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Wu X, Zhang S, Zhang Z, He Z, Xu Z, Wang W, Jin Z, You J, Guo Y, Zhang L, Huang W, Wang F, Liu X, Yan D, Cheng J, Yan J, Zhang S, Zhang B. Biologically interpretable multi-task deep learning pipeline predicts molecular alterations, grade, and prognosis in glioma patients. NPJ Precis Oncol 2024; 8:181. [PMID: 39152182 PMCID: PMC11329669 DOI: 10.1038/s41698-024-00670-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 08/01/2024] [Indexed: 08/19/2024] Open
Abstract
Deep learning models have been developed for various predictions in glioma; yet, they were constrained by manual segmentation, task-specific design, or a lack of biological interpretation. Herein, we aimed to develop an end-to-end multi-task deep learning (MDL) pipeline that can simultaneously predict molecular alterations and histological grade (auxiliary tasks), as well as prognosis (primary task) in gliomas. Further, we aimed to provide the biological mechanisms underlying the model's predictions. We collected multiscale data including baseline MRI images from 2776 glioma patients across two private (FAHZU and HPPH, n = 1931) and three public datasets (TCGA, n = 213; UCSF, n = 410; and EGD, n = 222). We trained and internally validated the MDL model using our private datasets, and externally validated it using the three public datasets. We used the model-predicted deep prognosis score (DPS) to stratify patients into low-DPS and high-DPS subtypes. Additionally, a radio-multiomics analysis was conducted to elucidate the biological basis of the DPS. In the external validation cohorts, the MDL model achieved average areas under the curve of 0.892-0.903, 0.710-0.894, and 0.850-0.879 for predicting IDH mutation status, 1p/19q co-deletion status, and tumor grade, respectively. Moreover, the MDL model yielded a C-index of 0.723 in the TCGA and 0.671 in the UCSF for the prediction of overall survival. The DPS exhibits significant correlations with activated oncogenic pathways, immune infiltration patterns, specific protein expression, DNA methylation, tumor mutation burden, and tumor-stroma ratio. Accordingly, our work presents an accurate and biologically meaningful tool for predicting molecular subtypes, tumor grade, and survival outcomes in gliomas, which provides personalized clinical decision-making in a global and non-invasive manner.
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Affiliation(s)
- Xuewei Wu
- Department of Radiology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Shuaitong Zhang
- School of Medical Technology, Beijing Institute of Technology, Beijing, China
| | - Zhenyu Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zicong He
- Department of Radiology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Zexin Xu
- School of Medical Technology, Beijing Institute of Technology, Beijing, China
| | - Weiwei Wang
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zhe Jin
- Department of Radiology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Jingjing You
- Department of Radiology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Yang Guo
- Department of Neurosurgery, The Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Lu Zhang
- Department of Radiology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Wenhui Huang
- Department of Radiology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Fei Wang
- Department of Radiology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Xianzhi Liu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Dongming Yan
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jingliang Cheng
- Department of MRI, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jing Yan
- Department of MRI, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| | - Shuixing Zhang
- Department of Radiology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China.
| | - Bin Zhang
- Department of Radiology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China.
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Pons-Escoda A, Garcia-Ruiz A, Naval-Baudin P, Martinez-Zalacain I, Castell J, Camins A, Vidal N, Bruna J, Cos M, Perez-Lopez R, Oleaga L, Warnert E, Smits M, Majos C. Differentiating IDH-mutant astrocytomas and 1p19q-codeleted oligodendrogliomas using DSC-PWI: high performance through cerebral blood volume and percentage of signal recovery percentiles. Eur Radiol 2024; 34:5320-5330. [PMID: 38282078 PMCID: PMC11255054 DOI: 10.1007/s00330-024-10611-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/13/2023] [Accepted: 01/01/2024] [Indexed: 01/30/2024]
Abstract
