Evaluation of TP53/PIK3CA mutations using texture and morphology analysis on breast MRI

Association of Pathological Features and Multiparametric MRI-Based Radiomics With TP53-Mutated Prostate Cancer

BACKGROUND

TP53 mutations are associated with prostate cancer (PCa) prognosis and therapy.

PURPOSE

To develop TP53 mutation classification models for PCa using MRI radiomics and clinicopathological features.

STUDY TYPE

Retrospective.

POPULATION

388 patients with PCa from two centers (Center 1: 281 patients; Center 2: 107 patients). Cases from Center 1 were randomly divided into training and internal validation sets (7:3). Cases from Center 2 were used for external validation.

FIELD STRENGTH/SEQUENCE

3.0T/T2-weighted imaging, dynamic contrast-enhanced imaging, diffusion-weighted imaging.

ASSESSMENT

Each patient's index tumor lesion was manually delineated on the above MRI images. Five clinicopathological and 428 radiomics features were obtained from each lesion. Radiomics features were selected by least absolute shrinkage and selection operator and binary logistic regression (LR) analysis, while clinicopathological features were selected using Mann-Whitney U test. Radiomics models were constructed using LR, support vector machine (SVM), and random forest (RF) classifiers. Clinicopathological-radiomics combined models were constructed using the selected radiomics and clinicopathological features with the aforementioned classifiers.

STATISTICAL TESTS

Mann-Whitney U test. Receiver operating characteristic (ROC) curve analysis and area under the curve (AUC). P value <0.05 indicates statistically significant.

RESULTS

In the internal validation set, the radiomics model had an AUC of 0.74 with the RF classifier, which was significantly higher than LR (AUC = 0.61), but similar to SVM (AUC = 0.69; P = 0.422). For the combined model, the AUC of RF model was 0.84, which was significantly higher than LR (0.64), but similar to SVM (0.80; P = 0.548). Both the combined RF and combined SVM models showed significantly higher AUCs than the radiomics models. In the external validation set, the combined RF and combined SVM models showed AUCs of 0.83 and 0.82.

DATA CONCLUSION

Pathological-radiomics combined models with RF, SVM show the association of TP53 mutations and pathological-radiomics features of PCa.

EVIDENCE LEVEL

3 TECHNICAL EFFICACY: Stage 2.

IMAGGS: a radiogenomic framework for identifying multi-way associations in breast cancer subtypes

Investigating correlations between radiomic and genomic profiling in breast cancer (BC) molecular subtypes is crucial for understanding disease mechanisms and providing personalized treatment. We present a well-designed radiogenomic framework image-gene-gene set (IMAGGS), which detects multi-way associations in BC subtypes by integrating radiomic and genomic features. Our dataset consists of 721 patients, each of whom has 12 ultrasound (US) images captured from different angles and gene mutation data. To better characterize tumor traits, 12 multi-angle US images are fused using two distinct strategies. Then, we analyze complex many-to-many associations between phenotypic and genotypic features using a machine learning algorithm, deviating from the prevalent one-to-one relationship pattern observed in previous studies. Key radiomic and genomic features are screened using these associations. In addition, gene set enrichment analysis is performed to investigate the joint effects of gene sets and delve deeper into the biological functions of BC subtypes. We further validate the feasibility of IMAGGS in a glioblastoma multiforme dataset to demonstrate the scalability of IMAGGS across different modalities and diseases. Taken together, IMAGGS provides a comprehensive characterization for diseases by associating imaging, genes, and gene sets, paving the way for biological interpretation of radiomics and development of targeted therapy.

Unraveling the Pivotal Network of Ultrasound and Somatic Mutations in Triple-Negative and Non-Triple-Negative Breast Cancer

Purpose

The emergence of genomic targeted therapy has improved the prospects of treatment for breast cancer (BC). However, genetic testing relies on invasive and sophisticated procedures.

Patients and Methods

Here, we performed ultrasound (US) and target sequencing to unravel the possible association between US radiomics features and somatic mutations in TNBC (n=83) and non-TNBC (n=83) patients. Least absolute shrinkage and selection operator (Lasso) were utilized to perform radiomic feature selection. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was utilized to identify the signaling pathways associated with radiomic features.

