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Pang L, Dunterman M, Guo S, Khan F, Liu Y, Taefi E, Bahrami A, Geula C, Hsu WH, Horbinski C, James CD, Chen P. Kunitz-type protease inhibitor TFPI2 remodels stemness and immunosuppressive tumor microenvironment in glioblastoma. Nat Immunol 2023; 24:1654-1670. [PMID: 37667051 PMCID: PMC10775912 DOI: 10.1038/s41590-023-01605-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 07/27/2023] [Indexed: 09/06/2023]
Abstract
Glioblastoma (GBM) tumors consist of multiple cell populations, including self-renewing glioblastoma stem cells (GSCs) and immunosuppressive microglia. Here we identified Kunitz-type protease inhibitor TFPI2 as a critical factor connecting these cell populations and their associated GBM hallmarks of stemness and immunosuppression. TFPI2 promotes GSC self-renewal and tumor growth via activation of the c-Jun N-terminal kinase-signal transducer and activator of transcription (STAT)3 pathway. Secreted TFPI2 interacts with its functional receptor CD51 on microglia to trigger the infiltration and immunosuppressive polarization of microglia through activation of STAT6 signaling. Inhibition of the TFPI2-CD51-STAT6 signaling axis activates T cells and synergizes with anti-PD1 therapy in GBM mouse models. In human GBM, TFPI2 correlates positively with stemness, microglia abundance, immunosuppression and poor prognosis. Our study identifies a function for TFPI2 and supports therapeutic targeting of TFPI2 as an effective strategy for GBM.
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Affiliation(s)
- Lizhi Pang
- Department of Neurological Surgery, Lou and Jean Malnati Brain Tumor Institute, Robert H Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Madeline Dunterman
- Department of Neurological Surgery, Lou and Jean Malnati Brain Tumor Institute, Robert H Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Songlin Guo
- Department of Neurological Surgery, Lou and Jean Malnati Brain Tumor Institute, Robert H Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Fatima Khan
- Department of Neurological Surgery, Lou and Jean Malnati Brain Tumor Institute, Robert H Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yang Liu
- Department of Neurological Surgery, Lou and Jean Malnati Brain Tumor Institute, Robert H Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Erfan Taefi
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease; Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Atousa Bahrami
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease; Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Changiz Geula
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease; Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Wen-Hao Hsu
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Craig Horbinski
- Department of Neurological Surgery, Lou and Jean Malnati Brain Tumor Institute, Robert H Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Charles David James
- Department of Neurological Surgery, Lou and Jean Malnati Brain Tumor Institute, Robert H Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Peiwen Chen
- Department of Neurological Surgery, Lou and Jean Malnati Brain Tumor Institute, Robert H Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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The Water Transport System in Astrocytes–Aquaporins. Cells 2022; 11:cells11162564. [PMID: 36010640 PMCID: PMC9406552 DOI: 10.3390/cells11162564] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/26/2022] [Accepted: 08/08/2022] [Indexed: 11/16/2022] Open
Abstract
Highlights (AQPs) are transmembrane proteins responsible for fast water movement across cell membranes, including those of astrocytes. The expression and subcellular localization of AQPs in astrocytes are highly dynamic under physiological and pathological conditions. Besides their primary function in water homeostasis, AQPs participate in many ancillary functions including glutamate clearance in tripartite synapses and cell migration.
Abstract Astrocytes have distinctive morphological and functional characteristics, and are found throughout the central nervous system. Astrocytes are now known to be far more than just housekeeping cells in the brain. Their functions include contributing to the formation of the blood–brain barrier, physically and metabolically supporting and communicating with neurons, regulating the formation and functions of synapses, and maintaining water homeostasis and the microenvironment in the brain. Aquaporins (AQPs) are transmembrane proteins responsible for fast water movement across cell membranes. Various subtypes of AQPs (AQP1, AQP3, AQP4, AQP5, AQP8 and AQP9) have been reported to be expressed in astrocytes, and the expressions and subcellular localizations of AQPs in astrocytes are highly correlated with both their physiological and pathophysiological functions. This review describes and summarizes the recent advances in our understanding of astrocytes and AQPs in regard to controlling water homeostasis in the brain. Findings regarding the features of different AQP subtypes, such as their expression, subcellular localization, physiological functions, and the pathophysiological roles of astrocytes are presented, with brain edema and glioma serving as two representative AQP-associated pathological conditions. The aim is to provide a better insight into the elaborate “water distribution” system in cells, exemplified by astrocytes, under normal and pathological conditions.
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Yang Z, Chen Z, Wang Y, Wang Z, Zhang D, Yue X, Zheng Y, Li L, Bian E, Zhao B. A Novel Defined Pyroptosis-Related Gene Signature for Predicting Prognosis and Treatment of Glioma. Front Oncol 2022; 12:717926. [PMID: 35433410 PMCID: PMC9008739 DOI: 10.3389/fonc.2022.717926] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 03/07/2022] [Indexed: 12/23/2022] Open
Abstract
Pyroptosis, a form of programmed cell death, that plays a significant role in the occurrence and progression of tumors, has been frequently investigated recently. However, the prognostic significance and therapeutic value of pyroptosis in glioma remain undetermined. In this research, we revealed the relationship of pyroptosis-related genes to glioma by analyzing whole transcriptome data from The Cancer Genome Atlas (TCGA) dataset serving as the training set and the Chinese Glioma Genome Atlas (CGGA) dataset serving as the validation set. We identified two subgroups of glioma patients with disparate prognostic and clinical features by performing consensus clustering analysis on nineteen pyroptosis-related genes that were differentially expressed between glioma and normal brain tissues. We further derived a risk signature, using eleven pyroptosis-related genes, that was demonstrated to be an independent prognostic factor for glioma. Furthermore, we used Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) to implement functional analysis of our gene set, and the results were closely related to immune and inflammatory responses in accordance with the characteristics of pyroptosis. Moreover, Gene Set Enrichment Analysis (GSEA) results showed that that the high-risk group exhibited enriched characteristics of malignant tumors in accordance with its poor prognosis. Next, we analyzed different immune cell infiltration between the two risk groups using ssGSEA. Finally, CASP1 was identified as a core gene, so we subsequently selected an inhibitor targeting CASP1 and simulated molecular docking. In addition, the inhibitory effect of belnacasan on glioma was verified at the cellular level. In conclusion, pyroptosis-related genes are of great significance for performing prognostic stratification and developing treatment strategies for glioma.