OBJECTIVE Presurgical differentiation between astrocytomas and oligodendrogliomas remains an unresolved challenge in neuro-oncology. This research aims to provide a comprehensive understanding of each tumor's DSC-PWI signatures, evaluate the discriminative capacity of cerebral blood volume (CBV) and percentage of signal recovery (PSR) percentile values, and explore the synergy of CBV and PSR combination for pre-surgical differentiation. METHODS Patients diagnosed with grade 2 and 3 IDH-mutant astrocytomas and IDH-mutant 1p19q-codeleted oligodendrogliomas were retrospectively retrieved (2010-2022). 3D segmentations of each tumor were conducted, and voxel-level CBV and PSR were extracted to compute mean, minimum, maximum, and percentile values. Statistical comparisons were performed using the Mann-Whitney U test and the area under the receiver operating characteristic curve (AUC-ROC). Lastly, the five most discriminative variables were combined for classification with internal cross-validation. RESULTS The study enrolled 52 patients (mean age 45-year-old, 28 men): 28 astrocytomas and 24 oligodendrogliomas. Oligodendrogliomas exhibited higher CBV and lower PSR than astrocytomas across all metrics (e.g., mean CBV = 2.05 and 1.55, PSR = 0.68 and 0.81 respectively). The highest AUC-ROCs and the smallest p values originated from CBV and PSR percentiles (e.g., PSRp70 AUC-ROC = 0.84 and p value = 0.0005, CBVp75 AUC-ROC = 0.8 and p value = 0.0006). The mean, minimum, and maximum values yielded lower results. Combining the best five variables (PSRp65, CBVp70, PSRp60, CBVp75, and PSRp40) achieved a mean AUC-ROC of 0.87 for differentiation. CONCLUSIONS Oligodendrogliomas exhibit higher CBV and lower PSR than astrocytomas, traits that are emphasized when considering percentiles rather than mean or extreme values. The combination of CBV and PSR percentiles results in promising classification outcomes. CLINICAL RELEVANCE STATEMENT The combination of histogram-derived percentile values of cerebral blood volume and percentage of signal recovery from DSC-PWI enhances the presurgical differentiation between astrocytomas and oligodendrogliomas, suggesting that incorporating these metrics into clinical practice could be beneficial. KEY POINTS • The unsupervised selection of percentile values for cerebral blood volume and percentage of signal recovery enhances presurgical differentiation of astrocytomas and oligodendrogliomas. • Oligodendrogliomas exhibit higher cerebral blood volume and lower percentage of signal recovery than astrocytomas. • Cerebral blood volume and percentage of signal recovery combined provide a broader perspective on tumor vasculature and yield promising results for this preoperative classification.
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Affiliation(s)
- Albert Pons-Escoda
- Radiology Department, Feixa Llarga SN, Hospital Universitari de Bellvitge, 08907, Barcelona, Spain.
- Neuro-oncology Unit, Feixa Llarga SN, Institut d'Investigació Biomèdica de Bellvitge- IDIBELL, 08907, Barcelona, Spain.
- Facultat de Medicina i Ciències de La Salut, Universitat de Barcelona (UB), Carrer de Casanova 143, 08036, Barcelona, Spain.
- Diagnostic Imaging and Nuclear Medicine Research Group, Institut d'Investigació Biomèdica de Bellvitge- IDIBELL, Feixa Llarga SN, 08907, Barcelona, Spain.
| | - Alonso Garcia-Ruiz
- Radiomics Group, Vall d'Hebron Institut d'Oncologia- VHIO, Carrer de Natzaret, 115-117, 08035, Barcelona, Spain
| | - Pablo Naval-Baudin
- Radiology Department, Feixa Llarga SN, Hospital Universitari de Bellvitge, 08907, Barcelona, Spain
- Diagnostic Imaging and Nuclear Medicine Research Group, Institut d'Investigació Biomèdica de Bellvitge- IDIBELL, Feixa Llarga SN, 08907, Barcelona, Spain
| | - Ignacio Martinez-Zalacain
- Radiology Department, Feixa Llarga SN, Hospital Universitari de Bellvitge, 08907, Barcelona, Spain
- Diagnostic Imaging and Nuclear Medicine Research Group, Institut d'Investigació Biomèdica de Bellvitge- IDIBELL, Feixa Llarga SN, 08907, Barcelona, Spain
| | - Josep Castell
- Radiology Department, Feixa Llarga SN, Hospital Universitari de Bellvitge, 08907, Barcelona, Spain
| | - Angels Camins
- Radiology Department, Feixa Llarga SN, Hospital Universitari de Bellvitge, 08907, Barcelona, Spain
| | - Noemi Vidal
- Neuro-oncology Unit, Feixa Llarga SN, Institut d'Investigació Biomèdica de Bellvitge- IDIBELL, 08907, Barcelona, Spain
- Pathology Department, Feixa Llarga SN, Hospital Universitari de Bellvitge, 08907, Barcelona, Spain
| | - Jordi Bruna
- Neuro-oncology Unit, Feixa Llarga SN, Institut d'Investigació Biomèdica de Bellvitge- IDIBELL, 08907, Barcelona, Spain
| | - Monica Cos
- Radiology Department, Feixa Llarga SN, Hospital Universitari de Bellvitge, 08907, Barcelona, Spain
| | - Raquel Perez-Lopez
- Radiomics Group, Vall d'Hebron Institut d'Oncologia- VHIO, Carrer de Natzaret, 115-117, 08035, Barcelona, Spain
| | - Laura Oleaga
- Radiology Department, Hospital Clinic de Barcelona, Villarroel 170, 08036, Barcelona, Spain
| | - Esther Warnert
- Department of Radiology & Nuclear Medicine, Erasmus MC, Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
