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Crouch SA, Krause J, Dandekar T, Breitenbach T. DataXflow: Synergizing data-driven modeling with best parameter fit and optimal control - An efficient data analysis for cancer research. Comput Struct Biotechnol J 2024; 23:1755-1772. [PMID: 38707537 PMCID: PMC11068525 DOI: 10.1016/j.csbj.2024.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 05/07/2024] Open
Abstract
Building data-driven models is an effective strategy for information extraction from empirical data. Adapting model parameters specifically to data with a best fitting approach encodes the relevant information into a mathematical model. Subsequently, an optimal control framework extracts the most efficient targets to steer the model into desired changes via external stimuli. The DataXflow software framework integrates three software pipelines, D2D for model fitting, a framework solving optimal control problems including external stimuli and JimenaE providing graphical user interfaces to employ the other frameworks lowering the barriers for the need of programming skills, and simultaneously automating reoccurring modeling tasks. Such tasks include equation generation from a graph and script generation allowing also to approach systems with many agents, like complex gene regulatory networks. A desired state of the model is defined, and therapeutic interventions are modeled as external stimuli. The optimal control framework purposefully exploits the model-encoded information by providing those external stimuli that effect the desired changes most efficiently. The implementation of DataXflow is available under https://github.com/MarvelousHopefull/DataXflow. We showcase its application by detecting specific drug targets for a therapy of lung cancer from measurement data to lower proliferation and increase apoptosis. By an iterative modeling process refining the topology of the model, the regulatory network of the tumor is generated from the data. An application of the optimal control framework in our example reveals the inhibition of AURKA and the activation of CDH1 as the most efficient drug target combination. DataXflow paves the way to an agile interplay between data generation and its analysis potentially accelerating cancer research by an efficient drug target identification, even in complex networks.
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Affiliation(s)
| | | | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland 97074, Würzburg, Germany
| | - Tim Breitenbach
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland 97074, Würzburg, Germany
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Yadav K, Vijayalakshmi R, Kumar Sahu K, Sure P, Chahal K, Yadav R, Sucheta, Dubey A, Jha M, Pradhan M. Exosome-Based Macromolecular neurotherapeutic drug delivery approaches in overcoming the Blood-Brain barrier for treating brain disorders. Eur J Pharm Biopharm 2024; 199:114298. [PMID: 38642716 DOI: 10.1016/j.ejpb.2024.114298] [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: 02/03/2024] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
Delivering drugs to the brain is a complex challenge in medical research, particularly for disorders like Alzheimer's and Parkinson's. The blood-brain barrier restricts the entry of many therapeutic molecules, hindering their effectiveness. Nanoparticles, a potential solution, face issues like toxicity and limited approvals. A new avenue explores the use of small extracellular vesicles (sEVs), i.e., exosomes, as natural carriers for drug delivery. sEVs, tiny structures below 150 nm, show promise due to their minimal immune response and ability to precisely deliver drugs. This review focuses on the potential of sEVs-based drug delivery systems for treating neurological disorders, brain cancers, and other brain-related issues. Notably, bioengineered sEVs-carrying therapeutic compounds exhibit promise in early studies. The unique features of sEVs, such as their small size and natural properties, position them as candidates to overcome challenges in drug delivery to the brain. Ongoing clinical trials and research into sEVs behavior within the body further highlight their potential for revolutionizing drug delivery and addressing complex brain conditions.
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Affiliation(s)
- Krishna Yadav
- Raipur Institute of Pharmaceutical Education and Research, Sarona, Raipur, Chhattisgarh 492010, India
| | - R Vijayalakshmi
- Department of Pharmaceutical Analysis, GIET School of Pharmacy, Chaitanya Knowledge City, Rajahmundry, AP, 533296, India
| | - Kantrol Kumar Sahu
- Institute of Pharmaceutical Research, GLA University, Mathura, Uttar Pradesh, 281406, India
| | - Pavani Sure
- Department of Pharmaceutics, Vignan Institute of Pharmaceutical Sciences, Hyderabad, Telangana, India
| | - Kavita Chahal
- Department of Botany, Government Model Science College Jabalpur, Madhya Pradesh, India
| | - Renu Yadav
- School of Medical and Allied Sciences, K. R. Mangalam University, Sohna Road, Gurugram, Haryana, 122103, India
| | - Sucheta
- School of Medical and Allied Sciences, K. R. Mangalam University, Sohna Road, Gurugram, Haryana, 122103, India
| | - Akhilesh Dubey
- Nitte (Deemed to be University), NGSM Institute of Pharmaceutical Sciences, Department of Pharmaceutics, Mangaluru-575018, Karnataka, India
| | - Megha Jha
- Department of Life Science, Mansarovar Global University, Sehore, M.P., India
| | - Madhulika Pradhan
- Gracious College of Pharmacy, Abhanpur, Chhattisgarh, 493661, India.
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3
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Lucke-Wold B, Rangwala BS, Shafique MA, Siddiq MA, Mustafa MS, Danish F, Nasrullah RMU, Zainab N, Haseeb A. Focus on current and emerging treatment options for glioma: A comprehensive review. World J Clin Oncol 2024; 15:482-495. [PMID: 38689623 PMCID: PMC11056857 DOI: 10.5306/wjco.v15.i4.482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/22/2024] [Accepted: 02/28/2024] [Indexed: 04/22/2024] Open
Abstract
This comprehensive review delves into the current updates and challenges associated with the management of low-grade gliomas (LGG), the predominant primary tumors in the central nervous system. With a general incidence rate of 5.81 per 100000, gliomas pose a significant global concern, necessitating advancements in treatment techniques to reduce mortality and morbidity. This review places a particular focus on immunotherapies, discussing promising agents such as Zotiraciclib and Lerapolturev. Zotiraciclib, a CDK9 inhibitor, has demonstrated efficacy in glioblastoma treatment in preclinical and clinical studies, showing its potential as a therapeutic breakthrough. Lerapolturev, a viral immunotherapy, induces inflammation in glioblastoma and displays positive outcomes in both adult and pediatric patients. Exploration of immunotherapy extends to Pembrolizumab, Nivolumab, and Entrectinib, revealing the challenges and variabilities in patient responses. Despite promising preclinical data, the monoclonal antibody Depatuxizumab has proven ineffective in glioblastoma treatment, emphasizing the critical need to understand resistance mechanisms. The review also covers the success of radiation therapy in pediatric LGG, with evolving techniques, such as proton therapy, showing potential improvements in patient quality of life. Surgical treatment is discussed in the context of achieving a balance between preserving the patient's quality of life and attaining gross total resection, with the extent of surgical resection significantly influencing the survival outcomes. In addition to advancements in cancer vaccine development, this review highlights the evolving landscape of LGG treatment, emphasizing a shift toward personalized and targeted therapies. Ongoing research is essential for refining strategies and enhancing outcomes in the management of LGG.