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Affiliation(s)
- Zhihao Yang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Zhigang Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Yu Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Zhiwei Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Deran Zhang
- 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
| | - Yinfei Zheng
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Lianxin Li
- 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
| | - 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
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Promoting Prognostic Model Application: A Review Based on Gliomas. JOURNAL OF ONCOLOGY 2021; 2021:7840007. [PMID: 34394352 PMCID: PMC8356003 DOI: 10.1155/2021/7840007] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/03/2021] [Indexed: 12/13/2022]
Abstract
Malignant neoplasms are characterized by poor therapeutic efficacy, high recurrence rate, and extensive metastasis, leading to short survival. Previous methods for grouping prognostic risks are based on anatomic, clinical, and pathological features that exhibit lower distinguishing capability compared with genetic signatures. The update of sequencing techniques and machine learning promotes the genetic panels-based prognostic model development, especially the RNA-panel models. Gliomas harbor the most malignant features and the poorest survival among all tumors. Currently, numerous glioma prognostic models have been reported. We systematically reviewed all 138 machine-learning-based genetic models and proposed novel criteria in assessing their quality. Besides, the biological and clinical significance of some highly overlapped glioma markers in these models were discussed. This study screened out markers with strong prognostic potential and 27 models presenting high quality. Conclusively, we comprehensively reviewed 138 prognostic models combined with glioma genetic panels and presented novel criteria for the development and assessment of clinically important prognostic models. This will guide the genetic models in cancers from laboratory-based research studies to clinical applications and improve glioma patient prognostic management.
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Abstract
Malignant neoplasms are characterized by poor therapeutic efficacy, high recurrence rate, and extensive metastasis, leading to short survival. Previous methods for grouping prognostic risks are based on anatomic, clinical, and pathological features that exhibit lower distinguishing capability compared with genetic signatures. The update of sequencing techniques and machine learning promotes the genetic panels-based prognostic model development, especially the RNA-panel models. Gliomas harbor the most malignant features and the poorest survival among all tumors. Currently, numerous glioma prognostic models have been reported. We systematically reviewed all 138 machine-learning-based genetic models and proposed novel criteria in assessing their quality. Besides, the biological and clinical significance of some highly overlapped glioma markers in these models were discussed. This study screened out markers with strong prognostic potential and 27 models presenting high quality. Conclusively, we comprehensively reviewed 138 prognostic models combined with glioma genetic panels and presented novel criteria for the development and assessment of clinically important prognostic models. This will guide the genetic models in cancers from laboratory-based research studies to clinical applications and improve glioma patient prognostic management.
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Pan T, Wu F, Li L, Wu S, Zhou F, Zhang P, Sun C, Xia L. The role m 6A RNA methylation is CNS development and glioma pathogenesis. Mol Brain 2021; 14:119. [PMID: 34281602 PMCID: PMC8290532 DOI: 10.1186/s13041-021-00831-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 05/31/2021] [Indexed: 12/22/2022] Open
Abstract
Epigenetic abnormalities play a crucial role in many tumors, including glioma. RNA methylation occurs as an epigenetic modification similar to DNA methylation and histone modification. m6A methylation is the most common and most intensively studied RNA methylation, which can be found throughout the RNA life cycle and exert biological functions by affecting RNA metabolism. The m6A modification is primarily associated with three types of protease, which are encoded by the writer, eraser and reader genes, respectively. It has been shown that the m6A methylation has close connections with the occurrence and development of many tumors, including glioma. In this study, the concept and the research progress of m6A methylation are reviewed, especially the role of m6A methylation in glioma. Moreover, we will discuss how glioma is paving the way to the development of new therapeutic options based on the inhibition of m6A deposition.
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Affiliation(s)
- Ting Pan
- School of the Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, China.,Department of Gynecological Oncology, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, People's Republic of China
| | - Fan Wu
- School of the Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Liwen Li
- Department of Neurosurgery, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, People's Republic of China.,Key Laboratory of Head & Neck Cancer, Translational Research of Zhejiang Province, Hangzhou, 310022, People's Republic of China
| | - Shiyan Wu
- School of the Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, China.,Department of Gynecological Oncology, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, People's Republic of China
| | - Fang Zhou
- School of the Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, China.,Department of Gynecological Oncology, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, People's Republic of China
| | - Ping Zhang
- Department of Gynecological Oncology, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, People's Republic of China.
| | - Caixing Sun
- Department of Neurosurgery, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, People's Republic of China. .,Key Laboratory of Head & Neck Cancer, Translational Research of Zhejiang Province, Hangzhou, 310022, People's Republic of China.
| | - Liang Xia
- Department of Neurosurgery, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, People's Republic of China. .,Key Laboratory of Head & Neck Cancer, Translational Research of Zhejiang Province, Hangzhou, 310022, People's Republic of China.