Results

Thirteen differently represented radiomic features were identified in TNBC and non-TNBC, including tumor shape, textual, and intensity features. The US radiomic-gene pairs were differently exhibited between TNBC and non-TNBC. Further investigation with KEGG verified radiomic-pathway (ie, JAK-STAT, MAPK, Ras, Wnt, microRNAs in cancer, PI3K-Akt) associations in TNBC and non-TNBC.

Conclusion

The pivotal network provided the connections of US radiogenomic signature and target sequencing for non-invasive genetic assessment of precise BC treatment.

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.

TP53 Mutation Estimation Based on MRI Radiomics Analysis for Breast Cancer

BACKGROUND

Noninvasive detection of TP53 mutations is useful for the molecular stratification of breast cancer.

PURPOSE

To explore MRI radiomics features reflecting TP53 mutations in breast cancer and propose a classifier for detecting such mutations.

STUDY TYPE

Retrospective.

POPULATION/SUBJECTS

A total of 139 breast cancer patients with TP53 expression profiling (98 with TP53 mutations and 41 without TP53 mutations).

FIELD STRENGTH/SEQUENCE

1.5 T, T1-weighted (T1W) DCE-MRI.

ASSESSMENT

Lesions were manually segmented using subtracted T1WI. A total of 944 radiomics features (including 744 wavelet-related features) and 7 clinicopathological features were extracted from each lesion. Principal component analysis and Pearson's correlation analysis were used to preprocess the features. Linear discriminant analysis, logistic regression (LR), support vector machine (SVM), and random forest (RF) were used as the classifiers.

STATISTICAL TESTS

Analysis of variance, Kruskal-Wallis and recursive features elimination were used to select features. Receiver operating characteristic (ROC) analysis was performed to compare the diagnostic accuracy.

RESULTS

For the radiomics model, the validation cohorts AUCs of the four classifiers ranged from 0.69 (RF) to 0.74 (LR), and LR (0.74) attained the highest AUCs. For the clinicopathological-radiomics combined model, the validation AUCs of the four classifiers ranged from 0.68 (RF) to 0.86 (SVM), and SVM (0.86) attained highest AUCs. In the subgroup analysis of triple-negative (TN) and luminal type breast cancer, RF achieved the highest AUCs (0.83 and 0.94).

DATA CONCLUSION

Clinicopathological-radiomics combined model with SVM could be used as noninvasive biomarkers for predicting TP53 mutations. RF was recommended for the detection of TP53 mutations in TN and luminal type breast cancer.

LEVEL OF EVIDENCE

3 TECHNICAL EFFICACY: Stage 2.

Multimodality MRI radiomics analysis of TP53 mutations in triple negative breast cancer

Objectives

To explore the value of T1-weighted imaging (T1WI), T2-weighted imaging (T2WI) and diffusion-weighted imaging (DWI) radiomics features reflecting TP53 mutations in patients with triple negative breast cancer (TNBC).

Study design

This retrospective study enrolled 91 patients with TNBC with TP53 testing (64 patients in the training cohort and 27 patients in the validation cohort). A total of 2832 radiomics features were extracted from the first phase of dynamic contrast-enhanced T1WI, T2WI and ADC maps. Analysis of variance (ANOVA) and the Kruskal-Wallis-test were used for feature selection. Then, linear discriminant analysis (LDA), multilayer perceptron (MLP), logistic regression (LR), LR with LASSO, decision tree (DT), naïve Bayes (NB), random forest (RF), and support vector machine (SVM) models were used for classification.

Results

The validation AUCs of the eight classifiers ranged from 0.74 (NB) to 0.85 (SVM). SVM attained the highest AUC (0.85) and diagnostic accuracy (0.82) of all tested models. The top 3 ranking features in the SVM model were T1-square-first order-skewness (coefficient: 1.735), T2-wavelet-LHH-GLCM-joint energy, and T2-wavelet-LHH-GLCM-inverse difference moment (coefficient: -0.654, -0.634).

Conclusions

Radiomics-based analysis with the SVM model is recommended for the detection of TP53 mutations in TNBC. Furthermore, T1WI- and T2WI-related features could be used as noninvasive biomarkers for predicting TP53 mutations.

Ultrasonic Features and Molecular Subtype Predict Somatic Mutations in TP53 and PIK3CA Genes in Breast Cancer

RATIONALE AND OBJECTIVES

To predict mutations in TP53 and PIK3CA genes in breast cancer using ultrasound (US) signatures and clinicopathology.

