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Turkarslan S, He Y, Hothi P, Murie C, Nicolas A, Kannan K, Park JH, Pan M, Awawda A, Cole ZD, Shapiro MA, Stuhlmiller TJ, Lee H, Patel AP, Cobbs C, Baliga NS. An atlas of causal and mechanistic drivers of interpatient heterogeneity in glioma. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.05.24305380. [PMID: 38633778 PMCID: PMC11023657 DOI: 10.1101/2024.04.05.24305380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Grade IV glioma, formerly known as glioblastoma multiforme (GBM) is the most aggressive and lethal type of brain tumor, and its treatment remains challenging in part due to extensive interpatient heterogeneity in disease driving mechanisms and lack of prognostic and predictive biomarkers. Using mechanistic inference of node-edge relationship (MINER), we have analyzed multiomics profiles from 516 patients and constructed an atlas of causal and mechanistic drivers of interpatient heterogeneity in GBM (gbmMINER). The atlas has delineated how 30 driver mutations act in a combinatorial scheme to causally influence a network of regulators (306 transcription factors and 73 miRNAs) of 179 transcriptional "programs", influencing disease progression in patients across 23 disease states. Through extensive testing on independent patient cohorts, we share evidence that a machine learning model trained on activity profiles of programs within gbmMINER significantly augments risk stratification, identifying patients who are super-responders to standard of care and those that would benefit from 2 nd line treatments. In addition to providing mechanistic hypotheses regarding disease prognosis, the activity of programs containing targets of 2 nd line treatments accurately predicted efficacy of 28 drugs in killing glioma stem-like cells from 43 patients. Our findings demonstrate that interpatient heterogeneity manifests from differential activities of transcriptional programs, providing actionable strategies for mechanistically characterizing GBM from a systems perspective and developing better prognostic and predictive biomarkers for personalized medicine.
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Luo Q, Zhuang J, Zheng D, Miao C, Luo H, Peng J, Zheng C, Qin C, Lan C, Chen M, Xia Y, Huang D, Chen Z. IGFBP2 from a novel copper metabolism-associated biomarker promoted glioma progression and response to immunotherapy. Front Immunol 2023; 14:1282734. [PMID: 37928523 PMCID: PMC10620745 DOI: 10.3389/fimmu.2023.1282734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/02/2023] [Indexed: 11/07/2023] Open
Abstract
Introduction Copper metabolism encompasses all cellular metabolic processes involving copper ions and plays a significant role in the pathogenesis of diseases, including cancer. Furthermore, copper is intricately involved in various processes related to nucleotide metabolism. However, a comprehensive analysis of copper metabolism in gliomas remains lacking despite its importance. Methods To address this gap, glioma patients were stratified based on the expression levels of copper metabolism-related genes. By utilizing machine learning techniques, a novel copper metabolism-associated biomarker was developed. The potential of this biomarker in prognosis, mutation analysis, and predicting immunotherapy response efficiency in gliomas was systematically investigated. Results Notably, IGFBP2, identified as a glioma tumor promoter, was found to promote disease progression and influence immunotherapy response. Additionally, glioma-derived IGFBP2 was observed to enhance microglial migration. High IGFBP2 expression in GBM cells facilitated macrophage interactions through the EGFR, CD63, ITGB1, and CD44 signaling pathways. Discussion: Overall, the copper metabolism-associated biomarker shows promising potential to enhance the clinical management of gliomas, offering valuable insights into disease prognosis and treatment strategies.
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Affiliation(s)
- Qisheng Luo
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Junhong Zhuang
- Department of Neurology, Affiliated Haikou Hospital of Xiangya Medical School, Central South University, Haikou, China
| | - Dandan Zheng
- Department of Radiation Oncology, The First Affiliated Hospital Zhejiang University, Hangzhou, China
| | - Changfeng Miao
- Department of Laboratory Medicine, Neurosurgery Second Branche, Hunan Provincial People’s Hospital (The First affiliated Hospital of Hunan Normal University), Changsha, Hunan, China
| | - Hongcheng Luo
- Department of Laboratory Medicine, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Jun Peng
- Department of Neurosurgery, Affiliated Haikou Hospital of Xiangya Medical School, Central South University, Haikou, China
| | - Chuanhua Zheng
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Chengjian Qin
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Chuanliu Lan
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Meiqin Chen
- Department of Radiation Oncology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Ying Xia
- Department of Neurosurgery, Affiliated Haikou Hospital of Xiangya Medical School, Central South University, Haikou, China
| | - Deyou Huang
- Department of Radiology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Zigui Chen
- Department of Neurosurgery, Affiliated Haikou Hospital of Xiangya Medical School, Central South University, Haikou, China
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Penkova A, Kuziakova O, Gulaia V, Tiasto V, Goncharov NV, Lanskikh D, Zhmenia V, Baklanov I, Farniev V, Kumeiko V. Comprehensive clinical assays for molecular diagnostics of gliomas: the current state and future prospects. Front Mol Biosci 2023; 10:1216102. [PMID: 37908227 PMCID: PMC10613994 DOI: 10.3389/fmolb.2023.1216102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/04/2023] [Indexed: 11/02/2023] Open
Abstract
Glioma is one of the most intractable types of cancer, due to delayed diagnosis at advanced stages. The clinical symptoms of glioma are unclear and due to a variety of glioma subtypes, available low-invasive testing is not effective enough to be introduced into routine medical laboratory practice. Therefore, recent advances in the clinical diagnosis of glioma have focused on liquid biopsy approaches that utilize a wide range of techniques such as next-generation sequencing (NGS), droplet-digital polymerase chain reaction (ddPCR), and quantitative PCR (qPCR). Among all techniques, NGS is the most advantageous diagnostic method. Despite the rapid cheapening of NGS experiments, the cost of such diagnostics remains high. Moreover, high-throughput diagnostics are not appropriate for molecular profiling of gliomas since patients with gliomas exhibit only a few diagnostic markers. In this review, we highlighted all available assays for glioma diagnosing for main pathogenic glioma DNA sequence alterations. In the present study, we reviewed the possibility of integrating routine molecular methods into the diagnosis of gliomas. We state that the development of an affordable assay covering all glioma genetic aberrations could enable early detection and improve patient outcomes. Moreover, the development of such molecular diagnostic kits could potentially be a good alternative to expensive NGS-based approaches.
