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Li M, Liu J, Weng J, Dong G, Chen X, Cui Y, Ren X, Shen S, Jiang H, Zhang X, Zhao X, Li M, Wang X, Ren H, Li Q, Zhang Y, Cheng Q, Yu Y, Lin S. Unveiling hierarchy and spatial distribution of O 6-methylguanine-DNA methyltransferase promoter methylation in World Health Organization grade 2-3 gliomas. Cancer Sci 2024. [PMID: 39101880 DOI: 10.1111/cas.16268] [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: 03/30/2024] [Revised: 06/13/2024] [Accepted: 06/24/2024] [Indexed: 08/06/2024] Open
Abstract
This study investigated the role of O6-methylguanine-DNA methyltransferase promoter (MGMTp) methylation hierarchy and heterogeneity in grade 2-3 gliomas, focusing on variations in chemotherapy benefits and resection dependency. A cohort of 668 newly diagnosed grade 2-3 gliomas, with comprehensive clinical, radiological, and molecular data, formed the basis of this analysis. The extent of resection was categorized into gross total resection (GTR ≥100%), subtotal resection (STR >90%), and partial resection (PR ≤90%). MGMTp methylation levels were examined using quantitative pyrosequencing. Our findings highlighted the critical role of GTR in improving the prognosis for astrocytomas (IDH1/2-mutant and 1p/19q non-codeleted), contrasting with its lesser significance for oligodendrogliomas (IDH1/2 mutation and 1p/19q codeletion). Oligodendrogliomas demonstrated the highest average MGMTp methylation levels (median: 28%), with a predominant percentage of methylated cases (average methylation levels >20%). Astrocytomas were more common in the low-methylated group (10%-20%), while IDH wild-type gliomas were mostly unmethylated (<10%). Spatial distribution analysis revealed a decrement in frontal lobe involvement from methylated, low-methylated to unmethylated cases (72.8%, 59.3%, and 47.8%, respectively). In contrast, low-methylated and unmethylated cases were more likely to invade the temporal-insular region (19.7%, 34.3%, and 40.4%, respectively). Astrocytomas with intermediate MGMTp methylation were notably associated with temporal-insular involvement, potentially indicating a moderate response to temozolomide and underscoring the importance of aggressive resection strategies. In conclusion, our study elucidates the complex interplay of MGMTp methylation hierarchy and heterogeneity among grade 2-3 gliomas, providing insights into why astrocytomas and IDH wild-type lower-grade glioma might derive less benefit from chemotherapy.
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Affiliation(s)
- Mingxiao Li
- Department of Neurosurgery, China-Japan Friendship Hospital, Beijing, China
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jiang Liu
- Department of Neurosurgery, China-Japan Friendship Hospital, Beijing, China
| | - Jiancong Weng
- Department of Neurosurgery, China-Japan Friendship Hospital, Beijing, China
| | - Gehong Dong
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Xuzhu Chen
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yong Cui
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Xiaohui Ren
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Shaoping Shen
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Haihui Jiang
- Department of Neurosurgery, Peking University Third Hospital, Beijing, China
| | - Xiaokang Zhang
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Xuzhe Zhao
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Ming Li
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Xijie Wang
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Hongxiang Ren
- Department of Neurosurgery, China-Japan Friendship Hospital, Beijing, China
| | - Qiang Li
- Department of Neurosurgery, China-Japan Friendship Hospital, Beijing, China
| | - Yulian Zhang
- Department of Neurosurgery, China-Japan Friendship Hospital, Beijing, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yanbing Yu
- Department of Neurosurgery, China-Japan Friendship Hospital, Beijing, China
| | - Song Lin
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
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Liu C, Wang J, Shen J, Chen X, Ji N, Yue S. Accurate and rapid molecular subgrouping of high-grade glioma via deep learning-assisted label-free fiber-optic Raman spectroscopy. PNAS NEXUS 2024; 3:pgae208. [PMID: 38860145 PMCID: PMC11164103 DOI: 10.1093/pnasnexus/pgae208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/17/2024] [Indexed: 06/12/2024]
Abstract
Molecular genetics is highly related with prognosis of high-grade glioma. Accordingly, the latest WHO guideline recommends that molecular subgroups of the genes, including IDH, 1p/19q, MGMT, TERT, EGFR, Chromosome 7/10, CDKN2A/B, need to be detected to better classify glioma and guide surgery and treatment. Unfortunately, there is no preoperative or intraoperative technology available for accurate and comprehensive molecular subgrouping of glioma. Here, we develop a deep learning-assisted fiber-optic Raman diagnostic platform for accurate and rapid molecular subgrouping of high-grade glioma. Specifically, a total of 2,354 fingerprint Raman spectra was obtained from 743 tissue sites (astrocytoma: 151; oligodendroglioma: 150; glioblastoma (GBM): 442) of 44 high-grade glioma patients. The convolutional neural networks (ResNet) model was then established and optimized for molecular subgrouping. The mean area under receiver operating characteristic curves (AUC) for identifying the molecular subgroups of high-grade glioma reached 0.904, with mean sensitivity of 83.3%, mean specificity of 85.0%, mean accuracy of 83.3%, and mean time expense of 10.6 s. The diagnosis performance using ResNet model was shown to be superior to PCA-SVM and UMAP models, suggesting that high dimensional information from Raman spectra would be helpful. In addition, for the molecular subgroups of GBM, the mean AUC reached 0.932, with mean sensitivity of 87.8%, mean specificity of 83.6%, and mean accuracy of 84.1%. Furthermore, according to saliency maps, the specific Raman features corresponding to tumor-associated biomolecules (e.g. nucleic acid, tyrosine, tryptophan, cholesteryl ester, fatty acid, and collagen) were found to contribute to the accurate molecular subgrouping. Collectively, this study opens up new opportunities for accurate and rapid molecular subgrouping of high-grade glioma, which would assist optimal surgical resection and instant post-operative decision-making.
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Affiliation(s)
- Chang Liu
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Xueyuan Road 37, Beijing 100191, China
| | - Jiejun Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, South Fourth Ring West Road 119, Beijing 100050, China
| | - Jianghao Shen
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Xueyuan Road 37, Beijing 100191, China
| | - Xun Chen
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Xueyuan Road 37, Beijing 100191, China
- School of Engineering Medicine, Beihang University, Xueyuan Road 37, Beijing 100191, China
| | - Nan Ji
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, South Fourth Ring West Road 119, Beijing 100050, China
| | - Shuhua Yue
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Xueyuan Road 37, Beijing 100191, China
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Liang B, Wang Y, Huang J, Lin S, Mao G, Zhou Z, Yan W, Shan C, Wu H, Etcheverry A, He Y, Liu F, Kang H, Yin A, Zhang S. Genome-wide DNA methylation analysis identifies potent CpG signature for temzolomide response in non-G-CIMP glioblastomas with unmethylated MGMT promoter: MGMT-dependent roles of GPR81. CNS Neurosci Ther 2024; 30:e14465. [PMID: 37830163 PMCID: PMC11017469 DOI: 10.1111/cns.14465] [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: 08/09/2022] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 10/14/2023] Open
Abstract
PURPOSES To identify potent DNA methylation candidates that could predict response to temozolomide (TMZ) in glioblastomas (GBMs) that do not have glioma-CpGs island methylator phenotype (G-CIMP) but have an unmethylated promoter of O-6-methylguanine-DNA methyltransferase (unMGMT). METHODS The discovery-validation approach was planned incorporating a series of G-CIMP-/unMGMT GBM cohorts with DNA methylation microarray data and clinical information, to construct multi-CpG prediction models. Different bioinformatic and experimental analyses were performed for biological exploration. RESULTS By analyzing discovery sets with radiotherapy (RT) plus TMZ versus RT alone, we identified a panel of 64 TMZ efficacy-related CpGs, from which a 10-CpG risk signature was further constructed. Both the 64-CpG panel and the 10-CpG risk signature were validated showing significant correlations with overall survival of G-CIMP-/unMGMT GBMs when treated with RT/TMZ, rather than RT alone. The 10-CpG risk signature was further observed for aiding TMZ choice by distinguishing differential outcomes to RT/TMZ versus RT within each risk subgroup. Functional studies on GPR81, the gene harboring one of the 10 CpGs, indicated its distinct impacts on TMZ resistance in GBM cells, which may be dependent on the status of MGMT expression. CONCLUSIONS The 64 TMZ efficacy-related CpGs and in particular the 10-CpG risk signature may serve as promising predictive biomarker candidates for guiding optimal usage of TMZ in G-CIMP-/unMGMT GBMs.