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Affiliation(s)
- Brandon Lucke-Wold
- Department of Neurosurgery, University of Florida, Gainesville, FL 32608, United States
| | | | | | - Mohammad Arham Siddiq
- Department of Neurosurgery, Jinnah Sindh Medical University, Karachi 75510, Pakistan
| | | | - Fnu Danish
- Department of Neurosurgery, Jinnah Sindh Medical University, Karachi 75510, Pakistan
| | | | - Noor Zainab
- Department of Neurosurgery, Army Medical College, Rawalpindi 46000, Pakistan
| | - Abdul Haseeb
- Department of Neurosurgery, Jinnah Sindh Medical University, Karachi 75510, Pakistan
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4
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Jiang H, Zhu Q, Wang X, Li M, Shen S, Yang C, Zhao X, Li M, Ma G, Zhao X, Chen X, Yang J, Lin S. Characterization and clinical implications of different malignant transformation patterns in diffuse low-grade gliomas. Cancer Sci 2023; 114:3708-3718. [PMID: 37332121 PMCID: PMC10475770 DOI: 10.1111/cas.15889] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/08/2023] [Accepted: 06/01/2023] [Indexed: 06/20/2023] Open
Abstract
Malignant transformation (MT) of low-grade gliomas (LGGs) to a higher-grade variant seems inevitable, yet it remains unclear which LGG patients will progress to grade 3 or even directly to grade 4 after receiving a long course of treatment. To elucidate this, we conducted a retrospective cohort study based on 229 adults with recurrent LGG. Our study aimed to disclose the characteristics of different MT patterns and to build predictive models for patients with LGG. Patients were allocated into group 2-2 (n = 81, 35.4%), group 2-3 (n = 91, 39.7%), and group 2-4 (n = 57, 24.9%), based on their MT patterns. Patients who underwent MT showed lower Karnofsky performance scale (KPS) scores, larger tumor sizes, smaller extents of resection (EOR), higher Ki-67 indices, lower rates of 1p/19q codeletion, but higher rates of subventricular involvement, radiotherapy, chemotherapy, astrocytoma, and post-progression enhancement (PPE) compared with those in group 2-2 (p < 0.01). On multivariate logistic regression, 1p/19q codeletion, Ki-67 index, radiotherapy, EOR, and KPS score were independently associated with MT (p < 0.05). Survival analyses demonstrated that patients in group 2-2 had the longest survival, followed by group 2-3 and then group 2-4 (p < 0.0001). Based on these independent parameters, we constructed a nomogram model that exhibited superior potential (sensitivity: 0.864, specificity: 0.814, and accuracy: 0.843) compared with PPE in early prediction of MT. Combining the factors of 1p/19q codeletion, Ki-67 index, radiotherapy, EOR, and KPS score that were presented at initial diagnosis could precisely forecast the subsequent MT patterns of patients with LGG.
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Affiliation(s)
- Haihui Jiang
- Department of NeurosurgeryPeking University Third Hospital, Peking UniversityBeijingChina
| | - Qinghui Zhu
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
| | - Xijie Wang
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
| | - Mingxiao Li
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
| | - Shaoping Shen
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
| | - Chuanwei Yang
- Department of Neurosurgery, Henan Provincial People's HospitalPeople's Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina
| | - Xuzhe Zhao
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
| | - Ming Li
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
| | - Guofo Ma
- Department of NeurosurgeryPeking University Third Hospital, Peking UniversityBeijingChina
| | - Xiaofang Zhao
- Department of NeurosurgeryPeking University Third Hospital, Peking UniversityBeijingChina
| | - Xiaodong Chen
- Department of NeurosurgeryPeking University Third Hospital, Peking UniversityBeijingChina
| | - Jun Yang
- Department of NeurosurgeryPeking University Third Hospital, Peking UniversityBeijingChina
| | - Song Lin
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
- National Clinical Research Center for Neurological Diseases, Center of Brain TumorBeijing Institute for Brain Disorders and Beijing Key Laboratory of Brain TumorBeijingChina
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5
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Kurimoto M, Rockenbach Y, Kato A, Natsume A. Prediction of Tumor Development and Urine-Based Liquid Biopsy for Molecule-Targeted Therapy of Gliomas. Genes (Basel) 2023; 14:1201. [PMID: 37372381 DOI: 10.3390/genes14061201] [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: 12/30/2022] [Revised: 05/21/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
The timing of the acquisition of tumor-specific gene mutations and the systems by which these gene mutations are acquired during tumorigenesis were clarified. Advances in our understanding of tumorigenesis are being made every day, and therapies targeting fundamental genetic alterations have great potential for cancer treatment. Moreover, our research team successfully estimated tumor progression using mathematical modeling and attempted early diagnosis of brain tumors. We developed a nanodevice that enables urinary genetic diagnosis in a simple and noninvasive manner. Mainly on the basis of our research and experience, this review article presents novel therapies being developed for central nervous system cancers and six molecules, which upon mutation cause tumorigenesis and tumor progression. Further understanding of the genetic characteristics of brain tumors will lead to the development of precise drugs and improve individual treatment outcomes.
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Affiliation(s)
- Michihiro Kurimoto
- Department of Neurosurgery, Aichi Children's Health and Medical Center, Obu 464-8710, Japan
| | - Yumi Rockenbach
- Institute of Innovation for Future Society, Nagoya University, Nagoya 464-8601, Japan
| | - Akira Kato
- Institute of Innovation for Future Society, Nagoya University, Nagoya 464-8601, Japan
| | - Atsushi Natsume
- Institute of Innovation for Future Society, Nagoya University, Nagoya 464-8601, Japan
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6
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Buckwar E, Conte M, Meddah A. A stochastic hierarchical model for low grade glioma evolution. J Math Biol 2023; 86:89. [PMID: 37147527 PMCID: PMC10163130 DOI: 10.1007/s00285-023-01909-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 03/17/2023] [Accepted: 03/22/2023] [Indexed: 05/07/2023]
Abstract
A stochastic hierarchical model for the evolution of low grade gliomas is proposed. Starting with the description of cell motion using a piecewise diffusion Markov process (PDifMP) at the cellular level, we derive an equation for the density of the transition probability of this Markov process based on the generalised Fokker-Planck equation. Then, a macroscopic model is derived via parabolic limit and Hilbert expansions in the moment equations. After setting up the model, we perform several numerical tests to study the role of the local characteristics and the extended generator of the PDifMP in the process of tumour progression. The main aim focuses on understanding how the variations of the jump rate function of this process at the microscopic scale and the diffusion coefficient at the macroscopic scale are related to the diffusive behaviour of the glioma cells and to the onset of malignancy, i.e., the transition from low-grade to high-grade gliomas.
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Affiliation(s)
- Evelyn Buckwar
- Institute of Stochastics, Johannes Kepler University, Altenberger Straße 69, 4040, Linz, Austria
- Centre for Mathematical Sciences, Lund University, 221 00, Lund, Sweden
| | - Martina Conte
- Department of Mathematical Sciences "G. L. Lagrange", Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129, Torino, Italy
| | - Amira Meddah
- Institute of Stochastics, Johannes Kepler University, Altenberger Straße 69, 4040, Linz, Austria.
