clinical success of adaptive therapy. Chief among these issues is the feasibility of real-time predictions of treatment response which represent a bedrock requirement of adaptive therapy. Generative artificial intelligence has the potential to learn prediction models of treatment response from clinical, molecular, and radiomics data about patients and their treatments. The article explores this potential through a proposed integration model of Generative Pre-Trained Transformers (GPTs) in a closed loop with adaptive treatments to predict the trajectories of disease progression. The conceptual model and the challenges facing its realization are discussed in the broader context of artificial intelligence integration in oncology.

Computed tomography-based radiomics to assess risk stratification in pediatric malignant peripheral neuroblastic tumors

This study aimed to develop and validate an analysis system based on preoperative computed tomography (CT) to predict the risk stratification in pediatric malignant peripheral neuroblastic tumors (PNTs). A total of 405 patients with malignant PNTs (184 girls and 221 boys; mean age, 33.8 ± 29.1 months) were retrospectively evaluated between January 2010 and June 2018. Radiomic features were extracted from manually segmented tumors on preoperative CT images. Spearman's rank correlation coefficient and the least absolute shrinkage and selection operator (LASSO) were used to eliminate redundancy and select features. A risk model was built to stratify low-, intermediate-, and high-risk groups. An image-defined risk factor (IDRFs) model was developed to classify 266 patients with malignant PNTs and one or more IDRFs into high-risk and non-high-risk groups. The performance of the predictive models was evaluated with respect to accuracy (Acc) and receiver operating characteristic (ROC) curve, including the area under the ROC curve (AUC). The risk model demonstrated good discrimination capability, with an area under the curve (AUC) of 0.903 to distinguish high-risk from non-high-risk groups, and 0.747 to classify intermediate- and low-risk groups. In the IDRF-based risk model with the number of IDRFs, the AUC was 0.876 for classifying the high-risk and non-high-risk groups. Radiomic analysis based on preoperative CT images has the potential to stratify the risk of pediatric malignant PNTs. It had outstanding efficiency in distinguishing patients in the high-risk group, and this predictive model of risk stratification could assist in selecting optimal aggressive treatment options.

Evaluation of Breast Cancer Tumor-Infiltrating Lymphocytes on Ultrasound Images Based on a Novel Multi-Cascade Residual U-Shaped Network

OBJECTIVE

Breast cancer has become the leading cancer of the 21st century. Tumor-infiltrating lymphocytes (TILs) have emerged as effective biomarkers for predicting treatment response and prognosis in breast cancer. The work described here was aimed at designing a novel deep learning network to assess the levels of TILs in breast ultrasound images.

METHODS

We propose the Multi-Cascade Residual U-Shaped Network (MCRUNet), which incorporates a gray feature enhancement (GFE) module for image reconstruction and normalization to achieve data synergy. Additionally, multiple residual U-shaped (RSU) modules are cascaded as the backbone network to maximize the fusion of global and local features, with a focus on the tumor's location and surrounding regions. The development of MCRUNet is based on data from two hospitals and uses a publicly available ultrasound data set for transfer learning.

RESULTS

MCRUNet exhibits excellent performance in assessing TILs levels, achieving an area under the receiver operating characteristic curve of 0.8931, an accuracy of 85.71%, a sensitivity of 83.33%, a specificity of 88.64% and an F1 score of 86.54% in the test group. It outperforms six state-of-the-art networks in terms of performance.

CONCLUSION

The MCRUNet network based on breast ultrasound images of breast cancer patients holds promise for non-invasively predicting TILs levels and aiding personalized treatment decisions.

Machine Learning Predicts Pathologic Complete Response to Neoadjuvant Chemotherapy for ER+HER2- Breast Cancer: Integrating Tumoral and Peritumoral MRI Radiomic Features

BACKGROUND

This study aimed to predict pathologic complete response (pCR) in neoadjuvant chemotherapy for ER+HER2- locally advanced breast cancer (LABC), a subtype with limited treatment response.