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Affiliation(s)
- Bao‐Bao Liang
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Yu‐Hong Wang
- The Emergency DepartmentThe Seventh Medical Center of Chinese PLA General HospitalBeijingChina
| | - Jing‐Jing Huang
- Department of Pediatric SurgeryThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Shuai Lin
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Guo‐Chao Mao
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Zhang‐Jian Zhou
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Wan‐Jun Yan
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Chang‐You Shan
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Hui‐Zi Wu
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Amandine Etcheverry
- CNRS, UMR 6290, Institut de Génétique et Développement de Rennes (IGdR)RennesFrance
| | - Ya‐Long He
- Department of Neurosurgery, Xijing HospitalAir Force Medical UniversityXi'anChina
| | - Fang‐Fang Liu
- Institute of Neurosciences, College of Basic MedicineAir Force Medical UniversityXi'anChina
| | - Hua‐Feng Kang
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - An‐An Yin
- Department of Biochemistry and Molecular BiologyAir Force Medical UniversityXi'anChina
- Department of Plastic and Reconstructive Surgery, Xijing HospitalAir Force Medical UniversityXi'anChina
| | - Shu‐Qun Zhang
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
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Wu X, Tao R, Zhang T, Liu X, Wang J, Zhang Z, Zhao X, Yang P. Biomedical applications of terahertz spectra in clinical and molecular pathology of human glioma. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 285:121933. [PMID: 36208578 DOI: 10.1016/j.saa.2022.121933] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/22/2022] [Accepted: 09/25/2022] [Indexed: 06/16/2023]
Abstract
Gliomas are the most common type of primary tumor originating in the central nervous system of adults. Tumor histological type, pathological grade, and molecular pathology are significant prognosis and predictive factors. In this study, we were aiming to predict histological type and molecular pathological features based on terahertz time-domain spectroscopy technology. Nine gliomas with different grades, one meningioma, and one lymphoma were enrolled. There were significant differences in terahertz absorption coefficient between normal brain tissue, tumoral-periphery, and tumoral-center tissue in specific frequency bands (0.2-1.4 THz). Histological type, pathological grade, and glioma-specific biomarkers were closely related to the terahertz absorption coefficient in both tumoral-periphery and tumoral-center tissues. Interestingly, tumoral-periphery showed more obvious differences than tumoral-center tissues in almost all aspects. All the results show that the terahertz technology has potential application value in the intraoperative real-time glioma recognition and diagnosis of glioma histological and molecular pathological features.
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Affiliation(s)
- Xianhao Wu
- School of Automation and Electrical Engineering, University of Science and Technology Beijing, Beijing, China
| | - Rui Tao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Tianyao Zhang
- School of Automation and Electrical Engineering, University of Science and Technology Beijing, Beijing, China
| | - Xing Liu
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jiangfei Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Zhaohui Zhang
- School of Automation and Electrical Engineering, University of Science and Technology Beijing, Beijing, China
| | - Xiaoyan Zhao
- School of Automation and Electrical Engineering, University of Science and Technology Beijing, Beijing, China.
| | - Pei Yang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.
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Chai R, Fang S, Pang B, Liu Y, Wang Y, Zhang W, Jiang T. Molecular pathology and clinical implications of diffuse glioma. Chin Med J (Engl) 2022; 135:2914-2925. [PMID: 36728558 PMCID: PMC10106158 DOI: 10.1097/cm9.0000000000002446] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Indexed: 02/03/2023] Open
Abstract
ABSTRACT The prognosis for diffusely infiltrating gliomas at World Health Organization (WHO) grade 2-4 remains dismal due to their heterogeneity. The rapid development of genome-wide molecular-profiling-associated studies has greatly promoted the accuracy of glioma classification. Thus, the latest version of the WHO classification of the central nervous system tumors published in 2021 has incorporated more molecular biomarkers together with histological features for the diagnosis of gliomas. Advanced usage of molecular pathology in clinical diagnostic practice provides also new opportunities for the therapy of patients with glioma, including surgery, radiotherapy and chemotherapy, targeted therapy, immunotherapy, and more precision clinical trials. Herein, we highlight the updates in the classification of gliomas according to the latest WHO guidelines and summarize the clinically relevant molecular markers by focusing on their applications in clinical practice. We also review the advances in molecular features of gliomas, which can facilitate the development of glioma therapies, thereby discussing the challenges and future directions of molecular pathology toward precision medicine for patients with glioma.
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Affiliation(s)
- Ruichao Chai
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Shengyu Fang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Bo Pang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Yuqing Liu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Yongzhi Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Wei Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Tao Jiang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- Research Unit of Accurate Diagnosis, Treatment, and Translational Medicine of Brain Tumors, Chinese Academy of Medical Sciences, Beijing 100070, China
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Volumetric Analysis of Glioblastoma for Determining Which CpG Sites Should Be Tested by Pyrosequencing to Predict Temozolomide Efficacy. Biomolecules 2022; 12:biom12101379. [DOI: 10.3390/biom12101379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/18/2022] [Accepted: 09/24/2022] [Indexed: 11/16/2022] Open
Abstract
The aim of the present study was to determine which individual or combined CpG sites among O6-methylguanine DNA methyltransferase CpG 74–89 in glioblastoma mainly affects the response to temozolomide resulting from CpG methylation using statistical analyses focused on the tumor volume ratio (TVR). We retrospectively examined 44 patients who had postoperative volumetrically measurable residual tumor tissue and received adjuvant temozolomide therapy for at least 6 months after initial chemoradiotherapy. TVR was defined as the tumor volume 6 months after the initial chemoradiotherapy divided by that before the start of chemoradiotherapy. Predictive values for TVR as a response to adjuvant therapy were compared among the averaged methylation percentages of individual or combined CpGs using the receiver operating characteristic curve. Our data revealed that combined CpG 78 and 79 showed a high area under the curve (AUC) and a positive likelihood ratio and that combined CpG 76–79 showed the highest AUC among all combinations. AUCs of consecutive CpG combinations tended to be higher for CpG 74–82 in exon 1 than for CpG 83–89 in intron 1. In conclusion, the methylation status at CpG sites in exon 1 was strongly associated with TVR reduction in glioblastoma.
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MGMT and Whole-Genome DNA Methylation Impacts on Diagnosis, Prognosis and Therapy of Glioblastoma Multiforme. Int J Mol Sci 2022; 23:ijms23137148. [PMID: 35806153 PMCID: PMC9266959 DOI: 10.3390/ijms23137148] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/21/2022] [Accepted: 06/23/2022] [Indexed: 12/15/2022] Open
Abstract
Epigenetic changes in DNA methylation contribute to the development of many diseases, including cancer. In glioblastoma multiforme, the most prevalent primary brain cancer and an incurable tumor with a median survival time of 15 months, a single epigenetic modification, the methylation of the O6-Methylguanine-DNA Methyltransferase (MGMT) gene, is a valid biomarker for predicting response to therapy with alkylating agents and also, independently, prognosis. More recently, the progress from single gene to whole-genome analysis of DNA methylation has allowed a better subclassification of glioblastomas. Here, we review the clinically relevant information that can be obtained by studying MGMT gene and whole-genome DNA methylation changes in glioblastomas, also highlighting benefits, including those of liquid biopsy, and pitfalls of the different detection methods. Finally, we discuss how changes in DNA methylation, especially in glioblastomas bearing mutations in the Isocitrate Dehydrogenase (IDH) 1 and 2 genes, can be exploited as targets for tailoring therapy.
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Chen Z, Zhang Z, Ding W, Zhang JH, Tan ZL, Mei YR, He W, Wang XJ. Expression and Potential Biomarkers of Regulators for M7G RNA Modification in Gliomas. Front Neurol 2022; 13:886246. [PMID: 35614925 PMCID: PMC9124973 DOI: 10.3389/fneur.2022.886246] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/11/2022] [Indexed: 12/15/2022] Open
Abstract
Gliomas are the most frequent primary malignant brain tumors of the central nervous system, causing significant impairment and death. There is mounting evidence that N7 methylguanosine (m7G) RNA dysmethylation plays a significant role in the development and progression of cancer. However, the expression patterns and function of the m7G RNA methylation regulator in gliomas are yet unknown. The goal of this study was to examine the expression patterns of 31 critical regulators linked with m7G RNA methylation and their prognostic significance in gliomas. To begin, we systematically analyzed patient clinical and prognostic data and mRNA gene expression data from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. We found that 17 key regulators of m7G RNA methylation showed significantly higher expression levels in gliomas. We then divided the sample into two subgroups by consensus clustering. Cluster 2 had a poorer prognosis than cluster 1 and was associated with a higher histological grade. In addition, cluster 2 was significantly enriched for cancer-related pathways. Based on this discovery, we developed a risk model involving three m7G methylation regulators. Patients were divided into high-risk and low-risk groups based on risk scores. Overall survival (OS) was significantly lower in the high-risk group than in the low-risk group. Further analysis showed that the risk score was an independent prognostic factor for gliomas.