- Erasmus MC Cancer Institute, Erasmus MC, Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Marion Smits
- Department of Radiology & Nuclear Medicine, Erasmus MC, Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
- Erasmus MC Cancer Institute, Erasmus MC, Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
- Medical Delta, Delft, The Netherlands
| | - Carles Majos
- Radiology Department, Feixa Llarga SN, Hospital Universitari de Bellvitge, 08907, Barcelona, Spain
- Neuro-oncology Unit, Feixa Llarga SN, Institut d'Investigació Biomèdica de Bellvitge- IDIBELL, 08907, Barcelona, Spain
- Diagnostic Imaging and Nuclear Medicine Research Group, Institut d'Investigació Biomèdica de Bellvitge- IDIBELL, Feixa Llarga SN, 08907, Barcelona, Spain
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Richter V, Ernemann U, Bender B. Novel Imaging Approaches for Glioma Classification in the Era of the World Health Organization 2021 Update: A Scoping Review. Cancers (Basel) 2024; 16:1792. [PMID: 38791871 PMCID: PMC11119220 DOI: 10.3390/cancers16101792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/22/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
The 2021 WHO classification of CNS tumors is a challenge for neuroradiologists due to the central role of the molecular profile of tumors. The potential of novel data analysis tools in neuroimaging must be harnessed to maintain its role in predicting tumor subgroups. We performed a scoping review to determine current evidence and research gaps. A comprehensive literature search was conducted regarding glioma subgroups according to the 2021 WHO classification and the use of MRI, radiomics, machine learning, and deep learning algorithms. Sixty-two original articles were included and analyzed by extracting data on the study design and results. Only 8% of the studies included pediatric patients. Low-grade gliomas and diffuse midline gliomas were represented in one-third of the research papers. Public datasets were utilized in 22% of the studies. Conventional imaging sequences prevailed; data on functional MRI (DWI, PWI, CEST, etc.) are underrepresented. Multiparametric MRI yielded the best prediction results. IDH mutation and 1p/19q codeletion status prediction remain in focus with limited data on other molecular subgroups. Reported AUC values range from 0.6 to 0.98. Studies designed to assess generalizability are scarce. Performance is worse for smaller subgroups (e.g., 1p/19q codeleted or IDH1/2 mutated gliomas). More high-quality study designs with diversity in the analyzed population and techniques are needed.
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Affiliation(s)
- Vivien Richter
- Department of Diagnostic and Interventional Neuroradiology, University Hospital Tübingen, 72076 Tübingen, Germany; (U.E.); (B.B.)
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Guan F, Wang Z, Qiu Y, Guo Y, Pei D, Wang M, Xing A, Liu Z, Yu B, Cheng J, Liu X, Ji Y, Yan D, Yan J, Zhang Z. Biological underpinnings of radiomic magnetic resonance imaging phenotypes for risk stratification in IDH wild-type glioblastoma. J Transl Med 2023; 21:841. [PMID: 37993907 PMCID: PMC10664532 DOI: 10.1186/s12967-023-04551-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 09/22/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND To develop and validate a conventional MRI-based radiomic model for predicting prognosis in patients with IDH wild-type glioblastoma (GBM) and reveal the biological underpinning of the radiomic phenotypes. METHODS A total of 801 adult patients (training set, N = 471; internal validation set, N = 239; external validation set, N = 91) diagnosed with IDH wild-type GBM were included. A 20-feature radiomic risk score (Radscore) was built for overall survival (OS) prediction by univariate prognostic analysis and least absolute shrinkage and selection operator (LASSO) Cox regression in the training set. GSEA and WGCNA were applied to identify the intersectional pathways underlying the prognostic radiomic features in a radiogenomic analysis set with paired MRI and RNA-seq data (N = 132). The biological meaning of the conventional MRI sequences was revealed using a Mantel test. RESULTS Radscore was demonstrated to be an independent prognostic factor (P < 0.001). Incorporating the Radscore into a clinical model resulted in a radiomic-clinical nomogram predicting survival better than either the Radscore model or the clinical model alone, with better calibration and classification accuracy (a total net reclassification improvement of 0.403, P < 0.001). Three pathway categories (proliferation, DNA damage response, and immune response) were significantly correlated with the prognostic radiomic phenotypes. CONCLUSION Our findings indicated that the prognostic radiomic phenotypes derived from conventional MRI are driven by distinct pathways involved in proliferation, DNA damage response, and immunity of IDH wild-type GBM.