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7
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Zhang Z, Chen J, Huo X, Zong G, Huang K, Cheng M, Sun L, Yue X, Bian E, Zhao B. Identification of a mesenchymal-related signature associated with clinical prognosis in glioma. Aging (Albany NY) 2021; 13:12431-12455. [PMID: 33875619 PMCID: PMC8148476 DOI: 10.18632/aging.202886] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/04/2021] [Indexed: 12/26/2022]
Abstract
Malignant glioma with a mesenchymal (MES) signature is characterized by shorter survival time due to aggressive dissemination and resistance to chemoradiotherapy. Here, this study used the TCGA database as the training set and the CGGA database as the testing set. Consensus clustering was performed on the two data sets, and it was found that two groups had distinguished prognostic and molecular features. Cox analysis and Lasso regression analysis were used to construct MES signature-based risk score model of glioma. Our results show that MES signature-based risk score model can be used to assess the prognosis of glioma. Three methods (ROC curve analyses, univariate Cox regression analysis, multivariate Cox regression analysis) were used to investigate the prognostic role of texture parameters. The result showed that the MES-related gene signature was proved to be an independent prognostic factor for glioma. Furthermore, functional analysis of the gene related to the risk signature showed that the genes sets were closely related to the malignant process of tumors. Finally, FCGR2A and EHD2 were selected for functional verification. Silencing these two genes inhibited the proliferation, migration and invasion of gliomas and reduced the expression of mesenchymal marker genes. Collectively, MES-related risk signature seems to provide a novel target for predicting the prognosis and treatment of glioma.
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Affiliation(s)
- Zhengwei Zhang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei 230601, China
| | - Jie Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei 230601, China
| | - Xiuhao Huo
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei 230601, China
| | - Gang Zong
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei 230601, China
| | - Kebing Huang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei 230601, China
| | - Meng Cheng
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei 230601, China
| | - Libo Sun
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei 230601, China
| | - Xiaoyu Yue
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei 230601, China
| | - Erbao Bian
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei 230601, China
| | - Bing Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei 230601, China
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Théret N, Bouezzeddine F, Azar F, Diab-Assaf M, Legagneux V. ADAM and ADAMTS Proteins, New Players in the Regulation of Hepatocellular Carcinoma Microenvironment. Cancers (Basel) 2021; 13:cancers13071563. [PMID: 33805340 PMCID: PMC8037375 DOI: 10.3390/cancers13071563] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Members of the adamalysin family are multi-domain proteins involved in many cancer-related functions. In this review, we will examine the literature on the involvement of adamalysins in hepatocellular carcinoma progression and their importance in the tumor microenvironment where they regulate the inflammatory response and the epithelial–mesenchymal transition. We complete this review with an analysis of adamalysin expression in a large cohort of patients with hepatocellular carcinoma from The Cancer Genome Atlas (TCGA) database. These original results give a new insight into the involvement of all adamalysins in the primary liver cancer. Abstract The tumor microenvironment plays a major role in tumor growth, invasion and resistance to chemotherapy, however understanding how all actors from microenvironment interact together remains a complex issue. The tumor microenvironment is classically represented as three closely connected components including the stromal cells such as immune cells, fibroblasts, adipocytes and endothelial cells, the extracellular matrix (ECM) and the cytokine/growth factors. Within this space, proteins of the adamalysin family (ADAM for a disintegrin and metalloproteinase; ADAMTS for ADAM with thrombospondin motifs; ADAMTSL for ADAMTS-like) play critical roles by modulating cell–cell and cell–ECM communication. During last decade, the implication of adamalysins in the development of hepatocellular carcinoma (HCC) has been supported by numerous studies however the functional characterization of most of them remain unsettled. In the present review we propose both an overview of the literature and a meta-analysis of adamalysins expression in HCC using data generated by The Cancer Genome Atlas (TCGA) Research Network.
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Affiliation(s)
- Nathalie Théret
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en santé, Environnement et Travail)-UMR_S1085, University of Rennes 1, 35000 Rennes, France; (F.A.); (V.L.)
- Correspondence:
| | - Fidaa Bouezzeddine
- Molecular Cancer and Pharmaceutical Biology Laboratory, Faculty of Sciences II, Lebanese University Fanar, 1500 Beirut, Lebanon; (F.B.); (M.D.-A.)
| | - Fida Azar
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en santé, Environnement et Travail)-UMR_S1085, University of Rennes 1, 35000 Rennes, France; (F.A.); (V.L.)
| | - Mona Diab-Assaf
- Molecular Cancer and Pharmaceutical Biology Laboratory, Faculty of Sciences II, Lebanese University Fanar, 1500 Beirut, Lebanon; (F.B.); (M.D.-A.)
| | - Vincent Legagneux
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en santé, Environnement et Travail)-UMR_S1085, University of Rennes 1, 35000 Rennes, France; (F.A.); (V.L.)
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Tan J, Zhu H, Tang G, Liu H, Wanggou S, Cao Y, Xin Z, Zhou Q, Zhan C, Wu Z, Guo Y, Jiang Z, Zhao M, Ren C, Jiang X, Yin W. Molecular Subtypes Based on the Stemness Index Predict Prognosis in Glioma Patients. Front Genet 2021; 12:616507. [PMID: 33732284 PMCID: PMC7957071 DOI: 10.3389/fgene.2021.616507] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 02/08/2021] [Indexed: 12/19/2022] Open
Abstract
Glioma is the common histological subtype of malignancy in the central nervous system, with high morbidity and mortality. Glioma cancer stem cells (CSCs) play essential roles in tumor recurrence and treatment resistance. Thus, exploring the stem cell-related genes and subtypes in glioma is important. In this study, we collected the RNA-sequencing (RNA-seq) data and clinical information of glioma patients from The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) databases. With the differentially expressed genes (DEGs) and weighted gene correlation network analysis (WGCNA), we identified 86 mRNA expression-based stemness index (mRNAsi)-related genes in 583 samples from TCGA RNA-seq dataset. Furthermore, these samples from TCGA database could be divided into two significantly different subtypes with different prognoses based on the mRNAsi corresponding gene, which could also be validated in the CGGA database. The clinical characteristics and immune cell infiltrate distribution of the two stemness subtypes are different. Then, functional enrichment analyses were performed to identify the different gene ontology (GO) terms and pathways in the two different subtypes. Moreover, we constructed a stemness subtype-related risk score model and nomogram to predict the prognosis of glioma patients. Finally, we selected one gene (ETV2) from the risk score model for experimental validation. The results showed that ETV2 can contribute to the invasion, migration, and epithelial-mesenchymal transition (EMT) process of glioma. In conclusion, we identified two distinct molecular subtypes and potential therapeutic targets of glioma, which could provide new insights for the development of precision diagnosis and prognostic prediction for glioma patients.
