Tumor habitat analysis by magnetic resonance imaging distinguishes tumor progression from radiation necrosis in brain metastases after stereotactic radiosurgery

Prediction of treatment response after stereotactic radiosurgery of brain metastasis using deep learning and radiomics on longitudinal MRI data

We developed artificial intelligence models to predict the brain metastasis (BM) treatment response after stereotactic radiosurgery (SRS) using longitudinal magnetic resonance imaging (MRI) data and evaluated prediction accuracy changes according to the number of sequential MRI scans. We included four sequential MRI scans for 194 patients with BM and 369 target lesions for the Developmental dataset. The data were randomly split (8:2 ratio) for training and testing. For external validation, 172 MRI scans from 43 patients with BM and 62 target lesions were additionally enrolled. The maximum axial diameter (Dmax), radiomics, and deep learning (DL) models were generated for comparison. We evaluated the simple convolutional neural network (CNN) model and a gated recurrent unit (Conv-GRU)-based CNN model in the DL arm. The Conv-GRU model performed superior to the simple CNN models. For both datasets, the area under the curve (AUC) was significantly higher for the two-dimensional (2D) Conv-GRU model than for the 3D Conv-GRU, Dmax, and radiomics models. The accuracy of the 2D Conv-GRU model increased with the number of follow-up studies. In conclusion, using longitudinal MRI data, the 2D Conv-GRU model outperformed all other models in predicting the treatment response after SRS of BM.

MRI-based intratumoral and peritumoral radiomics for preoperative prediction of glioma grade: a multicenter study

Background

Accurate preoperative prediction of glioma is crucial for developing individualized treatment decisions and assessing prognosis. In this study, we aimed to establish and evaluate the value of integrated models by incorporating the intratumoral and peritumoral features from conventional MRI and clinical characteristics in the prediction of glioma grade.

Methods

A total of 213 glioma patients from two centers were included in the retrospective analysis, among which, 132 patients were classified as the training cohort and internal validation set, and the remaining 81 patients were zoned as the independent external testing cohort. A total of 7728 features were extracted from MRI sequences and various volumes of interest (VOIs). After feature selection, 30 radiomic models depended on five sets of machine learning classifiers, different MRI sequences, and four different combinations of predictive feature sources, including features from the intratumoral region only, features from the peritumoral edema region only, features from the fusion area including intratumoral and peritumoral edema region (VOI-fusion), and features from the intratumoral region with the addition of features from peritumoral edema region (feature-fusion), were established to select the optimal model. A nomogram based on the clinical parameter and optimal radiomic model was constructed for predicting glioma grade in clinical practice.

Results

The intratumoral radiomic models based on contrast-enhanced T1-weighted and T2-flair sequences outperformed those based on a single MRI sequence. Moreover, the internal validation and independent external test underscored that the XGBoost machine learning classifier, incorporating features extracted from VOI-fusion, showed superior predictive efficiency in differentiating between low-grade gliomas (LGG) and high-grade gliomas (HGG), with an AUC of 0.805 in the external test. The radiomic models of VOI-fusion yielded higher prediction efficiency than those of feature-fusion. Additionally, the developed nomogram presented an optimal predictive efficacy with an AUC of 0.825 in the testing cohort.

Conclusion

This study systematically investigated the effect of intratumoral and peritumoral radiomics to predict glioma grading with conventional MRI. The optimal model was the XGBoost classifier coupled radiomic model based on VOI-fusion. The radiomic models that depended on VOI-fusion outperformed those that depended on feature-fusion, suggesting that peritumoral features should be rationally utilized in radiomic studies.

Component prediction in combined hepatocellular carcinoma-cholangiocarcinoma: habitat imaging and its biologic underpinnings

PURPOSE

To construct an MRI-based habitat imaging model to help predict component percentage in combined hepatocellular carcinoma-cholangiocarcinoma (cHCC-CCA) preoperatively, and investigate the biologic underpinnings of habitat imaging in cHCC-CCA.

METHODS

The study consisted of one retrospective model-building dataset and one prospective validation dataset from two hospitals. All voxels were assigned into different clusters according to the similarity of enhancement pattern by using K-means clustering method, and each habitat's volume fraction in each lesion was calculated. Least absolute shrinkage and selection operator (LASSO) regression analysis was performed to select optimal predictors, and then to establish an MRI-based habitat imaging model. R-squared was calculated to evaluate performance of the prediction models. Model performance was also verified in the prospective dataset with RNA sequencing data, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was then applied to investigate the biologic underpinnings of habitat imaging.