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Affiliation(s)
- Zhen Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhe Zhang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wei Ding
- Yifeng County People's Hospital, Yichun City, China
| | | | - Zi-long Tan
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yu-ran Mei
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wei He
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Wei He
| | - Xiao-jing Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Department of Neurology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- *Correspondence: Xiao-jing Wang
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MGMT gene promoter methylation by pyrosequencing method correlates volumetric response and neurological status in IDH wild-type glioblastomas. J Neurooncol 2022; 157:561-571. [PMID: 35397757 PMCID: PMC9072488 DOI: 10.1007/s11060-022-03999-5] [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: 02/25/2022] [Accepted: 03/24/2022] [Indexed: 01/03/2023]
Abstract
Purpose Although the usefulness of O6-methylguanine DNA methyltransferase (MGMT) promoter methylation analysis for predicting response to chemoradiotherapy and the prognosis of patients with glioblastoma has been widely reported, there is still no consensus regarding how to define MGMT promoter methylation percentage (MGMTpm%) cutoffs by pyrosequencing method. The aim of this study was to determine the optimal cutoff value of MGMT promoter methylation status using volumetric analysis focused on the tumor volume ratio (TVR) measured by MRI. Methods This retrospective study included newly diagnosed IDH wild-type glioblastoma patients with residual tumor after surgery, followed by local radiotherapy with temozolomide. TVR was defined as the tumor volume at 6 months after the initial chemoradiotherapy administration divided by the tumor volume before the start of therapy. The mean MGMTpm% of 16 CpG islands (74–89) was analyzed using pyrosequencing. We statistically analyzed the correlation between MGMTpm%, TVR, and change in Karnofsky performance status. Results The study included 44 patients with residual tumors. Thirteen (92.9%) of 14 patients with MGMTpm% ≥ 23.9% showed 50% or more volumetric response, leading to prolonged survival, and 17 (70.8%) of 24 patients with MGMTpm% < 8.2% had progressive disease after initial chemoradiotherapy administration. Three (50.0%) of six patients with MGMTpm% 8.2% to < 23.9% had stable disease or partial response. Conclusion Evaluation of MGMTpm% by pyrosequencing is important in predicting the volumetric response and prognosis of glioblastoma patients with residual tumors.
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Trillo Aliaga P, Spada F, Peveri G, Bagnardi V, Fumagalli C, Laffi A, Rubino M, Gervaso L, Guerini Rocco E, Pisa E, Curigliano G, Fazio N. Should temozolomide be used on the basis of O 6-methylguanine DNA methyltransferase status in patients with advanced neuroendocrine tumors? A systematic review and meta-analysis. Cancer Treat Rev 2021; 99:102261. [PMID: 34332293 DOI: 10.1016/j.ctrv.2021.102261] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Temozolomide (TEM) is an active treatment in metastatic neuroendocrine tumors (NETs). Patients affected by glioblastoma multiforme or advanced melanoma treated with TEM who have deficiency of O6-methylguanine DNA methyltransferase (MGMT) have a better responses and survival. However, the predictive role of MGMT in patients with NETs treated with TEM is still debated. METHODS We conducted a systematic review of the literature and meta-analysis, based on PRISMA methodology, searching in the main databases (PubMed, Embase, Scopus, Web of Science, Cochrane Library and clinical trial.gov) and the proceedings of the main international congresses, until April 26, 2021. RESULTS Twelve out of 616 articles were selected for our analysis, regarding a total of 858 NET patients treated with TEM-based chemotherapy. The status of MGMT had been tested in 513 (60%) patients, using various methods. The pooled overall response rate (ORR) was higher in MGMT-deficient compared with MGMT-proficient NETs, with a risk difference of 0.31 (95% confidence interval, CI: 0.13-0.50; p < 0.001; I2: 73%) and risk ratio of 2.29 (95% CI: 1.34-3.91; p < 0.001; I2: 55%). The pooled progression free survival (PFS) (hazard ratio, HR = 0.56; 95% CI: 0.43-0.74; p < 0.001) and overall survival (OS) (HR = 0.41; 95% CI: 0.20-0.62; p = 0.011) were longer in MGMT-deficient versus MGMT-proficient NETs. CONCLUSIONS Our meta-analysis suggested that MGMT status may be predictive of TEM efficacy. However, due to the high heterogeneity of the evaluated studies the risk of biases should be considered. On this hypothesis future homogeneous prospective studies are warranted.
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Affiliation(s)
- P Trillo Aliaga
- Division of New Drugs and Early Drug Development, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hematology, University of Milan, Milan, Italy
| | - F Spada
- Division of Gastrointestinal Medical Oncology and Neuroendocrine Tumors, European Institute of Oncology IRCCS, Milan, Italy
| | - G Peveri
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - V Bagnardi
- Department of Statistics and Quantitative Methods, University of Milan-Bicocca, Milan, Italy
| | - C Fumagalli
- Division of Pathology, European Institute of Oncology IRCCS, Milan, Italy
| | - A Laffi
- Division of Gastrointestinal Medical Oncology and Neuroendocrine Tumors, European Institute of Oncology IRCCS, Milan, Italy
| | - M Rubino
- Division of Gastrointestinal Medical Oncology and Neuroendocrine Tumors, European Institute of Oncology IRCCS, Milan, Italy
| | - L Gervaso
- Division of Gastrointestinal Medical Oncology and Neuroendocrine Tumors, European Institute of Oncology IRCCS, Milan, Italy; Molecular Medicine Department, University of Pavia, Pavia, Italy
| | - E Guerini Rocco
- Division of Pathology, European Institute of Oncology IRCCS, Milan, Italy
| | - E Pisa
- Division of Pathology, European Institute of Oncology IRCCS, Milan, Italy
| | - G Curigliano
- Division of New Drugs and Early Drug Development, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hematology, University of Milan, Milan, Italy
| | - N Fazio
- IEO, European Institute of Oncology, IRCCS, Milan, Italy.
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11
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Li M, Dong G, Zhang W, Ren X, Jiang H, Yang C, Zhao X, Zhu Q, Li M, Chen H, Yu K, Cui Y, Song L. Combining MGMT promoter pyrosequencing and protein expression to optimize prognosis stratification in glioblastoma. Cancer Sci 2021; 112:3699-3710. [PMID: 34115910 PMCID: PMC8409410 DOI: 10.1111/cas.15024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/16/2021] [Accepted: 06/10/2021] [Indexed: 12/12/2022] Open
Abstract
Pyrosequencing (PSQ) represents the golden standard for MGMT promoter status determination. Binary interpretation of results based on the threshold from the average of several CpGs tested would neglect the existence of the “gray zone”. How to define the gray zone and reclassify patients in this subgroup remains to be elucidated. A consecutive cohort of 312 primary glioblastoma patients were enrolled. CpGs 74‐81 in the promoter region of MGMT were tested by PSQ and the protein expression was assessed by immunohistochemistry (IHC). Receiver operating characteristic curves were constructed to calculate the area under the curves (AUC). Kaplan‐Meier plots were used to estimate the survival rate of patients compared by the log‐rank test. The optimal threshold of each individual CpG differed from 5% to 11%. Patients could be separated into the hypomethylated subgroup (all CpGs tested below the corresponding optimal thresholds, n = 126, 40.4%), hypermethylated subgroup (all CpGs tested above the corresponding optimal thresholds, n = 108, 34.6%), and the gray zone subgroup (remaining patients, n = 78, 25.0%). Patients in the gray zone harbored an intermediate prognosis. The IHC score instead of the average methylation levels could successfully predict the prognosis for the gray zone (AUC for overall survival, 0.653 and 0.519, respectively). Combining PSQ and IHC significantly improved the efficiency of survival prediction (AUC: 0.662, 0.648, and 0.720 for PSQ, IHC, and combined, respectively). Immunohistochemistry is a robust method to predict prognosis for patients in the gray zone defined by PSQ. Combining PSQ and IHC could significantly improve the predictive ability for clinical outcomes.
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Affiliation(s)
- Mingxiao Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Gehong Dong
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Weiwei Zhang
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Xiaohui Ren
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Haihui Jiang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Chuanwei Yang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Xuzhe Zhao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Qinghui Zhu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ming Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Hongyan Chen
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Kefu Yu
- Department of Pharmacy, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yong Cui
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Lin Song
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Center of Brain Tumor, Institute for Brain Disorders and Beijing Key Laboratory of Brain Tumor, Beijing, China.,Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
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12
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Cheng M, Sun L, Huang K, Yue X, Chen J, Zhang Z, Zhao B, Bian E. A Signature of Nine lncRNA Methylated Genes Predicts Survival in Patients With Glioma. Front Oncol 2021; 11:646409. [PMID: 33828990 PMCID: PMC8019920 DOI: 10.3389/fonc.2021.646409] [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: 12/26/2020] [Accepted: 02/24/2021] [Indexed: 12/20/2022] Open
Abstract
Glioma is one of the most common malignant tumors of the central nervous system, and its prognosis is extremely poor. Aberrant methylation of lncRNA promoter region is significantly associated with the prognosis of glioma patients. In this study, we investigated the potential impact of methylation of lncRNA promoter region in glioma patients to establish a signature of nine lncRNA methylated genes for determining glioma patient prognosis. Methylation data and clinical follow-up data were obtained from The Cancer Genome Atlas (TCGA). The multistep screening strategy identified nine lncRNA methylated genes that were significantly associated with the overall survival (OS) of glioma patients. Subsequently, we constructed a risk signature that containing nine lncRNA methylated genes. The risk signature successfully divided the glioma patients into high-risk and low-risk groups. Compared with the low-risk group, the high-risk group had a worse prognosis, higher glioma grade, and older age. Furthermore, we identified two lncRNAs termed PCBP1-AS1 and LINC02875 that may be involved in the malignant progression of glioma cells by using the TCGA database. Loss-of-function assays confirmed that knockdown of PCBP1-AS1 and LINC02875 inhibited the proliferation, migration, and invasion of glioma cells. Therefore, the nine lncRNA methylated genes signature may provide a novel predictor and therapeutic target for glioma patients.