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Affiliation(s)
- Jun Tan
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Hecheng Zhu
- Changsha Kexin Cancer Hospital, Changsha, China
| | - Guihua Tang
- Department of Clinical Laboratory, Hunan Provincial People's Hospital (First Affiliated Hospital of Hunan Normal University), Changsha, China
| | - Hongwei Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
| | - Siyi Wanggou
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
| | - Yudong Cao
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Zhaoqi Xin
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Quanwei Zhou
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Chaohong Zhan
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Zhaoping Wu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Youwei Guo
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Zhipeng Jiang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Ming Zhao
- Changsha Kexin Cancer Hospital, Changsha, China
| | - Caiping Ren
- Key Laboratory for Carcinogenesis of Chinese Ministry of Health, School of Basic Medical Science, Cancer Research Institute, Central South University, Changsha, China
| | - Xingjun Jiang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Wen Yin
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
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10
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Zhang W, Zhai Y, Li G, Jiang T. A novel gene signature based on five immune checkpoint genes predicts the survival of glioma. Chin Neurosurg J 2021; 7:15. [PMID: 33531060 PMCID: PMC7856730 DOI: 10.1186/s41016-020-00220-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 12/01/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Glioma is the most common and fatal type of nerve neoplasm in the central nervous system. Several biomarkers have been considered for prognosis prediction, which is not accurate enough. We aimed to carry out a gene signature related to the expression of immune checkpoints which was enough for its performance in prediction. METHODS Gene expression of immune checkpoints in TGGA database was filtrated. The 5 selected genes underwent verification by COX and Lasso-COX regression. Next, the selected genes were included to build a novel signature for further analysis. RESULTS Patients were sub-grouped into high and low risk according to the novel signature. Immune response, clinicopathologic characters, and survival showed significant differences between those 2 groups. Terms including "naive," "effector," and "IL-4" were screened out by GSEA. The results showed strong relevance between the signature and immune response. CONCLUSIONS We constructed a gene signature with 5 immune checkpoints. The signature predicted survival effectively. The novel signature performed more functional than previous biomarkers.
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Affiliation(s)
- 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
| | - You Zhai
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, No. 119 South Fourth Ring Road West, Fengtai District, Beijing, China
| | - Guanzhang Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, No. 119 South Fourth Ring Road West, Fengtai District, Beijing, China
| | - Tao Jiang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, No. 119 South Fourth Ring Road West, Fengtai District, 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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11
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Luo H, Tao C, Wang P, Li J, Huang K, Zhu X. Development of a prognostic index based on immunogenomic landscape analysis in glioma. IMMUNITY INFLAMMATION AND DISEASE 2021; 9:467-479. [PMID: 33503296 PMCID: PMC8127549 DOI: 10.1002/iid3.407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/05/2021] [Accepted: 01/09/2021] [Indexed: 12/21/2022]
Abstract
Background Glioma is the most common intracranial tumor. The inflammatory response actively participates in the malignancy of gliomas. There is still limited knowledge about the biological function of immune‐related genes (IRGs) and their potential involvement in the malignancy of gliomas. Methods We screened differentially expressed and survival‐associated IRGs, and explored their potential molecular characteristics. Then we developed a prognostic index derived from seven hub IRGs. A prognostic nomogram was built to indicate the prognostic value of the prognostic index and seven IRGs. We characterized the immune infiltration landscape to analyze tumor‐immune interactions. The real‐time quantitative polymerase chain reaction assay was performed to validate bioinformatics results. Results The differentially expressed IRGs are involved in cell chemotaxis, cytokine activity, and the chemokine‐mediated signaling pathway. The prognostic index derived from seven IRGs had clinical prognostic value in glioma, and positively correlated with the malignant clinicopathological characteristics. A nomogram further indicated that the prognostic index and seven hub IRGs had clinical prognostic value for gliomas. We revealed that the prognostic index could reflect the state of the glioma immune microenvironment. Conclusion This study demonstrates the importance of an IRG‐based prognostic index as a potential biomarker for predicting malignancy in gliomas.