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7
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Kreatsoulas D, Damante M, Gruber M, Duru O, Elder JB. Supratotal Surgical Resection for Low-Grade Glioma: A Systematic Review. Cancers (Basel) 2023; 15:cancers15092493. [PMID: 37173957 PMCID: PMC10177219 DOI: 10.3390/cancers15092493] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/20/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Low-grade gliomas (LGGs) are optimally treated with up-front maximal safe surgical resection, typically defined as maximizing the extent of tumor resection while minimizing neurologic risks of surgery. Supratotal resection of LGG may improve outcomes beyond gross total resection by removing tumor cells invading beyond the tumor border as defined on MRI. However, the evidence regarding supratotal resection of LGG, in terms of impact on clinical outcomes, such as overall survival and neurologic morbidities, remains unclear. Authors independently searched the PubMed, Medline, Ovid, CENTRAL (Cochrane Central Register of Controlled Trials), and Google Scholar databases for studies evaluating overall survival, time to progression, seizure outcomes, and postoperative neurologic and medical complications of supratotal resection/FLAIRectomy of WHO-defined LGGs. Papers in languages other than English, lacking full-text availability, evaluating supratotal resection of WHO-defined high-grade gliomas only, and nonhuman studies were excluded. After literature search, reference screening, and initial exclusions, 65 studies were screened for relevancy, of which 23 were evaluated via full-text review, and 10 were ultimately included in the final evidence review. Studies were evaluated for quality using the MINORS criteria. After data extraction, a total of 1301 LGG patients were included in the analysis, with 377 (29.0%) undergoing supratotal resection. The main measured outcomes were extent of resection, pre- and postoperative neurological deficits, seizure control, adjuvant treatment, neuropsychological outcomes, ability to return to work, progression-free survival, and overall survival. Overall, low- to moderate-quality evidence was supportive of aggressive, functional boundary-based resection of LGGs due to improvements in progression-free survival and seizure control. The published literature provides a moderate amount of low-quality evidence supporting supratotal surgical resection along functional boundaries for low-grade glioma. Among patients included in this analysis, the occurrence of postoperative neurological deficits was low, and nearly all patients recovered within 3 to 6 months after surgery. Notably, the surgical centers represented in this analysis have significant experience in glioma surgery in general, and supratotal resection specifically. In this setting, supratotal surgical resection along functional boundaries appears to be appropriate for both symptomatic and asymptomatic low-grade glioma patients. Larger clinical studies are needed to better define the role of supratotal resection in LGG.
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Affiliation(s)
- Daniel Kreatsoulas
- Department of Neurological Surgery, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Mark Damante
- Department of Neurological Surgery, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Maxwell Gruber
- Department of Neurological Surgery, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Olivia Duru
- College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - James Bradley Elder
- Department of Neurological Surgery, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
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8
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Vogelbaum MA. Balancing maximal resection and functional preservation in surgery for low-grade glioma. Neuro Oncol 2022; 24:794-795. [PMID: 35020909 PMCID: PMC9071335 DOI: 10.1093/neuonc/noac008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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9
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Lipková J, Menze B, Wiestler B, Koumoutsakos P, Lowengrub JS. Modelling glioma progression, mass effect and intracranial pressure in patient anatomy. J R Soc Interface 2022; 19:20210922. [PMID: 35317645 PMCID: PMC8941421 DOI: 10.1098/rsif.2021.0922] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/21/2022] [Indexed: 02/06/2023] Open
Abstract
Increased intracranial pressure is the source of most critical symptoms in patients with glioma, and often the main cause of death. Clinical interventions could benefit from non-invasive estimates of the pressure distribution in the patient's parenchyma provided by computational models. However, existing glioma models do not simulate the pressure distribution and they rely on a large number of model parameters, which complicates their calibration from available patient data. Here we present a novel model for glioma growth, pressure distribution and corresponding brain deformation. The distinct feature of our approach is that the pressure is directly derived from tumour dynamics and patient-specific anatomy, providing non-invasive insights into the patient's state. The model predictions allow estimation of critical conditions such as intracranial hypertension, brain midline shift or neurological and cognitive impairments. A diffuse-domain formalism is employed to allow for efficient numerical implementation of the model in the patient-specific brain anatomy. The model is tested on synthetic and clinical cases. To facilitate clinical deployment, a high-performance computing implementation of the model has been publicly released.
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Affiliation(s)
- Jana Lipková
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Bjoern Menze
- Department of Informatics, Technical University of Munich, Munich, Germany
- Department of Quantitative Biomedicine, University of Zürich, Zürich, Switzerland
- Department of Neuroradiology, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Benedikt Wiestler
- Department of Neuroradiology, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Petros Koumoutsakos
- Computational Science and Engineering Lab, ETH Zürich, Zürich, Switzerland
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - John S. Lowengrub
- Department of Mathematics, University of California, Irvine, CA, USA
- Department of Biomedical Engineering, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, Chao Family Comprehensive Cancer Center, University of California, Irvine, CA, USA
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10
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Xia M, Chen H, Chen T, Xue P, Dong X, Lin Y, Ma D, Zhou W, Shi W, Li H. Transcriptional Networks Identify BRPF1 as a Potential Drug Target Based on Inflammatory Signature in Primary Lower-Grade Gliomas. Front Oncol 2021; 11:766656. [PMID: 34926268 PMCID: PMC8674185 DOI: 10.3389/fonc.2021.766656] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/15/2021] [Indexed: 12/26/2022] Open
Abstract
Gliomas are the most common tumors of the central nervous system and are classified into grades I-IV based on their histological characteristics. Lower-grade gliomas (LGG) can be divided into grade II diffuse low-grade gliomas and grade III moderate gliomas and have a relatively good prognosis. However, LGG often develops into high-grade glioma within a few years. This study aimed to construct and identify the prognostic value of an inflammatory signature and discover potential drug targets for primary LGG. We first screened differentially expressed genes in primary LGG (TCGA) compared with normal brain tissue (GTEx) that overlapped with inflammation-related genes from MSigDB. After survival analysis, nine genes were selected to construct an inflammatory signature. LGG patients with a high inflammatory signature score had a poor prognosis, and the inflammatory signature was a strong independent prognostic factor in both the training cohort (TCGA) and validation cohort (CGGA). Compared with the low-inflammatory signature group, differentially expressed genes in the high-inflammatory signature group were mainly enriched in immune-related signaling pathways, which is consistent with the distribution of immune cells in the high- and low-inflammatory signature groups. Integrating driver genes, upregulated genes and drug targets data, bromodomain and PHD finger-containing protein 1 (BRPF1) was selected as a potential drug target. Inhibition of BRPF1 function or knockdown of BRPF1 expression attenuated glioma cell proliferation and colony formation.
