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Ocaña-Tienda B, Pérez-Beteta J, Ortiz de Mendivil A, Asenjo B, Albillo D, Pérez-Romasanta LA, LLorente M, Carballo N, Arana E, Pérez-García VM. Morphological MRI features as prognostic indicators in brain metastases. Cancer Imaging 2024; 24:111. [PMID: 39164779 PMCID: PMC11334491 DOI: 10.1186/s40644-024-00753-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 08/07/2024] [Indexed: 08/22/2024] Open
Abstract
BACKGROUND Stereotactic radiotherapy is the preferred treatment for managing patients with fewer than five brain metastases (BMs). However, some lesions recur after irradiation. The purpose of this study was to identify patients who are at a higher risk of failure, which can help in adjusting treatments and preventing recurrence. METHODS In this retrospective multicenter study, we analyzed the predictive significance of a set of interpretable morphological features derived from contrast-enhanced (CE) T1-weighted MR images as imaging biomarkers using Kaplan-Meier analysis. The feature sets studied included the total and necrotic volumes, the surface regularity and the CE rim width. Additionally, we evaluated other nonmorphological variables and performed multivariate Cox analysis. RESULTS A total of 183 lesions in 128 patients were included (median age 61 [31-95], 64 men and 64 women) treated with stereotactic radiotherapy (57% single fraction, 43% fractionated radiotherapy). None of the studied variables measured at diagnosis were found to have prognostic value. However, the total and necrotic volumes and the CE rim width measured at the first follow-up after treatment and the change in volume due to irradiation can be used as imaging biomarkers for recurrence. The optimal classification was achieved by combining the changes in tumor volume before and after treatment with the presence or absence of necrosis (p < < 0.001). CONCLUSION This study demonstrated the prognostic significance of interpretable morphological features extracted from routine clinical MR images following irradiation in brain metastases, offering valuable insights for personalized treatment strategies.
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Affiliation(s)
- Beatriz Ocaña-Tienda
- Mathematical Oncology Laboratory (MOLAB), University of Castilla-La Mancha, Ciudad Real, Spain.
| | - Julián Pérez-Beteta
- Mathematical Oncology Laboratory (MOLAB), University of Castilla-La Mancha, Ciudad Real, Spain
| | | | - Beatriz Asenjo
- Hospital Regional Universitario de Málaga, Málaga, Spain
| | | | | | | | | | | | - Víctor M Pérez-García
- Mathematical Oncology Laboratory (MOLAB), University of Castilla-La Mancha, Ciudad Real, Spain
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Setyawan NH, Choridah L, Nugroho HA, Malueka RG, Dwianingsih EK, Supriatna Y, Supriyadi B, Hartanto RA. Glioma Grade and Molecular Markers: Comparing Machine-Learning Approaches Using VASARI (Visually AcceSAble Rembrandt Images) Radiological Assessment. Cureus 2024; 16:e63873. [PMID: 39100020 PMCID: PMC11298015 DOI: 10.7759/cureus.63873] [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] [Accepted: 07/04/2024] [Indexed: 08/06/2024] Open
Abstract
OBJECTIVES This study aimed to leverage Visually AcceSAble Rembrandt Images (VASARI) radiological features, extracted from magnetic resonance imaging (MRI) scans, and machine-learning techniques to predict glioma grade, isocitrate dehydrogenase (IDH) mutation status, and O6-methylguanine-DNA methyltransferase (MGMT) methylation. METHODOLOGY A retrospective evaluation was undertaken, analyzing MRI and molecular data from 107 glioma patients treated at a tertiary hospital. Patients underwent MRI scans using established protocols and were evaluated based on VASARI criteria. Tissue samples were assessed for glioma grade and underwent molecular testing for IDH mutations and MGMT methylation. Four machine learning models, namely, Random Forest, Elastic-Net, multivariate adaptive regression spline (MARS), and eXtreme Gradient Boosting (XGBoost), were trained on 27 VASARI features using fivefold internal cross-validation. The models' predictive performances were assessed using the area under the curve (AUC), sensitivity, and specificity. RESULTS For glioma grade prediction, XGBoost exhibited the highest AUC (0.978), sensitivity (0.879), and specificity (0.964), with f6 (proportion of non-enhancing) and f12 (definition of enhancing margin) as the most important predictors. In predicting IDH mutation status, XGBoost achieved an AUC of 0.806, sensitivity of 0.364, and specificity of 0.880, with f1 (tumor location), f12, and f30 (perpendicular diameter to f29) as primary predictors. For MGMT methylation, XGBoost displayed an AUC of 0.580, sensitivity of 0.372, and specificity of 0.759, highlighting f29 (longest diameter) as the key predictor. CONCLUSIONS This study underscores the robust potential of combining VASARI radiological features with machine learning models in predicting glioma grade, IDH mutation status, and MGMT methylation. The best and most balanced performance was achieved using the XGBoost model. While the prediction of glioma grade showed promising results, the sensitivity in discerning IDH mutations and MGMT methylation still leaves room for improvement. Follow-up studies with larger datasets and more advanced artificial intelligence techniques can further refine our understanding and management of gliomas.
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Affiliation(s)
- Nurhuda H Setyawan
- Department of Radiology, Faculty of Medicine, Public Health, and Nursing, Dr. Sardjito General Hospital, Universitas Gadjah Mada, Yogyakarta, IDN
| | - Lina Choridah
- Department of Radiology, Faculty of Medicine, Public Health, and Nursing, Dr. Sardjito General Hospital, Universitas Gadjah Mada, Yogyakarta, IDN
| | - Hanung A Nugroho
- Department of Electrical and Information Engineering, Faculty of Engineering, Universitas Gadjah Mada, Yogyakarta, IDN
| | - Rusdy G Malueka
- Department of Neurology, Faculty of Medicine, Public Health, and Nursing, Dr. Sardjito General Hospital, Universitas Gadjah Mada, Yogyakarta, IDN
| | - Ery K Dwianingsih
- Department of Anatomical Pathology, Faculty of Medicine, Public Health, and Nursing, Dr. Sardjito General Hospital, Universitas Gadjah Mada, Yogyakarta, IDN
| | - Yana Supriatna
- Department of Radiology, Faculty of Medicine, Public Health, and Nursing,Dr. Sardjito General Hospital, Universitas Gadjah Mada, Yogyakarta, IDN
| | - Bambang Supriyadi
- Department of Radiology, Faculty of Medicine, Public Health, and Nursing, Dr. Sardjito General Hospital, Universitas Gadjah Mada, Yogyakarta, IDN
| | - Rachmat A Hartanto
- Department of Surgery, Faculty of Medicine, Public Health, and Nursing, Dr. Sardjito General Hospital, Universitas Gadjah Mada, Yogyakarta, IDN
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Chelliah A, Wood DA, Canas LS, Shuaib H, Currie S, Fatania K, Frood R, Rowland-Hill C, Thust S, Wastling SJ, Tenant S, McBain C, Foweraker K, Williams M, Wang Q, Roman A, Dragos C, MacDonald M, Lau YH, Linares CA, Bassiouny A, Luis A, Young T, Brock J, Chandy E, Beaumont E, Lam TC, Welsh L, Lewis J, Mathew R, Kerfoot E, Brown R, Beasley D, Glendenning J, Brazil L, Swampillai A, Ashkan K, Ourselin S, Modat M, Booth TC. Glioblastoma and radiotherapy: A multicenter AI study for Survival Predictions from MRI (GRASP study). Neuro Oncol 2024; 26:1138-1151. [PMID: 38285679 PMCID: PMC11145448 DOI: 10.1093/neuonc/noae017] [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: 09/15/2023] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND The aim was to predict survival of glioblastoma at 8 months after radiotherapy (a period allowing for completing a typical course of adjuvant temozolomide), by applying deep learning to the first brain MRI after radiotherapy completion. METHODS Retrospective and prospective data were collected from 206 consecutive glioblastoma, isocitrate dehydrogenase -wildtype patients diagnosed between March 2014 and February 2022 across 11 UK centers. Models were trained on 158 retrospective patients from 3 centers. Holdout test sets were retrospective (n = 19; internal validation), and prospective (n = 29; external validation from 8 distinct centers). Neural network branches for T2-weighted and contrast-enhanced T1-weighted inputs were concatenated to predict survival. A nonimaging branch (demographics/MGMT/treatment data) was also combined with the imaging model. We investigated the influence of individual MR sequences; nonimaging features; and weighted dense blocks pretrained for abnormality detection. RESULTS The imaging model outperformed the nonimaging model in all test sets (area under the receiver-operating characteristic curve, AUC P = .038) and performed similarly to a combined imaging/nonimaging model (P > .05). Imaging, nonimaging, and combined models applied to amalgamated test sets gave AUCs of 0.93, 0.79, and 0.91. Initializing the imaging model with pretrained weights from 10 000s of brain MRIs improved performance considerably (amalgamated test sets without pretraining 0.64; P = .003). CONCLUSIONS A deep learning model using MRI images after radiotherapy reliably and accurately determined survival of glioblastoma. The model serves as a prognostic biomarker identifying patients who will not survive beyond a typical course of adjuvant temozolomide, thereby stratifying patients into those who might require early second-line or clinical trial treatment.
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Affiliation(s)
- Alysha Chelliah
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, UK
| | - David A Wood
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, UK
| | - Liane S Canas
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, UK
| | - Haris Shuaib
- Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
- Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, UK
| | | | | | | | | | - Stefanie Thust
- University College London Hospitals NHS Foundation Trust, London, UK
- Institute of Neurology, University College London, London, UK
- Nottingham University Hospitals NHS Trust, Nottingham, UK
- Precision Imaging Beacon, School of Medicine, University of Nottingham, Nottingham, UK
| | - Stephen J Wastling
- University College London Hospitals NHS Foundation Trust, London, UK
- Institute of Neurology, University College London, London, UK
| | - Sean Tenant
- The Christie NHS Foundation Trust, Withington, Manchester, UK
| | | | | | - Matthew Williams
- Radiotherapy Department, Imperial College Healthcare NHS Trust, London, UK
- Institute for Global Health Improvement, Imperial College London, London, UK
| | - Qiquan Wang
- Radiotherapy Department, Imperial College Healthcare NHS Trust, London, UK
- Institute for Global Health Improvement, Imperial College London, London, UK
| | - Andrei Roman
- Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
- Oncology Institute Prof. Dr. Ion Chiricuta, Cluj-Napoca, Romania
| | | | | | - Yue Hui Lau
- King’s College Hospital NHS Foundation Trust, London, UK
| | | | - Ahmed Bassiouny
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, UK
- Department of Radiology, Mansoura University, Mansoura, Egypt
| | - Aysha Luis
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, UK
- King’s College Hospital NHS Foundation Trust, London, UK
| | - Thomas Young
- Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Juliet Brock
- Brighton and Sussex University Hospitals NHS Trust, England, UK
| | - Edward Chandy
- Brighton and Sussex University Hospitals NHS Trust, England, UK
| | - Erica Beaumont
- Lancashire Teaching Hospitals NHS Foundation Trust, England, UK
| | - Tai-Chung Lam
- Lancashire Teaching Hospitals NHS Foundation Trust, England, UK
| | - Liam Welsh
- The Royal Marsden NHS Foundation Trust, London, UK
| | - Joanne Lewis
- Newcastle upon Tyne Hospitals NHS Foundation Trust, England, UK
| | - Ryan Mathew
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
- School of Medicine, University of Leeds, Leeds, UK
| | - Eric Kerfoot
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, UK
| | - Richard Brown
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, UK
| | - Daniel Beasley
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, UK
- Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | | | - Lucy Brazil
- Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | | | - Keyoumars Ashkan
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- King’s College Hospital NHS Foundation Trust, London, UK
| | - Sébastien Ourselin
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, UK
| | - Marc Modat
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, UK
| | - Thomas C Booth
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, UK
- King’s College Hospital NHS Foundation Trust, London, UK
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Dono A, Torres J, Nunez L, Arevalo O, Rodriguez-Quinteros JC, Riascos RF, Kamali A, Tandon N, Ballester LY, Esquenazi Y. Imaging predictors of 4q12 amplified and RB1 mutated glioblastoma IDH-wildtype. J Neurooncol 2024; 167:99-109. [PMID: 38351343 PMCID: PMC11227885 DOI: 10.1007/s11060-024-04575-9] [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: 11/07/2023] [Accepted: 01/16/2024] [Indexed: 07/04/2024]
Abstract
INTRODUCTION Recent studies have identified that glioblastoma IDH-wildtype consists of different molecular subgroups with distinct prognoses. In order to accurately describe and classify gliomas, the Visually AcceSAble Rembrandt Images (VASARI) system was developed. The goal of this study was to evaluate the VASARI characteristics in molecular subgroups of IDH-wildtype glioblastoma. METHODS A retrospective analysis of glioblastoma IDH- wildtype with comprehensive next-generation sequencing and pre-operative and post-operative MRI was performed. VASARI characteristics and 205 genes were evaluated. Multiple comparison adjustment by the Bejamin-Hochberg false discovery rate (BH-FDR) was performed. A 1:3 propensity score match (PSM) with a Caliper of 0.2 was done. RESULTS 178 patients with GBM IDH-WT met the inclusion criteria. 4q12 amplified patients (n = 20) were associated with cyst presence (30% vs. 12%, p = 0.042), decreased hemorrhage (35% vs. 62%, p = 0.028), and non-restricting/mixed (35%/60%) rather than restricting diffusion pattern (5%), meanwhile, 4q12 non-amplified patients had mostly restricting (47.4%) rather than a non-restricting/mixed diffusion pattern (28.4%/23.4%). This remained statistically significant after BH-FDR adjustment (p = 0.002). PSM by 4q12 amplification showed that diffusion characteristics continued to be significantly different. Among RB1-mutant patients, 96% had well-defined enhancing margins vs. 70.6% of RB1-WT (p = 0.018), however, this was not significant after BH-FDR or PSM. CONCLUSIONS Patients with glioblastoma IDH-wildtype harboring 4q12 amplification rarely have restricting DWI patterns compared to their wildtype counterparts, in which this DWI pattern is present in ~ 50% of patients. This suggests that some phenotypic imaging characteristics can be identified among molecular subtypes of IDH-wildtype glioblastoma.
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Affiliation(s)
- Antonio Dono
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, 77030, Houston, TX, USA
| | - Jose Torres
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, 77030, Houston, TX, USA
| | - Luis Nunez
- Department of Diagnostic and Interventional Imaging, McGovern Medical School, The University of Texas Health Science Center at Houston, 77030, Houston, TX, USA
| | - Octavio Arevalo
- Department of Diagnostic and Interventional Imaging, McGovern Medical School, The University of Texas Health Science Center at Houston, 77030, Houston, TX, USA
- Department of Radiology, LSU Health Shreveport, 71103, Shreveport, LA, USA
| | - Juan Carlos Rodriguez-Quinteros
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, 77030, Houston, TX, USA
| | - Roy F Riascos
- Department of Diagnostic and Interventional Imaging, McGovern Medical School, The University of Texas Health Science Center at Houston, 77030, Houston, TX, USA
- Memorial Hermann Hospital-TMC, 77030, Houston, TX, USA
| | - Arash Kamali
- Department of Diagnostic and Interventional Imaging, McGovern Medical School, The University of Texas Health Science Center at Houston, 77030, Houston, TX, USA
- Memorial Hermann Hospital-TMC, 77030, Houston, TX, USA
| | - Nitin Tandon
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, 77030, Houston, TX, USA
- Memorial Hermann Hospital-TMC, 77030, Houston, TX, USA
| | - Leomar Y Ballester
- Department of Pathology, The University of Texas MD Anderson Cancer Center, 77030, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 77030, Houston, TX, USA
| | - Yoshua Esquenazi
- Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, 77030, Houston, TX, USA.
- Memorial Hermann Hospital-TMC, 77030, Houston, TX, USA.
- Center for Precision Health, School of Biomedical Informatics, the University of Texas Health Science Center at Houston, 77030, Houston, TX, USA.