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Affiliation(s)
- Haitao Luo
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Chuming Tao
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China.,East China Institute of Digital Medical Engineering, Shangrao, Jiangxi, China
| | - Peng Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Jingying Li
- Department of Comprehensive Intensive Care Unit, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Kai Huang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China.,Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi, China
| | - Xingen Zhu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China.,Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi, China
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12
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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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13
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Du S, Guan S, Zhu C, Guo Q, Cao J, Guan G, Cheng W, Cheng P, Wu A. Secretory Pathway Kinase FAM20C, a Marker for Glioma Invasion and Malignancy, Predicts Poor Prognosis of Glioma. Onco Targets Ther 2020; 13:11755-11768. [PMID: 33239887 PMCID: PMC7680683 DOI: 10.2147/ott.s275452] [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: 08/09/2020] [Accepted: 10/21/2020] [Indexed: 12/15/2022] Open
Abstract
Purpose Glioblastoma (GBM) is the most lethal primary cancer in adult central nervous system, and new strategies are desperately needed. The secretory pathway kinase or kinase-like proteins (SPKKPs) have been shown to mediate multiple physiological functions by phosphorylating extracellular proteins and proteoglycans. However, their roles in cancers, especially GBM, remain poorly defined. Methods The least absolute shrinkage and selection operator (LASSO) regression was employed for establishing the SPKKPs signature for IDH wild type (wt) GBM prognosis. Integrative analyses with multiple datasets were employed to identify the core member of this gene family in glioma. The receiver operator characteristic (ROC) curves and immunohistochemistry were further used for evaluating its association with progressive malignancy in glioma and GBM patients’ survival, respectively. Gene set enrichment analysis (GSEA) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to interpret its functions in GBM, which were further verified in vitro. Results A SPKKPs classifier was constructed with 3 genes of this family. This signature could effectively distinguish IDH wt GBM survival. Family with sequence similarity 20 C (FAM20C) was further identified as the core member of this family in glioma. Elevated FAM20C expression was not only closely correlated with glioma malignancy progression and the mesenchymal subtype of GBM but also indicated unfavorable survival of GBM patients. FAM20C was also found to be associated with the disrupted immune response in GBM microenvironment and was required for the migration of glioma and immune cells. Conclusion These data indicate that the potential of FAM20C serving as a predictive molecule and a therapeutic target for GBM.
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Affiliation(s)
- Shaonan Du
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, People's Republic of China
| | - Shu Guan
- Department of Surgical Oncology and Breast Surgery, The First Hospital of China Medical University, Shenyang, People's Republic of China
| | - Chen Zhu
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, People's Republic of China
| | - Qing Guo
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, People's Republic of China
| | - Jingyuan Cao
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, People's Republic of China
| | - Gefei Guan
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, People's Republic of China
| | - Wen Cheng
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, People's Republic of China
| | - Peng Cheng
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, People's Republic of China
| | - Anhua Wu
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, People's Republic of China.,College of Applied Technology, China Medical University, Shenyang, Liaoning 110122, People's Republic of China
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14
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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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15
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Chen BS, Wang KY, Yu SQ, Zhang CB, Li GZ, Wang ZL, Bao ZS. Whole-transcriptome sequencing profiling identifies functional and prognostic signatures in patients with PTPRZ1-MET fusion-negative secondary glioblastoma multiforme. Oncol Lett 2020; 20:187. [PMID: 32952656 PMCID: PMC7479526 DOI: 10.3892/ol.2020.12049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 02/21/2020] [Indexed: 11/24/2022] Open
Abstract
Gliomas are the most common type of primary brain tumor in adults with a high mortality rate. Low-grade gliomas progress to glioblastoma multiforme (GBM) in the majority of cases, forming secondary GBM (sGBM), followed by rapid fatal clinical outcomes. Protein tyrosine phosphatase receptor type Z1 (PTPRZ1)-MET proto-oncogene receptor tyrosine kinase (MET) (ZM) fusion has been identified as a biomarker for sGBM that is involved in glioma progression, but the mechanism of gliomagenesis and pathology of ZM-negative sGBM has remained to be fully elucidated. A whole-transcriptome signature is thus required to improve the outcome prediction for patients with sGBM without ZM fusion. In the present study, whole-transcriptome sequencing on 42 sGBM samples with or without ZM fusion from the Chinese Glioma Genome Atlas database identified mRNAs with differential expression between patients with and without ZM fusion and the most significant survival-associated genes were identified. A 6-gene signature was identified as a novel prognostic model reflecting survival probability in patients with ZM-negative sGBM. Clinical characteristics in patients with a high or low risk score value were analyzed with the Kaplan-Meier method and a two-sided log-rank test. In addition, ZM-negative sGBM patients with a high risk score exhibited an increase in immune cells, NF-κB-induced pathway activation and a decrease in endothelial cells compared with those with a low risk score. The present study demonstrated the potential use of a next-generation sequencing-based cancer gene signature in patients with ZM-negative sGBM, indicating possible clinical therapeutic strategies for further treatment of such patients.
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Affiliation(s)
- Bao-Shi Chen
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Kuan-Yu Wang
- Department of Gamma Knife Center, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China.,Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing 100069, P.R. China.,Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100050, P.R. China
| | - Shu-Qing Yu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Chuan-Bao Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Guan-Zhang Li
- Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100050, P.R. China
| | - Zhi-Liang Wang
- Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100050, P.R. China
| | - Zhao-Shi Bao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China.,Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing 100069, P.R. China.,Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100050, P.R. China
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16
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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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17
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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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18
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Xu G, Ou L, Liu Y, Wang X, Liu K, Li J, Li J, Wang S, Huang D, Zheng K, Wang S. Upregulated expression of MMP family genes is associated with poor survival in patients with esophageal squamous cell carcinoma via regulation of proliferation and epithelial‑mesenchymal transition. Oncol Rep 2020; 44:29-42. [PMID: 32627007 PMCID: PMC7251684 DOI: 10.3892/or.2020.7606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 03/13/2020] [Indexed: 12/19/2022] Open
Abstract
Matrix metalloproteinases (MMPs) are involved in the cleavage of several components of the extracellular matrix and serve important roles in tumor growth, metastasis and invasion. Previous studies have focused on the expression of one or several MMPs in esophageal squamous cell carcinoma (ESCC); however, in the present study, the transcriptomics of all 23 MMPs were systematically investigated with a focus on the prognostic value of the combination of MMPs. In this study, 8 overlapping differentially expressed genes of the MMP family were identified based on data obtained from Gene Expression Omnibus and The Cancer Genome Atlas. The prognostic value of these MMPs were investigated; the receiver operating characteristic curves, survival curves and nomograms showed that the combination of 6 selected MMPs possessed a good predictive ability, which was more accurate than the prediction model based on Tumor‑Node‑Metastasis stage. Gene set enrichment analysis and gene co‑expression analysis were performed to investigate the potential mechanism of action of MMPs in ESCC. The MMP family was associated with several signaling pathways, such as epithelial‑mesenchymal transition (EMT), Notch, TGF‑β, mTOR and P53. Cell Counting Kit‑8, colony formation, wound healing assays and western blotting were used to determine the effect of BB‑94, a pan‑MMP inhibitor, on proliferation and migration of ESCC cells. BB‑94 treatment decreased ESCC cell growth, migration and EMT. Therefore, MMPs may serve both as diagnostic and prognostic biomarkers of ESCC, and MMP inhibition may be a promising preventive and therapeutic strategy for patients with ESCC.
