Automatic Prediction of MGMT Status in Glioblastoma via Deep Learning-Based MR Image Analysis

Radiogenomics as an Integrated Approach to Glioblastoma Precision Medicine

PURPOSE OF REVIEW

Isocitrate dehydrogenase wild-type glioblastoma is the most aggressive primary brain tumour in adults. Its infiltrative nature and heterogeneity confer a dismal prognosis, despite multimodal treatment. Precision medicine is increasingly advocated to improve survival rates in glioblastoma management; however, conventional neuroimaging techniques are insufficient in providing the detail required for accurate diagnosis of this complex condition.

RECENT FINDINGS

Advanced magnetic resonance imaging allows more comprehensive understanding of the tumour microenvironment. Combining diffusion and perfusion magnetic resonance imaging to create a multiparametric scan enhances diagnostic power and can overcome the unreliability of tumour characterisation by standard imaging. Recent progress in deep learning algorithms establishes their remarkable ability in image-recognition tasks. Integrating these with multiparametric scans could transform the diagnosis and monitoring of patients by ensuring that the entire tumour is captured. As a corollary, radiomics has emerged as a powerful approach to offer insights into diagnosis, prognosis, treatment, and tumour response through extraction of information from radiological scans, and transformation of these tumour characteristics into quantitative data. Radiogenomics, which links imaging features with genomic profiles, has exhibited its ability in characterising glioblastoma, and determining therapeutic response, with the potential to revolutionise management of glioblastoma. The integration of deep learning algorithms into radiogenomic models has established an automated, highly reproducible means to predict glioblastoma molecular signatures, further aiding prognosis and targeted therapy. However, challenges including lack of large cohorts, absence of standardised guidelines and the 'black-box' nature of deep learning algorithms, must first be overcome before this workflow can be applied in clinical practice.

Quality assessment of the MRI-radiomics studies for MGMT promoter methylation prediction in glioma: a systematic review and meta-analysis

OBJECTIVES

To evaluate the methodological quality and diagnostic accuracy of MRI-based radiomic studies predicting O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation status in gliomas.

METHODS

PubMed Medline, EMBASE, and Web of Science were searched to identify MRI-based radiomic studies on MGMT methylation in gliomas published until December 31, 2022. Three raters evaluated the study methodological quality with Radiomics Quality Score (RQS, 16 components) and Transparent Reporting of a Multivariable Prediction Model for Individual Prognosis Or Diagnosis (TRIPOD, 22 items) scales. Risk of bias and applicability concerns were assessed with QUADAS-2 tool. A meta-analysis was performed to estimate the pooled area under the curve (AUC) and to assess inter-study heterogeneity.

RESULTS

We included 26 studies, published from 2016. The median RQS total score was 8 out of 36 (22%, range 8-44%). Thirteen studies performed external validation. All studies reported AUC or accuracy, but only 4 (15%) performed calibration and decision curve analysis. No studies performed phantom analysis, cost-effectiveness analysis, and prospective validation. The overall TRIPOD adherence score was between 50% and 70% in 16 studies and below 50% in 10 studies. The pooled AUC was 0.78 (95% CI, 0.73-0.83, I2 = 94.1%) with a high inter-study heterogeneity. Studies with external validation and including only WHO-grade IV gliomas had significantly lower AUC values (0.65; 95% CI, 0.57-0.73, p < 0.01).

CONCLUSIONS

Study RQS and adherence to TRIPOD guidelines was generally low. Radiomic prediction of MGMT methylation status showed great heterogeneity of results and lower performances in grade IV gliomas, which hinders its current implementation in clinical practice.

CLINICAL RELEVANCE STATEMENT

MGMT promoter methylation status appears to be variably correlated with MRI radiomic features; radiomic models are not sufficiently robust to be integrated into clinical practice to accurately predict MGMT promoter methylation status in patients with glioma before surgery.

KEY POINTS

• Adherence to the indications of TRIPOD guidelines was generally low, as was RQS total score. • MGMT promoter methylation status prediction with MRI radiomic features provided heterogeneous diagnostic accuracy results across studies. • Studies that included grade IV glioma only and performed external validation had significantly lower diagnostic accuracy than others.