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Affiliation(s)
- Mingyang Xia
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Huiyao Chen
- Center for Molecular Medicine, Children's Hospital of Fudan University, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Tong Chen
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Ping Xue
- Department of Neurosurgery, Children's Hospital of Fudan University, Shanghai, China
| | - Xinran Dong
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Yifeng Lin
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Duan Ma
- Key Laboratory of Neonatal Diseases, Division of Neonatology, Children's Hospital of Fudan University, Ministry of Health, Shanghai, China
| | - Wenhao Zhou
- Center for Molecular Medicine, Children's Hospital of Fudan University, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wei Shi
- Department of Neurosurgery, Children's Hospital of Fudan University, Shanghai, China
| | - Hao Li
- Department of Neurosurgery, Children's Hospital of Fudan University, Shanghai, China
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11
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Aoki K, Suzuki H, Yamamoto T, Yamamoto KN, Maeda S, Okuno Y, Ranjit M, Motomura K, Ohka F, Tanahashi K, Hirano M, Nishikawa T, Shimizu H, Kitano Y, Yamaguchi J, Yamazaki S, Nakamura H, Takahashi M, Narita Y, Nakada M, Deguchi S, Mizoguchi M, Momii Y, Muragaki Y, Abe T, Akimoto J, Wakabayashi T, Saito R, Ogawa S, Haeno H, Natsume A. Mathematical Modeling and Mutational Analysis Reveal Optimal Therapy to Prevent Malignant Transformation in Grade II IDH-Mutant Gliomas. Cancer Res 2021; 81:4861-4873. [PMID: 34333454 PMCID: PMC9635454 DOI: 10.1158/0008-5472.can-21-0985] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/10/2021] [Accepted: 07/23/2021] [Indexed: 01/07/2023]
Abstract
Isocitrate dehydrogenase-mutant low-grade gliomas (IDHmut-LGG) grow slowly but frequently undergo malignant transformation, which eventually leads to premature death. Chemotherapy and radiotherapy treatments prolong survival, but can also induce genetic (or epigenetic) alterations involved in transformation. Here, we developed a mathematical model of tumor progression based on serial tumor volume data and treatment history of 276 IDHmut-LGGs classified by chromosome 1p/19q codeletion (IDHmut/1p19qcodel and IDHmut/1p19qnoncodel) and performed genome-wide mutational analyses, including targeted sequencing and longitudinal whole-exome sequencing data. These analyses showed that tumor mutational burden correlated positively with malignant transformation rate, and chemotherapy and radiotherapy significantly suppressed tumor growth but increased malignant transformation rate per cell by 1.8 to 2.8 times compared with before treatment. This model revealed that prompt adjuvant chemoradiotherapy prolonged malignant transformation-free survival in small IDHmut-LGGs (≤ 50 cm3). Furthermore, optimal treatment differed according to genetic alterations for large IDHmut-LGGs (> 50 cm3); adjuvant therapies delayed malignant transformation in IDHmut/1p19qnoncodel but often accelerated it in IDHmut/1p19qcodel. Notably, PI3K mutation was not associated with malignant transformation but increased net postoperative proliferation rate and decreased malignant transformation-free survival, prompting the need for adjuvant therapy in IDHmut/1p19qcodel. Overall, this model uncovered therapeutic strategies that could prevent malignant transformation and, consequently, improve overall survival in patients with IDHmut-LGGs. SIGNIFICANCE: A mathematical model successfully estimates malignant transformation-free survival and reveals a link between genetic alterations and progression, identifying precision medicine approaches for optimal treatment of IDH-mutant low-grade gliomas.
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Affiliation(s)
- Kosuke Aoki
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Aichi, Japan.,Corresponding Authors: Kosuke Aoki, Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya 4668550, Japan. Phone: 815-2744-2353; E-mail: ; Hiroshi Haeno, ; and Atsushi Natsume,
| | - Hiromichi Suzuki
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Takashi Yamamoto
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Kimiyo N. Yamamoto
- Departments of General and Gastroenterological Surgery, Osaka Medical College Hospital, Takatsuki-shi, Osaka, Japan
| | - Sachi Maeda
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Yusuke Okuno
- Medical Genomics Center, Nagoya University Hospital, Nagoya, Aichi, Japan.,Department of Virology, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Melissa Ranjit
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Kazuya Motomura
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Fumiharu Ohka
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Kuniaki Tanahashi
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Masaki Hirano
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Tomohide Nishikawa
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Hiroyuki Shimizu
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Yotaro Kitano
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Junya Yamaguchi
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Shintaro Yamazaki
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Hideo Nakamura
- Department of Neurosurgery, Kumamoto University, Kumamoto, Japan.,Department of Neurosurgery, Kurume University, Kurume, Fukuoka, Japan
| | - Masamichi Takahashi
- Department of Neurosurgery and Neuro-oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yoshitaka Narita
- Department of Neurosurgery and Neuro-oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Mitsutoshi Nakada
- Department of Neurosurgery, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Shoichi Deguchi
- Division of Neurosurgery, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Masahiro Mizoguchi
- Department of Neurosurgery, Graduate School of Medical Sciences Kyushu University, Fukuoka, Japan
| | - Yasutomo Momii
- Department of Neurosurgery, Oita University, Yufu, Oita, Japan
| | - Yoshihiro Muragaki
- Department of Neurosurgery, Tokyo Women's Medical University, Tokyo, Japan
| | - Tatsuya Abe
- Department of Neurosurgery, Faculty of Medicine, Saga University, Saga, Japan
| | - Jiro Akimoto
- Department of Neurosurgery, Tokyo Medical University, Tokyo, Japan
| | - Toshihiko Wakabayashi
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Ryuta Saito
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroshi Haeno
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan.,Corresponding Authors: Kosuke Aoki, Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya 4668550, Japan. Phone: 815-2744-2353; E-mail: ; Hiroshi Haeno, ; and Atsushi Natsume,
| | - Atsushi Natsume
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Aichi, Japan.,Corresponding Authors: Kosuke Aoki, Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya 4668550, Japan. Phone: 815-2744-2353; E-mail: ; Hiroshi Haeno, ; and Atsushi Natsume,
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12
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Adenis L, Plaszczynski S, Grammaticos B, Pallud J, Badoual M. The Effect of Radiotherapy on Diffuse Low-Grade Gliomas Evolution: Confronting Theory with Clinical Data. J Pers Med 2021; 11:jpm11080818. [PMID: 34442462 PMCID: PMC8401413 DOI: 10.3390/jpm11080818] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 12/21/2022] Open
Abstract
Diffuse low-grade gliomas are slowly growing tumors that always recur after treatment. In this paper, we revisit the modeling of the evolution of the tumor radius before and after the radiotherapy process and propose a novel model that is simple yet biologically motivated and that remedies some shortcomings of previously proposed ones. We confront this with clinical data consisting of time series of tumor radii from 43 patient records by using a stochastic optimization technique and obtain very good fits in all cases. Since our model describes the evolution of a tumor from the very first glioma cell, it gives access to the possible age of the tumor. Using the technique of profile likelihood to extract all of the information from the data, we build confidence intervals for the tumor birth age and confirm the fact that low-grade gliomas seem to appear in the late teenage years. Moreover, an approximate analytical expression of the temporal evolution of the tumor radius allows us to explain the correlations observed in the data.