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Affiliation(s)
- Guifeng Xu
- School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen, Guangdong 518060, P.R. China
| | - Ling Ou
- Department of Pharmacy, The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen 518020, P.R. China
| | - Ying Liu
- Department of Pharmacy, The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen 518020, P.R. China
| | - Xiao Wang
- Department of Pharmacy, The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen 518020, P.R. China
| | - Kaisheng Liu
- Department of Pharmacy, The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen 518020, P.R. China
| | - Jieling Li
- School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen, Guangdong 518060, P.R. China
| | - Junjun Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau 999078, P.R. China
| | - Shaoqi Wang
- Department of Oncology, Hubei Provincial Corps Hospital, Chinese People Armed Police Forces, Wuhan, Hubei 430061, P.R. China
| | - Dane Huang
- Guangdong Province Engineering Technology Research Institute of Traditional Chinese Medicine, Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese Medicine, Guangzhou, Guangdong 510095, P.R. China
| | - Kai Zheng
- School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen, Guangdong 518060, P.R. China
| | - Shaoxiang Wang
- School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen, Guangdong 518060, P.R. China
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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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20
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Li J, Wang X, Zheng K, Liu Y, Li J, Wang S, Liu K, Song X, Li N, Xie S, Wang S. The clinical significance of collagen family gene expression in esophageal squamous cell carcinoma. PeerJ 2019; 7:e7705. [PMID: 31598423 PMCID: PMC6779144 DOI: 10.7717/peerj.7705] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 08/19/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) is a subtype of esophageal cancer with high incidence and mortality. Due to the poor 5-year survival rates of patients with ESCC, exploring novel diagnostic markers for early ESCC is emergent. Collagen, the abundant constituent of extracellular matrix, plays a critical role in tumor growth and epithelial-mesenchymal transition. However, the clinical significance of collagen genes in ESCC has been rarely studied. In this work, we systematically analyzed the gene expression of whole collagen family in ESCC, aiming to search for ideal biomarkers. METHODS Clinical data and gene expression profiles of ESCC patients were collected from The Cancer Genome Atlas and the gene expression omnibus databases. Bioinformatics methods, including differential expression analysis, survival analysis, gene sets enrichment analysis (GSEA) and co-expression network analysis, were performed to investigate the correlation between the expression patterns of 44 collagen family genes and the development of ESCC. RESULTS A total of 22 genes of collagen family were identified as differentially expressed genes in both the two datasets. Among them, COL1A1, COL10A1 and COL11A1 were particularly up-regulated in ESCC tissues compared to normal controls, while COL4A4, COL6A5 and COL14A1 were notably down-regulated. Besides, patients with low COL6A5 expression or high COL18A1 expression showed poor survival. In addition, a 7-gene prediction model was established based on collagen gene expression to predict patient survival, which had better predictive accuracy than the tumor-node-metastasis staging based model. Finally, GSEA results suggested that collagen genes might be tightly associated with PI3K/Akt/mTOR pathway, p53 pathway, apoptosis, cell cycle, etc. CONCLUSION Several collagen genes could be potential diagnostic and prognostic biomarkers for ESCC. Moreover, a novel 7-gene prediction model is probably useful for predicting survival outcomes of ESCC patients. These findings may facilitate early detection of ESCC and help improves prognosis of the patients.