MATERIALS AND METHODS

In this study, we developed and trained a model in 386 breast cancer patients to predict TP53 and PIK3CA mutations. The clinicopathological and US characteristics (including two-dimensional and color Doppler US) were investigated. Statistically significant variables were used to build predictive models, then a combined model was developed using the multivariate logistic regression analysis.

RESULTS

Univariate and multivariate analyses revealed that calcifications on US was an independent predictor of TP53 mutation (p < 0.05), whereas diameter on US and US type were independent predictors of PIK3CA mutation in breast cancer (all p < 0.05). Meanwhile, Luminal B/Human epidermal growth factor receptor two-positive (HER2+), HER2+/estrogen receptor-negative (ER-), and triple-negative breast cancer (TNBC) subtypes were strong predictors of TP53 mutation (odds ratio [OR] = 3.13, 3.18, 3.44, respectively, all p < 0.05). HER2+/ER- and TNBC subtypes were negative predictors of PIK3CA mutation (OR = 0.223, 0.241, respectively, all p < 0.05). The areas under curves (AUCs) for PIK3CA mutation in the training set increased from 0.553-0.610 to 0.741 in the multivariate model that combined US features and molecular subtype, with a sensitivity and specificity of 80.6% and 58.7%, respectively. The application of the multivariate model in the validation set achieved acceptable discrimination (AUC = 0.715). For TP53 mutation, the AUC was 0.653.

CONCLUSION

US is a non-invasive modality to recognize the presence of TP53 and PIK3CA mutation. The models combined with US features and molecular subtype have implications for the practical application of predicting gene mutation for individual decision-making regarding treatment planning.

Evaluation of physician performance using a concurrent-read artificial intelligence system to support breast ultrasound interpretation

Purpose

The purpose of this study was to compare the diagnostic performance and the interpretation time of breast ultrasound examination between reading without and with the artificial intelligence (AI) system as a concurrent reading aid.

Material and methods

A fully crossed multi-reader and multi-case (MRMC) reader study was conducted. Sixteen participating physicians were recruited and retrospectively interpreted 172 breast ultrasound cases in two reading scenarios, once without and once with the AI system (BU-CAD™, TaiHao Medical Inc.) assistance for concurrent reading. Interpretations of any given case set with and without the AI system were separated by at least 5 weeks. These reading results were compared to the reference standard and the area under the LROC curve (AUCLROC), sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated for performance evaluations. The interpretation time was also compared between the unaided and aided scenarios.

Results

With the help of the AI system, the readers had higher diagnostic performance with an increase in the average AUCLROC from 0.7582 to 0.8294 with statistically significant. The sensitivity, specificity, PPV, and NPV were also improved from 95.77%, 24.07%, 44.18%, and 93.50%–98.17%, 30.67%, 46.91%, and 96.10%, respectively. Of these, the improvement in specificity reached statistical significance. The average interpretation time was significantly reduced by approximately 40% when the readers were assisted by the AI system.

Conclusion

The concurrent-read AI system improves the diagnostic performance in detecting and diagnosing breast lesions on breast ultrasound images. In addition, the interpretation time is effectively reduced for the interpreting physicians.

•

A reader study was conducted to compare the breast ultrasound interpreting performance without and with the aid of AI system.

•

The performance of breast ultrasound interpretation was improved by the AI system as a concurrent reading aid.

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The breast ultrasound interpretation time is significantly reduced by the AI system as a concurrent reading aid.

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The reproducibility experiments of the same lesion cropped by different rectangular proved the robustness of the AI system.

Using an Improved Residual Network to Identify PIK3CA Mutation Status in Breast Cancer on Ultrasound Image

Background

The detection of phosphatidylinositol-3 kinase catalytic alpha (PIK3CA) gene mutations in breast cancer is a key step to design personalizing an optimal treatment strategy. Traditional genetic testing methods are invasive and time-consuming. It is urgent to find a non-invasive method to estimate the PIK3CA mutation status. Ultrasound (US), one of the most common methods for breast cancer screening, has the advantages of being non-invasive, fast imaging, and inexpensive. In this study, we propose to develop a deep convolutional neural network (DCNN) to identify PIK3CA mutations in breast cancer based on US images.