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Affiliation(s)
- Meng Cheng
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Libo Sun
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Kebing Huang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Xiaoyu Yue
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Jie Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Zhengwei Zhang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Bing Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Erbao Bian
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
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13
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Rosas-Alonso R, Colmenarejo-Fernandez J, Pernia O, Rodriguez-Antolín C, Esteban I, Ghanem I, Sanchez-Cabrero D, Losantos-Garcia I, Palacios-Zambrano S, Moreno-Bueno G, de Castro J, Martinez-Marin V, Ibanez-de-Caceres I. Clinical validation of a novel quantitative assay for the detection of MGMT methylation in glioblastoma patients. Clin Epigenetics 2021; 13:52. [PMID: 33750464 PMCID: PMC7941980 DOI: 10.1186/s13148-021-01044-2] [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: 11/11/2020] [Accepted: 02/28/2021] [Indexed: 12/03/2022] Open
Abstract
Background The promoter hypermethylation of the methylguanine-DNA methyltransferase gene is a frequently used biomarker in daily clinical practice as it is associated with a favorable prognosis in glioblastoma patients treated with temozolamide. Due to the absence of adequately standardized techniques, international harmonization of the MGMT methylation biomarker is still an unmet clinical need for the diagnosis and treatment of glioblastoma patients. Results In this study we carried out a clinical validation of a quantitative assay for MGMT methylation detection by comparing a novel quantitative MSP using double-probe (dp_qMSP) with the conventional MSP in 100 FFPE glioblastoma samples. We performed both technologies and established the best cutoff for the identification of positive-methylated samples using the quantitative data obtained from dp_qMSP. Kaplan–Meier curves and ROC time dependent curves were employed for the comparison of both methodologies. Conclusions We obtained similar results using both assays in the same cohort of patients, in terms of progression free survival and overall survival according to Kaplan–Meier curves. In addition, the results of ROC(t) curves showed that dp_qMSP increases the area under curve time-dependent in comparison with MSP for predicting progression free survival and overall survival over time. We concluded that dp_qMSP is an alternative methodology compatible with the results obtained with the conventional MSP. Our assay will improve the therapeutic management of glioblastoma patients, being a more sensitive and competitive alternative methodology that ensures the standardization of the MGMT-biomarker making it reliable and suitable for clinical use. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01044-2.
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Affiliation(s)
- Rocio Rosas-Alonso
- Epigenetics Laboratory. INGEMM, Paseo La Castellana 261. Edificio Bloque Quirúrgico Planta -2. University Hospital La Paz, 28046, Madrid, Spain. .,Experimental Therapies and Novel Biomarkers in Cancer. IdiPAZ, Madrid, Spain.
| | - Julian Colmenarejo-Fernandez
- Epigenetics Laboratory. INGEMM, Paseo La Castellana 261. Edificio Bloque Quirúrgico Planta -2. University Hospital La Paz, 28046, Madrid, Spain.,Experimental Therapies and Novel Biomarkers in Cancer. IdiPAZ, Madrid, Spain
| | - Olga Pernia
- Epigenetics Laboratory. INGEMM, Paseo La Castellana 261. Edificio Bloque Quirúrgico Planta -2. University Hospital La Paz, 28046, Madrid, Spain.,Experimental Therapies and Novel Biomarkers in Cancer. IdiPAZ, Madrid, Spain
| | - Carlos Rodriguez-Antolín
- Epigenetics Laboratory. INGEMM, Paseo La Castellana 261. Edificio Bloque Quirúrgico Planta -2. University Hospital La Paz, 28046, Madrid, Spain.,Experimental Therapies and Novel Biomarkers in Cancer. IdiPAZ, Madrid, Spain
| | - Isabel Esteban
- Experimental Therapies and Novel Biomarkers in Cancer. IdiPAZ, Madrid, Spain.,Pathology Department, La Paz University Hospital, Madrid, Spain
| | - Ismael Ghanem
- Medical Oncology Department, La Paz University Hospital, Madrid, Spain
| | | | | | | | - Gema Moreno-Bueno
- MD Anderson Cancer Center, Madrid, Spain.,Biochemistry Department, UAM/ IIBm (CSIC-UAM), IdiPaz, Fundación MD Anderson Internacional, Madrid, Spain.,CIBERONC, Madrid, Spain
| | - Javier de Castro
- Experimental Therapies and Novel Biomarkers in Cancer. IdiPAZ, Madrid, Spain.,Medical Oncology Department, La Paz University Hospital, Madrid, Spain
| | | | - Inmaculada Ibanez-de-Caceres
- Epigenetics Laboratory. INGEMM, Paseo La Castellana 261. Edificio Bloque Quirúrgico Planta -2. University Hospital La Paz, 28046, Madrid, Spain. .,Experimental Therapies and Novel Biomarkers in Cancer. IdiPAZ, Madrid, Spain.
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14
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Chai R, Li G, Liu Y, Zhang K, Zhao Z, Wu F, Chang Y, Pang B, Li J, Li Y, Jiang T, Wang Y. Predictive value of MGMT promoter methylation on the survival of TMZ treated IDH-mutant glioblastoma. Cancer Biol Med 2021; 18:272-282. [PMID: 33628600 PMCID: PMC7877176 DOI: 10.20892/j.issn.2095-3941.2020.0179] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/11/2020] [Indexed: 12/14/2022] Open
Abstract
Objective O6methylguanine-DNA methyltransferase (MGMT) promoter methylation is a biomarker widely used to predict the sensitivity of IDH-wildtype glioblastoma to temozolomide therapy. Given that the IDH status has critical effects on the survival and epigenetic features of glioblastoma, we aimed to assess the role of MGMT promoter methylation in IDH-mutant glioblastoma. Methods This study included 187 IDH-mutant glioblastomas and used 173 IDH-wildtype glioblastomas for comparison. Kaplan-Meier curves and multivariate Cox regression were used to study the predictive effects. Results Compared with IDH-wildtype glioblastomas, IDH-mutant glioblastomas showed significantly higher (P < 0.0001) MGMT promoter methylation. We demonstrated that MGMT promoter methylation status, as determined by a high cutoff value (≥30%) in pyrosequencing, could be used to significantly stratify the survival of 50 IDH-mutant glioblastomas receiving temozolomide therapy (cohort A); this result was validated in another cohort of 25 IDH-mutant glioblastomas (cohort B). The median progression-free survival and median overall survival in cohort A were 9.33 and 13.76 months for unmethylated cases, and 18.37 and 41.61 months for methylated cases, and in cohort B were 6.97 and 9.10 months for unmethylated cases, and 23.40 and 26.40 months for methylated cases. In addition, we confirmed that the MGMT promoter methylation was significantly (P = 0.0001) correlated with longer OS in IDH-mutant patients with GBM, independently of age, gender distribution, tumor type (primary or recurrent/secondary), and the extent of resection. Conclusions MGMT promoter methylation has predictive value in IDH-mutant glioblastoma, but its cutoff value should be higher than that for IDH-wildtype glioblastoma.
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Affiliation(s)
- Ruichao Chai
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute; Chinese Glioma Genome Atlas Network (CGGA), Capital Medical University, Beijing 100070, China
| | - Guanzhang Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute; Chinese Glioma Genome Atlas Network (CGGA), Capital Medical University, Beijing 100070, China
| | - Yuqing Liu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute; Chinese Glioma Genome Atlas Network (CGGA), Capital Medical University, Beijing 100070, China
| | - Kenan Zhang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute; Chinese Glioma Genome Atlas Network (CGGA), Capital Medical University, Beijing 100070, China
| | - Zheng Zhao
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute; Chinese Glioma Genome Atlas Network (CGGA), Capital Medical University, Beijing 100070, China
| | - Fan Wu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute; Chinese Glioma Genome Atlas Network (CGGA), Capital Medical University, Beijing 100070, China
| | - Yuzhou Chang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Bo Pang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute; Chinese Glioma Genome Atlas Network (CGGA), Capital Medical University, Beijing 100070, China
| | - Jingjun Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute; Chinese Glioma Genome Atlas Network (CGGA), Capital Medical University, Beijing 100070, China
| | - Yangfang Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute; Chinese Glioma Genome Atlas Network (CGGA), Capital Medical University, Beijing 100070, China
| | - Tao Jiang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute; Chinese Glioma Genome Atlas Network (CGGA), Capital Medical University, Beijing 100070, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Yongzhi Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute; Chinese Glioma Genome Atlas Network (CGGA), Capital Medical University, Beijing 100070, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
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15
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何 建, 李 晓, 吕 梦, 王 珏, 唐 健, 罗 胜, 钱 源. [ALKBH5 suppresses migration and invasion of human trophoblast cells by inhibiting epithelial-mesenchymal transition]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2020; 40:1720-1725. [PMID: 33380386 PMCID: PMC7835694 DOI: 10.12122/j.issn.1673-4254.2020.12.04] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To investigate the effects of ALKBH5 on migration, invasion and epithelial-mesenchymal transition (EMT) of human trophoblast cells. METHODS The expression plasmid of ALKBH5 or a negative control plasmid (ALKBH5-NC) was transfected in human trophoblast HTR-8 /SVneo cells, and the expressions of ALKBH5 mRNA and protein were detected by qRT-PCR and Western blotting. Transwell assay was used to assess the changes in migration and invasion abilities of the trophoblast cells after the transfection. Western blotting was performed to detect the expressions of EMT-related proteins in the cells including vimentin, fibronectin, E-cadherin, N-cadherin, MMP9 and MMP2. RESULTS ALKBH5 mRNA and protein expressions were significantly higher in ALKBH5 group than in the control group (P < 0.05). Over-expression of ALKBH5 significantly attenuated migration and invasion abilities of HTR-8/Svneo cells (P < 0.05). Compared with the control cells, the cells overexpressing ALKBH5 showed an up-regulated expression of E-cadherin and down-regulated expressions of vimentin, fibronectin, N-cadherin, MMP9 and MMP2 (P < 0.05). CONCLUSIONS ALKBH5 is involved in the pathogenesis of preeclampsia by inhibiting EMT of trophoblast cells and hence reducing their migration and invasion abilities.
