Tumour heterogeneity revealed by unsupervised decomposition of dynamic contrast-enhanced magnetic resonance imaging is associated with underlying gene expression patterns and poor survival in breast cancer patients

CT-based Machine Learning Radiomics Modeling: Survival Prediction and Mechanism Exploration in Ovarian Cancer Patients

RATIONALE AND OBJECTIVES

To create a radiomics model based on computed tomography (CT) to predict overall survival in ovarian cancer patients. To combine Rad-score with genomic data to explore the association between gene expression and Rad-score.

MATERIALS AND METHODS

Imaging and clinical data from 455 patients with ovarian cancer were retrospectively analyzed. Patients were categorized into training cohort, validation cohort and test cohort. Cox regression analysis and the least absolute shrinkage and selection operator (LASSO) methods were utilized to identify characteristics and develop the Rad-score. Radiomics models were developed and evaluated for predictive efficacy and clinical incremental value. Application of genomic data from the cancer genome atlas (TCGA) to reveal differential genes in different Rad-score groups. Screening hub genes and exploring the functions of hub genes through bioinformatics analysis and machine learning.

RESULTS

Prognostic models based on FIGO, tumor residual disease and Rad-score were developed. The receiver operating characteristic (ROC) curves showed that the 1, 3, and 5 year area under curves (AUCs) of the model were in the training group (0.816, 0.865 and 0.862, respectively), validation group (0.845, 0.877, 0.869, respectively) and test group (0.899, 0.906 and 0.869, respectively) had good predictive accuracy. Calibration curves showed good agreement between observations and predictions. Decision curve analysis revealed a high net benefit of the clinical-radiomics model. The clinical impact curve (CIC) showed good clinical applicability of the clinical-radiomics model. Analysis of sequencing data from the TCGA database revealed EMP1 as a hub gene for radiomics modeling. It revealed that its biological function may be associated with extracellular matrix organization and focal adhesion.

CONCLUSION

Prognostic models based on FIGO, Tumor residual disease, and Rad-score can effectively predict the overall survival (OS) of ovarian cancer patients. Rad-score may enable prognostic prediction of ovarian cancer patients by revealing the expression level of EMP1 and its biological function.

From Images to Genes: Radiogenomics Based on Artificial Intelligence to Achieve Non-Invasive Precision Medicine in Cancer Patients

With the increasing demand for precision medicine in cancer patients, radiogenomics emerges as a promising frontier. Radiogenomics is originally defined as a methodology for associating gene expression information from high-throughput technologies with imaging phenotypes. However, with advancements in medical imaging, high-throughput omics technologies, and artificial intelligence, both the concept and application of radiogenomics have significantly broadened. In this review, the history of radiogenomics is enumerated, related omics technologies, the five basic workflows and their applications across tumors, the role of AI in radiogenomics, the opportunities and challenges from tumor heterogeneity, and the applications of radiogenomics in tumor immune microenvironment. The application of radiogenomics in positron emission tomography and the role of radiogenomics in multi-omics studies is also discussed. Finally, the challenges faced by clinical transformation, along with future trends in this field is discussed.

Radiomics in breast cancer: Current advances and future directions

Breast cancer is a common disease that causes great health concerns to women worldwide. During the diagnosis and treatment of breast cancer, medical imaging plays an essential role, but its interpretation relies on radiologists or clinical doctors. Radiomics can extract high-throughput quantitative imaging features from images of various modalities via traditional machine learning or deep learning methods following a series of standard processes. Hopefully, radiomic models may aid various processes in clinical practice. In this review, we summarize the current utilization of radiomics for predicting clinicopathological indices and clinical outcomes. We also focus on radio-multi-omics studies that bridge the gap between phenotypic and microscopic scale information. Acknowledging the deficiencies that currently hinder the clinical adoption of radiomic models, we discuss the underlying causes of this situation and propose future directions for advancing radiomics in breast cancer research.

Network analysis of histopathological image features and genomics data improving prognosis performance in clear cell renal cell carcinoma

INTRODUCTION

Clear cell renal cell carcinoma is the most common type of kidney cancer, but the prediction of prognosis remains a challenge.

METHODS

We collected whole-slide histopathological images, corresponding clinical and genetic information from the The Cancer Imaging Archive and The Cancer Genome Atlas databases and randomly divided patients into training (n = 197) and validation (n = 84) cohorts. After feature extraction by CellProfiler, we used 2 different machine learning techniques (Least Absolute Shrinkage and Selector Operation-regularized Cox and Support Vector Machine-Recursive Feature Elimination) and weighted gene co-expression network analysis to select prognosis-related image features and genes, respectively. These features and genes were integrated into a joint model using random forest and used to create a nomogram that combines other predictive indicators.