RESULTS

A total of 129 patients were enrolled (mean age, 56.1 ± 10.4, 102 man), among which 104 patients were in the retrospective model-building set, while 25 patients in the prospective validation set. Three habitats, habitat1 (HCC-alike habitat), habitat2 (iCCA-alike habitat), and habitat3 (in-between habitat), were identified. Habitat 1's volume fraction, habitat 3's volume fraction, nonrim APHE, nonperipheral washout, and LI-RADS categorization were selected to develop an HCC percentage prediction model with R-squared of 0.611 in the model-building set and 0.541 in the validation set. Habitat 1's volume fraction was correlated with genes involved in regulation of actin cytoskeleton and Rap1 signaling pathway, which regulate cell migration and tumor metastasis.

CONCLUSION

Preoperative prediction of HCC percentage in patients with cHCC-CCA was achieved using an MRI-based habitat imaging model, which may correlate with signaling pathways regulating cell migration and tumor metastasis.

Do Habitat MRI and Fractal Analysis Help Distinguish Triple-Negative Breast Cancer From Non-Triple-Negative Breast Carcinoma

Purpose: To determine whether multiparametric MRI-based spatial habitats and fractal analysis can help distinguish triple-negative breast cancer (TNBC) from non-TNBC. Method: Multiparametric DWI and DCE-MRI at 3T were obtained from 142 biopsy- and surgery-proven breast cancer with 148 breast lesions (TNBC = 26 and non-TNBC = 122). The contrast-enhancing lesions were divided into 3 spatial habitats based on perfusion and diffusion patterns using K-means clustering. The fractal dimension (FD) of the tumour subregions was calculated. The accuracy of the habitat segmentation was measured using the Dice index. Inter- and intra-reader reliability were evaluated with the intraclass correlation coefficient (ICC). The ability to predict TNBC status was assessed using the receiver operating characteristic curve. Results: The Dice index for the whole tumour was 0.81 for inter-reader and 0.88 for intra-reader reliability. The inter- and intra-reader reliability were excellent for all 3 tumour habitats and fractal features (ICC > 0.9). TNBC had a lower hypervascular cellular habitat and higher FD 1 compared to non-TNBC (all P < .001). Multivariate analysis confirmed that hypervascular cellular habitat (OR = 0.88) and FD 1 (OR = 1.35) were independently associated with TNBC (all P < .001) after adjusting for rim enhancement, axillary lymph nodes status, and histological grade. The diagnostic model combining hypervascular cellular habitat and FD 1 showed excellent discriminatory ability for TNBC, with an AUC of 0.951 and an accuracy of 91.9%. Conclusions: The fraction of hypervascular cellular habitat and its FD may serve as useful imaging biomarkers for predicting TNBC status.

Non-invasive decision support for clinical treatment of non-small cell lung cancer using a multiscale radiomics approach

BACKGROUND

Selecting therapeutic strategies for cancer patients is typically based on key target-molecule biomarkers that play an important role in cancer onset, progression, and prognosis. Thus, there is a pressing need for novel biomarkers that can be utilized longitudinally to guide treatment selection.

METHODS

Using data from 508 non-small cell lung cancer (NSCLC) patients across three institutions, we developed and validated a comprehensive predictive biomarker that distinguishes six genotypes and infiltrative immune phenotypes. These features were analyzed to establish the association between radiological phenotypes and tumor genotypes/immune phenotypes and to create a radiological interpretation of molecular features. In addition, we assessed the sensitivity of the models by evaluating their performance at five different voxel intervals, resulting in improved generalizability of the proposed approach.

FINDINGS

The radiomics model we developed, which integrates clinical factors and multi-regional features, outperformed the conventional model that only uses clinical and intratumoral features. Our combined model showed significant performance for EGFR, KRAS, ALK, TP53, PIK3CA, and ROS1 mutation status with AUCs of 0.866, 0.874, 0.902, 0.850, 0.860, and 0.900, respectively. Additionally, the predictive performance for PD-1/PD-L1 was 0.852. Although the performance of all models decreased to different degrees at five different voxel space resolutions, the performance advantage of the combined model did not change.