Preoperative prediction of MGMT promoter methylation in glioblastoma based on multiregional and multi-sequence MRI radiomics analysis

O6-methylguanine-DNA methyltransferase (MGMT) has been demonstrated to be an important prognostic and predictive marker in glioblastoma (GBM). To establish a reliable radiomics model based on MRI data to predict the MGMT promoter methylation status of GBM. A total of 183 patients with glioblastoma were included in this retrospective study. The visually accessible Rembrandt images (VASARI) features were extracted for each patient, and a total of 14676 multi-region features were extracted from enhanced, necrotic, "non-enhanced, and edematous" areas on their multiparametric MRI. Twelve individual radiomics models were constructed based on the radiomics features from different subregions and different sequences. Four single-sequence models, three single-region models and the combined radiomics model combining all individual models were constructed. Finally, the predictive performance of adding clinical factors and VASARI characteristics was evaluated. The ComRad model combining all individual radiomics models exhibited the best performance in test set 1 and test set 2, with the area under the receiver operating characteristic curve (AUC) of 0.839 (0.709-0.963) and 0.739 (0.581-0.897), respectively. The results indicated that the radiomics model combining multi-region and multi-parametric MRI features has exhibited promising performance in predicting MGMT methylation status in GBM. The Modeling scheme that combining all individual radiomics models showed best performance among all constructed moels.

AI-driven estimation of O6 methylguanine-DNA-methyltransferase (MGMT) promoter methylation in glioblastoma patients: a systematic review with bias analysis

BACKGROUND

Accurate and non-invasive estimation of MGMT promoter methylation status in glioblastoma (GBM) patients is of paramount clinical importance, as it is a predictive biomarker associated with improved overall survival (OS). In response to the clinical need, recent studies have focused on the development of non-invasive artificial intelligence (AI)-based methods for MGMT estimation. In this systematic review, we not only delve into the technical aspects of these AI-driven MGMT estimation methods but also emphasize their profound clinical implications. Specifically, we explore the potential impact of accurate non-invasive MGMT estimation on GBM patient care and treatment decisions.

METHODS

Employing a PRISMA search strategy, we identified 33 relevant studies from reputable databases, including PubMed, ScienceDirect, Google Scholar, and IEEE Explore. These studies were comprehensively assessed using 21 diverse attributes, encompassing factors such as types of imaging modalities, machine learning (ML) methods, and cohort sizes, with clear rationales for attribute scoring. Subsequently, we ranked these studies and established a cutoff value to categorize them into low-bias and high-bias groups.

RESULTS

By analyzing the 'cumulative plot of mean score' and the 'frequency plot curve' of the studies, we determined a cutoff value of 6.00. A higher mean score indicated a lower risk of bias, with studies scoring above the cutoff mark categorized as low-bias (73%), while 27% fell into the high-bias category.

CONCLUSION

Our findings underscore the immense potential of AI-based machine learning (ML) and deep learning (DL) methods in non-invasively determining MGMT promoter methylation status. Importantly, the clinical significance of these AI-driven advancements lies in their capacity to transform GBM patient care by providing accurate and timely information for treatment decisions. However, the translation of these technical advancements into clinical practice presents challenges, including the need for large multi-institutional cohorts and the integration of diverse data types. Addressing these challenges will be critical in realizing the full potential of AI in improving the reliability and accessibility of MGMT estimation while lowering the risk of bias in clinical decision-making.

Systematic Literature Review of Machine Learning Algorithms Using Pretherapy Radiologic Imaging for Glioma Molecular Subtype Prediction

BACKGROUND

The molecular profile of gliomas is a prognostic indicator for survival, driving clinical decision-making for treatment. Pathology-based molecular diagnosis is challenging because of the invasiveness of the procedure, exclusion from neoadjuvant therapy options, and the heterogeneous nature of the tumor.

PURPOSE

We performed a systematic review of algorithms that predict molecular subtypes of gliomas from MR Imaging.

DATA SOURCES

Data sources were Ovid Embase, Ovid MEDLINE, Cochrane Central Register of Controlled Trials, Web of Science.