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Affiliation(s)
- 建萍 何
- 昆明市妇幼保健院医学遗传与产前诊断科,云南 昆明 650032Department of Medical Genetics and Prenatal Diagnosis, Kunming Maternal and Child Healthcare Hospital, Kunming 650031, China
| | - 晓娟 李
- 昆明医科大学第一附属医院产科,云南 昆明 650032Department of Obstetrics, First Affiliated Hospital of Kunming Medical University, Kunming 650032, China
- 云南省第一人民医院产科,云南 昆明 650032Department of Obstetrics, First People's Hospital of Yunnan Province, Kunming 650032, China
| | - 梦欣 吕
- 昆明市妇幼保健院医学遗传与产前诊断科,云南 昆明 650032Department of Medical Genetics and Prenatal Diagnosis, Kunming Maternal and Child Healthcare Hospital, Kunming 650031, China
| | - 珏 王
- 昆明医科大学第一附属医院医学检验科产前诊断室,云南 昆明 650032Prenatal Diagnosis Room, Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming 650032, China
| | - 健 唐
- 昆明市妇幼保健院医学遗传与产前诊断科,云南 昆明 650032Department of Medical Genetics and Prenatal Diagnosis, Kunming Maternal and Child Healthcare Hospital, Kunming 650031, China
| | - 胜军 罗
- 昆明市妇幼保健院医学遗传与产前诊断科,云南 昆明 650032Department of Medical Genetics and Prenatal Diagnosis, Kunming Maternal and Child Healthcare Hospital, Kunming 650031, China
| | - 源 钱
- 昆明市妇幼保健院医学遗传与产前诊断科,云南 昆明 650032Department of Medical Genetics and Prenatal Diagnosis, Kunming Maternal and Child Healthcare Hospital, Kunming 650031, China
- 昆明医科大学第一附属医院产科,云南 昆明 650032Department of Obstetrics, First Affiliated Hospital of Kunming Medical University, Kunming 650032, China
- 昆明医科大学第一附属医院医学检验科产前诊断室,云南 昆明 650032Prenatal Diagnosis Room, Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming 650032, China
- 云南省检验医学重点实验室,云南 昆明 650032Key Laboratory of Laboratory Medicine of Yunnan Province, Kunming 650032, China
- 云南省实验诊断研究所,云南 昆明 650032Institute of Practical Diagnosis of Yunnan Province, Kunming 650032, China; 7Research Institute in Yunnan Province, Kunming 650032, China
- 云南省内设研究机构,云南 昆明 650032Research Institute in Yunnan Province, Kunming 650032, China
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16
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Chang YZ, Li GZ, Pang B, Zhang KN, Zhang XH, Wang YZ, Jiang ZL, Chai RC. Transcriptional Characteristics of IDH-Wild Type Glioma Subgroups Highlight the Biological Processes Underlying Heterogeneity of IDH-Wild Type WHO Grade IV Gliomas. Front Cell Dev Biol 2020; 8:580464. [PMID: 33195221 PMCID: PMC7642517 DOI: 10.3389/fcell.2020.580464] [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: 07/06/2020] [Accepted: 09/24/2020] [Indexed: 12/11/2022] Open
Abstract
Isocitric dehydrogenase (IDH)-wild type diffuse gliomas, which have a poorer prognosis than their IDH-mutant counterparts, are also accompanied with high heterogeneity. Here, we aimed to identify the key biological processes associated with the three groups of IDH-wild type diffuse gliomas in 323 patients. By The Consortium to Inform Molecular and Practical Approaches to CNS Tumor Taxonomy (cIMPACT-NOW) update 3 recommendation, the three groups are Group A, diffuse astrocytic glioma, World Health Organization (WHO) grade II/III; Group B, diffuse astrocytic glioma, with one (or more) of the three genetic alterations: TERT promoter mutation, EGFR gene amplification, gain of chromosome 7 combined with loss of chromosome 10, WHO grade IV; and Group C, glioblastoma, WHO grade IV. Consistent with their histologic and genetic molecular features, we successfully identified that biological activities associated with “cell cycle” and “cell mitosis” are significantly elevated in Group B compared with Group A; microenvironment-related hallmarks “angiogenesis” and “hypoxia,” and biological processes of “extracellular matrix,” “immune response,” and “positive regulation of transcriptional activities” were more enriched in Group C than Group B. We also constructed a nine-gene signature from differentially expressed genes among the three groups to further stratify the WHO grade IV gliomas (Groups B and C) whose survival cannot be clearly stratified by current classification systems. This signature was an independent prognosis factor for WHO grade IV gliomas and had better prognostic value than other known factors in both training and validation dataset. In addition, the signature risk score was positively correlated with the amount of infiltrated immune cells, expression of immune checkpoints, and the genes enriched in biological processes of “immune response,” “cell cycle,” and “extracellular matrix.” The bioinformatic analysis results were also validated by immunohistochemistry and patient-derived cell proliferation assay. Overall, our findings revealed the key biological processes underlying the new classifications of IDH-wild type diffuse glioma. Meanwhile, we constructed a signature, which could properly stratify the prognosis, cell proliferation activates, extracellular matrix-mediated biological activities, and immune-microenvironment of IDH-wild type WHO grade IV gliomas.
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Affiliation(s)
- Yu-Zhou Chang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Guan-Zhang Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network, Beijing, China
| | - Bo Pang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network, Beijing, China
| | - Ke-Nan Zhang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network, Beijing, China
| | - Xiao-Hui Zhang
- Department of Neurosurgery, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yong-Zhi Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network, Beijing, China
| | - Zhong-Li Jiang
- Department of Neurosurgery, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Rui-Chao Chai
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network, Beijing, China
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17
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Brigliadori G, Goffredo G, Bartolini D, Tosatto L, Gurrieri L, Mercatali L, Ibrahim T. Influence of Intratumor Heterogeneity on the Predictivity of MGMT Gene Promoter Methylation Status in Glioblastoma. Front Oncol 2020; 10:533000. [PMID: 33194592 PMCID: PMC7606920 DOI: 10.3389/fonc.2020.533000] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 09/08/2020] [Indexed: 11/13/2022] Open
Abstract
Glioblastoma is the most aggressive tumor of the central nervous system. Prognosis is poor, even in the presence of a methylated state of MGMT gene promoter, which represents the biomarker with the highest prognostic/predictive value for the standard treatment of patients. Among patients with a methylated MGMT status, we identified an intermediate range of methylation above the standard 9% cut-off (gray zone) in which the predictive strength of the marker was lost. In an effort to improve the evaluation of the biomarker in clinical decision-making, we are carrying out a retrospective study, performing an in-depth analysis of samples used for diagnosis to understand how molecular heterogeneity, a hallmark of glioblastoma, impacts the evaluation of MGMT gene promoter methylation. Preliminary data from samples belonging to the "gray zone" tend to confirm the hypothesis of a mismatch between methylation values used for clinical decision-making and those included in our in-depth analysis. Confirmation of these data would help to better define the predictive power of MGMT promoter methylation status and greatly facilitate clinical decision-making.
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Affiliation(s)
- Giovanni Brigliadori
- Bioscience Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Giulia Goffredo
- Bioscience Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | | | | | - Lorena Gurrieri
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Laura Mercatali
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Toni Ibrahim
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
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18
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Huang R, Li G, Li Y, Wang Y, Yang P, Zhang C, Wang Z, Zhou D, Zhang W, Zhang Z, Jiang T. Long-term efficacy of surgical resection with or without adjuvant therapy for treatment of secondary glioblastoma in adults. Neurooncol Adv 2020; 2:vdaa098. [PMID: 33005897 PMCID: PMC7513886 DOI: 10.1093/noajnl/vdaa098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Background There are limited studies on treatment strategies and associated clinical outcomes in patients with secondary glioblastoma (sGBM). We sought to investigate the prognostic factors and treatment decisions in a retrospective cohort of patients with sGBM. Methods One hundred and seventy-one patients with sGBM who met the screening criteria were included in this study. Kaplan–Meier survival analysis and Cox survival analysis were used to detect prognostic factors. R (v3.5.0) and SPSS software (v25.0, IBM) were used to perform statistical analyses. Results The median overall survival was 303 days (range 23–2237 days) and the median progression-free survival was 229 days (range 33–1964 days) in patients with sGBM. When assessing the relationship between adjuvant treatment outcome and extent of resection (EOR), the results showed that patients underwent gross total resection can benefit from postoperative radiotherapy and chemotherapy, but not in patients underwent subtotal resection. In addition, we also found that aggressive adjuvant therapy can significantly improve clinical outcomes of IDH1-mutated patients but no significant prognostic value for IDH1-wildtyped patients. The univariate Cox regression analyses demonstrated that EOR, adjuvant therapy, and postoperative Karnofsky Performance Scores were prognostic factors for patients with sGBM, and multivariate COX analysis confirmed that adjuvant therapy and EOR were independent prognostic factors. Conclusions For patients with sGBM, aggressive postoperative adjuvant therapy after gross total resection was recommended. However, we did not detect a benefit in IDH1-wildtype patients in our cohort.