METHODS

We included 265 ER+HER2- LABC patients (2010-2020) with pre-treatment MRI, neoadjuvant chemotherapy, and confirmed pathology. Using data from January 2016, we divided them into training and validation cohorts. Volumes of interest (VOI) for the tumoral and peritumoral regions were segmented on preoperative MRI from three sequences: T1-weighted early and delayed contrast-enhanced sequences and T2-weighted fat-suppressed sequence (T2FS). We constructed seven machine learning models using tumoral, peritumoral, and combined texture features within and across the sequences, and evaluated their pCR prediction performance using AUC values.

RESULTS

The best single sequence model was SVM using a 1 mm tumor-to-peritumor VOI in the early contrast-enhanced phase (AUC = 0.9447). Among the combinations, the top-performing model was K-Nearest Neighbor, using 1 mm tumor-to-peritumor VOI in the early contrast-enhanced phase and 3 mm peritumoral VOI in T2FS (AUC = 0.9631).

CONCLUSIONS

We suggest that a combined machine learning model that integrates tumoral and peritumoral radiomic features across different MRI sequences can provide a more accurate pretreatment pCR prediction for neoadjuvant chemotherapy in ER+HER2- LABC.

Radiomic signatures based on pretreatment 18F-FDG PET/CT, combined with clinicopathological characteristics, as early prognostic biomarkers among patients with invasive breast cancer

Purpose

The aim of this study was to investigate the predictive role of fluorine-18 fluorodeoxyglucose positron emission tomography/computed tomography (18F-FDG PET/CT) in the prognostic risk stratification of patients with invasive breast cancer (IBC). To achieve this, we developed a clinicopathologic-radiomic-based model (C-R model) and established a nomogram that could be utilized in clinical practice.

Methods

We retrospectively enrolled a total of 91 patients who underwent preoperative 18F-FDG PET/CT and randomly divided them into training (n=63) and testing cohorts (n=28). Radiomic signatures (RSs) were identified using the least absolute shrinkage and selection operator (LASSO) regression algorithm and used to compute the radiomic score (Rad-score). Patients were assigned to high- and low-risk groups based on the optimal cut-off value of the receiver operating characteristic (ROC) curve analysis for both Rad-score and clinicopathological risk factors. Univariate and multivariate Cox regression analyses were performed to determine the association between these variables and progression-free survival (PFS) or overall survival (OS). We then plotted a nomogram integrating all these factors to validate the predictive performance of survival status.

Results

The Rad-score, age, clinical M stage, and minimum standardized uptake value (SUVmin) were identified as independent prognostic factors for predicting PFS, while only Rad-score, age, and clinical M stage were found to be prognostic factors for OS in the training cohort. In the testing cohort, the C-R model showed superior performance compared to single clinical or radiomic models. The concordance index (C-index) values for the C-R model, clinical model, and radiomic model were 0.816, 0.772, and 0.647 for predicting PFS, and 0.882, 0.824, and 0.754 for OS, respectively. Furthermore, decision curve analysis (DCA) and calibration curves demonstrated that the C-R model had a good ability for both clinical net benefit and application.

Conclusion

The combination of clinicopathological risks and baseline PET/CT-derived Rad-score could be used to evaluate the prognosis in patients with IBC. The predictive nomogram based on the C-R model further enhanced individualized estimation and allowed for more accurate prediction of patient outcomes.

Establishment of a N1-methyladenosine-related risk signature for breast carcinoma by bioinformatics analysis and experimental validation

OBJECTIVES

Breast carcinoma (BRCA) has resulted in a huge health burden globally. N1-methyladenosine (m¹A) RNA methylation has been proven to play key roles in tumorigenesis. Nevertheless, the function of m¹A RNA methylation-related genes in BRCA is indistinct.