RESULTS

A total of 4 overlapped features were identified, represented by the computed histopathological risk score in the random forest model, and showed predictive value for overall survival (test set: 1-year area under the curves (AUC) = 0.726, 3-year AUC = 0.727, and 5-year AUC = 0.764). The histopathological-genetic risk score (HGRS) integrating the genetic information computed performed better than the model that used image features only (test set: 1-year AUC = 0.682, 3-year AUC = 0.734, and 5-year AUC = 0.78). The nomogram (gender, stage, and HGRS) achieved the highest net benefit according to decision curve analysis compared to HGRS or clinical model.

CONCLUSION

This study developed a histopathological-genetic-related nomogram by combining histopathological features and clinical predictors, providing a more comprehensive prognostic assessment for clear cell renal cell carcinoma patients.

Comparative Evaluation of Machine Learning Models for Subtyping Triple-Negative Breast Cancer: A Deep Learning-Based Multi-Omics Data Integration Approach

Objective: Triple-negative breast cancer (TNBC) poses significant diagnostic challenges due to its aggressive nature. This research develops an innovative deep learning (DL) model based on the latest multi-omics data to enhance the accuracy of TNBC subtype and prognosis prediction. The study focuses on addressing the constraints of prior studies by showcasing a model with substantial advancements in data integration, statistical performance, and algorithmic optimization. Methods: Breast cancer-related molecular characteristic data, including mRNA, miRNA, gene mutations, DNA methylation, and magnetic resonance imaging (MRI) images, were retrieved from the TCGA and TCIA databases. This study not only compared single-omics with multi-omics machine learning models but also applied Bayesian optimization to innovatively optimize the neural network structure of a DL model for multi-omics data. Results: The DL model for multi-omics data significantly outperformed single-omics models in subtype prediction, achieving a 98.0% accuracy in cross-validation, 97.0% in the validation set, and 91.0% in an external test set. Additionally, the MRI radiomics model showed promising performance, especially with the training set; however, a decrease in performance during transfer testing underscored the advantages of the DL model for multi-omics data in data consistency and digital processing. Conclusion: Our multi-omics DL model presents notable innovations in statistical performance and transfer learning capability, bearing significant clinical relevance for TNBC classification and prognosis prediction. While the MRI radiomics model proved effective, it requires further optimization for cross-dataset application to enhance accuracy and consistency. Our findings offer new insights into improving TNBC classification and prognosis through multi-omics data and DL algorithms.

Deconvolution-Based Pharmacokinetic Analysis to Improve the Prediction of Pathological Information of Breast Cancer

Pharmacokinetic (PK) parameters, revealing changes in the tumor microenvironment, are related to the pathological information of breast cancer. Tracer kinetic models (e.g., Tofts-Kety model) with a nonlinear least square solver are commonly used to estimate PK parameters. However, the method is sensitive to noise in images. To relieve the effects of noise, a deconvolution (DEC) method, which was validated on synthetic concentration-time series, was proposed to accurately calculate PK parameters from breast dynamic contrast-enhanced magnetic resonance imaging. A time-to-peak-based tumor partitioning method was used to divide the whole tumor into three tumor subregions with different kinetic patterns. Radiomic features were calculated from the tumor subregion and whole tumor-based PK parameter maps. The optimal features determined by the fivefold cross-validation method were used to build random forest classifiers to predict molecular subtypes, Ki-67, and tumor grade. The diagnostic performance evaluated by the area under the receiver operating characteristic curve (AUC) was compared between the subregion and whole tumor-based PK parameters. The results showed that the DEC method obtained more accurate PK parameters than the Tofts method. Moreover, the results showed that the subregion-based Ktrans (best AUCs = 0.8319, 0.7032, 0.7132, 0.7490, 0.8074, and 0.6950) achieved a better diagnostic performance than the whole tumor-based Ktrans (AUCs = 0.8222, 0.6970, 0.6511, 0.7109, 0.7620, and 0.5894) for molecular subtypes, Ki-67, and tumor grade. These findings indicate that DEC-based Ktrans in the subregion has the potential to accurately predict molecular subtypes, Ki-67, and tumor grade.

Predicting histopathological types and molecular subtype of breast tumors: A comparative study using amide proton transfer-weighted imaging, intravoxel incoherent motion and diffusion kurtosis imaging

PURPOSE

To evaluate the predictive performance of multiparameter and histogram features derived from amide proton transfer-weighted imaging (APTWI), intravoxel incoherent motion (IVIM) and diffusion kurtosis imaging (DKI) for histopathological types of breast tumors.

METHODS

Region of interest (ROI) was delineated by outlining the largest slice of the tumor on the false-color images of the DKI, IVIM and APTWI parameters, and extracted the histogram features. Receiver operating characteristic (ROC) curve was used to evaluate the performance of parameters in predicting benign and malignant breast lesions, molecular prognostic biomarkers, lymph node status, and subtypes of breast lesions. The Spearman correlation coefficient was used to determine the correlations between each parameter and clinical-pathological factors.