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Hassan J, Saeed SM, Deka L, Uddin MJ, Das DB. Applications of Machine Learning (ML) and Mathematical Modeling (MM) in Healthcare with Special Focus on Cancer Prognosis and Anticancer Therapy: Current Status and Challenges. Pharmaceutics 2024; 16:260. [PMID: 38399314 PMCID: PMC10892549 DOI: 10.3390/pharmaceutics16020260] [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: 12/08/2023] [Revised: 01/29/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
The use of data-driven high-throughput analytical techniques, which has given rise to computational oncology, is undisputed. The widespread use of machine learning (ML) and mathematical modeling (MM)-based techniques is widely acknowledged. These two approaches have fueled the advancement in cancer research and eventually led to the uptake of telemedicine in cancer care. For diagnostic, prognostic, and treatment purposes concerning different types of cancer research, vast databases of varied information with manifold dimensions are required, and indeed, all this information can only be managed by an automated system developed utilizing ML and MM. In addition, MM is being used to probe the relationship between the pharmacokinetics and pharmacodynamics (PK/PD interactions) of anti-cancer substances to improve cancer treatment, and also to refine the quality of existing treatment models by being incorporated at all steps of research and development related to cancer and in routine patient care. This review will serve as a consolidation of the advancement and benefits of ML and MM techniques with a special focus on the area of cancer prognosis and anticancer therapy, leading to the identification of challenges (data quantity, ethical consideration, and data privacy) which are yet to be fully addressed in current studies.
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Affiliation(s)
- Jasmin Hassan
- Drug Delivery & Therapeutics Lab, Dhaka 1212, Bangladesh; (J.H.); (S.M.S.)
| | | | - Lipika Deka
- Faculty of Computing, Engineering and Media, De Montfort University, Leicester LE1 9BH, UK;
| | - Md Jasim Uddin
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Diganta B. Das
- Department of Chemical Engineering, Loughborough University, Loughborough LE11 3TU, UK
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Wu M, Luan J, Zhang D, Fan H, Qiao L, Zhang C. Development and validation of a clinical prediction model for glioma grade using machine learning. Technol Health Care 2024; 32:1977-1990. [PMID: 38306068 DOI: 10.3233/thc-231645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
BACKGROUND Histopathological evaluation is currently the gold standard for grading gliomas; however, this technique is invasive. OBJECTIVE This study aimed to develop and validate a diagnostic prediction model for glioma by employing multiple machine learning algorithms to identify risk factors associated with high-grade glioma, facilitating the prediction of glioma grading. METHODS Data from 1114 eligible glioma patients were obtained from The Cancer Genome Atlas (TCGA) database, which was divided into a training set (n= 781) and a test set (n= 333). Fifty machine learning algorithms were employed, and the optimal algorithm was selected to construct a prediction model. The performance of the machine learning prediction model was compared to the clinical prediction model in terms of discrimination, calibration, and clinical validity to assess the performance of the prediction model. RESULTS The area under the curve (AUC) values of the machine learning prediction models (training set: 0.870 vs. 0.740, test set: 0.863 vs. 0.718) were significantly improved from the clinical prediction models. Furthermore, significant improvement in discrimination was observed for the Integrated Discrimination Improvement (IDI) (training set: 0.230, test set: 0.270) and Net Reclassification Index (NRI) (training set: 0.170, test set: 0.170) from the clinical prognostic model. Both models showed a high goodness of fit and an increased net benefit. CONCLUSION A strong prediction accuracy model can be developed using machine learning algorithms to screen for high-grade glioma risk predictors, which can serve as a non-invasive prediction tool for preoperative diagnostic grading of glioma.
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Affiliation(s)
- Mingzhen Wu
- Department of Radiology, Liaocheng People's Hospital, Shandong First Medical University and Shandong Academy of Medical Sciences, Shandong, China
- Department of Radiology, Liaocheng People's Hospital, Shandong First Medical University and Shandong Academy of Medical Sciences, Shandong, China
| | - Jixin Luan
- Department of Radiology, China-Japan Friendship Hospital, Beijing, China
- China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Radiology, Liaocheng People's Hospital, Shandong First Medical University and Shandong Academy of Medical Sciences, Shandong, China
| | - Di Zhang
- Department of Radiology, Liaocheng People's Hospital, Shandong First Medical University and Shandong Academy of Medical Sciences, Shandong, China
| | - Hua Fan
- Department of Radiology, Liaocheng People's Hospital, Shandong First Medical University and Shandong Academy of Medical Sciences, Shandong, China
| | - Lishan Qiao
- School of Mathematics, Liaocheng University, Shandong, China
| | - Chuanchen Zhang
- Department of Radiology, Liaocheng People's Hospital, Shandong First Medical University and Shandong Academy of Medical Sciences, Shandong, China
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Meade SM, Salas-Vega S, Nagy MR, Sundar SJ, Steinmetz MP, Benzel EC, Habboub G. A Pilot Remote Curriculum to Enhance Resident and Medical Student Understanding of Machine Learning in Healthcare. World Neurosurg 2023; 180:e142-e148. [PMID: 37696433 DOI: 10.1016/j.wneu.2023.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/22/2023] [Accepted: 09/04/2023] [Indexed: 09/13/2023]
Abstract
BACKGROUND Despite the expanding role of machine learning (ML) in health care and patient expectations for clinicians to understand ML-based tools, few for-credit curricula exist specifically for neurosurgical trainees to learn basic principles and implications of ML for medical research and clinical practice. We implemented a novel, remotely delivered curriculum designed to develop literacy in ML for neurosurgical trainees. METHODS A 4-week pilot medical elective was designed specifically for trainees to build literacy in basic ML concepts. Qualitative feedback from interested and enrolled students was collected to assess students' and trainees' reactions, learning, and future application of course content. RESULTS Despite 15 interested learners, only 3 medical students and 1 neurosurgical resident completed the course. Enrollment included students and trainees from 3 different institutions. All learners who completed the course found the lectures relevant to their future practice as clinicians and researchers and reported improved confidence in applying and understanding published literature applying ML techniques in health care. Barriers to ample enrollment and retention (e.g., balancing clinical responsibilities) were identified. CONCLUSIONS This pilot elective demonstrated the interest, value, and feasibility of a remote elective to establish ML literacy; however, feedback to increase accessibility and flexibility of the course encouraged our team to implement changes. Future elective iterations will have a semiannual, 2-week format, splitting lectures more clearly between theory (the method and its value) and application (coding instructions) and will make lectures open-source prerequisites to allow tailoring of student learning to their planned application of these methods in their practice and research.
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Affiliation(s)
- Seth M Meade
- Department of Neurosurgery, Cleveland Clinic Lerner College of Medicine, Cleveland, Ohio, USA; Case Western School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA; Department of Neurosurgery, Neurologic Institute, Center for Spine Health, Cleveland Clinic Foundation, Cleveland, Ohio, USA.
| | - Sebastian Salas-Vega
- Case Western School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA; Department of Neurosurgery, Neurologic Institute, Center for Spine Health, Cleveland Clinic Foundation, Cleveland, Ohio, USA; Department of Neurosurgery, Inova Health System, Falls Church, Virginia, USA
| | - Matthew R Nagy
- Department of Neurosurgery, Cleveland Clinic Lerner College of Medicine, Cleveland, Ohio, USA; Case Western School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Swetha J Sundar
- Department of Neurosurgery, Cleveland Clinic Lerner College of Medicine, Cleveland, Ohio, USA; Department of Neurosurgery, Neurologic Institute, Center for Spine Health, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Michael P Steinmetz
- Department of Neurosurgery, Cleveland Clinic Lerner College of Medicine, Cleveland, Ohio, USA; Department of Neurosurgery, Neurologic Institute, Center for Spine Health, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Edward C Benzel
- Department of Neurosurgery, Cleveland Clinic Lerner College of Medicine, Cleveland, Ohio, USA; Department of Neurosurgery, Neurologic Institute, Center for Spine Health, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Ghaith Habboub
- Department of Neurosurgery, Cleveland Clinic Lerner College of Medicine, Cleveland, Ohio, USA; Department of Neurosurgery, Neurologic Institute, Center for Spine Health, Cleveland Clinic Foundation, Cleveland, Ohio, USA
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Au Yeung J, Wang YY, Kraljevic Z, Teo JTH. Artificial intelligence (AI) for neurologists: do digital neurones dream of electric sheep? Pract Neurol 2023; 23:476-488. [PMID: 37977806 DOI: 10.1136/pn-2023-003757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2023] [Indexed: 11/19/2023]
Abstract
Artificial intelligence (AI) is routinely mentioned in journals and newspapers, and non-technical outsiders may have difficulty in distinguishing hyperbole from reality. We present a practical guide to help non-technical neurologists to understand healthcare AI. AI is being used to support clinical decisions in treating neurological disorders. We introduce basic concepts of AI, such as machine learning and natural language processing, and explain how AI is being used in healthcare, giving examples its benefits and challenges. We also cover how AI performance is measured, and its regulatory aspects in healthcare. An important theme is that AI is a general-purpose technology like medical statistics, with broad utility applicable in various scenarios, such that niche approaches are outpaced by approaches that are broadly applicable in many disease areas and specialties. By understanding AI basics and its potential applications, neurologists can make informed decisions when evaluating AI used in their clinical practice. This article was written by four humans, with generative AI helping with formatting and image generation.
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Affiliation(s)
- Joshua Au Yeung
- CogStack team, Guy's and St Thomas' NHS Foundation Trust, London, UK
- CogStack team, King's College Hospital NHS Foundation Trust, London, London, UK
| | - Yang Yang Wang
- Medicine, Guy's and St Thomas' Hospitals NHS Trust, London, London, UK
| | - Zeljko Kraljevic
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - James T H Teo
- CogStack team, Guy's and St Thomas' NHS Foundation Trust, London, UK
- CogStack team, King's College Hospital NHS Foundation Trust, London, London, UK
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
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Chen Y, Hu D, Wang F, Huang C, Xie H, Jin L. A systematic framework for identifying prognostic necroptosis-related lncRNAs and verification of lncRNA CRNDE/miR-23b-3p/IDH1 regulatory axis in glioma. Aging (Albany NY) 2023; 15:12296-12313. [PMID: 37934582 PMCID: PMC10683586 DOI: 10.18632/aging.205180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/26/2023] [Indexed: 11/08/2023]
Abstract
Glioma remains the most frequent malignancy of the central nervous system. Recently, necroptosis has been identified as a cell death process that mediates the proliferation and development of tumor cells. LncRNAs play a key role in the diagnosis and treatment of various diseases. However, the impact that necrosis-related lncRNAs (NRLs) have on glioma remains unclear. In our studies, we selected 9 NRLs to construct a prognostic model. Meanwhile, we assessed the survival curves of these 9 NRLs. Our findings found ADGRA1-AS1 and WAC-AS1 were protective lncRNAs, while MIR210HG, LINC01503, CRNDE, HOXC-AS1, ZIM2-AS1, MIR22HG and PLBD1-AS1 were risk lncRNAs. Specifically, 12 immune cells, 25 immune-correlated pathways, and TME score were differentially expressed in the both risk groups. Additionally, the study predicted and validated the necroptosis-related lncRNA CRNDE/miR-23b-3p/IDH1 axis. CRNDE was strongly expressed in glioma specimens and several cell lines. Inhibiting CRNDE resulted in a substantial reduction in the proliferation and migration of U-118MG and U251 cells. Furthermore, the study predicted that CRNDE may exhibit oncogenic features by adsorbing miR-23b-3p and positively regulating IDH1 expression. Overall, the study constructed a prognostic model in glioma, and predicted a lncRNA CRNDE/miR-23b-3p/IDH1 axis, which could potentially be useful for gene therapy of glioma.
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Affiliation(s)
- Yangxia Chen
- Department of Dermatology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
- Department of Dermatology, Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Di Hu
- Department of Neurology and Stroke Centre, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Fang Wang
- Department of Neurology and Stroke Centre, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Cheng Huang
- Department of Neurology and Stroke Centre, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Hesong Xie
- Department of Neurology and Stroke Centre, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Ling Jin
- Department of Traditional Chinese Medicine, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
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10
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Geng X, Zhou ZA, Mi Y, Wang C, Wang M, Guo C, Qu C, Feng S, Kim I, Yu M, Ji H, Ren X. Glioma Single-Cell Biomechanical Analysis by Cyclic Conical Constricted Microfluidics. Anal Chem 2023; 95:15585-15594. [PMID: 37843131 DOI: 10.1021/acs.analchem.3c02434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Determining the grade of glioma is a critical step in choosing patients' treatment plans in clinical practices. The pathological diagnosis of patient's glioma samples requires extensive staining and imaging procedures, which are expensive and time-consuming. Current advanced uniform-width-constriction-channel-based microfluidics have proven to be effective in distinguishing cancer cells from normal tissues, such as breast cancer, ovarian cancer, prostate cancer, etc. However, the uniform-width-constriction channels can result in low yields on glioma cells with irregular morphologies and high heterogeneity. In this research, we presented an innovative cyclic conical constricted (CCC) microfluidic device to better differentiate glioma cells from normal glial cells. Compared with the widely used uniform-width-constriction microchannels, the new CCC configuration forces single cells to deform gradually and obtains the biophysical attributes from each deformation. The human-derived glioma cell lines U-87 and U-251, as well as the human-derived normal glial astrocyte cell line HA-1800 were selected as the proof of concept. The results showed that CCC channels can effectively obtain the biomechanical characteristics of different 12-25 μm glial cell lines. The patient glioma samples with WHO grades II, III, and IV were tested by CCC channels and compared between Elastic Net (ENet) and Lasso analysis. The results demonstrated that CCC channels and the ENet can successfully select critical biomechanical parameters to differentiate the grades of single-glioma cells. This CCC device can be potentially further applied to the extensive family of brain tumors at the single-cell level.
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Affiliation(s)
- Xin Geng
- Department of Neurosurgery, Shanxi Provincial People's Hospital, The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi 030012, China
| | - Zi-Ang Zhou
- Department of Microelectronics, Tianjin University, Tianjin 300072, China
| | - Yang Mi
- Department of Neurosurgery, Shanxi Provincial People's Hospital, The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi 030012, China
| | - Chunhong Wang
- Department of Neurosurgery, Shanxi Provincial People's Hospital, The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi 030012, China
| | - Meng Wang
- Department of Neurosurgery, Shanxi Provincial People's Hospital, The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi 030012, China
| | - Chenjia Guo
- Department of Pathology, Shanxi Provincial People's Hospital, The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi 030012, China
| | - Chongxiao Qu
- Department of Pathology, Shanxi Provincial People's Hospital, The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi 030012, China
| | - Shilun Feng
- Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
| | - Inyoung Kim
- Department of Statistics, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Miao Yu
- Department of Research and Development, Stedical Scientific, Carlsbad, California 92010, United States
| | - Hongming Ji
- Department of Neurosurgery, Shanxi Provincial People's Hospital, The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi 030012, China
| | - Xiang Ren
- Department of Neurosurgery, Shanxi Provincial People's Hospital, The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi 030012, China
- Department of Microelectronics, Tianjin University, Tianjin 300072, China
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11
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Jin W, Lin J, Wang P, Yang H, Jin C. Screening the predictors for live birth failure in women after the first frozen embryo transfer based on the Lasso algorithm: a retrospective study. ZYGOTE 2023; 31:350-358. [PMID: 37183670 DOI: 10.1017/s0967199423000217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
This study aimed to screen factors related to live birth outcomes of women with first frozen embryo transfer (FET). The enrolled women were divided into training and validation cohorts. The least absolute shrinkage and selection operator (Lasso) regression algorithm of machine learning and the multiple regression model were then used to screen factors relevant to live birth failure (LBF) for the training dataset. A nomogram risk prediction model was established on the basis of the screened factors, and the consistency index (C-index) and calibration curve were derived for evaluating the model. The validation cohort was utilized to validate the nomogram model further. In total, 2083 women who accepted the first FET in our hospital were included and 44 factors were initially screened in this study. On the basis of the training cohort, the screened risk factors via multiple regression analysis with odds ratio (OR) values were female age (OR: 3.092, 95%CI: 1.065-4.852), body mass index (BMI; OR: 1.106, 95%CI: 1.015-1.546), caesarean section (OR: 1.909, 95%CI: 1.318-2.814), number of high-quality embryos (OR: 0.698, 95%CI: 0.599-0.812), and endometrial thickness (OR: 0.957, CI: 0.904-0.980). The nomogram model was generated based on five predictors. Furthermore, favourable results with C-indexes and calibration curves close to ideal curves indicated the accurate predictive ability of the nomogram. Female age, BMI, caesarean section, number of high-quality embryos, and endometrial thickness were independent predictors for LBF. The five factors of the risk assessment model may help to identify LBF with high accuracy in women who accept FET.