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Affiliation(s)
- Léo Adenis
- CNRS/IN2P3, IJCLab, Université Paris-Saclay, 91405 Orsay, France; (L.A.); (B.G.); (M.B.)
- IJCLab, Université de Paris, 91405 Orsay, France
| | - Stéphane Plaszczynski
- CNRS/IN2P3, IJCLab, Université Paris-Saclay, 91405 Orsay, France; (L.A.); (B.G.); (M.B.)
- IJCLab, Université de Paris, 91405 Orsay, France
- Correspondence:
| | - Basile Grammaticos
- CNRS/IN2P3, IJCLab, Université Paris-Saclay, 91405 Orsay, France; (L.A.); (B.G.); (M.B.)
- IJCLab, Université de Paris, 91405 Orsay, France
| | - Johan Pallud
- Department of Neurosurgery, GHU Paris, Sainte-Anne Hospital, 75014 Paris, France;
- Université de Paris, Sorbonne Paris Cité, 75014 Paris, France
- Inserm, U1266, IMA-Brain, Institut de Psychiatrie et Neurosciences de Paris, 75014 Paris, France
| | - Mathilde Badoual
- CNRS/IN2P3, IJCLab, Université Paris-Saclay, 91405 Orsay, France; (L.A.); (B.G.); (M.B.)
- IJCLab, Université de Paris, 91405 Orsay, France
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13
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Liu H, Shen L, Huang X, Zhang G. Maximal tumor diameter in the preoperative tumor magnetic resonance imaging (MRI) T2 image is associated with prognosis of Grade II Glioma. Medicine (Baltimore) 2021; 100:e24850. [PMID: 33725839 PMCID: PMC7969255 DOI: 10.1097/md.0000000000024850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 01/28/2021] [Indexed: 11/26/2022] Open
Abstract
Factors associated with the prognosis of low-grade glioma remain undefined. In this study, we examined whether the maximal tumor diameter in the preoperative tumor magnetic resonance imaging (MRI) T2 image is associated with the prognosis of grade II gliomas patients, aiming to provide insights into the clinical prediction of patient outcome.We retrospectively analyzed the clinical data of patients with Grade II glioma, who were hospitalized in Xiangya Hospital, Central South University, from 2011 to 2016. Kaplan-Meier and Cox proportional hazards analyses were performed to determine the association between maximal tumor diameter and prognosis.A total of 90 patients with grade II glioma were included in this study. Mean patient age was 37.7 ± 13.0 years, and 58.9% of them were male. Kaplan-Meier survival analysis of overall survival (overall survival [OS], P = .009) and event-free survival (EFS, P = .002) revealed statistically significant differences between the patients with lesion diameter <7 cm and those with lesion diameter ≥7 cm. The maximal tumor diameter in the preoperative tumor MRI T2 image was identified as a prognostic factor of OS (P = .013), while constituting an independent risk factor for EFS (P = .002) alongside elevated histological grade after recurrence (P = .006).The maximal tumor diameter in the preoperative tumor MRI T2 image independently predicts OS and EFS in patients with grade II glioma.
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14
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Martínez-González A, Cabrera R, Lloret M, Lara PC. Pretreatment inflammatory indices predict Bevacizumab response in recurrent Glioma. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2020; 3:623-635. [PMID: 35582438 PMCID: PMC8992487 DOI: 10.20517/cdr.2020.33] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/18/2020] [Accepted: 06/07/2020] [Indexed: 12/26/2022]
Abstract
Aim: It remains unclear what the best therapeutic option for recurrent glioma patients after Stupp treatment is. Bevacizumab (BVZ) is commonly administered in progression, but it appears that only some patients benefit. It would be useful to find biomarkers that determine beforehand who these patients are. Methods: The protocol included 31 high-risk progressing glioma patients after Stupp treatment who received BVZ 5-10 mg/kg every 14 days and temozolomide (3-19 cycles, 150-200 mg five days each 28-day cycle) during a mean of eight cycles of BVZ or until tumor progression or unacceptable toxicity. We analyzed the clinical outcome values of inflammatory indices measured before BVZ administration. Results: Lymphocyte level before BVZ administration was the best independent predictor of overall survival (HR = 0.34; 95%CI: 0.145-0.81; P = 0.015). The area under the receiver operating characteristic (ROC) curve was 0.823, with 1.645 being the optimal cut-off value, and 0.80 and 0.85 the sensitivity and specificity values, respectively. Responder and non-responder survival curves were also significantly different, considering the first and second tertiles as cut-off points. The number of BVZ cycles was not related to lymphopenia. Pretreatment neutrophil, platelet levels, platelet-to-lymphocyte ratio (PLR), and neutrophil-to-lymphocyte ratio (NLR) did not have independent predictive value. Inflammatory variables were not correlated with each other. However, patients with high NLR and PLR simultaneously (double positive PLR-NLR) showed a worse clinical outcome than the rest (P = 0.043). Conclusion: Pretreatment lymphocyte levels and double positive PLR-NLR could be used as non-invasive hematological prognostic markers for recurrent gliomas treated with bevacizumab. A close relationship emerged between inflammation and angiogenesis.
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Affiliation(s)
- Alicia Martínez-González
- Department de Matemáticas, Universidad de Castilla-La Mancha, ETSI Industriales, Avda, Ciudad Real 13071, Spain
| | - Raquel Cabrera
- Oncología Radioterápica Hospital Universitario de Gran Canaria Dr Negrin, Barranco de la Ballena s/n, Las Palmas de Gran Canaria, Las Palmas 35010, Spain
| | - Marta Lloret
- Oncología Radioterápica Hospital Universitario de Gran Canaria Dr Negrin, Barranco de la Ballena s/n, Las Palmas de Gran Canaria, Las Palmas 35010, Spain.,Facultad de Ciencias de la Salud, Universidad de Las Palmas de Gran Canaria, Paseo de Blas Cabrera Felipe, s/n, Las Palmas de Gran Canaria, Las Palmas 35016, Spain.,Fundación Canaria del Instituto Canario de Investigación del Cáncer, Avda de la Trinidad 61 Torre Agustín Arevalo 7 planta La Laguna, Santa Cruz de Tenerife 38204, Spain
| | - Pedro C Lara
- Fundación Canaria del Instituto Canario de Investigación del Cáncer, Avda de la Trinidad 61 Torre Agustín Arevalo 7 planta La Laguna, Santa Cruz de Tenerife 38204, Spain.,San Roque University Hospitals, Dolores de la Rocha, 5, Las Palmas de Gran Canaria, Las Palmas 35001, Spain.,Fernando Pessoa Canarias University, Dolores dela Rocha 14, Las Palmas de Gran Canaria, Las Palmas 35016, Spain
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15
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Suárez-García JG, Hernández-López JM, Moreno-Barbosa E, de Celis-Alonso B. A simple model for glioma grading based on texture analysis applied to conventional brain MRI. PLoS One 2020; 15:e0228972. [PMID: 32413034 PMCID: PMC7228074 DOI: 10.1371/journal.pone.0228972] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/29/2020] [Indexed: 01/26/2023] Open
Abstract
Accuracy of glioma grading is fundamental for the diagnosis, treatment planning and prognosis of patients. The purpose of this work was to develop a low-cost and easy-to-implement classification model which distinguishes low-grade gliomas (LGGs) from high-grade gliomas (HGGs), through texture analysis applied to conventional brain MRI. Different combinations of MRI contrasts (T1Gd and T2) and one segmented glioma region (necrotic and non-enhancing tumor core, NCR/NET) were studied. Texture features obtained from the gray level size zone matrix (GLSZM) were calculated. An under-sampling method was proposed to divide the data into different training subsets and subsequently extract complementary information for the creation of distinct classification models. The sensitivity, specificity and accuracy of the models were calculated, and the best model explicitly reported. The best model included only three texture features and reached a sensitivity, specificity and accuracy of 94.12%, 88.24% and 91.18%, respectively. According to the features of the model, when the NCR/NET region was studied, HGGs had a more heterogeneous texture than LGGs in the T1Gd images, and LGGs had a more heterogeneous texture than HGGs in the T2 images. These novel results partially contrast with results from the literature. The best model proved to be useful for the classification of gliomas. Complementary results showed that the heterogeneity of gliomas depended on the MRI contrast studied. The chosen model stands out as a simple, low-cost, easy-to-implement, reproducible and highly accurate glioma classifier. Importantly, it should be accessible to populations with reduced economic and scientific resources.