Materials and Methods

We retrospectively collected 312 patients with pathologically confirmed breast cancer who underwent genetic testing. All US images (n=800) of breast cancer patients were collected and divided into the training set (n=600) and test set (n=200). A DCNN-Improved Residual Network (ImResNet) was designed to identify the PIK3CA mutations. We also compared the ImResNet model with the original ResNet50 model, classical machine learning models, and other deep learning models.

Results

The proposed ImResNet model has the ability to identify PIK3CA mutations in breast cancer based on US images. Notably, our ImResNet model outperforms the original ResNet50, DenseNet201, Xception, MobileNetv2, and two machine learning models (SVM and KNN), with an average area under the curve (AUC) of 0.775. Moreover, the overall accuracy, average precision, recall rate, and F1-score of the ImResNet model achieved 74.50%, 74.17%, 73.35%, and 73.76%, respectively. All of these measures were significantly higher than other models.

Conclusion

The ImResNet model gives an encouraging performance in predicting PIK3CA mutations based on breast US images, providing a new method for noninvasive gene prediction. In addition, this model could provide the basis for clinical adjustments and precision treatment.

Differentiating TP53 Mutation Status in Pancreatic Ductal Adenocarcinoma Using Multiparametric MRI-Derived Radiomics

Objectives

This study assessed the preoperative prediction of TP53 status based on multiparametric magnetic resonance imaging (mpMRI) radiomics extracted from two-dimensional (2D) and 3D images.

Methods

57 patients with pancreatic cancer who underwent preoperative MRI were included. The diagnosis and TP53 gene test were based on resections. Of the 57 patients included 37 mutated TP53 genes and the remaining 20 had wild-type TP53 genes. Two radiologists performed manual tumour segmentation on seven different MRI image acquisition sequences per patient, including multi-phase [pre-contrast, late arterial phase (ap), portal venous phase, and delayed phase] dynamic contrast enhanced (DCE) T1-weighted imaging, T2-weighted imaging (T2WI), Diffusion-weighted imaging (DWI), and apparent diffusion coefficient (ADC). PyRadiomics-package was used to generate 558 two-dimensional (2D) and 994 three-dimensional (3D) image features. Models were constructed by support vector machine (SVM) for differentiating TP53 status and DX score method were used for feature selection. The evaluation of the model performance included area under the curve (AUC), accuracy, calibration curves, and decision curve analysis.

Results

The 3D ADC-ap-DWI-T2WI model with 11 selected features yielded the best performance for differentiating TP53 status, with accuracy = 0.91 and AUC = 0.96. The model showed the good calibration. The decision curve analysis indicated that the radiomics model had clinical utility.

Conclusions

A non-invasive and quantitative mpMRI-based radiomics model can accurately predict TP53 mutation status in pancreatic cancer patients and contribute to the precision treatment.

MRI-based radiogenomics analysis for predicting genetic alterations in oncogenic signalling pathways in invasive breast carcinoma

AIM

To investigate the effect of radiomics in the assessment of alterations in canonical cancer pathways in breast cancer.

MATERIALS AND METHODS

Eighty-eight biopsy-proven breast cancer cases were included in the present study. Radiomics features were extracted from T1-weighted sagittal dynamic contrast-enhanced magnetic resonance imaging (MRI) images. Radiomics signatures were developed to predict genetic alterations in the cell cycle, Myc, PI3K, RTK/RAS, and p53 signalling pathways by using hypothesis testing combined with least absolute shrinkage and selection operator (LASSO) regression analysis. The predictive powers of the models were examined by the area under the curve (AUC) of the receiver operating characteristic curve.

RESULTS

A total of 5,234 radiomics features were obtained from MRI images based on the tumour region of interest. Hypothesis tests screened 250, 229, 156, 785, and 319 radiomics features that were differentially displayed between cell cycle, Myc, PI3K, RTK/RAS, and p53 alterations and no alteration status. According to the LASSO algorithm, 11, 12, 12, 15, and 13 features were identified for the construction of the radiomics signatures to predict cell cycle, Myc, PI3K, RTK/RAS, and p53 alterations, with AUC values of 0.933, 0.926, 0.956, 0.940, and 0.886, respectively. The cell cycle radiomics score correlated closely with the RTK/RAS and p53 radiomics scores. These signatures were also dysregulated in patients with different oestrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2 statuses.

CONCLUSION

MRI-based radiogenomics analysis exhibits excellent performance in predicting genetic pathways alterations, thus providing a novel approach for non-invasively obtaining genetic-level molecular characteristics of tumours.