RESULTS

All 52 breast lesions were enrolled in this prospective study, including 8 benign lesions and 44 breast cancers. To diagnose malignant and benign breast lesions, the value of APT (min) performed best, with the AUC reaching 0.983. According to the different imaging methods, the APTWI performed best. To predict the positive status of ER, PR, Ki67, the value of Dapp (uniformity), Dapp (uniformity), f (entropy) performed best, with the AUC values reaching 0.743, 0.770, 0.848, respectively. For the identification of Luminal B, HER2-enriched, and TNBC breast cancers, Kapp (max), f (kurtosis), and Dapp (uniformity) performed best, with AUC values reaching 0.679, 0.826, 0.771, respectively.

CONCLUSION

This study found the APTWI, IVIM and DKI parameters could diagnose breast cancer. The histogram features of DKI and IVIM, based on tumor heterogeneity, may help to predict breast cancer subtypes.

Efficient estimation of pharmacokinetic parameters from breast dynamic contrast-enhanced MRI based on a convolutional neural network for predicting molecular subtypes

Objective. Tracer kinetic models allow for estimating pharmacokinetic (PK) parameters, which are related to pathological characteristics, from breast dynamic contrast-enhanced magnetic resonance imaging. However, existing tracer kinetic models subject to inaccuracy are time-consuming for PK parameters estimation. This study aimed to accurately and efficiently estimate PK parameters for predicting molecular subtypes based on convolutional neural network (CNN).Approach. A CNN integrating global and local features (GL-CNN) was trained using synthetic data where known PK parameters map was used as the ground truth, and subsequently used to directly estimate PK parameters (volume transfer constantKtransand flux rate constantKep) map. The accuracy assessed by the peak signal-to-noise ratio (PSNR), structural similarity (SSIM), and concordance correlation coefficient (CCC) was compared between the GL-CNN and Tofts-based PK parameters in synthetic data. Radiomic features were calculated from the PK parameters map in 208 breast tumors. A random forest classifier was constructed to predict molecular subtypes using a discovery cohort (n= 144). The diagnostic performance evaluated on a validation cohort (n= 64) using the area under the receiver operating characteristic curve (AUC) was compared between the GL-CNN and Tofts-based PK parameters.Main results. The average PSNR (48.8884), SSIM (0.9995), and CCC (0.9995) between the GL-CNN-basedKtransmap and ground truth were significantly higher than those between the Tofts-basedKtransmap and ground truth. The GL-CNN-basedKtransobtained significantly better diagnostic performance (AUCs = 0.7658 and 0.8528) than the Tofts-basedKtransfor luminal B and HER2 tumors. The GL-CNN method accelerated the computation by speed approximately 79 times compared to the Tofts method for the whole breast of all patients.Significance. Our results indicate that the GL-CNN method can be used to accurately and efficiently estimate PK parameters for predicting molecular subtypes.

HLA-DQA1 expression is associated with prognosis and predictable with radiomics in breast cancer

BACKGROUND

High HLA-DQA1 expression is associated with a better prognosis in many cancers. However, the association between HLA-DQA1 expression and prognosis of breast cancer and the noninvasive assessment of HLA-DQA1 expression are still unclear. This study aimed to reveal the association and investigate the potential of radiomics to predict HLA-DQA1 expression in breast cancer.

METHODS

In this retrospective study, transcriptome sequencing data, medical imaging data, clinical and follow-up data were downloaded from the TCIA ( https://www.cancerimagingarchive.net/ ) and TCGA ( https://portal.gdc.cancer.gov/ ) databases. The clinical characteristic differences between the high HLA-DQA1 expression group (HHD group) and the low HLA-DQA1 expression group were explored. Gene set enrichment analysis, Kaplan‒Meier survival analysis and Cox regression were performed. Then, 107 dynamic contrast-enhanced magnetic resonance imaging features were extracted, including size, shape and texture. Using recursive feature elimination and gradient boosting machine, a radiomics model was established to predict HLA-DQA1 expression. Receiver operating characteristic (ROC) curves, precision-recall curves, calibration curves, and decision curves were used for model evaluation.

RESULTS

The HHD group had better survival outcomes. The differentially expressed genes in the HHD group were significantly enriched in oxidative phosphorylation (OXPHOS) and estrogen response early and late signalling pathways. The radiomic score (RS) output from the model was associated with HLA-DQA1 expression. The area under the ROC curves (95% CI), accuracy, sensitivity, specificity, positive predictive value, and negative predictive value of the radiomic model were 0.866 (0.775-0.956), 0.825, 0.939, 0.7, 0.775, and 0.913 in the training set and 0.780 (0.629-0.931), 0.659, 0.81, 0.5, 0.63, and 0.714 in the validation set, respectively, showing a good prediction effect.