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Affiliation(s)
- José Gerardo Suárez-García
- Faculty of Physics and Mathematics, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Puebla, México
| | | | - Eduardo Moreno-Barbosa
- Faculty of Physics and Mathematics, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Puebla, México
| | - Benito de Celis-Alonso
- Faculty of Physics and Mathematics, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Puebla, México
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16
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Cognitive Functions in Repeated Glioma Surgery. Cancers (Basel) 2020; 12:cancers12051077. [PMID: 32357421 PMCID: PMC7281009 DOI: 10.3390/cancers12051077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 04/21/2020] [Indexed: 12/12/2022] Open
Abstract
Low-grade gliomas (LGG) are slow-growing brain tumors infiltrating the central nervous system which tend to recur, often with malignant degeneration after primary treatment. Re-operations are not always recommended due to an assumed higher risk of neurological and cognitive deficits. However, this assumption is relatively ungrounded due to a lack of extensive neuropsychological testing. We retrospectively examined a series of 40 patients with recurrent glioma in eloquent areas of the left hemisphere, who all completed comprehensive pre- (T3) and post-surgical (T4) neuropsychological assessments after a second surgery (4-month follow up). The lesions were most frequent in the left insular cortex and the inferior frontal gyrus. Among this series, in 17 patients the cognitive outcomes were compared before the first surgery (T1), 4 months after the first surgery (T2), and at T3 and T4. There was no significant difference either in the number of patients scoring within the normal range between T3 and T4, or in their level of performance. Further addressing the T1-T4 evolution, there was no significant difference in the number of patients scoring within the normal range. As to their level of performance, the only significant change was in phonological fluency. This longitudinal follow-up study showed that repeated glioma surgery is possible without major damage to cognitive functions in the short-term period (4 months) after surgery.
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17
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Wang Q, He Z, Chen Y. Comprehensive Analysis Reveals a 4-Gene Signature in Predicting Response to Temozolomide in Low-Grade Glioma Patients. Cancer Control 2019; 26:1073274819855118. [PMID: 31167546 PMCID: PMC6558750 DOI: 10.1177/1073274819855118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Low-grade gliomas (LGGs) are a highly heterogeneous group of slow-growing,
lethal, diffusive brain tumors. Temozolomide (TMZ) is a frequently used primary
chemotherapeutic agent for LGGs. Currently there is no consensus as to the
optimal biomarkers to predict the efficacy of TMZ, which calls for
decision-making for each patient while considering molecular profiles. Low-grade
glioma data sets were retrieved from The Cancer Genome Atlas. Cox regression and
survival analyses were applied to identify clinical features significantly
associated with survival. Subsequently, Ordinal logistic regression,
co-expression, and Cox regression analyses were applied to identify genes that
correlate significantly with response rate, disease-free survival, and overall
survival of patients receiving TMZ as primary therapy. Finally, gene expression
and methylation analyses were exploited to explain the mechanism between these
gene expression and TMZ efficacy in LGG patients. Overall survival was
significantly correlated with age, Karnofsky Performance Status score, and
histological grade, but not with IDH1 mutation status. Using 3
distinct efficacy end points, regression and co-expression analyses further
identified a novel 4-gene signature of ASPM, CCNB1, EXO1, and
KIF23 which negatively correlated with response to TMZ
therapy. In addition, expression of the 4-gene signature was associated with
those of genes involved in homologous recombination. Finally, expression and
methylation profiling identified a largely unknown olfactory receptor
OR51F2 as potential mediator of the roles of the 4-gene
signature in reducing TMZ efficacy. Taken together, these findings propose the
4-gene signature as a novel panel of efficacy predictors of TMZ therapy, as well
as potential downstream mechanisms, including homologous recombination, OR51F2,
and DNA methylation independent of MGMT.
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Affiliation(s)
- Qi Wang
- 1 Department of Neurosurgery, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Sichuan, China
| | - Zongze He
- 1 Department of Neurosurgery, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Sichuan, China
| | - Yong Chen
- 1 Department of Neurosurgery, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Sichuan, China
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18
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Budia I, Alvarez-Arenas A, Woolley TE, Calvo GF, Belmonte-Beitia J. Radiation protraction schedules for low-grade gliomas: a comparison between different mathematical models. J R Soc Interface 2019; 16:20190665. [PMID: 31822220 DOI: 10.1098/rsif.2019.0665] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We optimize radiotherapy (RT) administration strategies for treating low-grade gliomas. Specifically, we consider different tumour growth laws, both with and without spatial effects. In each scenario, we find the optimal treatment in the sense of maximizing the overall survival time of a virtual low-grade glioma patient, whose tumour progresses according to the examined growth laws. We discover that an extreme protraction therapeutic strategy, which amounts to substantially extending the time interval between RT sessions, may lead to better tumour control. The clinical implications of our results are also presented.