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Affiliation(s)
- Jieling Li
- School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen, China
| | - Xiao Wang
- Department of Pharmacy, The Second Clinical Medical College (Shenzhen People’s Hospital), Jinan University, Shenzhen, China
| | - Kai Zheng
- School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen, China
| | - Ying Liu
- Department of Pharmacy, The Second Clinical Medical College (Shenzhen People’s Hospital), Jinan University, Shenzhen, China
| | - Junjun Li
- School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen, China
| | - Shaoqi Wang
- Department of Oncology, Hubei Provincial Corps Hospital, Chinese People Armed Police Forces, Wuhan, China
| | - Kaisheng Liu
- Department of Pharmacy, The Second Clinical Medical College (Shenzhen People’s Hospital), Jinan University, Shenzhen, China
| | - Xun Song
- School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen, China
| | - Nan Li
- Department of Pharmacy, The Second Clinical Medical College (Shenzhen People’s Hospital), Jinan University, Shenzhen, China
| | - Shouxia Xie
- Department of Pharmacy, The Second Clinical Medical College (Shenzhen People’s Hospital), Jinan University, Shenzhen, China
| | - Shaoxiang Wang
- School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen, China
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21
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Tang X, Xu P, Wang B, Luo J, Fu R, Huang K, Dai L, Lu J, Cao G, Peng H, Zhang L, Zhang Z, Chen Q. Identification of a Specific Gene Module for Predicting Prognosis in Glioblastoma Patients. Front Oncol 2019; 9:812. [PMID: 31508371 PMCID: PMC6718733 DOI: 10.3389/fonc.2019.00812] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 08/08/2019] [Indexed: 12/13/2022] Open
Abstract
Introduction: Glioblastoma (GBM) is the most common and malignant variant of intrinsic glial brain tumors. The poor prognosis of GBM has not significantly improved despite the development of innovative diagnostic methods and new therapies. Therefore, further understanding the molecular mechanism that underlies the aggressive behavior of GBM and the identification of appropriate prognostic markers and therapeutic targets is necessary to allow early diagnosis, to develop appropriate therapies and to improve prognoses. Methods: We used a weighted gene co-expression network analysis (WGCNA) to construct a gene co-expression network with 524 glioblastoma samples from The Cancer Genome Atlas (TCGA). A risk score was then constructed based on four module genes and the patients' overall survival (OS) rate. The prognostic and predictive accuracy of the risk score were verified in the GSE16011 cohort and the REMBRANDT cohort. Results: We identified a gene module (the green module) related to prognosis. Then, multivariate Cox analysis was performed on 4 hub genes to construct a Cox proportional hazards regression model from 524 glioblastoma patients. A risk score for predicting survival time was calculated with the following formula based on the top four genes in the green module: risk score = (0.00889 × EXPCLEC5A) + (0.0681 × EXPFMOD) + (0.1724 × EXPFKBP9) + (0.1557 × EXPLGALS8). The 5-year survival rate of the high-risk group (survival rate: 2.7%, 95% CI: 1.2–6.3%) was significantly lower than that of the low-risk group (survival rate: 8.8%, 95% CI: 5.5–14.1%). Conclusions: This study demonstrated the potential application of a WGCNA-based gene prognostic model for predicting the survival outcome of glioblastoma patients.
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Affiliation(s)
- Xiangjun Tang
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China.,Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China.,Department of Neurosurgery, Affiliated Hospital of Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Pengfei Xu
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Bin Wang
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Jie Luo
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Rui Fu
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Kuanming Huang
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Longjun Dai
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Junti Lu
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Gang Cao
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Hao Peng
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Li Zhang
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Zhaohui Zhang
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Qianxue Chen
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
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22
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Wang Z, Chen N, Yang J, Wang Q, Li A. Microarray gene profiling analysis of glioblastoma cell line U87 reveals suppression of the FANCD2/Fanconi anemia pathway by the combination of Y15 and temozolomide. Arch Med Sci 2019; 15:1035-1046. [PMID: 31360198 PMCID: PMC6657253 DOI: 10.5114/aoms.2019.86063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/16/2018] [Indexed: 12/03/2022] Open
Abstract
INTRODUCTION A recent study showed that a combination of Y15 (a FAK autophosphorylation inhibitor) with temozolomide (TMZ) treatment was effective in glioblastoma (GBM) therapy. In this study, we further investigated the pathways and genes that are differentially expressed in Y15 and TMZ treated U87 cells via bioinformatics analysis. MATERIAL AND METHODS The microarray gene profiling analysis screened out genes with differential expression in U87 cells treated with TMZ and Y15. Gene set enrichment analysis (GSEA) identified the key GO terms and KEGG pathways in TMZ + Y15 treated U87 cells. The functional partner genes of TMZ were predicted by the STICH database. FANCD2 expression in U87 cells was detected by qRT-PCR. MTT assay and colony formation assay were conducted for cell viability detection, and flow cytometry was performed for cell apoptosis detection. Western blot was conducted to determine the expression levels of the downstream proteins of the Fanconi anemia (FA) pathway, FAN1 and BRCA2. RESULTS The FA pathway was suppressed in U87 cells after treatment with TMZ and Y15. Genes involved in this pathway, including FANCD2, were also down-regulated. FANCD2 knockdown could restrain viability and promote apoptosis of U87 cells, as well as enhancing the inhibitory effect of TMZ + Y15 treatment. FANCD2 could regulate the FA pathway as the protein expression levels of FAN1 and BRCA2 were modulated by FANCD2. CONCLUSIONS The FA pathway and FANCD2 are down-regulated in U87 cells treated with TMZ and Y15. FANCD2 down-regulation by TMZ + Y15 treatment suppressed growth of U87 cells through inhibiting the FA pathway.
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Affiliation(s)
- Zichuan Wang
- College of Basic Medicine, Nanjing University of Chinese Medicine, Jiangsu, China
| | - Nan Chen
- College of Basic Medicine, Nanjing University of Chinese Medicine, Jiangsu, China
| | - Jin Yang
- College of Basic Medicine, Nanjing University of Chinese Medicine, Jiangsu, China
| | - Qingzhong Wang
- Department of Neurosurgery, People’s Hospital of Guanyun County, Jiangsu, China
| | - Aimin Li
- Department of Neurosurgery, First People’s Hospital of Lianyungang, Jiangsu, China
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23
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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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ADAMTSL4, a Secreted Glycoprotein, Is a Novel Immune-Related Biomarker for Primary Glioblastoma Multiforme. DISEASE MARKERS 2019; 2019:1802620. [PMID: 30728876 PMCID: PMC6341252 DOI: 10.1155/2019/1802620] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 09/09/2018] [Accepted: 10/03/2018] [Indexed: 02/06/2023]
Abstract
Background Researches on immunotherapy of glioblastoma multiforme (GBM, WHO grade IV) have increased exponentially in recent years. As a targeted therapy, a series of biomarkers have been identified in local tumor tissue, while circulating marker which could be detected in the body fluids is still lacking. ADAMTSL4, a secreted glycoprotein, was earlier found to play a critical role in a prognostic signature for primary GBM (pGBM). We aimed to investigate the role of ADAMTSL4 at transcriptome level and its relationship with clinical practice in pGBM. Methods A cohort of 88 pGBM patients with RNA-seq data from the Chinese Glioma Genome Atlas (CGGA) was analyzed, and 168 pGBM patients from TCGA were included as validation. Several bioinformatic methods and predictive tools were applied to investigate the ADAMTSL4-associated immune microenvironment status. Results We found that ADAMTSL4 was enriched in GBM (WHO grade IV), especially for those with IDH1/2 wild-type and MGMT unmethylated groups. According to the TCGA classification scheme, ADAMTSL4 can act as a potential marker for subtypes with poorer prognosis. Bioinformatic analyses revealed that ADAMTSL4 was significantly correlated to the immune-related processes in GBM (WHO grade IV), especially representing the infiltration of immune cells and complicated tumor microenvironment. Clinically, high expression of ADAMTSL4 was an independent indicator for poor prognosis. Conclusion The expression of ADAMTSL4 is closely related to the clinicopathologic characteristics of pGBM. Meanwhile, it may play a critical role in immune-related processes. As a secreted glycoprotein, ADAMTSL4 is a promising circulating biomarker for pGBM, deserving further investigations.