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Affiliation(s)
- Wumin Jin
- Department of Reproductive Medicine Centre, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jia Lin
- Department of Reproductive Medicine Centre, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Peiyu Wang
- Department of Reproductive Medicine Centre, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Haiyan Yang
- Department of Reproductive Medicine Centre, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Congcong Jin
- Department of Reproductive Medicine Centre, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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12
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Wijethilake N, MacCormac O, Vercauteren T, Shapey J. Imaging biomarkers associated with extra-axial intracranial tumors: a systematic review. Front Oncol 2023; 13:1131013. [PMID: 37182138 PMCID: PMC10167010 DOI: 10.3389/fonc.2023.1131013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 03/27/2023] [Indexed: 05/16/2023] Open
Abstract
Extra-axial brain tumors are extra-cerebral tumors and are usually benign. The choice of treatment for extra-axial tumors is often dependent on the growth of the tumor, and imaging plays a significant role in monitoring growth and clinical decision-making. This motivates the investigation of imaging biomarkers for these tumors that may be incorporated into clinical workflows to inform treatment decisions. The databases from Pubmed, Web of Science, Embase, and Medline were searched from 1 January 2000 to 7 March 2022, to systematically identify relevant publications in this area. All studies that used an imaging tool and found an association with a growth-related factor, including molecular markers, grade, survival, growth/progression, recurrence, and treatment outcomes, were included in this review. We included 42 studies, comprising 22 studies (50%) of patients with meningioma; 17 studies (38.6%) of patients with pituitary tumors; three studies (6.8%) of patients with vestibular schwannomas; and two studies (4.5%) of patients with solitary fibrous tumors. The included studies were explicitly and narratively analyzed according to tumor type and imaging tool. The risk of bias and concerns regarding applicability were assessed using QUADAS-2. Most studies (41/44) used statistics-based analysis methods, and a small number of studies (3/44) used machine learning. Our review highlights an opportunity for future work to focus on machine learning-based deep feature identification as biomarkers, combining various feature classes such as size, shape, and intensity. Systematic Review Registration: PROSPERO, CRD42022306922.
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Affiliation(s)
- Navodini Wijethilake
- School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
| | - Oscar MacCormac
- School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
- Department of Neurosurgery, King’s College Hospital NHS Foundation Trust, London, United Kingdom
| | - Tom Vercauteren
- School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
| | - Jonathan Shapey
- School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
- Department of Neurosurgery, King’s College Hospital NHS Foundation Trust, London, United Kingdom
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13
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Din M, Agarwal S, Grzeda M, Wood DA, Modat M, Booth TC. Detection of cerebral aneurysms using artificial intelligence: a systematic review and meta-analysis. J Neurointerv Surg 2023; 15:262-271. [PMID: 36375834 PMCID: PMC9985742 DOI: 10.1136/jnis-2022-019456] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/11/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND Subarachnoid hemorrhage from cerebral aneurysm rupture is a major cause of morbidity and mortality. Early aneurysm identification, aided by automated systems, may improve patient outcomes. Therefore, a systematic review and meta-analysis of the diagnostic accuracy of artificial intelligence (AI) algorithms in detecting cerebral aneurysms using CT, MRI or DSA was performed. METHODS MEDLINE, Embase, Cochrane Library and Web of Science were searched until August 2021. Eligibility criteria included studies using fully automated algorithms to detect cerebral aneurysms using MRI, CT or DSA. Following Preferred Reporting Items for Systematic Reviews and Meta-Analysis: Diagnostic Test Accuracy (PRISMA-DTA), articles were assessed using Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS-2). Meta-analysis included a bivariate random-effect model to determine pooled sensitivity, specificity, and area under the receiver operator characteristic curve (ROC-AUC). PROSPERO CRD42021278454. RESULTS 43 studies were included, and 41/43 (95%) were retrospective. 34/43 (79%) used AI as a standalone tool, while 9/43 (21%) used AI assisting a reader. 23/43 (53%) used deep learning. Most studies had high bias risk and applicability concerns, limiting conclusions. Six studies in the standalone AI meta-analysis gave (pooled) 91.2% (95% CI 82.2% to 95.8%) sensitivity; 16.5% (95% CI 9.4% to 27.1%) false-positive rate (1-specificity); 0.936 ROC-AUC. Five reader-assistive AI studies gave (pooled) 90.3% (95% CI 88.0% - 92.2%) sensitivity; 7.9% (95% CI 3.5% to 16.8%) false-positive rate; 0.910 ROC-AUC. CONCLUSION AI has the potential to support clinicians in detecting cerebral aneurysms. Interpretation is limited due to high risk of bias and poor generalizability. Multicenter, prospective studies are required to assess AI in clinical practice.
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Affiliation(s)
- Munaib Din
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Siddharth Agarwal
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Mariusz Grzeda
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - David A Wood
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Marc Modat
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Thomas C Booth
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
- Department of Neuroradiology, King's College Hospital NHS Foundation Trust, London, UK
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14
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Wamelink IJHG, Kuijer JPA, Padrela BE, Zhang Y, Barkhof F, Mutsaerts HJMM, Petr J, van de Giessen E, Keil VC. Reproducibility of 3 T APT-CEST in Healthy Volunteers and Patients With Brain Glioma. J Magn Reson Imaging 2023; 57:206-215. [PMID: 35633282 PMCID: PMC10084114 DOI: 10.1002/jmri.28239] [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: 02/23/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Amide proton transfer (APT) imaging is a chemical exchange saturation transfer (CEST) technique offering potential clinical applications such as diagnosis, characterization, and treatment planning and monitoring in glioma patients. While APT-CEST has demonstrated high potential, reproducibility remains underexplored. PURPOSE To investigate whether cerebral APT-CEST with clinically feasible scan time is reproducible in healthy tissue and glioma for clinical use at 3 T. STUDY TYPE Prospective, longitudinal. SUBJECTS Twenty-one healthy volunteers (11 females; mean age ± SD: 39 ± 11 years) and 6 glioma patients (3 females; 50 ± 17 years: 4 glioblastomas, 1 oligodendroglioma, 1 radiologically suspected low-grade glioma). FIELD STRENGTH/SEQUENCE 3 T, Turbo Spin Echo - ampling perfection with application optimized contrasts using different flip angle evolution - chemical exchange saturation transfer (TSE SPACE-CEST). ASSESSMENT APT-CEST measurement reproducibility was assessed within-session (glioma patients, scan session 1; healthy volunteers scan sessions 1, 2, and 3), between-sessions (healthy volunteers scan sessions 1 and 2), and between-days (healthy volunteers, scan sessions 1 and 3). The mean APTCEST values and standard deviation of the within-subject difference (SDdiff ) were calculated in whole tumor enclosed by regions of interest (ROIs) in patients, and eight ROIs in healthy volunteers-whole-brain, cortical gray matter, putamen, thalami, orbitofrontal gyri, occipital lobes, central brain-and compared. STATISTICAL TESTS Brown-Forsythe tests and variance component analysis (VCA) were used to assess the reproducibility of ROIs for the three time intervals. Significance was set at P < 0.003 after Bonferroni correction. RESULTS Intratumoral mean APTCEST was significantly higher than APTCEST in healthy-appearing tissue in patients (0.5 ± 0.46%). The average within-session, between-sessions, and between-days SDdiff of healthy control brains was 0.2% and did not differ significantly with each other (0.76 > P > 0.22). The within-session SDdiff of whole-brain was 0.2% in both healthy volunteers and patients, and 0.21% in the segmented tumor. VCA showed that within-session factors were the most important (60%) for scanning variance. DATA CONCLUSION Cerebral APT-CEST imaging may show good scan-rescan reproducibility in healthy tissue and tumors with clinically feasible scan times at 3 T. Short-term measurement effects may be the dominant components for reproducibility. LEVEL OF EVIDENCE 2 TECHNICAL EFFICACY: Stage 2.
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Affiliation(s)
- Ivar J H G Wamelink
- Department of Radiology and Nuclear Medicine, Cancer Center Amsterdam, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Joost P A Kuijer
- Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Beatriz E Padrela
- Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Yi Zhang
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China
| | - Frederik Barkhof
- Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Center, Amsterdam, The Netherlands.,Queen Square Institute of Neurology and Centre for Medical Image Computing, University College London, London, UK
| | - Henk J M M Mutsaerts
- Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Jan Petr
- Department of Radiology and Nuclear Medicine, Cancer Center Amsterdam, Amsterdam University Medical Center, Amsterdam, The Netherlands.,Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
| | - Elsmarieke van de Giessen
- Department of Radiology and Nuclear Medicine, Cancer Center Amsterdam, Amsterdam University Medical Center, Amsterdam, The Netherlands.,Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Vera C Keil
- Department of Radiology and Nuclear Medicine, Cancer Center Amsterdam, Amsterdam University Medical Center, Amsterdam, The Netherlands
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15
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Shuaib H, Barker GJ, Sasieni P, De Vita E, Chelliah A, Andrei R, Ashkan K, Beaumont E, Brazil L, Rowland-Hill C, Lau YH, Luis A, Powell J, Swampillai A, Tenant S, Thust SC, Wastling S, Young T, Booth TC. Overcoming challenges of translating deep-learning models for glioblastoma: the ZGBM consortium. Br J Radiol 2023; 96:20220206. [PMID: 35616700 PMCID: PMC10997010 DOI: 10.1259/bjr.20220206] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 04/25/2022] [Indexed: 11/05/2022] Open
Abstract
OBJECTIVE To report imaging protocol and scheduling variance in routine care of glioblastoma patients in order to demonstrate challenges of integrating deep-learning models in glioblastoma care pathways. Additionally, to understand the most common imaging studies and image contrasts to inform the development of potentially robust deep-learning models. METHODS MR imaging data were analysed from a random sample of five patients from the prospective cohort across five participating sites of the ZGBM consortium. Reported clinical and treatment data alongside DICOM header information were analysed to understand treatment pathway imaging schedules. RESULTS All sites perform all structural imaging at every stage in the pathway except for the presurgical study, where in some sites only contrast-enhanced T1-weighted imaging is performed. Diffusion MRI is the most common non-structural imaging type, performed at every site. CONCLUSION The imaging protocol and scheduling varies across the UK, making it challenging to develop machine-learning models that could perform robustly at other centres. Structural imaging is performed most consistently across all centres. ADVANCES IN KNOWLEDGE Successful translation of deep-learning models will likely be based on structural post-treatment imaging unless there is significant effort made to standardise non-structural or peri-operative imaging protocols and schedules.
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Affiliation(s)
- Haris Shuaib
- Guy’s & St Thomas’ NHS Foundation Trust,
King’s College, London, United Kingdom
| | | | | | | | | | - Roman Andrei
- The Oncology Institute "Prof. Dr. Ion Chiricuţă"
Cluj-Napoca, Cluj-Napoca, Romania
| | - Keyoumars Ashkan
- King’s College Hospital NHS Foundation
Trust, London, United Kingdom
| | - Erica Beaumont
- Lancashire Teaching Hospitals NHS Foundation
Trust, Lancashire, United Kingdom
| | - Lucy Brazil
- Guy’s & St Thomas’ NHS Foundation Trust,
King’s College, London, United Kingdom
| | | | - Yue Hui Lau
- King’s College Hospital NHS Foundation
Trust, London, United Kingdom
| | - Aysha Luis
- King's College London, London, United
Kingdom
| | - James Powell
- Velindre University NHS Trust, Wales, United
Kingdom
| | - Angela Swampillai
- Guy’s & St Thomas’ NHS Foundation Trust,
King’s College, London, United Kingdom
| | - Sean Tenant
- The Christie NHS Foundation Trust, Manchester,
United Kingdom
| | - Stefanie C Thust
- National Hospital for Neurology and Neurosurgery, UCL
Institute of Neurology, London, United Kingdom
| | - Stephen Wastling
- National Hospital for Neurology and Neurosurgery, UCL
Institute of Neurology, London, United Kingdom
| | - Tom Young
- Guy’s & St Thomas’ NHS Foundation Trust,
King’s College, London, United Kingdom
| | - Thomas C Booth
- Guy’s & St Thomas’ NHS Foundation Trust,
King’s College, London, United Kingdom
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16
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Cost Matrix of Molecular Pathology in Glioma-Towards AI-Driven Rational Molecular Testing and Precision Care for the Future. Biomedicines 2022; 10:biomedicines10123029. [PMID: 36551786 PMCID: PMC9775648 DOI: 10.3390/biomedicines10123029] [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: 10/20/2022] [Revised: 11/09/2022] [Accepted: 11/19/2022] [Indexed: 11/27/2022] Open
Abstract
Gliomas are the most common and aggressive primary brain tumors. Gliomas carry a poor prognosis because of the tumor's resistance to radiation and chemotherapy leading to nearly universal recurrence. Recent advances in large-scale genomic research have allowed for the development of more targeted therapies to treat glioma. While precision medicine can target specific molecular features in glioma, targeted therapies are often not feasible due to the lack of actionable markers and the high cost of molecular testing. This review summarizes the clinically relevant molecular features in glioma and the current cost of care for glioma patients, focusing on the molecular markers and meaningful clinical features that are linked to clinical outcomes and have a realistic possibility of being measured, which is a promising direction for precision medicine using artificial intelligence approaches.
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17
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Pálsson S, Cerri S, Poulsen HS, Urup T, Law I, Van Leemput K. Predicting survival of glioblastoma from automatic whole-brain and tumor segmentation of MR images. Sci Rep 2022; 12:19744. [PMID: 36396681 PMCID: PMC9671967 DOI: 10.1038/s41598-022-19223-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 08/25/2022] [Indexed: 11/18/2022] Open
Abstract
Survival prediction models can potentially be used to guide treatment of glioblastoma patients. However, currently available MR imaging biomarkers holding prognostic information are often challenging to interpret, have difficulties generalizing across data acquisitions, or are only applicable to pre-operative MR data. In this paper we aim to address these issues by introducing novel imaging features that can be automatically computed from MR images and fed into machine learning models to predict patient survival. The features we propose have a direct anatomical-functional interpretation: They measure the deformation caused by the tumor on the surrounding brain structures, comparing the shape of various structures in the patient's brain to their expected shape in healthy individuals. To obtain the required segmentations, we use an automatic method that is contrast-adaptive and robust to missing modalities, making the features generalizable across scanners and imaging protocols. Since the features we propose do not depend on characteristics of the tumor region itself, they are also applicable to post-operative images, which have been much less studied in the context of survival prediction. Using experiments involving both pre- and post-operative data, we show that the proposed features carry prognostic value in terms of overall- and progression-free survival, over and above that of conventional non-imaging features.