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Affiliation(s)
- Ruoyu Huang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Guanzhang Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Yiming Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yinyan Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Pei Yang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Chuanbao Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Zheng Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Dabiao Zhou
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wei Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), Beijing, China
| | - Zhong Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Tao Jiang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), Beijing, China
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19
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Zhang YW, Chai RC, Cao R, Jiang WJ, Liu WH, Xu YL, Yang J, Wang YZ, Jia WQ. Clinicopathological characteristics and survival of spinal cord astrocytomas. Cancer Med 2020; 9:6996-7006. [PMID: 32777166 PMCID: PMC7541164 DOI: 10.1002/cam4.3364] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 06/13/2020] [Accepted: 07/14/2020] [Indexed: 11/13/2022] Open
Abstract
Background Due to their rarity, the clinicopathological characteristics and prognostic factors of spinal cord gliomas are still unclear. Here, we aimed to clarify these issues in a cohort of 108 spinal cord astrocytomas. Methods We characterized the clinicopathological characteristics, including 2016 World Health Organization (WHO) grade, age, sex, location, segment length, resection, pre‐ and postsurgery, Modified McCormick Scale (MMS), radio‐ and chemotherapy, and Ki‐67 and H3 K27M mutations, in 108 spinal cord astrocytomas through heatmaps. The Cox regression analysis and Kaplan‐Meier curves were used to study the prognostic value of these clinicopathological features. Results There are a total 38 H3 K27M‐mutant tumors, including 31 cases with histological grade II/III tumors. The age of low‐grade astrocytoma patients (WHO grade I/II, n = 54) was significantly younger (27.0 vs 35.5 years, P = .001) than those with high‐grade tumors (WHO grade III/IV, n = 54). All patients underwent surgical resection with neurophysiological monitoring, and the surgery did not result in significant changes in MMS. The presurgery MMS was associated with overall survival in the high‐grade subgroup (P = .008) but not in the low‐grade subgroup (P = .312). While, the high content of resection improved the survival of only patients with low‐grade astrocytomas (P = .016) but not those with high‐grade astrocytomas (P = .475). Both the low‐grade and high‐grade astrocytomas had no obvious benefit from neither adjuvant chemotherapy nor radiotherapy (all P > .05). Conclusions We characterized the clinicopathological characteristics and their prognostic values in 108 spinal cord astrocytomas, which could help with evidence‐based management of spinal cord astrocytomas.
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Affiliation(s)
- Yao-Wu Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Rui-Chao Chai
- China National Clinical Research Center for Neurological Diseases, Beijing, China.,Department of Molecular Neuropathology, Beijing neurosurgical institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA), Beijing, China
| | - Ren Cao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Wen-Ju Jiang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Wei-Hao Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Yu-Lun Xu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Jun Yang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Yong-Zhi Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China.,Department of Molecular Neuropathology, Beijing neurosurgical institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA), Beijing, China
| | - Wen-Qing Jia
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
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20
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Wongsurawat T, Jenjaroenpun P, De Loose A, Alkam D, Ussery DW, Nookaew I, Leung YK, Ho SM, Day JD, Rodriguez A. A novel Cas9-targeted long-read assay for simultaneous detection of IDH1/2 mutations and clinically relevant MGMT methylation in fresh biopsies of diffuse glioma. Acta Neuropathol Commun 2020; 8:87. [PMID: 32563269 PMCID: PMC7305623 DOI: 10.1186/s40478-020-00963-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 06/11/2020] [Indexed: 12/20/2022] Open
Abstract
Molecular biomarkers provide both diagnostic and prognostic results for patients with diffuse glioma, the most common primary brain tumor in adults. Here, we used a long-read nanopore-based sequencing technique to simultaneously assess IDH mutation status and MGMT methylation level in 4 human cell lines and 8 fresh human brain tumor biopsies. Currently, these biomarkers are assayed separately, and results can take days to weeks. We demonstrated the use of nanopore Cas9-targeted sequencing (nCATS) to identify IDH1 and IDH2 mutations within 36 h and compared this approach against currently used clinical methods. nCATS was also able to simultaneously provide high-resolution evaluation of MGMT methylation levels not only at the promoter region, as with currently used methods, but also at CpGs across the proximal promoter region, the entirety of exon 1, and a portion of intron 1. We compared the methylation levels of all CpGs to MGMT expression in all cell lines and tumors and observed a positive correlation between intron 1 methylation and MGMT expression. Finally, we identified single nucleotide variants in 3 target loci. This pilot study demonstrates the feasibility of using nCATS as a clinical tool for cancer precision medicine.
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Affiliation(s)
- Thidathip Wongsurawat
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.
| | - Piroon Jenjaroenpun
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Annick De Loose
- Department of Neurosurgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Duah Alkam
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - David W Ussery
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Yuet-Kin Leung
- Department of Pharmacology and Toxicology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Shuk-Mei Ho
- Department of Pharmacology and Toxicology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - John D Day
- Department of Neurosurgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Analiz Rodriguez
- Department of Neurosurgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.
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21
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Chai RC, Zhang KN, Chang YZ, Wu F, Liu YQ, Zhao Z, Wang KY, Chang YH, Jiang T, Wang YZ. Systematically characterize the clinical and biological significances of 1p19q genes in 1p/19q non-codeletion glioma. Carcinogenesis 2020; 40:1229-1239. [PMID: 31157866 DOI: 10.1093/carcin/bgz102] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 05/26/2019] [Accepted: 06/01/2019] [Indexed: 11/13/2022] Open
Abstract
1p/19q codeletion, which leads to the abnormal expression of 1p19q genes in oligodendroglioma, is associated with chemosensitivity and favorable prognosis. Here, we aimed to explore the clinical implications of 1p19q gene expression in 1p/19q non-codel gliomas. We analyzed expression of 1p19q genes in 668 1p/19q non-codel gliomas obtained from The Cancer Genome Atlas (n = 447) and the Chinese Glioma Genome Atlas (n = 221) for training and validation, respectively. The expression of 1p19q genes was significantly correlated with the clinicopathological features and overall survival of 1p/19q non-codel gliomas. Then, we derived a risk signature of 25 selected 1p19q genes that not only had prognosis value in total 1p/19q non-codel gliomas but also had prognosis value in stratified gliomas. The prognosis value of the risk signature was superior than known clinicopathological features in 1p/19q non-codel gliomas and was also highly associated with the following features: loss of CDKN2A/B copy number in mutant-IDH-astrocytoma; telomerase reverse transcriptase (TERT) promoter mutation, combined chromosome 7 gain/chromosome 10 loss and epidermal growth factor receptor amplification in wild-type-IDH-astrocytoma; classical and mesenchymal subtypes in glioblastoma. Furthermore, genes enriched in the biological processes of cell division, extracellular matrix, angiogenesis significantly correlated to the signature risk score, and this is also supported by the immunohistochemistry and cell biology experiments. In conclusion, the expression profile of 1p19q genes is highly associated with the malignancy and prognosis of 1p/19q non-codel gliomas. A 25-1p19q-gene signature has powerfully predictive value for both malignant molecular pathological features and prognosis across distinct subgroups of 1p/19q non-codel gliomas.
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Affiliation(s)
- Rui-Chao Chai
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA), Beijing, China.,China National Clinical Research Center for Neurological Diseases
| | - Ke-Nan Zhang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA), Beijing, China
| | - Yu-Zhou Chang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Fan Wu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA), Beijing, China
| | - Yu-Qing Liu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA), Beijing, China
| | - Zheng Zhao
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA), Beijing, China
| | - Kuan-Yu Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA), Beijing, China
| | - Yuan-Hao Chang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA), Beijing, China
| | - Tao Jiang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA), Beijing, China.,China National Clinical Research Center for Neurological Diseases.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yong-Zhi Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA), Beijing, China.,China National Clinical Research Center for Neurological Diseases.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
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22
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Chai RC, Wu F, Wang QX, Zhang S, Zhang KN, Liu YQ, Zhao Z, Jiang T, Wang YZ, Kang CS. m 6A RNA methylation regulators contribute to malignant progression and have clinical prognostic impact in gliomas. Aging (Albany NY) 2020; 11:1204-1225. [PMID: 30810537 PMCID: PMC6402513 DOI: 10.18632/aging.101829] [Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 02/12/2019] [Indexed: 12/22/2022]
Abstract
N6-methyladenosine (m6A) RNA methylation, associated with cancer initiation and progression, is dynamically regulated by the m6A RNA methylation regulators (“writers”, “erasers” and “readers”). Here, we demonstrate that most of the thirteen main m6A RNA methylation regulators are differentially expressed among gliomas stratified by different clinicopathological features in 904 gliomas. We identified two subgroups of gliomas (RM1/2) by applying consensus clustering to m6A RNA methylation regulators. Compared with the RM1 subgroup, the RM2 subgroup correlates with a poorer prognosis, higher WHO grade, and lower frequency of IDH mutation. Moreover, the hallmarks of epithelial-mesenchymal transition and TNFα signaling via NF-κB are also significantly enriched in the RM2 subgroup. This finding indicates that m6A RNA methylation regulators are closely associated with glioma malignancy. Based on this finding, we derived a risk signature, using seven m6A RNA methylation regulators, that is not only an independent prognostic marker but can also predict the clinicopathological features of gliomas. Moreover, m6A regulators are associated with the mesenchymal subtype and TMZ sensitivity in GBM. In conclusion, m6A RNA methylation regulators are crucial participants in the malignant progression of gliomas and are potentially useful for prognostic stratification and treatment strategy development.