CONCLUSIONS

High HLA-DQA1 expression is associated with a better prognosis in breast cancer. Quantitative radiomics as a noninvasive imaging biomarker has potential value for predicting HLA-DQA1 expression.

Radiomics Nomogram: Prediction of 2-Year Disease-Free Survival in Young Age Breast Cancer

This study aimed to predict early breast cancer recurrence in women under 40 years of age using radiomics signature and clinicopathological information. We retrospectively investigated 155 patients under 40 years of age with invasive breast cancer who underwent MRI and surgery. Through stratified random sampling, 111 patients were assigned as the training set, and 44 were assigned as the validation set. Recurrence-associated factors were investigated based on recurrence within 5 years during the total follow-up period. A Rad-score was generated through texture analysis (3D slicer, ver. 4.8.0) of breast MRI using the least absolute shrinkage and selection operator Cox regression model. The Rad-score showed a significant association with disease-free survival (DFS) in the training set (p = 0.003) and validation set (p = 0.020) in the Kaplan–Meier analysis. The nomogram was generated through Cox proportional hazards models, and its predictive ability was validated. The nomogram included the Rad-score and estrogen receptor negativity as predictive factors and showed fair DFS predictive ability in both the training and validation sets (C-index 0.63, 95% CI 0.45–0.79). In conclusion, the Rad-score can predict the disease recurrence of invasive breast cancer in women under 40 years of age, and the Rad-score-based nomogram showed reasonably high DFS predictive ability, especially within 2 years of surgery.

Machine learning radiomics can predict early liver recurrence after resection of intrahepatic cholangiocarcinoma

BACKGROUND

Most patients recur after resection of intrahepatic cholangiocarcinoma (IHC). We studied whether machine-learning incorporating radiomics and tumor size could predict intrahepatic recurrence within 1-year.

METHODS

This was a retrospective analysis of patients with IHC resected between 2000 and 2017 who had evaluable computed tomography imaging. Texture features (TFs) were extracted from the liver, tumor, and future liver remnant (FLR). Random forest classification using training (70.3%) and validation cohorts (29.7%) was used to design a predictive model.

RESULTS

138 patients were included for analysis. Patients with early recurrence had a larger tumor size (7.25 cm [IQR 5.2-8.9] vs. 5.3 cm [IQR 4.0-7.2], P = 0.011) and a higher rate of lymph node metastasis (28.6% vs. 11.6%, P = 0.041), but were not more likely to have multifocal disease (21.4% vs. 17.4%, P = 0.643). Three TFs from the tumor, FD1, FD30, and IH4 and one from the FLR, ACM15, were identified by feature selection. Incorporation of TFs and tumor size achieved the highest AUC of 0.84 (95% CI 0.73-0.95) in predicting recurrence in the validation cohort.

CONCLUSION

This study demonstrates that radiomics and machine-learning can reliably predict patients at risk for early intrahepatic recurrence with good discrimination accuracy.

Radiomics predicts the prognosis of patients with locally advanced breast cancer by reflecting the heterogeneity of tumor cells and the tumor microenvironment

Background

This study investigated the efficacy of radiomics to predict survival outcome for locally advanced breast cancer (LABC) patients and the association of radiomics with tumor heterogeneity and microenvironment.

Methods

Patients with LABC from 2010 to 2015 were retrospectively reviewed. Radiomics features were extracted from enhanced MRI. We constructed the radiomics score using lasso and assessed its prognostic value. An external validation cohort from The Cancer Imaging Archive was used to assess phenotype reproducibility. Sequencing data from TCGA and our center were applied to reveal genomic landscape of different radiomics score groups. Tumor infiltrating lymphocytes map and bioinformatics methods were applied to evaluate the heterogeneity of tumor microenvironment. Computational histopathology was also applied.

Results

A total of 278 patients were divided into training cohort and validation cohort. Radiomics score was constructed and significantly associated with disease-free survival (DFS) of the patients in training cohort, validation cohort and external validation cohort (p < 0.001, p = 0.014 and p = 0.041, respectively). The radiomics-based nomogram showed better predictive performance of DFS compared with TNM model. Distinct gene expression patterns were identified. Immunophenotype and immune cell composition was different in each radiomics score group. The link between radiomics and computational histopathology was revealed.

Conclusions

The radiomics score could effectively predict prognosis of LABC after neoadjuvant chemotherapy and radiotherapy. Radiomics revealed heterogeneity of tumor cell and tumor microenvironment and holds great potential to facilitate individualized DFS estimation and guide personalized care.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13058-022-01516-0.