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Affiliation(s)
- Sveinn Pálsson
- grid.5170.30000 0001 2181 8870Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Stefano Cerri
- grid.5170.30000 0001 2181 8870Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Hans Skovgaard Poulsen
- grid.475435.4Department of Oncology, The Finsen Center, Rigshospitalet, Copenhagen, Denmark
| | - Thomas Urup
- grid.475435.4Department of Oncology, The Finsen Center, Rigshospitalet, Copenhagen, Denmark
| | - Ian Law
- grid.475435.4Department of Clinical Physiology, Nuclear Medicine and PET, Center of Diagnostic Investigation, Rigshospitalet, Copenhagen, Denmark
| | - Koen Van Leemput
- grid.5170.30000 0001 2181 8870Department of Health Technology, Technical University of Denmark, Lyngby, Denmark ,grid.32224.350000 0004 0386 9924Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, USA
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18
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Ershadi MM, Rise ZR, Niaki STA. A hierarchical machine learning model based on Glioblastoma patients' clinical, biomedical, and image data to analyze their treatment plans. Comput Biol Med 2022; 150:106159. [PMID: 36257277 DOI: 10.1016/j.compbiomed.2022.106159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 08/28/2022] [Accepted: 09/24/2022] [Indexed: 11/03/2022]
Abstract
AIM OF STUDY Glioblastoma Multiforme (GBM) is an aggressive brain cancer in adults that kills most patients in the first year due to ineffective treatment. Different clinical, biomedical, and image data features are needed to analyze GBM, increasing complexities. Besides, they lead to weak performances for machine learning models due to ignoring physicians' knowledge. Therefore, this paper proposes a hierarchical model based on Fuzzy C-mean (FCM) clustering, Wrapper feature selection, and twelve classifiers to analyze treatment plans. METHODOLOGY/APPROACH The proposed method finds the effectiveness of previous and current treatment plans, hierarchically determining the best decision for future treatment plans for GBM patients using clinical data, biomedical data, and different image data. A case study is presented based on the Cancer Genome Atlas Glioblastoma Multiforme dataset to prove the effectiveness of the proposed model. This dataset is analyzed using data preprocessing, experts' knowledge, and a feature reduction method based on the Principal Component Analysis. Then, the FCM clustering method is utilized to reinforce classifier learning. OUTCOMES OF STUDY The proposed model finds the best combination of Wrapper feature selection and classifier for each cluster based on different measures, including accuracy, sensitivity, specificity, precision, F-score, and G-mean according to a hierarchical structure. It has the best performance among other reinforced classifiers. Besides, this model is compatible with real-world medical processes for GBM patients based on clinical, biomedical, and image data.
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Affiliation(s)
- Mohammad Mahdi Ershadi
- Department of Industrial Engineering and Management Systems, Amirkabir University of Technology, Tehran, Iran.
| | - Zeinab Rahimi Rise
- Department of Industrial Engineering and Management Systems, Amirkabir University of Technology, Tehran, Iran.
| | - Seyed Taghi Akhavan Niaki
- Department of Industrial Engineering, Sharif University of Technology, PO Box 11155-9414, Tehran, 1458889694, Iran.
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19
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Short SC, Noushmehr H. Unmet need for liquid biomarkers and the Brain-Liquid Biopsy Consortium. Neurooncol Adv 2022; 4:ii1-ii3. [PMID: 36380869 PMCID: PMC9650471 DOI: 10.1093/noajnl/vdac020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023] Open
Affiliation(s)
- Susan C Short
- Department of Oncology, Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Houtan Noushmehr
- Department of Neurosurgery, Henry Ford Health System, Detroit, Michigan, USA
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20
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Zhao R, Zhuge Y, Camphausen K, Krauze AV. Machine learning based survival prediction in Glioma using large-scale registry data. Health Informatics J 2022; 28:14604582221135427. [PMID: 36264067 PMCID: PMC10673681 DOI: 10.1177/14604582221135427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2023]
Abstract
Gliomas are the most common central nervous system tumors exhibiting poor clinical outcomes. The ability to estimate prognosis is crucial for both patients and providers in order to select the most appropriate treatment. Machine learning (ML) allows for sophisticated approaches to survival prediction using real world clinical parameters needed to achieve superior predictive accuracy. We employed Cox Proportional hazards (CPH) model, Support Vector Machine (SVM) model, Random Forest (RF) model in a large glioma dataset (3462 patients, diagnosed 2000-2018) to explore the most optimal approach to survival prediction. Features employed were age, sex, surgical resection status, tumor histology and tumor site, administration of radiation therapy (RT) and chemotherapy status. Concordance index (c-index) was employed to assess the accuracy of survival time prediction. All three models performed well with prediction accuracy (CI 0.767, 0.771, 0.57 for CPH, SVM, RF models respectively) with the best performance achieved when incorporating RT and chemotherapy administration status which emerged as key predictive features. Within the subset of glioblastoma patients, similar prediction accuracy was achieved. These findings should prompt stricter clinician oversight over registry data accuracy through quality assurance as we move towards meaningful predictive ability using ML approaches in glioma.
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Affiliation(s)
| | | | | | - Andra V Krauze
- 3421National Cancer Institute, NIH, USA; 184934BC Cancer Surrey, Canada
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21
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Liu H, Xing K, Jiang Y, Liu Y, Wang C, Ding X. Using Machine Learning to Identify Biomarkers Affecting Fat Deposition in Pigs by Integrating Multisource Transcriptome Information. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:10359-10370. [PMID: 35953074 PMCID: PMC9413214 DOI: 10.1021/acs.jafc.2c03339] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Fat deposition in pigs is not only closely related to pig production efficiency and pork quality but also an ideal model for human obesity. Transcriptome sequencing is widely used to study fat deposition. However, due to small sample sizes, high false positive rates, and poor consistency of results from different studies, new strategies are urgently needed. Machine learning, a new analysis method, can effectively fit complex data and accurately identify samples and genes. In this study, 36 samples of adipose tissue, muscle tissue, and liver tissue were collected from Songliao black pigs and Landrace pigs, and the mRNA of all the samples was sequenced. In addition, we collected transcriptome data for 64 samples in the GEO database from four different sources. After standardization and imputation of missing values in the data set comprising 100 samples, traditional differential expression analysis was carried out, and different numbers of expressed genes were selected as features for the training model of eight machine learning methods. In the 1000 replications of fourfold cross validation with 100 samples, AdaBoost performed best, with an average prediction accuracy greater than 93% and the highest mean area under the curve in predicting the high- and low-fat content groups among the eight ML methods. According to their performance-based ranks inferred by AdaBoost, 12 genes related to fat deposition were identified; among them, FASN and APOD were specifically expressed in adipose tissue, and APOA1 was specifically expressed in the liver, which could be important candidate biomarkers affecting fat deposition.
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22
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Detection of mutation profiles and tumor mutation burden of cerebrospinal fluid circulating DNA by a cancer genomic panel sequencing in glioma patients. Clin Chim Acta 2022; 534:81-92. [PMID: 35810802 DOI: 10.1016/j.cca.2022.07.001] [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: 06/09/2022] [Accepted: 07/03/2022] [Indexed: 11/23/2022]
Abstract
BACKGROUND AND AIMS Circulating tumor DNA (ctDNA) has been recognized as a reliable source to reflect the molecular and genetic landscape of corresponding tumors in recent years. In this study, we tested the application of a cancer genomic panel sequencing on the cerebrospinal fluid (CSF)-derived ctDNA for the less invasive detection and diagnosis of glioma. MATERIALS AND METHODS CtDNA was extracted from 26 CSF samples and subject to a cancer genomic panel sequencing of 520 genes to analyze the mutation profiles and tumor mutation burden (TMB), which were compared with their corresponding tumor DNA samples. Associations between mutations or TMB and clinical characteristics were also evaluated. RESULTS A high detection rate of ctDNA (24/26, 92.3%) was observed in CSF. CtDNA mutations had high concordance rates with tumor DNA, especially in non-copy number variations and in glioblastoma. CSF ctDNA TMB also exhibited a strong correlation with tumor DNA TMB (R2 = 0.879, P < 0.001), particularly in glioblastoma (R2 = 0.992, P < 0.001). Age was significantly associated with CSF ctDNA TMB in glioma patients. CONCLUSION We established a less invasive but effective molecular diagnostic approach using a cancer genomic panel sequencing system targeting CSF ctDNA for glioma, especially in glioblastoma.
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23
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Jian A, Liu S, Di Ieva A. Artificial Intelligence for Survival Prediction in Brain Tumors on Neuroimaging. Neurosurgery 2022; 91:8-26. [PMID: 35348129 DOI: 10.1227/neu.0000000000001938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 01/08/2022] [Indexed: 12/30/2022] Open
Abstract
Survival prediction of patients affected by brain tumors provides essential information to guide surgical planning, adjuvant treatment selection, and patient counseling. Current reliance on clinical factors, such as Karnofsky Performance Status Scale, and simplistic radiological characteristics are, however, inadequate for survival prediction in tumors such as glioma that demonstrate molecular and clinical heterogeneity with variable survival outcomes. Advances in the domain of artificial intelligence have afforded powerful tools to capture a large number of hidden high-dimensional imaging features that reflect abundant information about tumor structure and physiology. Here, we provide an overview of current literature that apply computational analysis tools such as radiomics and machine learning methods to the pipeline of image preprocessing, tumor segmentation, feature extraction, and construction of classifiers to establish survival prediction models based on neuroimaging. We also discuss challenges relating to the development and evaluation of such models and explore ethical issues surrounding the future use of machine learning predictions.
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Affiliation(s)
- Anne Jian
- Computational NeuroSurgery (CNS) Lab, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
- Royal Melbourne Hospital, Melbourne, Australia
| | - Sidong Liu
- Computational NeuroSurgery (CNS) Lab, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
- Centre for Health Informatics, Australian Institute of Health Innovation, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Antonio Di Ieva
- Computational NeuroSurgery (CNS) Lab, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
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24
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Tozzi AE, Fabozzi F, Eckley M, Croci I, Dell’Anna VA, Colantonio E, Mastronuzzi A. Gaps and Opportunities of Artificial Intelligence Applications for Pediatric Oncology in European Research: A Systematic Review of Reviews and a Bibliometric Analysis. Front Oncol 2022; 12:905770. [PMID: 35712463 PMCID: PMC9194810 DOI: 10.3389/fonc.2022.905770] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 05/04/2022] [Indexed: 12/23/2022] Open
Abstract
The application of artificial intelligence (AI) systems is emerging in many fields in recent years, due to the increased computing power available at lower cost. Although its applications in various branches of medicine, such as pediatric oncology, are many and promising, its use is still in an embryonic stage. The aim of this paper is to provide an overview of the state of the art regarding the AI application in pediatric oncology, through a systematic review of systematic reviews, and to analyze current trends in Europe, through a bibliometric analysis of publications written by European authors. Among 330 records found, 25 were included in the systematic review. All papers have been published since 2017, demonstrating only recent attention to this field. The total number of studies included in the selected reviews was 674, with a third including an author with a European affiliation. In bibliometric analysis, 304 out of the 978 records found were included. Similarly, the number of publications began to dramatically increase from 2017. Most explored AI applications regard the use of diagnostic images, particularly radiomics, as well as the group of neoplasms most involved are the central nervous system tumors. No evidence was found regarding the use of AI for process mining, clinical pathway modeling, or computer interpreted guidelines to improve the healthcare process. No robust evidence is yet available in any of the domains investigated by systematic reviews. However, the scientific production in Europe is significant and consistent with the topics covered in systematic reviews at the global level. The use of AI in pediatric oncology is developing rapidly with promising results, but numerous gaps and challenges persist to validate its utilization in clinical practice. An important limitation is the need for large datasets for training algorithms, calling for international collaborative studies.
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Affiliation(s)
- Alberto Eugenio Tozzi
- Multifactorial and Complex Diseases Research Area, Bambino Gesù Children’s Hospital, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Francesco Fabozzi
- Department of Onco Hematology and Cell and Gene Therapy, Bambino Gesù Pediatric Hospital, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Department of Pediatrics, University of Rome Tor Vergata, Rome, Italy
| | - Megan Eckley
- Department of Onco Hematology and Cell and Gene Therapy, Bambino Gesù Pediatric Hospital, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Ileana Croci
- Multifactorial and Complex Diseases Research Area, Bambino Gesù Children’s Hospital, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Vito Andrea Dell’Anna
- Department of Onco Hematology and Cell and Gene Therapy, Bambino Gesù Pediatric Hospital, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Erica Colantonio
- Department of Onco Hematology and Cell and Gene Therapy, Bambino Gesù Pediatric Hospital, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Angela Mastronuzzi
- Department of Onco Hematology and Cell and Gene Therapy, Bambino Gesù Pediatric Hospital, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- *Correspondence: Angela Mastronuzzi,
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25
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Lv K, Cao X, Wang R, Du P, Fu J, Geng D, Zhang J. Neuroplasticity of Glioma Patients: Brain Structure and Topological Network. Front Neurol 2022; 13:871613. [PMID: 35645982 PMCID: PMC9136300 DOI: 10.3389/fneur.2022.871613] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/26/2022] [Indexed: 11/19/2022] Open
Abstract
Glioma is the most common primary malignant brain tumor in adults. It accounts for about 75% of such tumors and occurs more commonly in men. The incidence rate has been increasing in the past 30 years. Moreover, the 5-year overall survival rate of glioma patients is < 35%. Different locations, grades, and molecular characteristics of gliomas can lead to different behavioral deficits and prognosis, which are closely related to patients' quality of life and associated with neuroplasticity. Some advanced magnetic resonance imaging (MRI) technologies can explore the neuroplasticity of structural, topological, biochemical metabolism, and related mechanisms, which may contribute to the improvement of prognosis and function in glioma patients. In this review, we summarized the studies conducted on structural and topological plasticity of glioma patients through different MRI technologies and discussed future research directions. Previous studies have found that glioma itself and related functional impairments can lead to structural and topological plasticity using multimodal MRI. However, neuroplasticity caused by highly heterogeneous gliomas is not fully understood, and should be further explored through multimodal MRI. In addition, the individualized prediction of functional prognosis of glioma patients from the functional level based on machine learning (ML) is promising. These approaches and the introduction of ML can further shed light on the neuroplasticity and related mechanism of the brain, which will be helpful for management of glioma patients.
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Affiliation(s)
- Kun Lv
- Department of Radiology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xin Cao
- Department of Radiology, Huashan Hospital, Fudan University, Shanghai, China
- Institute of Functional and Molecular Medical Imaging, Fudan University, Shanghai, China
- Center for Shanghai Intelligent Imaging for Critical Brain Diseases Engineering and Technology Reasearch, Shanghai, China
- Institute of Intelligent Imaging Phenomics, International Human Phenome Institutes (Shanghai), Shanghai, China
| | - Rong Wang
- Department of Radiology, Huashan Hospital, Fudan University, Shanghai, China
- Institute of Functional and Molecular Medical Imaging, Fudan University, Shanghai, China
- Center for Shanghai Intelligent Imaging for Critical Brain Diseases Engineering and Technology Reasearch, Shanghai, China
- Institute of Intelligent Imaging Phenomics, International Human Phenome Institutes (Shanghai), Shanghai, China
| | - Peng Du
- Department of Radiology, Huashan Hospital, Fudan University, Shanghai, China
| | - Junyan Fu
- Department of Radiology, Huashan Hospital, Fudan University, Shanghai, China
| | - Daoying Geng
- Department of Radiology, Huashan Hospital, Fudan University, Shanghai, China
- Institute of Functional and Molecular Medical Imaging, Fudan University, Shanghai, China
- Center for Shanghai Intelligent Imaging for Critical Brain Diseases Engineering and Technology Reasearch, Shanghai, China
- Institute of Intelligent Imaging Phenomics, International Human Phenome Institutes (Shanghai), Shanghai, China
- *Correspondence: Daoying Geng
| | - Jun Zhang
- Department of Radiology, Huashan Hospital, Fudan University, Shanghai, China
- Institute of Functional and Molecular Medical Imaging, Fudan University, Shanghai, China
- Center for Shanghai Intelligent Imaging for Critical Brain Diseases Engineering and Technology Reasearch, Shanghai, China
- Institute of Intelligent Imaging Phenomics, International Human Phenome Institutes (Shanghai), Shanghai, China
- Jun Zhang
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26
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Cassinelli Petersen GI, Shatalov J, Verma T, Brim WR, Subramanian H, Brackett A, Bahar RC, Merkaj S, Zeevi T, Staib LH, Cui J, Omuro A, Bronen RA, Malhotra A, Aboian MS. Machine Learning in Differentiating Gliomas from Primary CNS Lymphomas: A Systematic Review, Reporting Quality, and Risk of Bias Assessment. AJNR Am J Neuroradiol 2022; 43:526-533. [PMID: 35361577 PMCID: PMC8993193 DOI: 10.3174/ajnr.a7473] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 01/31/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND Differentiating gliomas and primary CNS lymphoma represents a diagnostic challenge with important therapeutic ramifications. Biopsy is the preferred method of diagnosis, while MR imaging in conjunction with machine learning has shown promising results in differentiating these tumors. PURPOSE Our aim was to evaluate the quality of reporting and risk of bias, assess data bases with which the machine learning classification algorithms were developed, the algorithms themselves, and their performance. DATA SOURCES Ovid EMBASE, Ovid MEDLINE, Cochrane Central Register of Controlled Trials, and the Web of Science Core Collection were searched according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. STUDY SELECTION From 11,727 studies, 23 peer-reviewed studies used machine learning to differentiate primary CNS lymphoma from gliomas in 2276 patients. DATA ANALYSIS Characteristics of data sets and machine learning algorithms were extracted. A meta-analysis on a subset of studies was performed. Reporting quality and risk of bias were assessed using the Transparent Reporting of a multivariable prediction model for Individual Prognosis Or Diagnosis (TRIPOD) and Prediction Model Study Risk Of Bias Assessment Tool. DATA SYNTHESIS The highest area under the receiver operating characteristic curve (0.961) and accuracy (91.2%) in external validation were achieved by logistic regression and support vector machines models using conventional radiomic features. Meta-analysis of machine learning classifiers using these features yielded a mean area under the receiver operating characteristic curve of 0.944 (95% CI, 0.898-0.99). The median TRIPOD score was 51.7%. The risk of bias was high for 16 studies. LIMITATIONS Exclusion of abstracts decreased the sensitivity in evaluating all published studies. Meta-analysis had high heterogeneity. CONCLUSIONS Machine learning-based methods of differentiating primary CNS lymphoma from gliomas have shown great potential, but most studies lack large, balanced data sets and external validation. Assessment of the studies identified multiple deficiencies in reporting quality and risk of bias. These factors reduce the generalizability and reproducibility of the findings.