CONCLUSIONS

We validated multiscale radiomic signatures across tumor genotypes and immunophenotypes in a multi-institutional cohort. This imaging-based biomarker offers a non-invasive approach to select patients with NSCLC who are sensitive to targeted therapies or immunotherapy, which is promising for developing personalized treatment strategies during therapy.

Evaluate the Microvascular Invasion of Hepatocellular Carcinoma (≤5 cm) and Recurrence Free Survival with Gadoxetate Disodium-Enhanced MRI-Based Habitat Imaging

BACKGROUND

Tumors are heterogenous and consist of subregions, also known as tumoral habitats, each exhibiting varied biological characteristics. Each habitat corresponds to a cluster of tissue sharing similar structural, metabolic, or functional characteristics. The habitat imaging technique facilitates both the visualization and quantification of these tumoral habitats.

PURPOSE

To evaluate the microvascular invasion (MVI) in hepatocellular carcinoma (HCC) (≤5 cm) and assess the recurrence-free survival (RFS) using gadoxetate disodium-enhanced MRI-based habitat imaging.

STUDY TYPE

Retrospective.

SUBJECTS

180 patients (52.9 years ± 11.7, 156 men) with HCC.

FIELD STRENGTH/SEQUENCE

1.5T/contrast-enhanced T1-weighted gradient-echo sequence.

ASSESSMENT

The enhancement ratio of signal intensity at the arterial phase (AER) and hepatobiliary phase (HBPER) were calculated. The HCC lesions and their peritumoral tissues of 3, 5, and 7 mm were encoded into four habitats. The volume fraction of each habitat was then quantified. The diagnostic performance was assessed using the receiver operating characteristic analysis with 5-fold cross-validation. The RFS was evaluated with Kaplan-Meier curves.

RESULTS

Habitat 2 (with median to high AER and low HBPER) within the peritumoral tissue of 3 mm (f2 -P3 ) and tumor diameter could serve as independent risk factors for MVI and showed the statistical significance (odds ratio (OR) of f2 -P3  = 1.170, 95% CI = 1.099-1.246; OR of tumor diameter: 6.112, 95% CI = 2.162-17.280). A nomogram was developed by incorporating f2 -P3 and tumor diameter, demonstrating high diagnostic accuracy. The area under the curve from 5-fold cross-validation ranged from 0.880 to 1.000. Additionally, the nomogram model demonstrated high efficacy in risk stratification for RFS.

CONCLUSION

Habitat imaging of HCC and its peritumoral microenvironment has the potential for noninvasive and preoperative identification of MVI and prognostic assessment.

LEVEL OF EVIDENCE

3 TECHNICAL EFFICACY: Stage 2.

Habitat Radiomics Based on MRI for Predicting Platinum Resistance in Patients with High-Grade Serous Ovarian Carcinoma: A Multicenter Study

RATIONALE AND OBJECTIVES

This study aims to explore the feasibility of MRI-based habitat radiomics for predicting response of platinum-based chemotherapy in patients with high-grade serous ovarian carcinoma (HGSOC), and compared to conventional radiomics and deep learning models.

MATERIALS AND METHODS

A retrospective study was conducted on HGSOC patients from three hospitals. K-means algorithm was used to perform clustering on T2-weighted images (T2WI), contrast-enhanced T1-weighted images (CE-T1WI), and apparent diffusion coefficient (ADC) maps. After feature extraction and selection, the radiomics model, habitat model, and deep learning model were constructed respectively to identify platinum-resistant and platinum-sensitive patients. A nomogram was developed by integrating the optimal model and clinical independent predictors. The model performance and benefit was assessed using the area under the receiver operating characteristic curve (AUC), net reclassification index (NRI), and integrated discrimination improvement (IDI).

RESULTS

A total of 394 eligible patients were incorporated. Three habitats were clustered, a significant difference in habitat 2 (weak enhancement, high ADC values, and moderate T2WI signal) was found between the platinum-resistant and platinum-sensitive groups (P < 0.05). Compared to the radiomics model (0.640) and deep learning model (0.603), the habitat model had a higher AUC (0.710). The nomogram, combining habitat signatures with a clinical independent predictor (neoadjuvant chemotherapy), yielded a highest AUC (0.721) among four models, with positive NRI and IDI.