Effectiveness of 5-Fluorouracil and gemcitabine hydrochloride loaded iron‑based chitosan-coated MIL-100 composite as an advanced, biocompatible, pH-sensitive and smart drug delivery system on breast cancer therapy

This study was planned to evolve the bioavailability and therapeutic efficiency of Gemcitabine (GEM) and 5-Fluorouracil with decreased side effects using MIL-100 nano-composite as carrier. Impregnation approach was used for encapsulation of 5-Fluorouracil alone and with GEM inside the MIL-100. The formed 5-Fluorouracil@MIL-100 and 5-Fluorouracil-GEM@MIL-100 were then coated with chitosan, sequentially chelated with iron(III) and conjugated with quercetin, eventually obtaining a multifunctional MIL-100 nanocarrier. The hybrid nanocarrier nascency was verified by different characterization results. pH-sensitive releases of 5-Fluorouracil and GEM were observed because of the inherent pH-dependent stability of MIL-100. Additionally, we evaluated the anti-cancer activity of these nanocarriers through WST-1 analysis and acridine orange staining in MCF-7 human breast cancer and HUVEC control cell lines. Our findings showed that all nanocarriers exhibited anti-cancer activity and induced apoptosis in MCF-7 cells. However, 5-Fluorouracil@MIL-100 and chitosan-coated 5-Fluorouracil@MIL-100 with quercetin were more effective than other nanocarriers in MCF-7 cells (p < 0.05). Moreover, we observed cytotoxicity in HUVEC cells due to the adverse side effects of chemotherapy drugs. However, chitosan coated nanocarriers with quercetin were less toxic on HUVEC cells at particularly 1 µg/mL. Therefore, MIL-100 could be used for a promising chemotherapeutic drugs delivery and chitosan coated drugs with quercetin could be useful for reducing toxicity on normal cells.

Artificial intelligence in clinical research of cancers

Several factors, including advances in computational algorithms, the availability of high-performance computing hardware, and the assembly of large community-based databases, have led to the extensive application of Artificial Intelligence (AI) in the biomedical domain for nearly 20 years. AI algorithms have attained expert-level performance in cancer research. However, only a few AI-based applications have been approved for use in the real world. Whether AI will eventually be capable of replacing medical experts has been a hot topic. In this article, we first summarize the cancer research status using AI in the past two decades, including the consensus on the procedure of AI based on an ideal paradigm and current efforts of the expertise and domain knowledge. Next, the available data of AI process in the biomedical domain are surveyed. Then, we review the methods and applications of AI in cancer clinical research categorized by the data types including radiographic imaging, cancer genome, medical records, drug information and biomedical literatures. At last, we discuss challenges in moving AI from theoretical research to real-world cancer research applications and the perspectives toward the future realization of AI participating cancer treatment.

A deep matrix factorization framework for identifying underlying tissue-specific patterns of DCE-MRI: applications for molecular subtype classification in breast cancer

Objective.Breast cancer is heterogeneous in that different angiogenesis and blood flow characteristics could be present within a tumor. The pixel kinetics of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) can assume several distinct signal patterns related to specific tissue characteristics. Identification of the latent, tissue-specific dynamic patterns of intratumor heterogeneity can shed light on the biological mechanisms underlying the heterogeneity of tumors.Approach.To mine this information, we propose a deep matrix factorization-based dynamic decomposition (DMFDE) model specifically designed according to DCE-MRI characteristics. The time-series imaging data were decomposed into tissue-specific dynamic patterns and their corresponding proportion maps. The image pixel matrix and the reference matrix of population-level kinetics obtained by clustering the dynamic signals were used as the inputs. Two multilayer neural network branches were designed to collaboratively project the input matrix into a latent dynamic pattern and a dynamic proportion matrix, which was justified using simulated data. Clinical implications of DMFDE were assessed by radiomics analysis of proportion maps obtained from the tumor/parenchyma region for classifying the luminal A subtype.Main results.The decomposition performance of DMFDE was evaluated by the root mean square error and was shown to be better than that of the conventional convex analysis of mixtures (CAM) method. The predictive model withK = 3, 4, and 5 dynamic proportion maps generated AUC values of 0.780, 0.786 and 0.790, respectively, in distinguishing between luminal A and nonluminal A tumors, which are better than the CAM method (AUC = 0.726). The combination of statistical features from images with different proportion maps has the highest prediction value (AUC = 0.813), which is significantly higher than that based on CAM.Conclusion.This proposed method identified the latent dynamic patterns associated with different molecular subtypes, and radiomics analysis based on the pixel compositions of the uncovered dynamic patterns was able to determine molecular subtypes of breast cancer.