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Affiliation(s)
- G I Cassinelli Petersen
- From the Department of Radiology and Biomedical Imaging (G.I.C.P., T.V., H.S., R.C.B., S.M., T.Z., L.H.S., J.C., R.A.B., A.M., M.S.A.)
- Universitätsmedizin Göttingen (G.I.C.P.), Göttingen, Germany
| | - J Shatalov
- University of Richmond (J.S.), Richmond, Virginia
| | - T Verma
- From the Department of Radiology and Biomedical Imaging (G.I.C.P., T.V., H.S., R.C.B., S.M., T.Z., L.H.S., J.C., R.A.B., A.M., M.S.A.)
- New York University (T.V.), New York, New York
| | - W R Brim
- Whiting School of Engineering (W.R.B.), Johns Hopkins University, Baltimore, Maryland
| | - H Subramanian
- From the Department of Radiology and Biomedical Imaging (G.I.C.P., T.V., H.S., R.C.B., S.M., T.Z., L.H.S., J.C., R.A.B., A.M., M.S.A.)
| | | | - R C Bahar
- From the Department of Radiology and Biomedical Imaging (G.I.C.P., T.V., H.S., R.C.B., S.M., T.Z., L.H.S., J.C., R.A.B., A.M., M.S.A.)
| | - S Merkaj
- From the Department of Radiology and Biomedical Imaging (G.I.C.P., T.V., H.S., R.C.B., S.M., T.Z., L.H.S., J.C., R.A.B., A.M., M.S.A.)
| | - T Zeevi
- From the Department of Radiology and Biomedical Imaging (G.I.C.P., T.V., H.S., R.C.B., S.M., T.Z., L.H.S., J.C., R.A.B., A.M., M.S.A.)
| | - L H Staib
- From the Department of Radiology and Biomedical Imaging (G.I.C.P., T.V., H.S., R.C.B., S.M., T.Z., L.H.S., J.C., R.A.B., A.M., M.S.A.)
| | - J Cui
- From the Department of Radiology and Biomedical Imaging (G.I.C.P., T.V., H.S., R.C.B., S.M., T.Z., L.H.S., J.C., R.A.B., A.M., M.S.A.)
| | - A Omuro
- Department of Neurology (A.O.), Yale School of Medicine, New Haven, Connecticut
| | - R A Bronen
- From the Department of Radiology and Biomedical Imaging (G.I.C.P., T.V., H.S., R.C.B., S.M., T.Z., L.H.S., J.C., R.A.B., A.M., M.S.A.)
| | - A Malhotra
- From the Department of Radiology and Biomedical Imaging (G.I.C.P., T.V., H.S., R.C.B., S.M., T.Z., L.H.S., J.C., R.A.B., A.M., M.S.A.)
| | - M S Aboian
- From the Department of Radiology and Biomedical Imaging (G.I.C.P., T.V., H.S., R.C.B., S.M., T.Z., L.H.S., J.C., R.A.B., A.M., M.S.A.)
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27
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Henriksen OM, del Mar Álvarez-Torres M, Figueiredo P, Hangel G, Keil VC, Nechifor RE, Riemer F, Schmainda KM, Warnert EAH, Wiegers EC, Booth TC. High-Grade Glioma Treatment Response Monitoring Biomarkers: A Position Statement on the Evidence Supporting the Use of Advanced MRI Techniques in the Clinic, and the Latest Bench-to-Bedside Developments. Part 1: Perfusion and Diffusion Techniques. Front Oncol 2022; 12:810263. [PMID: 35359414 PMCID: PMC8961422 DOI: 10.3389/fonc.2022.810263] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 01/05/2022] [Indexed: 01/16/2023] Open
Abstract
Objective Summarize evidence for use of advanced MRI techniques as monitoring biomarkers in the clinic, and highlight the latest bench-to-bedside developments. Methods Experts in advanced MRI techniques applied to high-grade glioma treatment response assessment convened through a European framework. Current evidence regarding the potential for monitoring biomarkers in adult high-grade glioma is reviewed, and individual modalities of perfusion, permeability, and microstructure imaging are discussed (in Part 1 of two). In Part 2, we discuss modalities related to metabolism and/or chemical composition, appraise the clinic readiness of the individual modalities, and consider post-processing methodologies involving the combination of MRI approaches (multiparametric imaging) or machine learning (radiomics). Results High-grade glioma vasculature exhibits increased perfusion, blood volume, and permeability compared with normal brain tissue. Measures of cerebral blood volume derived from dynamic susceptibility contrast-enhanced MRI have consistently provided information about brain tumor growth and response to treatment; it is the most clinically validated advanced technique. Clinical studies have proven the potential of dynamic contrast-enhanced MRI for distinguishing post-treatment related effects from recurrence, but the optimal acquisition protocol, mode of analysis, parameter of highest diagnostic value, and optimal cut-off points remain to be established. Arterial spin labeling techniques do not require the injection of a contrast agent, and repeated measurements of cerebral blood flow can be performed. The absence of potential gadolinium deposition effects allows widespread use in pediatric patients and those with impaired renal function. More data are necessary to establish clinical validity as monitoring biomarkers. Diffusion-weighted imaging, apparent diffusion coefficient analysis, diffusion tensor or kurtosis imaging, intravoxel incoherent motion, and other microstructural modeling approaches also allow treatment response assessment; more robust data are required to validate these alone or when applied to post-processing methodologies. Conclusion Considerable progress has been made in the development of these monitoring biomarkers. Many techniques are in their infancy, whereas others have generated a larger body of evidence for clinical application.
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Affiliation(s)
- Otto M. Henriksen
- Department of Clinical Physiology, Nuclear Medicine and PET, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | | | - Patricia Figueiredo
- Department of Bioengineering and Institute for Systems and Robotics-Lisboa, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Gilbert Hangel
- Department of Neurosurgery, Medical University, Vienna, Austria
- High-Field MR Centre, Department of Biomedical Imaging and Image-Guided Therapy, Medical University, Vienna, Austria
| | - Vera C. Keil
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, Amsterdam, Netherlands
| | - Ruben E. Nechifor
- International Institute for the Advanced Studies of Psychotherapy and Applied Mental Health, Department of Clinical Psychology and Psychotherapy, Babes-Bolyai University, Cluj-Napoca, Romania
| | - Frank Riemer
- Mohn Medical Imaging and Visualization Centre (MMIV), Department of Radiology, Haukeland University Hospital, Bergen, Norway
| | - Kathleen M. Schmainda
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI, United States
| | | | - Evita C. Wiegers
- Department of Radiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Thomas C. Booth
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School of Biomedical Engineering and Imaging Sciences, St. Thomas’ Hospital, King’s College London, London, United Kingdom
- Department of Neuroradiology, King’s College Hospital NHS Foundation Trust, London, United Kingdom
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28
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Booth TC, Wiegers EC, Warnert EAH, Schmainda KM, Riemer F, Nechifor RE, Keil VC, Hangel G, Figueiredo P, Álvarez-Torres MDM, Henriksen OM. High-Grade Glioma Treatment Response Monitoring Biomarkers: A Position Statement on the Evidence Supporting the Use of Advanced MRI Techniques in the Clinic, and the Latest Bench-to-Bedside Developments. Part 2: Spectroscopy, Chemical Exchange Saturation, Multiparametric Imaging, and Radiomics. Front Oncol 2022; 11:811425. [PMID: 35340697 PMCID: PMC8948428 DOI: 10.3389/fonc.2021.811425] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/28/2021] [Indexed: 01/16/2023] Open
Abstract
Objective To summarize evidence for use of advanced MRI techniques as monitoring biomarkers in the clinic, and to highlight the latest bench-to-bedside developments. Methods The current evidence regarding the potential for monitoring biomarkers was reviewed and individual modalities of metabolism and/or chemical composition imaging discussed. Perfusion, permeability, and microstructure imaging were similarly analyzed in Part 1 of this two-part review article and are valuable reading as background to this article. We appraise the clinic readiness of all the individual modalities and consider methodologies involving machine learning (radiomics) and the combination of MRI approaches (multiparametric imaging). Results The biochemical composition of high-grade gliomas is markedly different from healthy brain tissue. Magnetic resonance spectroscopy allows the simultaneous acquisition of an array of metabolic alterations, with choline-based ratios appearing to be consistently discriminatory in treatment response assessment, although challenges remain despite this being a mature technique. Promising directions relate to ultra-high field strengths, 2-hydroxyglutarate analysis, and the use of non-proton nuclei. Labile protons on endogenous proteins can be selectively targeted with chemical exchange saturation transfer to give high resolution images. The body of evidence for clinical application of amide proton transfer imaging has been building for a decade, but more evidence is required to confirm chemical exchange saturation transfer use as a monitoring biomarker. Multiparametric methodologies, including the incorporation of nuclear medicine techniques, combine probes measuring different tumor properties. Although potentially synergistic, the limitations of each individual modality also can be compounded, particularly in the absence of standardization. Machine learning requires large datasets with high-quality annotation; there is currently low-level evidence for monitoring biomarker clinical application. Conclusion Advanced MRI techniques show huge promise in treatment response assessment. The clinical readiness analysis highlights that most monitoring biomarkers require standardized international consensus guidelines, with more facilitation regarding technique implementation and reporting in the clinic.
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Affiliation(s)
- Thomas C. Booth
- School of Biomedical Engineering and Imaging Sciences, King’s College London, St. Thomas’ Hospital, London, United Kingdom
- Department of Neuroradiology, King’s College Hospital NHS Foundation Trust, London, United Kingdom
| | - Evita C. Wiegers
- Department of Radiology, University Medical Center Utrecht, Utrecht, Netherlands
| | | | - Kathleen M. Schmainda
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Frank Riemer
- Mohn Medical Imaging and Visualization Centre (MMIV), Department of Radiology, Haukeland University Hospital, Bergen, Norway
| | - Ruben E. Nechifor
- Department of Clinical Psychology and Psychotherapy International Institute for the Advanced Studies of Psychotherapy and Applied Mental Health, Babes-Bolyai University, Cluj-Napoca, Romania
| | - Vera C. Keil
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, location VUmc, Amsterdam, Netherlands
| | - Gilbert Hangel
- Department of Neurosurgery & High-Field MR Centre, Department of Biomedical Imaging and Image-Guided Therapy, Medical University Vienna, Vienna, Austria
| | - Patrícia Figueiredo
- Department of Bioengineering and Institute for Systems and Robotics - Lisboa, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | | | - Otto M. Henriksen
- Department of Clinical Physiology, Nuclear medicine and PET, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
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29
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Booth TC, Grzeda M, Chelliah A, Roman A, Al Busaidi A, Dragos C, Shuaib H, Luis A, Mirchandani A, Alparslan B, Mansoor N, Lavrador J, Vergani F, Ashkan K, Modat M, Ourselin S. Imaging Biomarkers of Glioblastoma Treatment Response: A Systematic Review and Meta-Analysis of Recent Machine Learning Studies. Front Oncol 2022; 12:799662. [PMID: 35174084 PMCID: PMC8842649 DOI: 10.3389/fonc.2022.799662] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/03/2022] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVE Monitoring biomarkers using machine learning (ML) may determine glioblastoma treatment response. We systematically reviewed quality and performance accuracy of recently published studies. METHODS Following Preferred Reporting Items for Systematic Reviews and Meta-Analysis: Diagnostic Test Accuracy, we extracted articles from MEDLINE, EMBASE and Cochrane Register between 09/2018-01/2021. Included study participants were adults with glioblastoma having undergone standard treatment (maximal resection, radiotherapy with concomitant and adjuvant temozolomide), and follow-up imaging to determine treatment response status (specifically, distinguishing progression/recurrence from progression/recurrence mimics, the target condition). Using Quality Assessment of Diagnostic Accuracy Studies Two/Checklist for Artificial Intelligence in Medical Imaging, we assessed bias risk and applicability concerns. We determined test set performance accuracy (sensitivity, specificity, precision, F1-score, balanced accuracy). We used a bivariate random-effect model to determine pooled sensitivity, specificity, area-under the receiver operator characteristic curve (ROC-AUC). Pooled measures of balanced accuracy, positive/negative likelihood ratios (PLR/NLR) and diagnostic odds ratio (DOR) were calculated. PROSPERO registered (CRD42021261965). RESULTS Eighteen studies were included (1335/384 patients for training/testing respectively). Small patient numbers, high bias risk, applicability concerns (particularly confounding in reference standard and patient selection) and low level of evidence, allow limited conclusions from studies. Ten studies (10/18, 56%) included in meta-analysis gave 0.769 (0.649-0.858) sensitivity [pooled (95% CI)]; 0.648 (0.749-0.532) specificity; 0.706 (0.623-0.779) balanced accuracy; 2.220 (1.560-3.140) PLR; 0.366 (0.213-0.572) NLR; 6.670 (2.800-13.500) DOR; 0.765 ROC-AUC. CONCLUSION ML models using MRI features to distinguish between progression and mimics appear to demonstrate good diagnostic performance. However, study quality and design require improvement.