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Affiliation(s)
- Fangzhan Guan
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Zilong Wang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Yuning Qiu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Yu Guo
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Dongling Pei
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Minkai Wang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Aoqi Xing
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Zhongyi Liu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Bin Yu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Jingliang Cheng
- Department of MRI, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Xianzhi Liu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Yuchen Ji
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Dongming Yan
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
| | - Jing Yan
- Department of MRI, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
| | - Zhenyu Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
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Zhang H, Fan X, Zhang J, Wei Z, Feng W, Hu Y, Ni J, Yao F, Zhou G, Wan C, Zhang X, Wang J, Liu Y, You Y, Yu Y. Deep-learning and conventional radiomics to predict IDH genotyping status based on magnetic resonance imaging data in adult diffuse glioma. Front Oncol 2023; 13:1143688. [PMID: 37711207 PMCID: PMC10499353 DOI: 10.3389/fonc.2023.1143688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 08/17/2023] [Indexed: 09/16/2023] Open
Abstract
Objectives In adult diffuse glioma, preoperative detection of isocitrate dehydrogenase (IDH) status helps clinicians develop surgical strategies and evaluate patient prognosis. Here, we aim to identify an optimal machine-learning model for prediction of IDH genotyping by combining deep-learning (DL) signatures and conventional radiomics (CR) features as model predictors. Methods In this study, a total of 486 patients with adult diffuse gliomas were retrospectively collected from our medical center (n=268) and the public database (TCGA, n=218). All included patients were randomly divided into the training and validation sets by using nested 10-fold cross-validation. A total of 6,736 CR features were extracted from four MRI modalities in each patient, namely T1WI, T1CE, T2WI, and FLAIR. The LASSO algorithm was performed for CR feature selection. In each MRI modality, we applied a CNN+LSTM-based neural network to extract DL features and integrate these features into a DL signature after the fully connected layer with sigmoid activation. Eight classic machine-learning models were analyzed and compared in terms of their prediction performance and stability in IDH genotyping by combining the LASSO-selected CR features and integrated DL signatures as model predictors. In the validation sets, the prediction performance was evaluated by using accuracy and the area under the curve (AUC) of the receiver operating characteristics, while the model stability was analyzed by using the relative standard deviation of the AUC (RSDAUC). Subgroup analyses of DL signatures and CR features were also individually conducted to explore their independent prediction values. Results Logistic regression (LR) achieved favorable prediction performance (AUC: 0.920 ± 0.043, accuracy: 0.843 ± 0.044), whereas support vector machine with the linear kernel (l-SVM) displayed low prediction performance (AUC: 0.812 ± 0.052, accuracy: 0.821 ± 0.050). With regard to stability, LR also showed high robustness against data perturbation (RSDAUC: 4.7%). Subgroup analyses showed that DL signatures outperformed CR features (DL, AUC: 0.915 ± 0.054, accuracy: 0.835 ± 0.061, RSDAUC: 5.9%; CR, AUC: 0.830 ± 0.066, accuracy: 0.771 ± 0.051, RSDAUC: 8.0%), while DL and DL+CR achieved similar prediction results. Conclusion In IDH genotyping, LR is a promising machine-learning classification model. Compared with CR features, DL signatures exhibit markedly superior prediction values and discriminative capability.
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Affiliation(s)
- Hongjian Zhang
- Department of Medical Informatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiao Fan
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Junxia Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhiyuan Wei
- Department of Medical Informatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wei Feng
- Department of Medical Informatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yifang Hu
- Department of Geriatric Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jiaying Ni
- Department of Medical Informatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Fushen Yao
- Department of Medical Informatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Gaoxin Zhou
- Department of Medical Informatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu, China
- Institute of Medical Informatics and Management, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Cheng Wan
- Department of Medical Informatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu, China
- Institute of Medical Informatics and Management, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xin Zhang
- Department of Medical Informatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu, China
- Institute of Medical Informatics and Management, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Junjie Wang
- Department of Medical Informatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu, China
- Institute of Medical Informatics and Management, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yun Liu
- Department of Medical Informatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu, China
- Institute of Medical Informatics and Management, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yongping You
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yun Yu
- Department of Medical Informatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu, China
- Institute of Medical Informatics and Management, Nanjing Medical University, Nanjing, Jiangsu, China
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