Radiomic Analysis of Pharmacokinetic Heterogeneity Within Tumor Based on the Unsupervised Decomposition of Dynamic Contrast-Enhanced MRI for Predicting Histological Characteristics of Breast Cancer

BACKGROUND

Breast tumor heterogeneity is associated with histological characteristics. However, pharmacokinetic (PK) heterogeneity within tumor might merit further exploration.

PURPOSE

To enhance the predictive power of molecular subtypes, Ki-67, and tumor grade by analyzing PK heterogeneity within tumor based on dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI).

STUDY TYPE

Retrospective.

POPULATION

Two hundred and eight biopsy-proven breast cancer patients, randomly divided into a training cohort (N = 144) and a testing cohort (N = 64).

FIELD STRENGTH/SEQUENCE

T₁ -weighted DCE-MRI at 3.0 T.

ASSESSMENT

A convex analysis of mixtures-compartmental modeling decomposition method was used to estimate the PK parameter (i.e., the volume transfer constant K^trans ) in tumor subregions with distinct physiological kinetic patterns, including fast-flow kinetics, slow-flow kinetics, and plasma input. Radiomic features based on the PK parameter were calculated from each tumor subregion.

STATISTICAL TESTS

The training cohort was used to build random forest classifiers based on the optimal features determined by the 5-fold cross-validation method. The performance was assessed on the testing cohort using the area under the receiver operating characteristic curve (AUC). The AUCs derived from the tumor subregion-based PK parameter were compared with those of the original images of the entire tumor using the DeLong test. A P-value of <0.05 was considered statistically significant.

RESULTS

The tumor subregion-based PK parameter, which yielded the highest AUCs of 0.8782, 0.7568, 0.7019, 0.7963, 0.8080, and 0.7375 for luminal A, luminal B, basal-like, human epidermal growth factor receptor 2, Ki-67, and tumor grade, respectively, obtained better diagnostic performance than the original images in the entire tumor (highest AUCs = 0.8612, 0.6191, 0.5593, 0.7704, 0.7494, and 0.6261, respectively). In particular, statistically significant improvement in the diagnostic performance was obtained for luminal B.

DATA CONCLUSION

Radiomic analysis of PK heterogeneity within tumor can enhance the predictive performance of radiomic models compared with that of the entire tumor.

LEVEL OF EVIDENCE

4 TECHNICAL EFFICACY STAGE: 3.

Artificial intelligence in tumor subregion analysis based on medical imaging: A review

Medical imaging is widely used in the diagnosis and treatment of cancer, and artificial intelligence (AI) has achieved tremendous success in medical image analysis. This paper reviews AI-based tumor subregion analysis in medical imaging. We summarize the latest AI-based methods for tumor subregion analysis and their applications. Specifically, we categorize the AI-based methods by training strategy: supervised and unsupervised. A detailed review of each category is presented, highlighting important contributions and achievements. Specific challenges and potential applications of AI in tumor subregion analysis are discussed.

Texture analysis using machine learning-based 3-T magnetic resonance imaging for predicting recurrence in breast cancer patients treated with neoadjuvant chemotherapy

OBJECTIVES

To determine whether texture analysis for magnetic resonance imaging (MRI) can predict recurrence in patients with breast cancer treated with neoadjuvant chemotherapy (NAC).

METHODS

This retrospective study included 130 women who received NAC and underwent subsequent surgery for breast cancer between January 2012 and August 2017. We assessed common features, including standard morphologic MRI features and clinicopathologic features. We used a  commercial software and analyzed texture features from pretreatment and midtreatment MRI. A random forest (RF) method was performed to build a model for predicting recurrence. The diagnostic performance of this model for predicting recurrence was assessed and compared with those of five other machine learning classifiers using the Wald test.

RESULTS

Of the 130 women, 21 (16.2%) developed recurrence at a median follow-up of 35.4 months. The RF classifier with common features including clinicopathologic and morphologic MRI features showed the lowest diagnostic performance (area under the receiver operating characteristic curve [AUC], 0.83). The texture analysis with the RF method showed the highest diagnostic performances for pretreatment T2-weighted images and midtreatment DWI and ADC maps showed better diagnostic performance than that of an analysis of common features (AUC, 0.94 vs. 0.83, p < 0.05). The RF model based on all sequences showed a better diagnostic performance for predicting recurrence than did the five other machine learning classifiers.

CONCLUSIONS

Texture analysis using an RF model for pretreatment and midtreatment MRI may provide valuable prognostic information for predicting recurrence in patients with breast cancer treated with NAC and surgery.

KEY POINTS

• RF model-based texture analysis showed a superior diagnostic performance than traditional MRI and clinicopathologic features (AUC, 0.94 vs.0.83, p < 0.05) for predicting recurrence in breast cancer after NAC. • Texture analysis using RF classifier showed the highest diagnostic performances (AUC, 0.94) for pretreatment T2-weighted images and midtreatment DWI and ADC maps. • RF model showed a better diagnostic performance for predicting recurrence than did the five other machine learning classifiers.