CONCLUSION

MRI-based habitat radiomics had the potential to predict response of platinum-based chemotherapy in patients with HGSOC. The nomogram combining with habitat signature had a best performance and good model gains for identifying platinum-resistant patients.

Multiparametric MRI: From Simultaneous Rapid Acquisition Methods and Analysis Techniques Using Scoring, Machine Learning, Radiomics, and Deep Learning to the Generation of Novel Metrics

ABSTRACT

With the recent advancements in rapid imaging methods, higher numbers of contrasts and quantitative parameters can be acquired in less and less time. Some acquisition models simultaneously obtain multiparametric images and quantitative maps to reduce scan times and avoid potential issues associated with the registration of different images. Multiparametric magnetic resonance imaging (MRI) has the potential to provide complementary information on a target lesion and thus overcome the limitations of individual techniques. In this review, we introduce methods to acquire multiparametric MRI data in a clinically feasible scan time with a particular focus on simultaneous acquisition techniques, and we discuss how multiparametric MRI data can be analyzed as a whole rather than each parameter separately. Such data analysis approaches include clinical scoring systems, machine learning, radiomics, and deep learning. Other techniques combine multiple images to create new quantitative maps associated with meaningful aspects of human biology. They include the magnetic resonance g-ratio, the inner to the outer diameter of a nerve fiber, and the aerobic glycolytic index, which captures the metabolic status of tumor tissues.

Tumor Habitat Analysis Using Longitudinal Physiological MRI to Predict Tumor Recurrence After Stereotactic Radiosurgery for Brain Metastasis

OBJECTIVE

It is difficult to predict the treatment response of tissue after stereotactic radiosurgery (SRS) because radiation necrosis (RN) and tumor recurrence can coexist. Our study aimed to predict tumor recurrence, including the recurrence site, after SRS of brain metastasis by performing a longitudinal tumor habitat analysis.

MATERIALS AND METHODS

Two consecutive multiparametric MRI examinations were performed for 83 adults (mean age, 59.0 years; range, 27-82 years; 44 male and 39 female) with 103 SRS-treated brain metastases. Tumor habitats based on contrast-enhanced T1- and T2-weighted images (structural habitats) and those based on the apparent diffusion coefficient (ADC) and cerebral blood volume (CBV) images (physiological habitats) were defined using k-means voxel-wise clustering. The reference standard was based on the pathology or Response Assessment in Neuro-Oncologycriteria for brain metastases (RANO-BM). The association between parameters of single-time or longitudinal tumor habitat and the time to recurrence and the site of recurrence were evaluated using the Cox proportional hazards regression analysis and Dice similarity coefficient, respectively.

RESULTS

The mean interval between the two MRI examinations was 99 days. The longitudinal analysis showed that an increase in the hypovascular cellular habitat (low ADC and low CBV) was associated with the risk of recurrence (hazard ratio [HR], 2.68; 95% confidence interval [CI], 1.46-4.91; P = 0.001). During the single-time analysis, a solid low-enhancing habitat (low T2 and low contrast-enhanced T1 signal) was associated with the risk of recurrence (HR, 1.54; 95% CI, 1.01-2.35; P = 0.045). A hypovascular cellular habitat was indicative of the future recurrence site (Dice similarity coefficient = 0.423).

CONCLUSION

After SRS of brain metastases, an increased hypovascular cellular habitat observed using a longitudinal MRI analysis was associated with the risk of recurrence (i.e., treatment resistance) and was indicative of recurrence site. A tumor habitat analysis may help guide future treatments for patients with brain metastases.

Diagnostic accuracy of MRI techniques for treatment response evaluation in patients with brain metastasis: A systematic review and meta-analysis

BACKGROUND

Treatment response assessment in patients with brain metastasis uses contrast enhanced T1-weighted MRI. Advanced MRI techniques have been studied, but the diagnostic accuracy is not well known. Therefore, we performed a metaanalysis to assess the diagnostic accuracy of the currently available MRI techniques for treatment response.

METHODS

A systematic literature search was done. Study selection and data extraction were done by two authors independently. Meta-analysis was performed using a bivariate random effects model. An independent cohort was used for DSC perfusion external validation of diagnostic accuracy.