STUDY SELECTION

Per the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, 12,318 abstracts were screened and 1323 underwent full-text review, with 85 articles meeting the inclusion criteria.

DATA ANALYSIS

We compared prediction results from different machine learning approaches for predicting molecular subtypes of gliomas. Bias analysis was conducted for each study, following the Prediction model Risk Of Bias Assessment Tool (PROBAST) guidelines.

DATA SYNTHESIS

Isocitrate dehydrogenase mutation status was reported with an area under the curve and accuracy of 0.88 and 85% in internal validation and 0.86 and 87% in limited external validation data sets, respectively. For the prediction of O6-methylguanine-DNA methyltransferase promoter methylation, the area under the curve and accuracy in internal validation data sets were 0.79 and 77%, and in limited external validation, 0.89 and 83%, respectively. PROBAST scoring demonstrated high bias in all articles.

LIMITATIONS

The low number of external validation and studies with incomplete data resulted in unequal data analysis. Comparing the best prediction pipelines of each study may introduce bias.

CONCLUSIONS

While the high area under the curve and accuracy for the prediction of molecular subtypes of gliomas are reported in internal and external validation data sets, limited use of external validation and the increased risk of bias in all articles may present obstacles for clinical translation of these techniques.

Predicting MGMT Promoter Methylation in Diffuse Gliomas Using Deep Learning with Radiomics

This study aimed to investigate the feasibility of predicting oxygen 6-methylguanine-DNA methyltransferase (MGMT) promoter methylation in diffuse gliomas by developing a deep learning approach using MRI radiomics. A total of 111 patients with diffuse gliomas participated in the retrospective study (56 patients with MGMT promoter methylation and 55 patients with MGMT promoter unmethylation). The radiomics features of the two regions of interest (ROI) (the whole tumor area and the tumor core area) for four sequences, including T1 weighted image (T1WI), T2 weighted image (T2WI), apparent diffusion coefficient (ADC) maps, and T1 contrast-enhanced (T1CE) MR images were extracted and jointly fed into the residual network. Then the deep learning method was developed and evaluated with a five-fold cross-validation, where in each fold, the dataset was randomly divided into training (80%) and validation (20%) cohorts. We compared the performance of all models using area under the curve (AUC) and average accuracy of validation cohorts and calculated the 10 most important features of the best model via a class activation map. Based on the ROI of the whole tumor, the predictive capacity of the T1CE and ADC model achieved the highest AUC value of 0.85. Based on the ROI of the tumor core, the T1CE and ADC model achieved the highest AUC value of 0.90. After comparison, the T1CE combined with the ADC model based on the ROI of the tumor core exhibited the best performance, with the highest average accuracy (0.91) and AUC (0.90) among all models. The deep learning method using MRI radiomics has excellent diagnostic performance with a high accuracy in predicting MGMT promoter methylation in diffuse gliomas.

Radiogenomic Predictors of Recurrence in Glioblastoma—A Systematic Review

Glioblastoma, as the most aggressive brain tumor, is associated with a poor prognosis and outcome. To optimize prognosis and clinical therapy decisions, there is an urgent need to stratify patients with increased risk for recurrent tumors and low therapeutic success to optimize individual treatment. Radiogenomics establishes a link between radiological and pathological information. This review provides a state-of-the-art picture illustrating the latest developments in the use of radiogenomic markers regarding prognosis and their potential for monitoring recurrence. Databases PubMed, Google Scholar, and Cochrane Library were searched. Inclusion criteria were defined as diagnosis of glioblastoma with histopathological and radiological follow-up. Out of 321 reviewed articles, 43 articles met these inclusion criteria. Included studies were analyzed for the frequency of radiological and molecular tumor markers whereby radiogenomic associations were analyzed. Six main associations were described: radiogenomic prognosis, MGMT status, IDH, EGFR status, molecular subgroups, and tumor location. Prospective studies analyzing prognostic features of glioblastoma together with radiological features are lacking. By reviewing the progress in the development of radiogenomic markers, we provide insights into the potential efficacy of such an approach for clinical routine use eventually enabling early identification of glioblastoma recurrence and therefore supporting a further personalized monitoring and treatment strategy.