Prediction of the clinicopathological subtypes of breast cancer using a fisher discriminant analysis model based on radiomic features of diffusion-weighted MRI

BACKGROUND

The clinicopathological classification of breast cancer is proposed according to therapeutic purposes. It is simplified and can be conducted easily in clinical practice, and this subtyping undoubtedly contributes to the treatment selection of breast cancer. This study aims to investigate the feasibility of using a Fisher discriminant analysis model based on radiomic features of diffusion-weighted MRI for predicting the clinicopathological subtypes of breast cancer.

METHODS

Patients who underwent breast magnetic resonance imaging were confirmed by retrieving data from our institutional picture archiving and communication system (PACS) between March 2013 and September 2017. Five clinicopathological subtypes were determined based on the status of ER, PR, HER2 and Ki-67 from the immunohistochemical test. The radiomic features of diffusion-weighted imaging were derived from the volume of interest (VOI) of each tumour. Fisher discriminant analysis was performed for clinicopathological subtyping by using a backward selection method. To evaluate the diagnostic performance of the radiomic features, ROC analyses were performed to differentiate between immunohistochemical biomarker-positive and -negative groups.

RESULTS

A total of 84 radiomic features of four statistical methods were included after preprocessing. The overall accuracy for predicting the clinicopathological subtypes was 96.4% by Fisher discriminant analysis, and the weighted accuracy was 96.6%. For predicting diverse clinicopathological subtypes, the prediction accuracies ranged from 92 to 100%. According to the cross-validation, the overall accuracy of the model was 82.1%, and the accuracies of the model for predicting the luminal A, luminal B_HER2-, luminal B_HER2+, HER2 positive and triple negative subtypes were 79, 77, 88, 92 and 73%, respectively. According to the ROC analysis, the radiomic features had excellent performance in differentiating between different statuses of ER, PR, HER2 and Ki-67.

CONCLUSIONS

The Fisher discriminant analysis model based on radiomic features of diffusion-weighted MRI is a reliable method for the prediction of clinicopathological breast cancer subtypes.

Can Magnetic Resonance Radiomics Analysis Discriminate Parotid Gland Tumors? A Pilot Study

Our purpose is to evaluate the performance of magnetic resonance (MR) radiomics analysis for differentiating between malignant and benign parotid neoplasms and, among the latter, between pleomorphic adenomas and Warthin tumors. We retrospectively evaluated 75 T2-weighted images of parotid gland lesions, of which 61 were benign tumors (32 pleomorphic adenomas, 23 Warthin tumors and 6 oncocytomas) and 14 were malignant tumors. A receiver operating characteristics (ROC) curve analysis was performed to find the threshold values for the most discriminative features and determine their sensitivity, specificity and area under the ROC curve (AUROC). The most discriminative features were used to train a support vector machine classifier. The best classification performance was obtained by comparing a pleomorphic adenoma with a Warthin tumor (yielding sensitivity, specificity and a diagnostic accuracy as high as 0.8695, 0.9062 and 0.8909, respectively) and a pleomorphic adenoma with malignant tumors (sensitivity, specificity and a diagnostic accuracy of 0.6666, 0.8709 and 0.8043, respectively). Radiomics analysis of parotid tumors on conventional T2-weighted MR images allows the discrimination of pleomorphic adenomas from Warthin tumors and malignant tumors with a high sensitivity, specificity and diagnostic accuracy.

The role of histogram analysis in diffusion-weighted imaging in the differential diagnosis of benign and malignant breast lesions

Background

The present study aims to investigate the role of histogram analysis of intravoxel incoherent motion (IVIM) in the differential diagnosis of benign and malignant breast lesions.

Methods

The magnetic resonance imaging and clinical data of 55 patients (63 lesions) were retrospectively analyzed. The multi-b-valued diffusion-weighted imaging image was processed using the MADC software to obtain the gray-scaled maps of apparent diffusion coefficient (ADC)-slow, ADC-fast and f. The MaZda software was used to extract the histogram metrics of these maps. Combined with the conventional sequence images, the region of interest (ROI) was manually drawn along the edge of the lesion at the maximum level of the gray-scale image, and the difference of the data was analyzed between the benign and malignant breast lesions.

Results

There were 29 patients with 37 benign lesions, which included 23 fibroadenomas, 6 adenosis, 1 breast cysts, 4 intraductal papillomas, and 3 inflammations of breast. Furthermore, 26 malignant lesions in 26 patients, which included 20 non-specific invasive ductal carcinomas, 5 intraductal carcinomas and 1 patient with squamous cell carcinoma. The ADC-slow (mean and the 50th percentile) and f (minimum, mean, kurtosis, the 10th percentile and 50th percentile) of these malignant breast lesions were significantly lower than those of benign lesions (P < 0.05), while ADC-fast (kurtosis) and f (variance, skewness) of these malignant breast lesions were significantly higher than those of benign lesions (P < 0.05).