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25
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A novel analytical model of MGMT methylation pyrosequencing offers improved predictive performance in patients with gliomas. Mod Pathol 2019; 32:4-15. [PMID: 30291347 DOI: 10.1038/s41379-018-0143-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/29/2018] [Accepted: 08/31/2018] [Indexed: 12/28/2022]
Abstract
The methylation status of the promoter of MGMT gene is a crucial factor influencing clinical decision-making in patients with gliomas. MGMT pyrosequencing results are often dichotomized by a cut-off value based on an average of several tested CpGs. However, this method frequently results in a "gray zone", representing a dilemma for physicians. We therefore propose a novel analytical model for MGMT methylation pyrosequencing. MGMT CpG heterogeneity was investigated in 213 glioma patients in two tested cohorts: cohort A in which CpGs 75-82 were tested and cohort B in which CpGs 72-78 were tested. The predictive performances of the novel and traditional averaging models were compared in 135 patients who received temozolomide using receiver operating characteristic curves and Kaplan-Meier curves, and in patients stratified according to isocitrate dehydrogenase gene mutation status. The results were validated in an independent cohort of 65 consecutive patients with high-grade gliomas from the Chinese Glioma Genome Atlas database. Heterogeneity of MGMT promoter CpG methylation level was observed in most gliomas. The optimal cut-off value for each individual CpG varied from 4-16%. The current analysis defined MGMT promoter methylation as occurring when at least three CpGs exceeded their respective cut-off values. This novel analysis could accurately predict the prognosis of patients in the methylation "gray zone" according to the standard averaging method, and improved the area under the curves from 0.67, 0.76, and 0.67 to 0.70, 0.84, and 0.72 in cohorts A, B, and the validation cohort, respectively, demonstrating superiority of this analytical method in all three cohorts. Furthermore, the advantages of the novel analysis were retained regardless of WHO grade and isocitrate dehydrogenase gene mutation status. In conclusion, this novel analytical model offers an improved clinical predictive performance for MGMT pyrosequencing results and is suitable for clinical use in patients with gliomas.
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Chai RC, Zhang KN, Liu YQ, Wu F, Zhao Z, Wang KY, Jiang T, Wang YZ. Combinations of four or more CpGs methylation present equivalent predictive value for MGMT expression and temozolomide therapeutic prognosis in gliomas. CNS Neurosci Ther 2018; 25:314-322. [PMID: 30117294 DOI: 10.1111/cns.13040] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 12/19/2022] Open
Abstract
AIMS The pyrosequencing (PSQ) has been regarded as the gold standard for MGMT promoter methylation testing in gliomas. However, various CpG combinations are currently used in clinical practice. We aimed to clarify how and how many CpGs combined is robust enough to predict MGMT mRNA expression and therapeutic prognosis of patients. METHODS Total 223 patients with WHO III/IV gliomas were enrolled from Chinese Glioma Genome Atlas, including two independent cohorts, the eight-site cohort (with CpGs 75-82 tested) and the seven-site cohort (with CpGs 72-78 tested). Spearman's correlation and ROC curves were employed to investigate the value of different CpG combinations on predicting MGMT mRNA expression. The ROC curves and Kaplan-Meier steps were performed to compare the TMZ therapeutic prognostic values of different CpG combinations. RESULTS The methylation level of all individual CpG and CpG combinations for the eleven CpGs (CpGs 72-82), significantly correlated to MGMT mRNA expression (Spearman, all P < 0.0001), could effectively predict the mRNA expression (AUC, 0.86-0.91 in the eight-site cohort, 0.83-0.90 in the seven-site cohort). Moreover, the correlation coefficients and the predictive values presented equivalent when four or more CpGs combinedly used (AUC, 0.88-0.90 in the eight-site cohort, 0.87-0.88 in the seven-site cohort). Finally, similar results were also observed when using selected CpG combinations to predict therapeutic prognosis of patients. CONCLUSIONS Four-CpG combinations of pyrosequencing are sufficient for evaluating the methylation status of MGMT and predicting therapeutic prognosis in 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 (CGGA), Beijing, China
| | - Ke-Nan Zhang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas (CGGA), Beijing, China.,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 (CGGA), Beijing, China
| | - Fan Wu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas (CGGA), Beijing, China
| | - Zheng Zhao
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas (CGGA), Beijing, China
| | - Kuan-Yu Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas (CGGA), Beijing, China.,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.,Chinese Glioma Genome Atlas (CGGA), Beijing, China.,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 (CGGA), Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
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