An Attentive Multi-Modal CNN for Brain Tumor Radiogenomic Classification

Medical images of brain tumors are critical for characterizing the pathology of tumors and early diagnosis. There are multiple modalities for medical images of brain tumors. Fusing the unique features of each modality of the magnetic resonance imaging (MRI) scans can accurately determine the nature of brain tumors. The current genetic analysis approach is time-consuming and requires surgical extraction of brain tissue samples. Accurate classification of multi-modal brain tumor images can speed up the detection process and alleviate patient suffering. Medical image fusion refers to effectively merging the significant information of multiple source images of the same tissue into one image, which will carry abundant information for diagnosis. This paper proposes a novel attentive deep-learning-based classification model that integrates multi-modal feature aggregation, lite attention mechanism, separable embedding, and modal-wise shortcuts for performance improvement. We evaluate our model on the RSNA-MICCAI dataset, a scenario-specific medical image dataset, and demonstrate that the proposed method outperforms the state-of-the-art (SOTA) by around 3%.

A Hybrid CNN-GLCM Classifier For Detection And Grade Classification Of Brain Tumor

A supervised CNN Deep net classifier is proposed for the detection, classification and diagnosis of meningioma brain tumor using deep learning approach. This proposed method includes preprocessing, classification, and segmentation of the primary occurring brain tumor in adults. The proposed CNN Deep Net classifier extracts the features internally from the enhanced image and classifies them into normal and abnormal tumor images. The segmentation of tumor region is performed by global thresholding along with an area morphological function. This proposed method of fully automated classification and segmentation of brain tumor preserves the spatial invariance and inheritance. Furthermore, based on its feature attributes the proposed CNN Deep net classifier, classifies the detected tumor image either as (low grade) benign or (high grade) malignant. This proposed CNN Deep net classification approach with grading system is evaluated both quantitatively and qualitatively. The quantitative measures such as sensitivity, specificity, accuracy, Dice similarity coefficient, precision, F-score of the proposed classifier states a better segmentation accuracy and classification rate of 99.4% and 99.5% with respect to ground truth images.

Diagnostic performance of radiomics using machine learning algorithms to predict MGMT promoter methylation status in glioma patients: a meta-analysis

PURPOSE

We aimed to assess the diagnostic performance of radiomics using machine learning algorithms to predict the methylation status of the O6-methylguanine-DNA methyltransferase (MGMT) promoter in glioma patients.

METHODS

A comprehensive literature search of PubMed, EMBASE, and Web of Science until 27 July 2021 was performed to identify eligible studies. Stata SE 15.0 and Meta-Disc 1.4 were used for data analysis.

RESULTS

A total of fifteen studies with 1663 patients were included: five studies with training and validation cohorts and ten with only training cohorts. The pooled sensitivity and specificity of machine learning for predicting MGMT promoter methylation in gliomas were 85% (95% CI 79%-90%) and 84% (95% CI 78%-88%) in the training cohort (n=15) and 84% (95% CI 70%-92%) and 78% (95% CI 63%-88%) in the validation cohort (n=5). The AUC was 0.91 (95% CI 0.88-0.93) in the training cohort and 0.88 (95% CI 0.85-0.91) in the validation cohort. The meta-regression demonstrated that magnetic resonance imaging sequences were related to heterogeneity. The sensitivity analysis showed that heterogeneity was reduced by excluding one study with the lowest diagnostic performance.

CONCLUSION

This meta-analysis demonstrated that machine learning is a promising, reliable and repeatable candidate method for predicting MGMT promoter methylation status in glioma and showed a higher performance than non-machine learning methods.