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Affiliation(s)
- Thomas C. Booth
- School of Biomedical Engineering & Imaging Sciences, King’s College London, St. Thomas’ Hospital, London, United Kingdom
- Department of Neuroradiology, King’s College Hospital National Health Service Foundation Trust, London, United Kingdom
| | - Mariusz Grzeda
- School of Biomedical Engineering & Imaging Sciences, King’s College London, St. Thomas’ Hospital, London, United Kingdom
| | - Alysha Chelliah
- School of Biomedical Engineering & Imaging Sciences, King’s College London, St. Thomas’ Hospital, London, United Kingdom
| | - Andrei Roman
- Department of Radiology, Guy’s & St. Thomas’ National Health Service Foundation Trust, London, United Kingdom
- Department of Radiology, The Oncology Institute “Prof. Dr. Ion Chiricuţă” Cluj-Napoca, Cluj-Napoca, Romania
| | - Ayisha Al Busaidi
- Department of Neuroradiology, King’s College Hospital National Health Service Foundation Trust, London, United Kingdom
| | - Carmen Dragos
- Department of Radiology, Buckinghamshire Healthcare National Health Service Trust, Amersham, United Kingdom
| | - Haris Shuaib
- Department of Medical Physics, Guy’s & St. Thomas’ National Health Service Foundation Trust, London, United Kingdom
- Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
| | - Aysha Luis
- Department of Neuroradiology, King’s College Hospital National Health Service Foundation Trust, London, United Kingdom
| | - Ayesha Mirchandani
- Department of Radiology, Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, United Kingdom
| | - Burcu Alparslan
- Department of Neuroradiology, King’s College Hospital National Health Service Foundation Trust, London, United Kingdom
- Department of Radiology, Kocaeli University, İzmit, Turkey
| | - Nina Mansoor
- Department of Neuroradiology, King’s College Hospital National Health Service Foundation Trust, London, United Kingdom
| | - Jose Lavrador
- Department of Neurosurgery, King’s College Hospital National Health Service Foundation Trust, London, United Kingdom
| | - Francesco Vergani
- Department of Neurosurgery, King’s College Hospital National Health Service Foundation Trust, London, United Kingdom
| | - Keyoumars Ashkan
- Department of Neurosurgery, King’s College Hospital National Health Service Foundation Trust, London, United Kingdom
| | - Marc Modat
- School of Biomedical Engineering & Imaging Sciences, King’s College London, St. Thomas’ Hospital, London, United Kingdom
| | - Sebastien Ourselin
- School of Biomedical Engineering & Imaging Sciences, King’s College London, St. Thomas’ Hospital, London, United Kingdom
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Mládek A, Gerla V, Skalický P, Vlasák A, Zazay A, Lhotská L, Beneš V, Beneš V, Bradáč O. Prediction of Shunt Responsiveness in Suspected Patients With Normal Pressure Hydrocephalus Using the Lumbar Infusion Test: A Machine Learning Approach. Neurosurgery 2022; 90:407-418. [PMID: 35080523 DOI: 10.1227/neu.0000000000001838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 10/27/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Machine learning (ML) approaches can significantly improve the classical Rout-based evaluation of the lumbar infusion test (LIT) and the clinical management of the normal pressure hydrocephalus. OBJECTIVE To develop a ML model that accurately identifies patients as candidates for permanent cerebral spinal fluid shunt implantation using only intracranial pressure and electrocardiogram signals recorded throughout LIT. METHODS This was a single-center cohort study of prospectively collected data of 96 patients who underwent LIT and 5-day external lumbar cerebral spinal fluid drainage (external lumbar drainage) as a reference diagnostic method. A set of selected 48 intracranial pressure/electrocardiogram complex signal waveform features describing nonlinear behavior, wavelet transform spectral signatures, or recurrent map patterns were calculated for each patient. After applying a leave-one-out cross-validation training-testing split of the data set, we trained and evaluated the performance of various state-of-the-art ML algorithms. RESULTS The highest performing ML algorithm was the eXtreme Gradient Boosting. This model showed a good calibration and discrimination on the testing data, with an area under the receiver operating characteristic curve of 0.891 (accuracy: 82.3%, sensitivity: 86.1%, and specificity: 73.9%) obtained for 8 selected features. Our ML model clearly outperforms the classical Rout-based manual classification commonly used in clinical practice with an accuracy of 62.5%. CONCLUSION This study successfully used the ML approach to predict the outcome of a 5-day external lumbar drainage and hence which patients are likely to benefit from permanent shunt implantation. Our automated ML model thus enhances the diagnostic utility of LIT in management.
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Affiliation(s)
- Arnošt Mládek
- Department of Neurosurgery and Neurooncology, Military University Hospital, 1st Faculty of Medicine, Charles University in Prague, Prague, Czech Republic.,Department of Neurosurgery, Motol University Hospital, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic.,Czech Technical University, Prague, Czech Republic
| | - Václav Gerla
- Department of Cognitive Systems and Neurosciences, Czech Institute of Informatics, Robotics and Cybernetics, Czech Technical University, Prague, Czech Republic
| | - Petr Skalický
- Department of Neurosurgery and Neurooncology, Military University Hospital, 1st Faculty of Medicine, Charles University in Prague, Prague, Czech Republic.,Department of Neurosurgery, Motol University Hospital, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Aleš Vlasák
- Department of Neurosurgery and Neurooncology, Military University Hospital, 1st Faculty of Medicine, Charles University in Prague, Prague, Czech Republic.,Department of Neurosurgery, Motol University Hospital, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Awista Zazay
- Institute of Pathological Physiology, 1st Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Lenka Lhotská
- Department of Cognitive Systems and Neurosciences, Czech Institute of Informatics, Robotics and Cybernetics, Czech Technical University, Prague, Czech Republic.,Department of Natural Sciences, Faculty of Biomedical Engineering, Czech Technical University, Prague, Czech Republic
| | - Vladimír Beneš
- Department of Neurosurgery and Neurooncology, Military University Hospital, 1st Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Vladimír Beneš
- Department of Neurosurgery, Motol University Hospital, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Ondřej Bradáč
- Department of Neurosurgery and Neurooncology, Military University Hospital, 1st Faculty of Medicine, Charles University in Prague, Prague, Czech Republic.,Department of Neurosurgery, Motol University Hospital, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
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Krauze AV, Camphausen K. Molecular Biology in Treatment Decision Processes-Neuro-Oncology Edition. Int J Mol Sci 2021; 22:13278. [PMID: 34948075 PMCID: PMC8703419 DOI: 10.3390/ijms222413278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 11/30/2022] Open
Abstract
Computational approaches including machine learning, deep learning, and artificial intelligence are growing in importance in all medical specialties as large data repositories are increasingly being optimised. Radiation oncology as a discipline is at the forefront of large-scale data acquisition and well positioned towards both the production and analysis of large-scale oncologic data with the potential for clinically driven endpoints and advancement of patient outcomes. Neuro-oncology is comprised of malignancies that often carry poor prognosis and significant neurological sequelae. The analysis of radiation therapy mediated treatment and the potential for computationally mediated analyses may lead to more precise therapy by employing large scale data. We analysed the state of the literature pertaining to large scale data, computational analysis, and the advancement of molecular biomarkers in neuro-oncology with emphasis on radiation oncology. We aimed to connect existing and evolving approaches to realistic avenues for clinical implementation focusing on low grade gliomas (LGG), high grade gliomas (HGG), management of the elderly patient with HGG, rare central nervous system tumors, craniospinal irradiation, and re-irradiation to examine how computational analysis and molecular science may synergistically drive advances in personalised radiation therapy (RT) and optimise patient outcomes.
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Affiliation(s)
- Andra V. Krauze
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, 9000 Rockville Pike, Building 10, Bethesda, MD 20892, USA;
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Xie QY, Wang MW, Hu ZY, Cao CJ, Wang C, Kang JY, Fu XY, Zhang XW, Chu YM, Feng ZH, Cheng YR. Screening the Influence of Biomarkers for Metabolic Syndrome in Occupational Population Based on the Lasso Algorithm. Front Public Health 2021; 9:743731. [PMID: 34712642 PMCID: PMC8545799 DOI: 10.3389/fpubh.2021.743731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/14/2021] [Indexed: 12/23/2022] Open
Abstract
Aim: Metabolic syndrome (MS) screening is essential for the early detection of the occupational population. This study aimed to screen out biomarkers related to MS and establish a risk assessment and prediction model for the routine physical examination of an occupational population. Methods: The least absolute shrinkage and selection operator (Lasso) regression algorithm of machine learning was used to screen biomarkers related to MS. Then, the accuracy of the logistic regression model was further verified based on the Lasso regression algorithm. The areas under the receiving operating characteristic curves were used to evaluate the selection accuracy of biomarkers in identifying MS subjects with risk. The screened biomarkers were used to establish a logistic regression model and calculate the odds ratio (OR) of the corresponding biomarkers. A nomogram risk prediction model was established based on the selected biomarkers, and the consistency index (C-index) and calibration curve were derived. Results: A total of 2,844 occupational workers were included, and 10 biomarkers related to MS were screened. The number of non-MS cases was 2,189 and that of MS was 655. The area under the curve (AUC) value for non-Lasso and Lasso logistic regression was 0.652 and 0.907, respectively. The established risk assessment model revealed that the main risk biomarkers were absolute basophil count (OR: 3.38, CI:1.05–6.85), platelet packed volume (OR: 2.63, CI:2.31–3.79), leukocyte count (OR: 2.01, CI:1.79–2.19), red blood cell count (OR: 1.99, CI:1.80–2.71), and alanine aminotransferase level (OR: 1.53, CI:1.12–1.98). Furthermore, favorable results with C-indexes (0.840) and calibration curves closer to ideal curves indicated the accurate predictive ability of this nomogram. Conclusions: The risk assessment model based on the Lasso logistic regression algorithm helped identify MS with high accuracy in physically examining an occupational population.
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Affiliation(s)
- Qiao-Ying Xie
- Occupational Disease Department, Hangzhou Occupational Disease Prevention and Control Hospital, Hangzhou, China
| | - Ming-Wei Wang
- Metabolic Disease Center, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Zu-Ying Hu
- Occupational Disease Department, Hangzhou Occupational Disease Prevention and Control Hospital, Hangzhou, China
| | - Cheng-Jian Cao
- Occupational Disease Department, Hangzhou Occupational Disease Prevention and Control Hospital, Hangzhou, China
| | - Cong Wang
- School of Mathematics and Statistics, Jiangsu Normal University, Xuzhou, China
| | - Jing-Yu Kang
- School of Mathematics and Statistics, Jiangsu Normal University, Xuzhou, China
| | - Xin-Yan Fu
- Metabolic Disease Center, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Xing-Wei Zhang
- Metabolic Disease Center, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Yan-Ming Chu
- Zhejiang Geriatric Care Hospital, Hangzhou, China
| | - Zhan-Hui Feng
- Neurological Department, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Yong-Ran Cheng
- School of Public Health, Hangzhou Medical College, Hangzhou, China
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MRI-based machine learning for determining quantitative and qualitative characteristics affecting the survival of glioblastoma multiforme. Magn Reson Imaging 2021; 85:222-227. [PMID: 34687850 DOI: 10.1016/j.mri.2021.10.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/16/2021] [Accepted: 10/17/2021] [Indexed: 11/22/2022]
Abstract
PURPOSE Our current study aims to consider the image biomarkers extracted from the MRI images for exploring their effects on glioblastoma multiforme (GBM) patients' survival. Determining its biomarker helps better manage the disease and evaluate treatments. It has been proven that imaging features could be used as a biomarker. The purpose of this study is to investigate the features in MRI and clinical features as the biomarker association of survival of GBM. METHODS 55 patients were considered with five clinical features, 10 qualities pre-operative MRI image features, and six quantitative features obtained using BraTumIA software. It was run ANN, C5, Bayesian, and Cox models in two phases for determining important variables. In the first phase, we selected the quality features that occur at least in three models and quantitative in two models. In the second phase, models were run with the extracted features, and then the probability value of variables in each model was calculated. RESULTS The mean of accuracy, sensitivity, specificity, and area under curve (AUC) after running four machine learning techniques were 80.47, 82.54, 79.78, and 0.85, respectively. In the second step, the mean of accuracy, sensitivity, specificity, and AUC were 79.55, 78.71, 79.83, and 0.87, respectively. CONCLUSION We found the largest size of the width, the largest size of length, radiotherapy, volume of enhancement, volume of nCET, satellites, enhancing margin, and age feature are important features.
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Abdel Razek AAK, Alksas A, Shehata M, AbdelKhalek A, Abdel Baky K, El-Baz A, Helmy E. Clinical applications of artificial intelligence and radiomics in neuro-oncology imaging. Insights Imaging 2021; 12:152. [PMID: 34676470 PMCID: PMC8531173 DOI: 10.1186/s13244-021-01102-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/26/2021] [Indexed: 12/15/2022] Open
Abstract
This article is a comprehensive review of the basic background, technique, and clinical applications of artificial intelligence (AI) and radiomics in the field of neuro-oncology. A variety of AI and radiomics utilized conventional and advanced techniques to differentiate brain tumors from non-neoplastic lesions such as inflammatory and demyelinating brain lesions. It is used in the diagnosis of gliomas and discrimination of gliomas from lymphomas and metastasis. Also, semiautomated and automated tumor segmentation has been developed for radiotherapy planning and follow-up. It has a role in the grading, prediction of treatment response, and prognosis of gliomas. Radiogenomics allowed the connection of the imaging phenotype of the tumor to its molecular environment. In addition, AI is applied for the assessment of extra-axial brain tumors and pediatric tumors with high performance in tumor detection, classification, and stratification of patient's prognoses.
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Affiliation(s)
| | - Ahmed Alksas
- Biomaging Lab, Department of Bioengineering, University of Louisville, Louisville, KY, 40292, USA
| | - Mohamed Shehata
- Biomaging Lab, Department of Bioengineering, University of Louisville, Louisville, KY, 40292, USA
| | - Amr AbdelKhalek
- Internship at Mansoura University Hospital, Mansoura Faculty of Medicine, Mansoura, Egypt
| | - Khaled Abdel Baky
- Department of Diagnostic Radiology, Faculty of Medicine, Port Said University, Port Said, Egypt
| | - Ayman El-Baz
- Biomaging Lab, Department of Bioengineering, University of Louisville, Louisville, KY, 40292, USA
| | - Eman Helmy
- Department of Diagnostic Radiology, Faculty of Medicine, Mansoura University, Elgomheryia Street, Mansoura, 3512, Egypt.
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Abstract
Amongst the several types of brain cancers known to humankind, glioma is one of the most severe and life-threatening types of cancer, comprising 40% of all primary brain tumors. Recent reports have shown the incident rate of gliomas to be 6 per 100,000 individuals per year globally. Despite the various therapeutics used in the treatment of glioma, patient survival rate remains at a median of 15 months after undergoing first-line treatment including surgery, radiation, and chemotherapy with Temozolomide. As such, the discovery of newer and more effective therapeutic agents is imperative for patient survival rate. The advent of computer-aided drug design in the development of drug discovery has emerged as a powerful means to ascertain potential hit compounds with distinctively high therapeutic effectiveness against glioma. This review encompasses the recent advances of bio-computational in-silico modeling that have elicited the discovery of small molecule inhibitors and/or drugs against various therapeutic targets in glioma. The relevant information provided in this report will assist researchers, especially in the drug design domains, to develop more effective therapeutics against this global disease.
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Chromatin insulation dynamics in glioblastoma: challenges and future perspectives of precision oncology. Clin Epigenetics 2021; 13:150. [PMID: 34332627 PMCID: PMC8325855 DOI: 10.1186/s13148-021-01139-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/23/2021] [Indexed: 12/13/2022] Open
Abstract
Glioblastoma (GBM) is the most aggressive primary brain tumor, having a poor prognosis and a median overall survival of less than two years. Over the last decade, numerous findings regarding the distinct molecular and genetic profiles of GBM have led to the emergence of several therapeutic approaches. Unfortunately, none of them has proven to be effective against GBM progression and recurrence. Epigenetic mechanisms underlying GBM tumor biology, including histone modifications, DNA methylation, and chromatin architecture, have become an attractive target for novel drug discovery strategies. Alterations on chromatin insulator elements (IEs) might lead to aberrant chromatin remodeling via DNA loop formation, causing oncogene reactivation in several types of cancer, including GBM. Importantly, it is shown that mutations affecting the isocitrate dehydrogenase (IDH) 1 and 2 genes, one of the most frequent genetic alterations in gliomas, lead to genome-wide DNA hypermethylation and the consequent IE dysfunction. The relevance of IEs has also been observed in a small population of cancer stem cells known as glioma stem cells (GSCs), which are thought to participate in GBM tumor initiation and drug resistance. Recent studies revealed that epigenomic alterations, specifically chromatin insulation and DNA loop formation, play a crucial role in establishing and maintaining the GSC transcriptional program. This review focuses on the relevance of IEs in GBM biology and their implementation as a potential theranostic target to stratify GBM patients and develop novel therapeutic approaches. We will also discuss the state-of-the-art emerging technologies using big data analysis and how they will settle the bases on future diagnosis and treatment strategies in GBM patients.