Conclusion

The histogram analysis of ADC-slow (mean and the 50th percentile), ADC-fast (kurtosis) and f (minimum, mean, kurtosis, the 10th percentile and 50th percentile. Variance, skewness) can provide a more objective and accurate basis for the differential diagnosis of benign and malignant breast lesions.

Preliminary study on discriminating HER2 2+ amplification status of breast cancers based on texture features semi-automatically derived from pre-, post-contrast, and subtraction images of DCE-MRI

Objective

To investigate whether texture features extracted from dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) are associated with human epidermal growth factor receptor type 2 (HER2) 2+ status of breast cancer.

Materials and methods

92 MRI cases including 52 HER2 2+ positive and 40 negative patients confirmed by fluorescence in situ hybridization were retrospectively selected. The lesion area was semi-automatically delineated, and a total of 488 texture features were respectively extracted from precontrast, postcontrast, and subtraction images. The Student’s t-test or Mann-Whitney U test was performed to identify statistically significant features between different HER2 2+ amplification groups. Least absolute shrinkage and selection operator (LASSO) was used to search for the optimal feature subsets. Three machine learning classifiers, logistic regression analysis (LRA), quadratic discriminant analysis (QDA), and support vector machine (SVM), were used with a leave-one-out cross validation method to establish the classification models of HER2 2+ status. Classification performance was evaluated by receiver operating characteristic (ROC) analysis.

Results

Based on the texture analysis with SVM model, the areas under the ROC curve (AUCs) were 0.890 for subtraction images, 0.736 for postcontrast images, and 0.672 for precontrast images, respectively. For LRA model, the AUCs were 0.884, 0.733, and 0.623, respectively. For QDA model, the AUCs were 0.831, 0.726, and 0.568, respectively. LRA and the SVM model with subtraction images reached significantly better performance than the QDA model (P = 0.0227 and P = 0.0088, respectively).

Conclusion

Texture features of breast cancer extracted from DCE-MRI are associated with HER2 2+ status. Additional studies are necessary to confirm the present preliminary findings.

The Association Between Ultrasound Features and Biological Properties of Invasive Breast Carcinoma Is Modified by Age, Tumor Size, and the Preoperative Axilla Status

OBJECTIVES

To investigate the value of ultrasound (US) feature-based models in predicting the proliferation and invasiveness of invasive breast cancer (IBC) and to compare the performance of models based solely on US features with models that combined US features, patient age, tumor size, and axilla status from US.

METHODS

With ethical approval, 746 patients with a pathologic diagnosis of IBC were reviewed for preoperative clinical, US, and postoperative pathologic data. The proliferation and invasiveness properties of the IBC included the histologic grade and Ki-67 status and lymphovascular invasion (LVI) and axillary lymph node metastasis (ALNM), respectively. Logistic regression analyses were used to identify independent risk factors for tumor proliferation and invasiveness.

RESULTS

Posterior echo enhancement, calcification, a tumor size larger than 2 cm, and suspicion of ALNM from axillary US were independent risk factors for a high histologic grade and high Ki-67 expression of IBC (P < .05). A posterior echo shadow, patient age younger than 45 years, and suspicious findings on axillary US imaging were independent variables for predicting the presence of LVI and ALNM in IBC (P < .05). Calcification was the independent factor for predicting LVI (P = .013). The predictive performance of the combined models was improved compared with the US feature-based models, with a higher accuracy rate and negative predictive value. The area under curve of the combined models was also significantly higher than that of the single models (P < .05).

CONCLUSIONS

Compared with the US feature-based models, the combined models yielded better predictive performance. This may provide a more robust model to predict the tumor biological properties of IBC before surgery.

TCGA-TCIA Impact on Radiogenomics Cancer Research: A Systematic Review

In the last decade, the development of radiogenomics research has produced a significant amount of papers describing relations between imaging features and several molecular 'omic signatures arising from next-generation sequencing technology and their potential role in the integrated diagnostic field. The most vulnerable point of many of these studies lies in the poor number of involved patients. In this scenario, a leading role is played by The Cancer Genome Atlas (TCGA) and The Cancer Imaging Archive (TCIA), which make available, respectively, molecular 'omic data and linked imaging data. In this review, we systematically collected and analyzed radiogenomic studies based on TCGA-TCIA data. We organized literature per tumor type and molecular 'omic data in order to discuss salient imaging genomic associations and limitations of each study. Finally, we outlined the potential clinical impact of radiogenomics to improve the accuracy of diagnosis and the prediction of patient outcomes in oncology.