Imaging-Genomics in Glioblastoma: Combining Molecular and Imaging Signatures

Based on artificial intelligence (AI), computer-assisted medical diagnosis can scientifically and efficiently deal with a large quantity of medical imaging data. AI technologies including deep learning have shown remarkable progress across medical image recognition and genome analysis. Imaging-genomics attempts to explore the associations between potential gene expression patterns and specific imaging phenotypes. These associations provide potential cellular pathophysiology information, allowing sampling of the lesion habitat with high spatial resolution. Glioblastoma (GB) poses spatial and temporal heterogeneous characteristics, challenging to current precise diagnosis and treatments for the disease. Imaging-genomics provides a powerful tool for non-invasive global assessment of GB and its response to treatment. Imaging-genomics also has the potential to advance our understanding of underlying cancer biology, gene alterations, and corresponding biological processes. This article reviews the recent progress in the utilization of the imaging-genomics analysis in GB patients, focusing on its implications and prospects in individualized diagnosis and management.

A Systematic Approach for MRI Brain Tumor Localization and Segmentation Using Deep Learning and Active Contouring

One of the main requirements of tumor extraction is the annotation and segmentation of tumor boundaries correctly. For this purpose, we present a threefold deep learning architecture. First, classifiers are implemented with a deep convolutional neural network (CNN) and second a region-based convolutional neural network (R-CNN) is performed on the classified images to localize the tumor regions of interest. As the third and final stage, the concentrated tumor boundary is contoured for the segmentation process by using the Chan-Vese segmentation algorithm. As the typical edge detection algorithms based on gradients of pixel intensity tend to fail in the medical image segmentation process, an active contour algorithm defined with the level set function is proposed. Specifically, the Chan-Vese algorithm was applied to detect the tumor boundaries for the segmentation process. To evaluate the performance of the overall system, Dice Score, Rand Index (RI), Variation of Information (VOI), Global Consistency Error (GCE), Boundary Displacement Error (BDE), Mean Absolute Error (MAE), and Peak Signal to Noise Ratio (PSNR) were calculated by comparing the segmented boundary area which is the final output of the proposed, against the demarcations of the subject specialists which is the gold standard. Overall performance of the proposed architecture for both glioma and meningioma segmentation is with an average Dice Score of 0.92 (also, with RI of 0.9936, VOI of 0.0301, GCE of 0.004, BDE of 2.099, PSNR of 77.076, and MAE of 52.946), pointing to the high reliability of the proposed architecture.

To Explore MR Imaging Radiomics for the Differentiation of Orbital Lymphoma and IgG4-Related Ophthalmic Disease

Among orbital lymphoproliferative disorders, about 55% of diagnosed cancerous tumors are orbital lymphomas, and nearly 50% of benign cases are immunoglobulin G4-related ophthalmic disease (IgG4-ROD). However, due to nonspecific characteristics, the differentiation of the two diseases is challenging. In this study, conventional magnetic resonance imaging-based radiomics approaches were explored for clinical recognition of orbital lymphomas and IgG4-ROD. We investigated the value of radiomics features of axial T1- (T1WI-) and T2-weighted (T2WI), contrast-enhanced T1WI in axial (CE-T1WI) and coronal (CE-T1WI-cor) planes, and 78 patients (orbital lymphoma, 36; IgG4-ROD, 42) were retrospectively reviewed. The mass lesions were manually annotated and represented with 99 features. The performance of elastic net-based radiomics models using single or multiple modalities with or without feature selection was compared. The demographic features showed orbital lymphoma patients were significantly older than IgG4-ROD patients (p < 0.01), and most of the patients were male (72% in the orbital lymphoma group vs. 23% in the IgG4-ROD group; p = 0.03). The MR imaging findings revealed orbital lymphomas were mostly unilateral (81%, p = 0.02) and wrapped eyeballs or optic nerves frequently (78%, p = 0.02). In addition, orbital lymphomas showed isointense in T1WI (100%, p < 0.01), and IgG4-ROD was isointense (60%, p < 0.01) or hyperintense (40%, p < 0.01) in T1WI with well-defined shape (64%, p < 0.01). The experimental comparison indicated that using CE-T1WI radiomics features achieved superior results, and the features in combination with CE-T1WI-cor features and the feature preselection method could further improve the classification performance. In conclusion, this study comparatively analyzed orbital lymphoma and IgG4-ROD from demographic features, MR imaging findings, and radiomics features. It might deepen our understanding and benefit disease management.