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Sasi S D, Gupta RK, Patir R, Ahlawat S, Vaishya S, Singh A. A comprehensive evaluation and impact of normalization of generalized tracer kinetic model parameters to characterize blood-brain-barrier permeability in normal-appearing and tumor tissue regions of patients with glioma. Magn Reson Imaging 2021; 83:77-88. [PMID: 34311065 DOI: 10.1016/j.mri.2021.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 07/04/2021] [Accepted: 07/20/2021] [Indexed: 11/27/2022]
Abstract
RATIONALE AND OBJECTIVES To comprehensively evaluate robustness and variations of DCE-MRI derived generalized-tracer-kinetic-model (GTKM) parameters in healthy and tumor tissues and impact of normalization in mitigating these variations on application to glioma. MATERIALS (PATIENTS) AND METHODS A retrospective study included pre-operative 31 high-grade-glioma(HGG), 22 low-grade-glioma(LGG) and 33 follow-up data from 10 patients a prospective study with 4 HGG subjects. Voxel-wise GTKM was fitted to DCE-MRI data to estimate Ktrans, ve, vb. Simulations were used to evaluate noise sensitivity. Variation of parameters with-respect-to arterial-input-function (AIF) variation and data length were studied. Normalization of parameters with-respect-to mean values in gray-matter (GM) and white-matter (WM) regions (GM-Type-2, WM-Type-2) and mean curves (GM-Type-1, WM-Type-1) were also evaluated. Co-efficient-of-variation(CoV), relative-percentage-error (RPE), Box-Whisker plots, bar graphs and t-test were used for comparison. RESULTS GTKM was fitted well in all tissue regions. Ktrans and ve in contrast-enhancing (CE) has shown improved noise sensitivity in longer data. vb was reliable in all tissues. Mean AIF and C(t) peaks showed ~38% and ~35% variations. During simulation, normalizations have mitigated variations due to changes in AIF amplitude in Ktrans and vb.. ve was less sensitive to normalizations. CoV of Ktrans and vb has reduced ~70% after GM-Type-1 normalization and ~80% after GM-Type-2 normalization, respectively. GM-Type-1 (p = 0.003) and GM-Type-2 (p = 0.006) normalizations have significantly improved differentiation of HGG and LGG using Ktrans. CONCLUSION Ktrans and vb can be reliably estimated in normal-appearing brain tissues and can be used for normalization of corresponding parameters in tumor tissues for mitigating inter-subject variability due to errors in AIF. Normalized Ktrans and vb provided improved differentiation of HGG and LGG.
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Affiliation(s)
- Dinil Sasi S
- Centre for Biomedical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Rakesh K Gupta
- Department of Radiology and Imaging, Fortis Memorial Research Institute, Gurugram, India
| | - Rana Patir
- Department of Neurosurgery, Fortis Memorial Research Institute, Gurugram, India
| | - Suneeta Ahlawat
- SRL Diagnostics, Fortis Memorial Research Institute, Gurugram, India
| | - Sandeep Vaishya
- Department of Neurosurgery, Fortis Memorial Research Institute, Gurugram, India
| | - Anup Singh
- Centre for Biomedical Engineering, Indian Institute of Technology Delhi, New Delhi, India; Department of Biomedical Engineering, All India Institute of Medical Sciences, New Delhi, India.
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Liu D, Chen J, Hu X, Yang K, Liu Y, Hu G, Ge H, Zhang W, Liu H. Imaging-Genomics in Glioblastoma: Combining Molecular and Imaging Signatures. Front Oncol 2021; 11:699265. [PMID: 34295824 PMCID: PMC8290166 DOI: 10.3389/fonc.2021.699265] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/23/2021] [Indexed: 12/12/2022] Open
Abstract
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.
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Affiliation(s)
- Dongming Liu
- Department of Neurosurgery, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Jiu Chen
- Institute of Neuropsychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Fourth Clinical College of Nanjing Medical University, Nanjing, China.,Department of Neurosurgery, Institute of Brain Sciences, The Affilated Nanjing Brain Hosptial of Nanjing Medical University, Nanjing, China
| | - Xinhua Hu
- Department of Neurosurgery, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China.,Department of Neurosurgery, Institute of Brain Sciences, The Affilated Nanjing Brain Hosptial of Nanjing Medical University, Nanjing, China
| | - Kun Yang
- Department of Neurosurgery, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Yong Liu
- Department of Neurosurgery, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Guanjie Hu
- Department of Neurosurgery, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Honglin Ge
- Department of Neurosurgery, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Wenbin Zhang
- Department of Neurosurgery, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China.,Department of Neurosurgery, Institute of Brain Sciences, The Affilated Nanjing Brain Hosptial of Nanjing Medical University, Nanjing, China
| | - Hongyi Liu
- Department of Neurosurgery, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China.,Department of Neurosurgery, Institute of Brain Sciences, The Affilated Nanjing Brain Hosptial of Nanjing Medical University, Nanjing, China
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Dagi TF, Barker FG, Glass J. Machine Learning and Artificial Intelligence in Neurosurgery: Status, Prospects, and Challenges. Neurosurgery 2021; 89:133-142. [PMID: 34015816 DOI: 10.1093/neuros/nyab170] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- T Forcht Dagi
- Queen's University Belfast and The William J. Clinton Leadership Institute, Belfast, UK
- Mayo Clinic College of Medicine and Science, Rochester, Minnesota, USA
| | - Fred G Barker
- Department of Neurosurgery, Harvard Medical School, Boston, Massachusetts, USA
- The Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jacob Glass
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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Baptiste M, Moinuddeen SS, Soliz CL, Ehsan H, Kaneko G. Making Sense of Genetic Information: The Promising Evolution of Clinical Stratification and Precision Oncology Using Machine Learning. Genes (Basel) 2021; 12:722. [PMID: 34065872 PMCID: PMC8151328 DOI: 10.3390/genes12050722] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 12/16/2022] Open
Abstract
Precision medicine is a medical approach to administer patients with a tailored dose of treatment by taking into consideration a person's variability in genes, environment, and lifestyles. The accumulation of omics big sequence data led to the development of various genetic databases on which clinical stratification of high-risk populations may be conducted. In addition, because cancers are generally caused by tumor-specific mutations, large-scale systematic identification of single nucleotide polymorphisms (SNPs) in various tumors has propelled significant progress of tailored treatments of tumors (i.e., precision oncology). Machine learning (ML), a subfield of artificial intelligence in which computers learn through experience, has a great potential to be used in precision oncology chiefly to help physicians make diagnostic decisions based on tumor images. A promising venue of ML in precision oncology is the integration of all available data from images to multi-omics big data for the holistic care of patients and high-risk healthy subjects. In this review, we provide a focused overview of precision oncology and ML with attention to breast cancer and glioma as well as the Bayesian networks that have the flexibility and the ability to work with incomplete information. We also introduce some state-of-the-art attempts to use and incorporate ML and genetic information in precision oncology.
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Affiliation(s)
| | | | | | | | - Gen Kaneko
- School of Arts & Sciences, University of Houston-Victoria, Victoria, TX 77901, USA; (M.B.); (S.S.M.); (C.L.S.); (H.E.)
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Patel M, Zhan J, Natarajan K, Flintham R, Davies N, Sanghera P, Grist J, Duddalwar V, Peet A, Sawlani V. Machine learning-based radiomic evaluation of treatment response prediction in glioblastoma. Clin Radiol 2021; 76:628.e17-628.e27. [PMID: 33941364 DOI: 10.1016/j.crad.2021.03.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 03/29/2021] [Indexed: 11/16/2022]
Abstract
AIM To investigate machine learning based models combining clinical, radiomic, and molecular information to distinguish between early true progression (tPD) and pseudoprogression (psPD) in patients with glioblastoma. MATERIALS AND METHODS A retrospective analysis was undertaken of 76 patients (46 tPD, 30 psPD) with early enhancing disease following chemoradiotherapy for glioblastoma. Outcome was determined on follow-up until 6 months post-chemoradiotherapy. Models comprised clinical characteristics, O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation status, and 307 quantitative imaging features extracted from enhancing disease and perilesional oedema masks on early post-chemoradiotherapy contrast-enhanced T1-weighted imaging, T2-weighted imaging (T2WI), and apparent diffusion coefficient (ADC) maps. Feature selection was performed within bootstrapped cross-validated recursive feature elimination with a random forest algorithm. Naive Bayes five-fold cross-validation was used to validate the final model. RESULTS Top selected features included age, MGMT promoter methylation status, two shape-based features from the enhancing disease mask, three radiomic features from the enhancing disease mask on ADC, and one radiomic feature from the perilesional oedema mask on T2WI. The final model had an area under the receiver operating characteristics curve (AUC) of 0.80, sensitivity 78.2%, specificity 66.7%, and accuracy of 73.7%. CONCLUSION Incorporating a machine learning-based approach using quantitative radiomic features from standard-of-care magnetic resonance imaging (MRI), in combination with clinical characteristics and MGMT promoter methylation status has a complementary effect and improves model performance for early prediction of glioblastoma treatment response.
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Affiliation(s)
- M Patel
- University of Birmingham, Birmingham, UK; Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - J Zhan
- Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK; The Affiliated Hospital of Qingdao University, Qingdao Shi, Shandong Sheng, China
| | - K Natarajan
- Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - R Flintham
- Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - N Davies
- Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - P Sanghera
- University of Birmingham, Birmingham, UK; Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - J Grist
- University of Birmingham, Birmingham, UK
| | - V Duddalwar
- Departments of Radiology, Urology and Biomedical Engineering, University of Southern California, USA
| | - A Peet
- University of Birmingham, Birmingham, UK; Birmingham Children's Hospital, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - V Sawlani
- University of Birmingham, Birmingham, UK; Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.
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42
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Cheung HMC, Rubin D. Challenges and opportunities for artificial intelligence in oncological imaging. Clin Radiol 2021; 76:728-736. [PMID: 33902889 DOI: 10.1016/j.crad.2021.03.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/15/2021] [Indexed: 02/08/2023]
Abstract
Imaging plays a key role in oncology, including the diagnosis and detection of cancer, determining clinical management, assessing treatment response, and complications of treatment or disease. The current use of clinical oncology is predominantly qualitative in nature with some relatively crude size-based measurements of tumours for assessment of disease progression or treatment response; however, it is increasingly understood that there may be significantly more information about oncological disease that can be obtained from imaging that is not currently utilized. Artificial intelligence (AI) has the potential to harness quantitative techniques to improve oncological imaging. These may include improving the efficiency or accuracy of traditional roles of imaging such as diagnosis or detection. These may also include new roles for imaging such as risk-stratifying patients for different types of therapy or determining biological tumour subtypes. This review article outlines several major areas in oncological imaging where there may be opportunities for AI technology. These include (1) screening and detection of cancer, (2) diagnosis and risk stratification, (3) tumour segmentation, (4) precision oncology, and (5) predicting prognosis and assessing treatment response. This review will also address some of the potential barriers to AI research in oncological imaging.
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Affiliation(s)
- H M C Cheung
- Department of Medical Imaging, Sunnybrook Health Sciences Centre, University of Toronto, Canada
| | - D Rubin
- Department of Radiology, Stanford University, CA, USA.
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Hajjo R, Sabbah DA, Bardaweel SK, Tropsha A. Identification of Tumor-Specific MRI Biomarkers Using Machine Learning (ML). Diagnostics (Basel) 2021; 11:742. [PMID: 33919342 PMCID: PMC8143297 DOI: 10.3390/diagnostics11050742] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 02/06/2023] Open
Abstract
The identification of reliable and non-invasive oncology biomarkers remains a main priority in healthcare. There are only a few biomarkers that have been approved as diagnostic for cancer. The most frequently used cancer biomarkers are derived from either biological materials or imaging data. Most cancer biomarkers suffer from a lack of high specificity. However, the latest advancements in machine learning (ML) and artificial intelligence (AI) have enabled the identification of highly predictive, disease-specific biomarkers. Such biomarkers can be used to diagnose cancer patients, to predict cancer prognosis, or even to predict treatment efficacy. Herein, we provide a summary of the current status of developing and applying Magnetic resonance imaging (MRI) biomarkers in cancer care. We focus on all aspects of MRI biomarkers, starting from MRI data collection, preprocessing and machine learning methods, and ending with summarizing the types of existing biomarkers and their clinical applications in different cancer types.
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Affiliation(s)
- Rima Hajjo
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman 11733, Jordan;
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carlina at Chapel Hill, Chapel Hill, NC 27599, USA;
- National Center for Epidemics and Communicable Disease Control, Amman 11118, Jordan
| | - Dima A. Sabbah
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman 11733, Jordan;
| | - Sanaa K. Bardaweel
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Jordan, Amman 11942, Jordan;
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carlina at Chapel Hill, Chapel Hill, NC 27599, USA;
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Chuntova P, Chow F, Watchmaker PB, Galvez M, Heimberger AB, Newell EW, Diaz A, DePinho RA, Li MO, Wherry EJ, Mitchell D, Terabe M, Wainwright DA, Berzofsky JA, Herold-Mende C, Heath JR, Lim M, Margolin KA, Chiocca EA, Kasahara N, Ellingson BM, Brown CE, Chen Y, Fecci PE, Reardon DA, Dunn GP, Liau LM, Costello JF, Wick W, Cloughesy T, Timmer WC, Wen PY, Prins RM, Platten M, Okada H. Unique challenges for glioblastoma immunotherapy-discussions across neuro-oncology and non-neuro-oncology experts in cancer immunology. Meeting Report from the 2019 SNO Immuno-Oncology Think Tank. Neuro Oncol 2021; 23:356-375. [PMID: 33367885 PMCID: PMC7992879 DOI: 10.1093/neuonc/noaa277] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cancer immunotherapy has made remarkable advances with over 50 separate Food and Drug Administration (FDA) approvals as first- or second-line indications since 2015. These include immune checkpoint blocking antibodies, chimeric antigen receptor-transduced T cells, and bispecific T-cell-engaging antibodies. While multiple cancer types now benefit from these immunotherapies, notable exceptions thus far include brain tumors, such as glioblastoma. As such, it seems critical to gain a better understanding of unique mechanistic challenges underlying the resistance of malignant gliomas to immunotherapy, as well as to acquire insights into the development of future strategies. An Immuno-Oncology Think Tank Meeting was held during the 2019 Annual Society for Neuro-Oncology Scientific Conference. Discussants in the fields of neuro-oncology, neurosurgery, neuro-imaging, medical oncology, and cancer immunology participated in the meeting. Sessions focused on topics such as the tumor microenvironment, myeloid cells, T-cell dysfunction, cellular engineering, and translational aspects that are critical and unique challenges inherent with primary brain tumors. In this review, we summarize the discussions and the key messages from the meeting, which may potentially serve as a basis for advancing the field of immune neuro-oncology in a collaborative manner.
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Affiliation(s)
- Pavlina Chuntova
- Department of Neurological Surgery, UCSF, San Francisco, California
| | - Frances Chow
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | | | - Mildred Galvez
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, Los Angeles, California
| | - Amy B Heimberger
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Aaron Diaz
- Department of Neurological Surgery, UCSF, San Francisco, California
| | - Ronald A DePinho
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ming O Li
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - E John Wherry
- Department of Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Duane Mitchell
- Department of Neurosurgery, University of Florida College of Medicine, Gainesville, Florida
| | - Masaki Terabe
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Derek A Wainwright
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Jay A Berzofsky
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | | | | | - Michael Lim
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kim A Margolin
- Department of Medical Oncology & Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, California
| | - E Antonio Chiocca
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts
| | | | - Benjamin M Ellingson
- Department of Radiological Sciences, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Christine E Brown
- Department of Immuno-Oncology, Beckman Research Institute of the City of Hope, Duarte, California
| | - Yvonne Chen
- Department of Microbiology, Immunology & Molecular Genetics, UCLA, Los Angeles, California
| | - Peter E Fecci
- Department of Neurosurgery, Duke University School of Medicine, Durham, North Carolina
| | - David A Reardon
- Department of Medicine/Medical Oncology, Harvard Medical School, Boston, Massachusetts
| | - Gavin P Dunn
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri
| | - Linda M Liau
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, Los Angeles, California
| | | | - Wolfgang Wick
- Department of Neurology, University Hospital Heidelberg, Heidelberg, Germany
| | - Timothy Cloughesy
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - William C Timmer
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, Maryland
| | - Patrick Y Wen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Robert M Prins
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, Los Angeles, California.,Parker Institute for Cancer Immunotherapy, San Francisco, California
| | - Michael Platten
- Department of Neurology, Medical Faculty Mannheim, MCTN, University of Heidelberg, Mannheim, Germany.,DKTK CCU Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hideho Okada
- Department of Neurological Surgery, UCSF, San Francisco, California.,Parker Institute for Cancer Immunotherapy, San Francisco, California
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Rogachev AD, Alemasov NA, Ivanisenko VA, Ivanisenko NV, Gaisler EV, Oleshko OS, Cheresiz SV, Mishinov SV, Stupak VV, Pokrovsky AG. Correlation of Metabolic Profiles of Plasma and Cerebrospinal Fluid of High-Grade Glioma Patients. Metabolites 2021; 11:metabo11030133. [PMID: 33669010 PMCID: PMC7996604 DOI: 10.3390/metabo11030133] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/09/2021] [Accepted: 02/22/2021] [Indexed: 01/17/2023] Open
Abstract
This work compares the metabolic profiles of plasma and the cerebrospinal fluid (CSF) of the patients with high-grade (III and IV) gliomas and the conditionally healthy controls using the wide-range targeted screening of low molecular metabolites by HPLC-MS/MS. The obtained data were analyzed using robust linear regression with Huber’s M-estimates, and a number of metabolites with correlated content in plasma and CSF was identified. The statistical analysis shows a significant correlation of metabolite content in plasma and CSF samples for the majority of metabolites. Several metabolites were shown to have high correlation in the control samples, but not in the glioma patients. This can be due to the specific metabolic processes in the glioma patients or to the damaged integrity of blood-brain barrier. The results of our study may be useful for the understanding of molecular mechanisms underlying the development of gliomas, as well as for the search of potential biomarkers for the minimally invasive diagnostic procedures of gliomas.