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Affiliation(s)
- Rui-Chao Chai
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing 100160, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA)
| | - Fan Wu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing 100160, China.,Chinese Glioma Genome Atlas Network (CGGA)
| | - Qi-Xue Wang
- Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Department of Neurosurgery, Tianjin Medical University General Hospital and Key Laboratory of Neurotrauma, Variation, and Regeneration, Ministry of Education and Tianjin Municipal Government, Tianjin 300052, China.,Chinese Glioma Genome Atlas Network (CGGA)
| | - Shu Zhang
- Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Department of Neurosurgery, Tianjin Medical University General Hospital and Key Laboratory of Neurotrauma, Variation, and Regeneration, Ministry of Education and Tianjin Municipal Government, Tianjin 300052, China
| | - Ke-Nan Zhang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing 100160, China.,Chinese Glioma Genome Atlas Network (CGGA)
| | - Yu-Qing Liu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing 100160, China.,Chinese Glioma Genome Atlas Network (CGGA)
| | - Zheng Zhao
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing 100160, China.,Chinese Glioma Genome Atlas Network (CGGA)
| | - Tao Jiang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing 100160, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100160, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA)
| | - Yong-Zhi Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing 100160, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100160, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA)
| | - Chun-Sheng Kang
- Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Department of Neurosurgery, Tianjin Medical University General Hospital and Key Laboratory of Neurotrauma, Variation, and Regeneration, Ministry of Education and Tianjin Municipal Government, Tianjin 300052, China.,Chinese Glioma Genome Atlas Network (CGGA).,Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou 510095, China
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23
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Chai RC, Zhang YW, Liu YQ, Chang YZ, Pang B, Jiang T, Jia WQ, Wang YZ. The molecular characteristics of spinal cord gliomas with or without H3 K27M mutation. Acta Neuropathol Commun 2020; 8:40. [PMID: 32228694 PMCID: PMC7106747 DOI: 10.1186/s40478-020-00913-w] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/09/2020] [Indexed: 12/11/2022] Open
Abstract
Due to the rare incidence of spinal cord astrocytomas, their molecular features remain unclear. Here, we characterized the landscapes of mutations in H3 K27M, isocitrate dehydrogenase 1 (IDH1) R132H, BRAF V600E, and the TERT promoter in 83 diffuse spinal cord astrocytic tumors. Among these samples, thirty-five patients had the H3 K27M mutation; this mutant could be observed in histological grade II (40%), III (40%), and IV (20%) astrocytomas. IDH1 mutations were absent in 58 of 58 cases tested. The BRAF V600E mutation (7/57) was only observed in H3-wildtype astrocytomas, and was associated with a better prognosis in all histological grade II/III astrocytomas. TERT promoter mutations were observed in both H3 K27M-mutant (4/25) and -wildtype (9/33) astrocytomas, and were associated with a poor prognosis in H3-wildtype histological grade II/III astrocytomas. In the 2016 WHO classification of CNS tumors, H3 K27M-mutant diffuse midline gliomas, including spinal cord astrocytomas, are categorized as WHO grade IV. Here, we noticed that the median overall survival of histological grade II/III H3 K27M-mutant cases (n = 28) was significantly longer than that of either the total histological grade IV cases (n = 12) or the H3 K27M-mutant histological grade IV cases (n = 7). We also directly compared H3 K27M-mutant astrocytomas to H3-wildtype astrocytomas of the same histological grade. In histological grade II astrocytomas, compared to H3-wildtype cases (n = 37), H3 K27M-mutant patients (n = 14) had showed a significantly higher Ki-67-positive rate and poorer survival rate. However, no significant differences in these parameters were observed in histological grade III and IV astrocytoma patients. In conclusion, these findings indicate that spinal cord astrocytomas are considerably different from hemispheric and brainstem astrocytomas in terms of their molecular profiles, and that the histological grade cannot be ignored when assessing the prognosis of H3 K27M-mutant spinal cord astrocytomas.
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Liu YQ, Wu F, Li JJ, Li YF, Liu X, Wang Z, Chai RC. Gene Expression Profiling Stratifies IDH-Wildtype Glioblastoma With Distinct Prognoses. Front Oncol 2019; 9:1433. [PMID: 31921684 PMCID: PMC6929203 DOI: 10.3389/fonc.2019.01433] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 12/02/2019] [Indexed: 12/31/2022] Open
Abstract
Objectives: In the present study, we aimed to determine the candidate genes that may function as biomarkers to further distinguish patients with isocitrate dehydrogenase (IDH)-wildtype glioblastoma (GBM), which are heterogeneous with respect to clinical outcomes. Materials and Methods: We selected 41 candidate genes associated with overall survival (OS) using univariate Cox regression from IDH-wildtype GBM patients based on RNA sequencing (RNAseq) expression data from the Chinese Glioma Genome Atlas (CGGA, n = 105) and The Cancer Genome Atlas (TCGA, n = 139) cohorts. Next, a seven-gene-based risk signature was formulated according to Least Absolute Shrinkage and Selection Operator (LASSO) regression algorithm in the CGGA RNAseq database as a training set, while another 525 IDH-wildtype GBM patient TCGA datasets, consisting of RNA sequencing and microarray data, were used for validation. Patient survival in the low- and high-risk groups was calculated using Kaplan-Meier survival curve analysis and the log-rank test. Uni-and multivariate Cox regression analysis was used to assess the prognosis value. Gene oncology (GO) and gene set enrichment analysis (GSEA) were performed for the functional analysis of the seven-gene-based risk signature. Results: We developed a seven-gene-based signature, which allocated each patient to a risk group (low or high). Patients in the high-risk group had dramatically shorter overall survival than their low-risk counterparts in three independent cohorts. Univariate and multivariate analysis showed that the seven-gene signature remained an independent prognostic factor. Moreover, the seven-gene risk signature exhibited a striking prognostic validity, with AUC of 78.4 and 73.9%, which was higher than for traditional “age” (53.7%, 62.4%) and “GBM sub-type” (57.7%, 52.9%) in the CGGA- and TCGA-RNAseq databases, respectively. Subsequent bioinformatics analysis predicted that the seven-gene signature was involved in the inflammatory response, immune response, cell adhesion, and apoptotic process. Conclusions: Our findings indicate that the seven-gene signature could be a potential prognostic biomarker. This study refined the current classification system of IDH-wildtype GBM and may provide a novel perspective for the research and individual therapy of IDH-wildtype GBM.
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Affiliation(s)
- Yu-Qing Liu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing, China.,Chinese Glioma Genome Atlas Network, Beijing, China
| | - Fan Wu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing, China.,Chinese Glioma Genome Atlas Network, Beijing, China
| | - Jing-Jun Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing, China.,Chinese Glioma Genome Atlas Network, Beijing, China
| | - Yang-Fang Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing, China.,Chinese Glioma Genome Atlas Network, Beijing, China
| | - Xing Liu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing, China.,Chinese Glioma Genome Atlas Network, Beijing, China
| | - Zheng Wang
- Chinese Glioma Genome Atlas Network, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Rui-Chao Chai
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing, China.,Chinese Glioma Genome Atlas Network, Beijing, China
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25
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Chai RC, Chang YZ, Wang QW, Zhang KN, Li JJ, Huang H, Wu F, Liu YQ, Wang YZ. A Novel DNA Methylation-Based Signature Can Predict the Responses of MGMT Promoter Unmethylated Glioblastomas to Temozolomide. Front Genet 2019; 10:910. [PMID: 31611911 PMCID: PMC6776832 DOI: 10.3389/fgene.2019.00910] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/28/2019] [Indexed: 12/22/2022] Open
Abstract
Glioblastoma (GBM) is the most malignant glioma, with a median overall survival (OS) of 14–16 months. Temozolomide (TMZ) is the first-line chemotherapy drug for glioma, but whether TMZ should be withheld from patients with GBMs that lack O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation is still under debate. DNA methylation profiling holds great promise for further stratifying the responses of MGMT promoter unmethylated GBMs to TMZ. In this study, we studied 147 TMZ-treated MGMT promoter unmethylated GBM, whose methylation information was obtained from the HumanMethylation27 (HM-27K) BeadChips (n = 107) and the HumanMethylation450 (HM-450K) BeadChips (n = 40) for training and validation, respectively. In the training set, we performed univariate Cox regression and identified that 3,565 CpGs were significantly associated with the OS of the TMZ-treated MGMT promoter unmethylated GBMs. Functional analysis indicated that the genes corresponding to these CpGs were enriched in the biological processes or pathways of mitochondrial translation, cell cycle, and DNA repair. Based on these CpGs, we developed a 31-CpGs methylation signature utilizing the least absolute shrinkage and selection operator (LASSO) Cox regression algorithm. In both training and validation datasets, the signature identified the TMZ-sensitive GBMs in the MGMT promoter unmethylated GBMs, and only the patients in the low-risk group appear to benefit from the TMZ treatment. Furthermore, these identified TMZ-sensitive MGMT promoter unmethylated GBMs have a similar OS when compared with the MGMT promoter methylated GBMs after TMZ treatment in both two datasets. Multivariate Cox regression demonstrated the independent prognostic value of the signature in TMZ-treated MGMT promoter unmethylated GBMs. Moreover, we also noticed that the hallmark of epithelial–mesenchymal transition, ECM related biological processes and pathways were highly enriched in the MGMT unmethylated GBMs with the high-risk score, indicating that enhanced ECM activities could be involved in the TMZ-resistance of GBM. In conclusion, our findings promote our understanding of the roles of DNA methylation in MGMT umethylated GBMs and offer a very promising TMZ-sensitivity predictive signature for these GBMs that could be tested prospectively.