RESULTS

Anatomical MRI (16 studies, 726 lesions) showed a pooled sensitivity of 79% and a specificity of 76%. DCE perfusion (4 studies, 114 lesions) showed a pooled sensitivity of 74% and a specificity of 92%. DSC perfusion (12 studies, 418 lesions) showed a pooled sensitivity was 83% with a specificity of 78%. Diffusion weighted imaging (7 studies, 288 lesions) showed a pooled sensitivity of 67% and a specificity of 79%. MRS (4 studies, 54 lesions) showed a pooled sensitivity of 80% and a specificity of 78%. Combined techniques (6 studies, 375 lesions) showed a pooled sensitivity of 84% and a specificity of 88%. External validation of DSC showed a lower sensitivity and a higher specificity for the reported cut-off values included in this metaanalysis.

CONCLUSION

A combination of techniques shows the highest diagnostic accuracy differentiating tumor progression from treatment induced abnormalities. External validation of imaging results is important to better define the reliability of imaging results with the different techniques.

Visualising spatial heterogeneity in glioblastoma using imaging habitats

Glioblastoma is a high-grade aggressive neoplasm characterised by significant intra-tumoral spatial heterogeneity. Personalising therapy for this tumour requires non-invasive tools to visualise its heterogeneity to monitor treatment response on a regional level. To date, efforts to characterise glioblastoma's imaging features and heterogeneity have focussed on individual imaging biomarkers, or high-throughput radiomic approaches that consider a vast number of imaging variables across the tumour as a whole. Habitat imaging is a novel approach to cancer imaging that identifies tumour regions or 'habitats' based on shared imaging characteristics, usually defined using multiple imaging biomarkers. Habitat imaging reflects the evolution of imaging biomarkers and offers spatially preserved assessment of tumour physiological processes such perfusion and cellularity. This allows for regional assessment of treatment response to facilitate personalised therapy. In this review, we explore different methodologies to derive imaging habitats in glioblastoma, strategies to overcome its technical challenges, contrast experiences to other cancers, and describe potential clinical applications.

Chemical Exchange Saturation Transfer MRI for Differentiating Radiation Necrosis From Tumor Progression in Brain Metastasis-Application in a Clinical Setting

BACKGROUND

High radiation doses of stereotactic radiosurgery (SRS) for brain metastases (BM) can increase the likelihood of radiation necrosis (RN). Advanced MRI sequences can improve the differentiation between RN and tumor progression (TP).

PURPOSE

To use saturation transfer MRI methods including chemical exchange saturation transfer (CEST) and magnetization transfer (MT) to distinguish RN from TP.

STUDY TYPE

Prospective cohort study.

SUBJECTS

Seventy patients (median age 60; 73% females) with BM (75 lesions) post-SRS.

FIELD STRENGTH/SEQUENCE

3-T, CEST imaging using low/high-power (saturation B₁  = 0.52 and 2.0 μT), quantitative MT imaging using B₁  = 1.5, 3.0, and 5.0 μT, WAter Saturation Shift Referencing (WASSR), WAter Shift And B₁ (WASABI), T₁ , and T₂ mapping. All used gradient echoes except T₂ mapping (gradient and spin echo).

ASSESSMENT

Voxel-wise metrics included: magnetization transfer ratio (MTR); apparent exchange-dependent relaxation (AREX); MTR asymmetry; normalized MT exchange rate and pool size product; direct water saturation peak width; and the observed T₁ and T₂ . Regions of interests (ROIs) were manually contoured on the post-Gd T₁ w. The mean (of median ROI values) was compared between groups. Clinical outcomes were determined by clinical and radiologic follow-up or histopathology.

STATISTICAL TESTS

t-Test, univariable and multivariable logistic regression, receiver operating characteristic, and area under the curve (AUC) with sensitivity/specificity values with the optimal cut point using the Youden index, Akaike information criterion (AIC), Cohen's d. P < 0.05 with Bonferroni correction was considered significant.

RESULTS

Seven metrics showed significant differences between RN and TP. The high-power MTR showed the highest AUC of 0.88, followed by low-power MTR (AUC = 0.87). The combination of low-power CEST scans improved the separation compared to individual parameters (with an AIC of 70.3 for low-power MTR/AREX). Cohen's d effect size showed that the MTR provided the largest effect sizes among all metrics.

DATA CONCLUSION

Significant differences between RN and TP were observed based on saturation transfer MRI.

EVIDENCE LEVEL

3 Technical Efficacy: Stage 2.