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Affiliation(s)
- Artem D. Rogachev
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, Pirogov str., 2, 630090 Novosibirsk, Russia; (E.V.G.); (O.S.O.); (S.V.C.); (A.G.P.)
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, acad. Lavrentiev ave., 9, 630090 Novosibirsk, Russia
- Correspondence: ; Tel.: +7-(383)-330-97-47
| | - Nikolay A. Alemasov
- Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences, acad. Lavrentiev ave., 10, 630090 Novosibirsk, Russia; (N.A.A.); (V.A.I.); (N.V.I.)
| | - Vladimir A. Ivanisenko
- Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences, acad. Lavrentiev ave., 10, 630090 Novosibirsk, Russia; (N.A.A.); (V.A.I.); (N.V.I.)
| | - Nikita V. Ivanisenko
- Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences, acad. Lavrentiev ave., 10, 630090 Novosibirsk, Russia; (N.A.A.); (V.A.I.); (N.V.I.)
| | - Evgeniy V. Gaisler
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, Pirogov str., 2, 630090 Novosibirsk, Russia; (E.V.G.); (O.S.O.); (S.V.C.); (A.G.P.)
| | - Olga S. Oleshko
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, Pirogov str., 2, 630090 Novosibirsk, Russia; (E.V.G.); (O.S.O.); (S.V.C.); (A.G.P.)
| | - Sergey V. Cheresiz
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, Pirogov str., 2, 630090 Novosibirsk, Russia; (E.V.G.); (O.S.O.); (S.V.C.); (A.G.P.)
| | - Sergey V. Mishinov
- FSBI “Novosibirsk Research Institute of Traumatology and Orthopedics Named after Ya. L. Tsiviyan”, Frunze str., 17, 630091 Novosibirsk, Russia; (S.V.M.); (V.V.S.)
| | - Vyacheslav V. Stupak
- FSBI “Novosibirsk Research Institute of Traumatology and Orthopedics Named after Ya. L. Tsiviyan”, Frunze str., 17, 630091 Novosibirsk, Russia; (S.V.M.); (V.V.S.)
| | - Andrey G. Pokrovsky
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, Pirogov str., 2, 630090 Novosibirsk, Russia; (E.V.G.); (O.S.O.); (S.V.C.); (A.G.P.)
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Vitale A, Villa R, Ugga L, Romeo V, Stanzione A, Cuocolo R. Artificial intelligence applied to neuroimaging data in Parkinsonian syndromes: Actuality and expectations. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2021; 18:1753-1773. [PMID: 33757209 DOI: 10.3934/mbe.2021091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Idiopathic Parkinson's Disease (iPD) is a common motor neurodegenerative disorder. It affects more frequently the elderly population, causing a significant emotional burden both for the patient and caregivers, due to the disease-related onset of motor and cognitive disabilities. iPD's clinical hallmark is the onset of cardinal motor symptoms such as bradykinesia, rest tremor, rigidity, and postural instability. However, these symptoms appear when the neurodegenerative process is already in an advanced stage. Furthermore, the greatest challenge is to distinguish iPD from other similar neurodegenerative disorders, "atypical parkinsonisms", such as Multisystem Atrophy, Progressive Supranuclear Palsy and Cortical Basal Degeneration, since they share many phenotypic manifestations, especially in the early stages. The diagnosis of these neurodegenerative motor disorders is essentially clinical. Consequently, the diagnostic accuracy mainly depends on the professional knowledge and experience of the physician. Recent advances in artificial intelligence have made it possible to analyze the large amount of clinical and instrumental information in the medical field. The application machine learning algorithms to the analysis of neuroimaging data appear to be a promising tool for identifying microstructural alterations related to the pathological process in order to explain the onset of symptoms and the spread of the neurodegenerative process. In this context, the search for quantitative biomarkers capable of identifying parkinsonian patients in the prodromal phases of the disease, of correctly distinguishing them from atypical parkinsonisms and of predicting clinical evolution and response to therapy represent the main goal of most current clinical research studies. Our aim was to review the recent literature and describe the current knowledge about the contribution given by machine learning applications to research and clinical management of parkinsonian syndromes.
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Affiliation(s)
- Annalisa Vitale
- Department of Advanced Biomedical Sciences, University of Naples "Federico Ⅱ", Via S. Pansini 5, 80131-Naples, Italy
| | - Rossella Villa
- Department of Advanced Biomedical Sciences, University of Naples "Federico Ⅱ", Via S. Pansini 5, 80131-Naples, Italy
| | - Lorenzo Ugga
- Department of Advanced Biomedical Sciences, University of Naples "Federico Ⅱ", Via S. Pansini 5, 80131-Naples, Italy
| | - Valeria Romeo
- Department of Advanced Biomedical Sciences, University of Naples "Federico Ⅱ", Via S. Pansini 5, 80131-Naples, Italy
| | - Arnaldo Stanzione
- Department of Advanced Biomedical Sciences, University of Naples "Federico Ⅱ", Via S. Pansini 5, 80131-Naples, Italy
| | - Renato Cuocolo
- Department of Clinical Medicine and Surgery, University of Naples "Federico Ⅱ", Via S. Pansini 5, 80131-Naples, Italy
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Sheng C, Chen Z, Lei J, Zhu J, Song S. Development and Multi-Data Set Verification of an RNA Binding Protein Signature for Prognosis Prediction in Glioma. Front Med (Lausanne) 2021; 8:637803. [PMID: 33634155 PMCID: PMC7900154 DOI: 10.3389/fmed.2021.637803] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/11/2021] [Indexed: 12/13/2022] Open
Abstract
Objective: Increasing evidence emphasizes the clinical implications of RNA binding proteins (RBPs) in cancers. This study aimed to develop a RBP signature for predicting prognosis in glioma. Methods: Two glioma datasets as training (n = 693) and validation (n = 325) sets were retrieved from the CGGA database. In the training set, univariate Cox regression analysis was conducted to screen prognosis-related RBPs based on differentially expressed RBPs between WHO grade II and IV. A ten-RBP signature was then established. The predictive efficacy was evaluated by ROCs. The applicability was verified in the validation set. The pathways involving the risk scores were analyzed by ssGSEA. scRNA-seq was utilized for evaluating their expression in different glioma cell types. Moreover, their expression was externally validated between glioma and control samples. Results: Based on 39 prognosis-related RBPs, a ten RBP signature was constructed. High risk score distinctly indicated a poorer prognosis than low risk score. AUCs were separately 0.838 and 0.822 in the training and validation sets, suggesting its well performance for prognosis prediction. Following adjustment of other clinicopathological characteristics, the signature was an independent risk factor. Various cancer-related pathways were significantly activated in samples with high risk score. The scRNA-seq identified that risk RBPs were mainly expressed in glioma malignant cells. Their high expression was also found in glioma than control samples. Conclusion: This study developed a novel RBP signature for robustly predicting prognosis of glioma following multi-data set verification. These RBPs may affect the progression of glioma.
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Affiliation(s)
- Chunpeng Sheng
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhihua Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jianwei Lei
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jianming Zhu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Shuxin Song
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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Booth TC, Thompson G, Bulbeck H, Boele F, Buckley C, Cardoso J, Dos Santos Canas L, Jenkinson D, Ashkan K, Kreindler J, Huskens N, Luis A, McBain C, Mills SJ, Modat M, Morley N, Murphy C, Ourselin S, Pennington M, Powell J, Summers D, Waldman AD, Watts C, Williams M, Grant R, Jenkinson MD. A Position Statement on the Utility of Interval Imaging in Standard of Care Brain Tumour Management: Defining the Evidence Gap and Opportunities for Future Research. Front Oncol 2021; 11:620070. [PMID: 33634034 PMCID: PMC7900557 DOI: 10.3389/fonc.2021.620070] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/06/2021] [Indexed: 12/19/2022] Open
Abstract
OBJECTIV E To summarise current evidence for the utility of interval imaging in monitoring disease in adult brain tumours, and to develop a position for future evidence gathering while incorporating the application of data science and health economics. METHODS Experts in 'interval imaging' (imaging at pre-planned time-points to assess tumour status); data science; health economics, trial management of adult brain tumours, and patient representatives convened in London, UK. The current evidence on the use of interval imaging for monitoring brain tumours was reviewed. To improve the evidence that interval imaging has a role in disease management, we discussed specific themes of data science, health economics, statistical considerations, patient and carer perspectives, and multi-centre study design. Suggestions for future studies aimed at filling knowledge gaps were discussed. RESULTS Meningioma and glioma were identified as priorities for interval imaging utility analysis. The "monitoring biomarkers" most commonly used in adult brain tumour patients were standard structural MRI features. Interval imaging was commonly scheduled to provide reported imaging prior to planned, regular clinic visits. There is limited evidence relating interval imaging in the absence of clinical deterioration to management change that alters morbidity, mortality, quality of life, or resource use. Progression-free survival is confounded as an outcome measure when using structural MRI in glioma. Uncertainty from imaging causes distress for some patients and their caregivers, while for others it provides an important indicator of disease activity. Any study design that changes imaging regimens should consider the potential for influencing current or planned therapeutic trials, ensure that opportunity costs are measured, and capture indirect benefits and added value. CONCLUSION Evidence for the value, and therefore utility, of regular interval imaging is currently lacking. Ongoing collaborative efforts will improve trial design and generate the evidence to optimise monitoring imaging biomarkers in standard of care brain tumour management.
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Affiliation(s)
- Thomas C. Booth
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, United Kingdom
- Department of Neuroradiology, King’s College Hospital NHS Foundation Trust, London, United Kingdom
| | - Gerard Thompson
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Florien Boele
- Leeds Institute of Medical Research at St James’s, St James’s University Hospital, Leeds, United Kingdom
- Faculty of Medicine and Health, Leeds Institute of Health Sciences, University of Leeds, Leeds, United Kingdom
| | | | - Jorge Cardoso
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, United Kingdom
| | - Liane Dos Santos Canas
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, United Kingdom
| | | | - Keyoumars Ashkan
- Department of Neurosurgery, King’s College Hospital NHS Foundation Trust, London, United Kingdom
| | | | - Nicky Huskens
- The Tessa Jowell Brain Cancer Mission, London, United Kingdom
| | - Aysha Luis
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, United Kingdom
- Lysholm Department of Neuroradiology, National Hospital for Neurology and Neurosurgery, London, United Kingdom
| | - Catherine McBain
- Department of Oncology, Christie Hospital NHS Foundation Trust, Manchester, United Kingdom
| | - Samantha J. Mills
- Department of Neuroradiology, The Walton Centre NHS Foundation Trust, Liverpool, United Kingdom
| | - Marc Modat
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, United Kingdom
| | - Nick Morley
- Department of Radiology, Wales Research and Diagnostic PET Imaging Centre, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Caroline Murphy
- King’s College Trials Unit, King’s College London, London, United Kingdom
| | - Sebastian Ourselin
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, United Kingdom
| | - Mark Pennington
- King’s Health Economics, King’s College London, London, United Kingdom
| | - James Powell
- Department of Oncology, Velindre Cancer Centre, Cardiff, United Kingdom
| | - David Summers
- Department of Neuroradiology, Western General Hospital, Edinburgh, United Kingdom
| | - Adam D. Waldman
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Colin Watts
- Birmingham Brain Cancer Program, University of Birmingham, Birmingham, United Kingdom
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Matthew Williams
- Department of Neuro-oncology, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Robin Grant
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Michael D. Jenkinson
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
- Department of Neurosurgery, The Walton Centre NHS Foundation Trust, Liverpool, United Kingdom
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GLIMPSE: a glioblastoma prognostication model using ensemble learning-a surveillance, epidemiology, and end results study. Health Inf Sci Syst 2021; 9:5. [PMID: 33489102 DOI: 10.1007/s13755-020-00134-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/04/2020] [Indexed: 12/21/2022] Open
Abstract
Purpose Glioblastoma is one of the most common and aggressive brain tumors in the world with a poor prognosis. A glioblastoma prognostication model has the potential to improve the cancer's standard of care. No other paper has looked at using ensemble learning with a population database to predict multiple binary glioblastoma survival outcomes. Methods We utilized ensemble learning to design, build, and test a prognostication system for glioblastoma for short-, intermediate- and long-term survival, based on various clinical features. We used the population database SEER which covers 17 different registries. The most important prognostic features were identified and used as a clinical feature set. The statistical feature set was determined using Random Forests. The accuracy, sensitivity, specificity, area under the receiver operating characteristic (AUROC), positive predictive value (PPV), and negative predictive value (NPV) were reported. Results Statistically-determined feature sets had the best performance. All the top models for short, intermediate, and long-term survival were random forests. With regards to short-term survival, top model had metrics AUROC = 0.937, accuracy = 86%, specificity = 88%, sensitivity = 85%, NPV = 85%, and PPV = 87%. For long-term survival, the top model had AUROC = 0.893, accuracy = 81%, specificity = 79%, sensitivity = 83%, NPV = 82%, and PPV = 79%. The top intermediate-term survival prediction had AUROC ≥ 0.780 and the other metrics were at least 70%. Conclusions Our ensemble models were high-performing and achieved AUROCs as high as 0.94, highlighting the importance of balancing, using ensemble techniques and statistical feature selection. Our models can potentially be used by clinicians after external validation.
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Favorable role of IDH1/2 mutations aided with MGMT promoter gene methylation in the outcome of patients with malignant glioma. Future Sci OA 2020; 7:FSO663. [PMID: 33552543 PMCID: PMC7849969 DOI: 10.2144/fsoa-2020-0057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Aim The implications of molecular biomarkers IDH1/2 mutations and MGMT gene promoter methylation were evaluated for prognostic outcome of glioma patients. Materials & methods Glioma cases were analyzed for IDH1/2 mutations and MGMT promoter methylation by DNA sequencing and methylation-specific PCR, respectively. Results Mutations found in IDH1/2 genes totaled 63.4% (N = 40) wherein IDH1 mutations were significantly associated with oligidendrioglioma (p = 0.005) and astrocytoma (p = 0.0002). IDH1 mutants presented more, 60.5% in MGMT promoter-methylated cases (p = 0.03). IDH1 mutant cases had better survival for glioblastoma and oligodendrioglioma (log-rank p = 0.01). Multivariate analysis confirmed better survival in MGMT methylation carriers (hazard ratio [HR]: 0.59; p = 0.031). Combination of both biomarkers showed better prognosis on temozolomide (p < 0.05). Conclusion IDH1/2 mutations proved independent prognostic factors in glioma and associated with MGMT methylation for better survival.
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