METHODS

The RNA sequencing (RNA-seq), copy-number variation (CNV), single-nucleotide variant (SNV), and clinical data of BRCA were acquired via The Cancer Genome Atlas (TCGA) database. In addition, the GSE20685 dataset, the external validation set, was acquired from the Gene Expression Omnibus (GEO) database. 10 m¹A RNA methylation regulators were obtained from the previous literature, and further analyzed through differential expression analysis by rank-sum test, mutation by SNV data, and mutual correlation by Pearson Correlation Analysis. Furthermore, the differentially expressed m¹A-related genes were selected through overlapping m¹A-related module genes obtained by weighted gene co-expression network analysis (WGCNA), differentially expressed genes (DEGs) in BRCA and DEGs between high- and low- m¹A score subgroups. The m¹A-related model genes in the risk signature were derived by univariate Cox and least absolute shrinkage and selection operator (LASSO) regression analyses. In addition, a nomogram was built through univariate and multivariate Cox analyses. After that, the immune infiltration between the high- and low-risk groups was investigated through ESTIMATE and CIBERSORT. Finally, the expression trends of model genes in clinical BRCA samples were further confirmed by quantitative real-time PCR (RT‒qPCR).

RESULTS

Eighty-five differentially expressed m¹A-related genes were obtained. Among them, six genes were selected as prognostic biomarkers to build the risk model. The validation results of the risk model showed that its prediction was reliable. In addition, Cox independent prognosis analysis revealed that age, risk score, and stage were independent prognostic factors for BRCA. Moreover, 13 types of immune cells were different between the high- and low-risk groups and the immune checkpoint molecules TIGIT, IDO1, LAG3, ICOS, PDCD1LG2, PDCD1, CD27, and CD274 were significantly different between the two risk groups. Ultimately, RT-qPCR results confirmed that the model genes MEOX1, COL17A1, FREM1, TNN, and SLIT3 were significantly up-regulated in BRCA tissues versus normal tissues.

CONCLUSIONS

An m¹A RNA methylation regulator-related prognostic model was constructed, and a nomogram based on the prognostic model was constructed to provide a theoretical reference for individual counseling and clinical preventive intervention in BRCA.

Radiomic Models Predict Tumor Microenvironment Using Artificial Intelligence-the Novel Biomarkers in Breast Cancer Immune Microenvironment

Breast cancer is the most common malignancy in women, and some subtypes are associated with a poor prognosis with a lack of efficacious therapy. Moreover, immunotherapy and the use of other novel antibody‒drug conjugates have been rapidly incorporated into the standard management of advanced breast cancer. To extract more benefit from these therapies, clarifying and monitoring the tumor microenvironment (TME) status is critical, but this is difficult to accomplish based on conventional approaches. Radiomics is a method wherein radiological image features are comprehensively collected and assessed to build connections with disease diagnosis, prognosis, therapy efficacy, the TME, etc In recent years, studies focused on predicting the TME using radiomics have increasingly emerged, most of which demonstrate meaningful results and show better capability than conventional methods in some aspects. Beyond predicting tumor-infiltrating lymphocytes, immunophenotypes, cytokines, infiltrating inflammatory factors, and other stromal components, radiomic models have the potential to provide a completely new approach to deciphering the TME and facilitating tumor management by physicians.

Tumor Microenvironment, Radiology, and Artificial Intelligence: Should We Consider Tumor Periphery?

OBJECTIVES

The tumor microenvironment (TME) consists of cellular and noncellular components which enable the tumor to interact with its surroundings and plays an important role in the tumor progression and how the immune system reacts to the malignancy. In the present study, we investigate the diagnostic potential of the TME in differentiating benign and malignant lesions using image quantification and machine learning.

METHODS

A total of 229 breast lesions and 220 cervical lymph nodes were included in the study. A group of expert radiologists first performed medical imaging and segmented the lesions, after which a rectangular mask was drawn, encompassing all of the contouring. The mask was extended in each axis up to 50%, and 29 radiomics features were extracted from each mask. Radiomics features that showed a significant difference in each contour were used to develop a support vector machine (SVM) classifier for benign and malignant lesions in breast and lymph node images separately.

RESULTS

Single radiomics features extracted from extended contours outperformed radiologists' contours in both breast and lymph node lesions. Furthermore, when fed into the SVM model, the extended models also outperformed the radiologist's contour, achieving an area under the receiver operating characteristic curve of 0.887 and 0.970 in differentiating breast and lymph node lesions, respectively.

CONCLUSIONS

Our results provide convincing evidence regarding the importance of the tumor periphery and TME in medical imaging diagnosis. We propose that the immediate tumor periphery should be considered for differentiating benign and malignant lesions in image quantification studies.