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Affiliation(s)
- Rui-Chao Chai
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yu-Zhou Chang
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Qiang-Wei Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ke-Nan Zhang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jing-Jun Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Hua Huang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Fan Wu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yu-Qing Liu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yong-Zhi Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
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Chai RC, Li YM, Zhang KN, Chang YZ, Liu YQ, Zhao Z, Wang ZL, Chang YH, Li GZ, Wang KY, Wu F, Wang YZ. RNA processing genes characterize RNA splicing and further stratify lower-grade glioma. JCI Insight 2019; 5:130591. [PMID: 31408440 DOI: 10.1172/jci.insight.130591] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Aberrant expression of RNA processing genes may drive the alterative RNA profile in lower-grade gliomas (LGGs). Thus, we aimed to further stratify LGGs based on the expression of RNA processing genes. METHODS This study included 446 LGGs from The Cancer Genome Atlas (TCGA, training set) and 171 LGGs from the Chinese Glioma Genome Atlas (CGGA, validation set). The least absolute shrinkage and selection operator (LASSO) Cox regression algorithm was conducted to develop a risk-signature. The receiver operating characteristic (ROC) curves and Kaplan-Meier curves were used to study the prognosis value of the risk-signature. RESULTS Among the tested 784 RNA processing genes, 276 were significantly correlated with the OS of LGGs. Further LASSO Cox regression identified a 19-gene risk-signature, whose risk score was also an independently prognosis factor (P<0.0001, multiplex Cox regression) in the validation dataset. The signature had better prognostic value than the traditional factors "age", "grade" and "WHO 2016 classification" for 3- and 5-year survival both two datasets (AUCs > 85%). Importantly, the risk-signature could further stratify the survival of LGGs in specific subgroups of WHO 2016 classification. Furthermore, alternative splicing events for genes such as EGFR and FGFR were found to be associated with the risk score. mRNA expression levels for genes, which participated in cell proliferation and other processes, were significantly correlated to the risk score. CONCLUSIONS Our results highlight the role of RNA processing genes for further stratifying the survival of patients with LGGs and provide insight into the alternative splicing events underlying this role.
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Affiliation(s)
- Rui-Chao Chai
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China.,China National Clinical Research Center for Neurological Diseases and
| | - Yi-Ming Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ke-Nan Zhang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China
| | - Yu-Zhou Chang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yu-Qing Liu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China
| | - Zheng Zhao
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China
| | - Zhi-Liang Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China
| | - Yuan-Hao Chang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China
| | - Guan-Zhang Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China
| | - Kuan-Yu Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China
| | - Fan Wu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China
| | - Yong-Zhi Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China.,China National Clinical Research Center for Neurological Diseases and.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
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Pyrosequencing versus methylation-specific PCR for assessment of MGMT methylation in tumor and blood samples of glioblastoma patients. Sci Rep 2019; 9:11125. [PMID: 31366977 PMCID: PMC6668570 DOI: 10.1038/s41598-019-47642-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 07/16/2019] [Indexed: 12/20/2022] Open
Abstract
Circulating biomarkers in blood may provide an interesting alternative to risky tissue biopsies in the diagnosis and follow-up of glioblastoma patients. We have assessed MGMT methylation status in blood and tissue samples from unresected glioblastoma patients who had been included in the randomized GENOM-009 trial. Paired blood and tissue samples were assessed by methylation-specific PCR (MSP) and pyrosequencing (PYR). After establishing the minimum PYR cut-off that could yield a significant difference in overall survival, we assessed the sensitivity, specificity, positive predictive value and negative predictive value (NPV) of the analyses. Methylation could be detected in cfDNA by both MSP and PYR but with low concordance with results in tissue. Sensitivity was low for both methods (31% and 38%, respectively), while specificity was higher for MSP in blood than for PYR in plasma (96% vs 76%) and NPV was similar (56 vs 57%). Concordance of results in tissue by MSP and PYR was 84.3% (P < 0.001) and correlated with outcome. We conclude that detection of cfDNA in the blood of glioblastoma patients can be an alternative when tumor tissue is not available but methods for the detection of cfDNA in blood must improve before it can replace analysis in tumor tissue.
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Radiogenomic analysis of PTEN mutation in glioblastoma using preoperative multi-parametric magnetic resonance imaging. Neuroradiology 2019; 61:1229-1237. [DOI: 10.1007/s00234-019-02244-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 06/05/2019] [Indexed: 02/07/2023]
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Chai RC, Wang N, Chang YZ, Zhang KN, Li JJ, Niu JJ, Wu F, Liu YQ, Wang YZ. Systematically profiling the expression of eIF3 subunits in glioma reveals the expression of eIF3i has prognostic value in IDH-mutant lower grade glioma. Cancer Cell Int 2019; 19:155. [PMID: 31171919 PMCID: PMC6549376 DOI: 10.1186/s12935-019-0867-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/27/2019] [Indexed: 12/14/2022] Open
Abstract
Background Abnormal expression of the eukaryotic initiation factor 3 (eIF3) subunits plays critical roles in tumorigenesis and progression, and also has potential prognostic value in cancers. However, the expression and clinical implications of eIF3 subunits in glioma remain unknown. Methods Expression data of eIF3 for patients with gliomas were obtained from the Chinese Glioma Genome Atlas (CGGA) (n = 272) and The Cancer Genome Atlas (TCGA) (n = 595). Cox regression, the receiver operating characteristic (ROC) curves and Kaplan–Meier analysis were used to study the prognostic value. Gene oncology (GO) and gene set enrichment analysis (GSEA) were utilized for functional prediction. Results In both the CGGA and TCGA datasets, the expression levels of eIF3d, eIF3e, eIF3f, eIF3h and eIF3l highly were associated with the IDH mutant status of gliomas. The expression of eIF3b, eIF3i, eIF3k and eIF3m was increased with the tumor grade, and was associated with poorer overall survival [All Hazard ratio (HR) > 1 and P < 0.05]. By contrast, the expression of eIF3a and eIF3l was decreased in higher grade gliomas and was associated with better overall survival (Both HR < 1 and P < 0.05). Importantly, the expression of eIF3i (located on chromosome 1p) and eIF3k (Located on chromosome 19q) were the two highest risk factors in both the CGGA [eIF3i HR = 2.068 (1.425–3.000); eIF3k HR = 1.737 (1.166–2.588)] and TCGA [eIF3i HR = 1.841 (1.642–2.064); eIF3k HR = 1.521 (1.340–1.726)] databases. Among eIF3i, eIF3k alone or in combination, the expression of eIF3i was the more robust in stratifying the survival of glioma in various pathological subgroups. The expression of eIF3i was an independent prognostic factor in IDH-mutant lower grade glioma (LGG) and could also predict the 1p/19q codeletion status of IDH-mutant LGG. Finally, GO and GSEA analysis showed that the elevated expression of eIF3i was significantly correlated with the biological processes of cell proliferation, mRNA processing, translation, T cell receptor signaling, NF-κB signaling and others. Conclusions Our study reveals the expression alterations during glioma progression, and highlights the prognostic value of eIF3i in IDH-mutant LGG. Electronic supplementary material The online version of this article (10.1186/s12935-019-0867-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rui-Chao Chai
- 1Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100160 China.,4China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100160 China.,Chinese Glioma Genome Atlas Network (CGGA), Beijing, China
| | - Ning Wang
- 2Department of Clinical Laboratory, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020 China
| | - Yu-Zhou Chang
- 3Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100160 China
| | - Ke-Nan Zhang
- 1Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100160 China.,Chinese Glioma Genome Atlas Network (CGGA), Beijing, China
| | - Jing-Jun Li
- 1Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100160 China.,Chinese Glioma Genome Atlas Network (CGGA), Beijing, China
| | - Jun-Jie Niu
- Xiang Fen Centers for Disease Control and Prevention, Xiangfen, 041500 Shanxi China
| | - Fan Wu
- 1Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100160 China.,Chinese Glioma Genome Atlas Network (CGGA), Beijing, China
| | - Yu-Qing Liu
- 1Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100160 China.,Chinese Glioma Genome Atlas Network (CGGA), Beijing, China
| | - Yong-Zhi Wang
- 1Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100160 China.,3Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100160 China.,4China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100160 China.,Chinese Glioma Genome Atlas Network (CGGA), Beijing, China
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