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Affiliation(s)
- I Budia
- Department of Mathematics and MôLAB-Mathematical Oncology Laboratory, University of Castilla-La Mancha, 13071 Ciudad Real, Spain
| | - A Alvarez-Arenas
- Department of Mathematics and MôLAB-Mathematical Oncology Laboratory, University of Castilla-La Mancha, 13071 Ciudad Real, Spain
| | - T E Woolley
- School of Mathematics, Cardiff University, Senghennydd Road, Cardiff CF24 4AG, UK
| | - G F Calvo
- Department of Mathematics and MôLAB-Mathematical Oncology Laboratory, University of Castilla-La Mancha, 13071 Ciudad Real, Spain
| | - J Belmonte-Beitia
- Department of Mathematics and MôLAB-Mathematical Oncology Laboratory, University of Castilla-La Mancha, 13071 Ciudad Real, Spain
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19
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Pérez-García VM, Ayala-Hernández LE, Belmonte-Beitia J, Schucht P, Murek M, Raabe A, Sepúlveda J. Computational design of improved standardized chemotherapy protocols for grade II oligodendrogliomas. PLoS Comput Biol 2019; 15:e1006778. [PMID: 31306418 PMCID: PMC6629055 DOI: 10.1371/journal.pcbi.1006778] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 06/24/2019] [Indexed: 11/18/2022] Open
Abstract
Here we put forward a mathematical model describing the response of low-grade (WHO grade II) oligodendrogliomas (LGO) to temozolomide (TMZ). The model describes the longitudinal volumetric dynamics of tumor response to TMZ of a cohort of 11 LGO patients treated with TMZ. After finding patient-specific parameters, different therapeutic strategies were tried computationally on the 'in-silico twins' of those patients. Chemotherapy schedules with larger-than-standard rest periods between consecutive cycles had either the same or better long-term efficacy than the standard 28-day cycles. The results were confirmed in a large trial of 2000 virtual patients. These long-cycle schemes would also have reduced toxicity and defer the appearance of resistances. On the basis of those results, a combination scheme consisting of five induction TMZ cycles given monthly plus 12 maintenance cycles given every three months was found to provide substantial survival benefits for the in-silico twins of the 11 LGO patients (median 5.69 years, range: 0.67 to 68.45 years) and in a large virtual trial including 2000 patients. We used 220 sets of experiments in-silico to show that a clinical trial incorporating 100 patients per arm (standard intensive treatment versus 5 + 12 scheme) could demonstrate the superiority of the novel scheme after a follow-up period of 10 years. Thus, the proposed treatment plan could be the basis for a standardized TMZ treatment for LGO patients with survival benefits.
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Affiliation(s)
- Víctor M. Pérez-García
- Department of Mathematics, Mathematical Oncology Laboratory (MOLAB), Universidad de Castilla-La Mancha, Avda. Camilo José Cela, 3, 13071 Ciudad Real, Spain
| | - Luis E. Ayala-Hernández
- Departamento de Ciencias Exactas y Tecnología Centro Universitario de los Lagos, Universidad de Guadalajara, Lagos de Moreno, Mexico
| | - Juan Belmonte-Beitia
- Department of Mathematics, Mathematical Oncology Laboratory (MOLAB), Universidad de Castilla-La Mancha, Avda. Camilo José Cela, 3, 13071 Ciudad Real, Spain
| | - Philippe Schucht
- Universitätsklinik für Neurochirurgie, Bern University Hospital, CH-3010 Bern, Switzerland
| | - Michael Murek
- Universitätsklinik für Neurochirurgie, Bern University Hospital, CH-3010 Bern, Switzerland
| | - Andreas Raabe
- Universitätsklinik für Neurochirurgie, Bern University Hospital, CH-3010 Bern, Switzerland
| | - Juan Sepúlveda
- Oncology Unit, Hospital 12 de Octubre, Avda. de Córdoba s/n, 28041 Madrid, Spain
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20
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Wang L, Wang S, Chen R, Qu X, Chen Y, Huang S, Liu C. Nested Dilation Networks for Brain Tumor Segmentation Based on Magnetic Resonance Imaging. Front Neurosci 2019; 13:285. [PMID: 31024229 PMCID: PMC6460997 DOI: 10.3389/fnins.2019.00285] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/11/2019] [Indexed: 12/11/2022] Open
Abstract
Aim: Brain tumors are among the most fatal cancers worldwide. Diagnosing and manually segmenting tumors are time-consuming clinical tasks, and success strongly depends on the doctor's experience. Automatic quantitative analysis and accurate segmentation of brain tumors are greatly needed for cancer diagnosis. Methods:This paper presents an advanced three-dimensional multimodal segmentation algorithm called nested dilation networks (NDNs). It is inspired by the U-Net architecture, a convolutional neural network (CNN) developed for biomedical image segmentation and is modified to achieve better performance for brain tumor segmentation. Thus, we propose residual blocks nested with dilations (RnD) in the encoding part to enrich the low-level features and use squeeze-and-excitation (SE) blocks in both the encoding and decoding parts to boost significant features. To prove the reliability of the network structure, we compare our results with those of the standard U-Net and its transmutation networks. Different loss functions are considered to cope with class imbalance problems to maximize the brain tumor segmentation results. A cascade training strategy is employed to run NDNs for coarse-to-fine tumor segmentation. This strategy decomposes the multiclass segmentation problem into three binary segmentation problems and trains each task sequentially. Various augmentation techniques are utilized to increase the diversity of the data to avoid overfitting. Results: This approach achieves Dice similarity scores of 0.6652, 0.5880, and 0.6682 for edema, non-enhancing tumors, and enhancing tumors, respectively, in which the Dice loss is used for single-pass training. After cascade training, the Dice similarity scores rise to 0.7043, 0.5889, and 0.7206, respectively. Conclusion: Experiments show that the proposed deep learning algorithm outperforms other U-Net transmutation networks for brain tumor segmentation. Moreover, applying cascade training to NDNs facilitates better performance than other methods. The findings of this study provide considerable insight into the automatic and accurate segmentation of brain tumors.
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Affiliation(s)
- Liansheng Wang
- Fujian Key Laboratory of Sensing and Computing for Smart City, School of Information Science and Engineering, Xiamen University, Xiamen, China
- Department of Computer Science, School of Information Science and Engineering, Xiamen University, Xiamen, China
| | - Shuxin Wang
- Department of Computer Science, School of Information Science and Engineering, Xiamen University, Xiamen, China
| | - Rongzhen Chen
- Department of Computer Science, School of Information Science and Engineering, Xiamen University, Xiamen, China
| | - Xiaobo Qu
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, School of Electronic Science and Engineering (National Model Microelectronics College), Xiamen University, Xiamen, China
| | - Yiping Chen
- Fujian Key Laboratory of Sensing and Computing for Smart City, School of Information Science and Engineering, Xiamen University, Xiamen, China
- Department of Computer Science, School of Information Science and Engineering, Xiamen University, Xiamen, China
| | - Shaohui Huang
- Department of Computer Science, School of Information Science and Engineering, Xiamen University, Xiamen, China
| | - Changhua Liu
- Department of Medical Imaging, Chenggong Hospital Affiliated to Xiamen University, Xiamen, China
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21
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Texture analysis on conventional MRI images accurately predicts early malignant transformation of low-grade gliomas. Eur Radiol 2019; 29:2751-2759. [PMID: 30617484 DOI: 10.1007/s00330-018-5921-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/31/2018] [Accepted: 11/27/2018] [Indexed: 12/20/2022]
Abstract
OBJECTIVES Texture analysis performed on MRI images can provide additional quantitative information that is invisible to human assessment. This study aimed to evaluate the feasibility of texture analysis on preoperative conventional MRI images in predicting early malignant transformation from low- to high-grade glioma and compare its utility to histogram analysis alone. METHODS A total of 68 patients with low-grade glioma (LGG) were included in this study, 15 of which showed malignant transformation. Patients were randomly divided into training (60%) and testing (40%) sets. Texture analyses were performed to obtain the most discriminant factor (MDF) values for both training and testing data. Receiver operating characteristic (ROC) curve analyses were performed on MDF values and 9 histogram parameters in the training data to obtain cutoff values for determining the correct rates of discrimination between two groups in the testing data. RESULTS The ROC analyses on MDF values resulted in an area under the curve (AUC) of 0.90 (sensitivity 85%, specificity 84%) for T2w FLAIR, 0.92 (86%, 94%) for ADC, 0.96 (97%, 84%) for T1w, and 0.82 (78%, 75%) for T1w + Gd and correctly discriminated between the two groups in 93%, 100%, 93%, and 92% of cases in testing data, respectively. In the astrocytoma subgroup, AUCs were 0.92 (88%, 83%) for T2w FLAIR and 0.90 (92%, 74%) for T1w + Gd and correctly discriminated two groups in 100% and 92% of cases. The MDF outperformed all 9 of the histogram parameters. CONCLUSION Texture analysis on conventional preoperative MRI images can accurately predict early malignant transformation of LGGs, which may guide therapeutic planning. KEY POINTS • Texture analysis performed on MRI images can provide additional quantitative information that is invisible to human assessment. • Texture analysis based on conventional preoperative MR images can accurately predict early malignant transformation from low- to high-grade glioma. • Texture analysis is a clinically feasible technique that may provide an alternative and effective way of determining the likelihood of early malignant transformation and help guide therapeutic decisions.
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Chammas M, Saadeh F, Maaliki M, Assi H. Therapeutic Interventions in Adult Low-Grade Gliomas. J Clin Neurol 2018; 15:1-8. [PMID: 30198226 PMCID: PMC6325362 DOI: 10.3988/jcn.2019.15.1.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/18/2018] [Accepted: 06/19/2018] [Indexed: 01/05/2023] Open
Abstract
Treating adult low-grade gliomas (LGGs) is particularly challenging due to the highly infiltrative nature of this type of brain cancer. Although surgery, radiotherapy, and chemotherapy are the mainstay treatment modalities for LGGs, the optimal combination management plan for a particular patient based on individual symptoms and the risk of treatment-induced toxicity remains unclear. This review highlights the competency and limitations of standard treatment options while providing an essential therapeutic update regarding current clinical trials aimed at implementing targeted therapies with morbidity rates lower than those for current LGG treatments and also augmenting the killing of cancerous cells while maintaining an improved quality of life.
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Affiliation(s)
- Majid Chammas
- American University of Beirut, Faculty of Medicine, Beirut, Lebanon
| | - Fadi Saadeh
- American University of Beirut, Faculty of Medicine, Beirut, Lebanon
| | - Maya Maaliki
- American University of Beirut, Faculty of Medicine, Beirut, Lebanon
| | - Hazem Assi
- Department of Internal Medicine, Naef K. Basile Cancer Institute, American University of Beirut Medical Center, Beirut, Lebanon.
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Dufour A, Gontran E, Deroulers C, Varlet P, Pallud J, Grammaticos B, Badoual M. Modeling the dynamics of oligodendrocyte precursor cells and the genesis of gliomas. PLoS Comput Biol 2018; 14:e1005977. [PMID: 29590097 PMCID: PMC5903643 DOI: 10.1371/journal.pcbi.1005977] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 04/17/2018] [Accepted: 01/10/2018] [Indexed: 11/24/2022] Open
Abstract
Oligodendrocyte precursor cells (OPCs) have remarkable properties: they represent the most abundant cycling cell population in the adult normal brain and they manage to achieve a uniform and constant density throughout the adult brain. This equilibrium is obtained by the interplay of four processes: division, differentiation or death, migration and active self-repulsion. They are also strongly suspected to be at the origin of gliomas, when their equilibrium is disrupted. In this article, we present a model of the dynamics of OPCs, first in a normal tissue. This model is based on a cellular automaton and its rules are mimicking the ones that regulate the dynamics of real OPCs. The model is able to reproduce the homeostasis of the cell population, with the maintenance of a constant and uniform cell density and the healing of a lesion. We show that there exists a fair quantitative agreement between the simulated and experimental parameters, such as the cell velocity, the time taken to close a lesion, and the duration of the cell cycle. We present three possible scenarios of disruption of the equilibrium: the appearance of an over-proliferating cell, of a deadless/non-differentiating cell, or of a cell that lost any contact-inhibition. We show that the appearance of an over-proliferating cell is sufficient to trigger the growth of a tumor that has low-grade glioma features: an invasive behaviour, a linear radial growth of the tumor with a corresponding growth velocity of less than 2 mm per year, as well a cell density at the center which exceeds the one in normal tissue by a factor of less than two. The loss of contact inhibition leads to a more high-grade-like glioma. The results of our model contribute to the body of evidence that identify OPCs as possible cells of origin of gliomas. Gliomas are the most common brain tumors and result in more years of life lost than any other tumor. Standard treatments only confer a limited improvement in overall survival, underscoring the need for new therapies. Finding the type of cells at the origin of these tumors could lead to the development of new drugs, specifically targeted towards these cells. The oligodendrocyte precursor cells are suspected to be these cells of origin, because they continue to proliferate through all the adult life. In this article, we present a model of the dynamics of these cells, first in the normal brain, and then we extrapolate our model to the pathological situation. We study several scenarios where, from the normal situation, a cell appears with one property different from those of the normal cells. We show that the alteration of only one of the properties of these cells in the model can lead to the formation of gliomas with different aggressiveness and very similar to real gliomas, reinforcing the suspicion that the precursor cells are at the origin of gliomas.
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Affiliation(s)
- Aloys Dufour
- IMNC Laboratory, CNRS, Univ Paris Saclay, Univ Paris-Sud, Univ Paris Diderot, France
| | - Emilie Gontran
- IMNC Laboratory, CNRS, Univ Paris Saclay, Univ Paris-Sud, Univ Paris Diderot, France
| | - Christophe Deroulers
- IMNC Laboratory, CNRS, Univ Paris Saclay, Univ Paris-Sud, Univ Paris Diderot, France
| | - Pascale Varlet
- Department of Neuropathology, Sainte-Anne Hospital, IMA-Brain, INSERM U894, Univ Paris Descartes, Paris, France
| | - Johan Pallud
- Department of Neurosurgery, Sainte-Anne Hospital, IMA-Brain, INSERM U894, Univ Paris Descartes, Paris, France
| | - Basile Grammaticos
- IMNC Laboratory, CNRS, Univ Paris Saclay, Univ Paris-Sud, Univ Paris Diderot, France
| | - Mathilde Badoual
- IMNC Laboratory, CNRS, Univ Paris Saclay, Univ Paris-Sud, Univ Paris Diderot, France
- * E-mail:
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