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Affiliation(s)
- Alina Penkova
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Olga Kuziakova
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Valeriia Gulaia
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Vladlena Tiasto
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Nikolay V. Goncharov
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- A. V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, Russia
| | - Daria Lanskikh
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Valeriia Zhmenia
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Ivan Baklanov
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- A. V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, Russia
| | - Vladislav Farniev
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Vadim Kumeiko
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- A. V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, Russia
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Chen Z, Zheng D, Lin Z, Zhang C, Wei C, Deng X, Yan P, Zheng C, Lan C, Qin C, Wei X, Qin D, Wu Y, Peng J, Miao C, Lu L, Xia Y, Luo Q. GPX8 regulates pan-apoptosis in gliomas to promote microglial migration and mediate immunotherapy responses. Front Immunol 2023; 14:1260169. [PMID: 37795080 PMCID: PMC10545954 DOI: 10.3389/fimmu.2023.1260169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/23/2023] [Indexed: 10/06/2023] Open
Abstract
Introduction Gliomas have emerged as the predominant brain tumor type in recent decades, yet the exploration of non-apoptotic cell death regulated by the pan-optosome complex, known as pan-apoptosis, remains largely unexplored in this context. This study aims to illuminate the molecular properties of pan-apoptosis-related genes in glioma patients, classifying them and developing a signature using machine learning techniques. Methods The prognostic significance, mutation features, immunological characteristics, and pharmaceutical prediction performance of this signature were comprehensively investigated. Furthermore, GPX8, a gene of interest, was extensively examined for its prognostic value, immunological characteristics, medication prediction performance, and immunotherapy prediction potential. Results Experimental techniques such as CCK-8, Transwell, and EdU investigations revealed that GPX8 acts as a tumor accelerator in gliomas. At the single-cell RNA sequencing level, GPX8 appeared to facilitate cell contact between tumor cells and macrophages, potentially enhancing microglial migration. Conclusions The incorporation of pan-apoptosis-related features shows promising potential for clinical applications in predicting tumor progression and advancing immunotherapeutic strategies. However, further in vitro and in vivo investigations are necessary to validate the tumorigenic and immunogenic processes associated with GPX8 in gliomas.
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Affiliation(s)
- Zigui Chen
- Department of Neurosurgery, Affiliated Haikou Hospital of Xiangya Medical School, Central South University, Haikou, China
| | - Dandan Zheng
- Department of Radiation Oncology, The First Affiliated Hospital Zhejiang University, Hangzhou, China
| | - Ziren Lin
- Department of Wound Repair Surgery, The People’s Hospital of Baise, Baise, Guangxi, China
| | - Chunyuan Zhang
- Life Science and Clinical Research Center, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Cheng Wei
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Xiandong Deng
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Peng Yan
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Chuanhua Zheng
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Chuanliu Lan
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Chengjian Qin
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Xuanlei Wei
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Deling Qin
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Yongfang Wu
- Department of Wound Repair Surgery, The People’s Hospital of Baise, Baise, Guangxi, China
| | - Jun Peng
- Department of Neurosurgery, Affiliated Haikou Hospital of Xiangya Medical School, Central South University, Haikou, China
| | - Changfeng Miao
- Department of Laboratory Medicine, Neurosurgery Second Branche, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, China
| | - Liuxue Lu
- Department of Medicine, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Ying Xia
- Department of Neurosurgery, Affiliated Haikou Hospital of Xiangya Medical School, Central South University, Haikou, China
| | - Qisheng Luo
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
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Guo Y, Bao J, Lin D, Hong K, Cen K, Sun J, Wang Z, Wu Z. Novel immune checkpoint-related gene model to predict prognosis and treatment responsiveness in low-grade gliomas. Heliyon 2023; 9:e20178. [PMID: 37809899 PMCID: PMC10559968 DOI: 10.1016/j.heliyon.2023.e20178] [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: 04/03/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 10/10/2023] Open
Abstract
Recently, studies have shown that immune checkpoint-related genes (ICGs) are instrumental in maintaining immune homeostasis and can be regarded as potential therapeutic targets. However, the prognostic applications of ICGs require further elucidation in low-grade glioma (LGG) cases. In the present study, a unique prognostic gene signature in LGG has been identified and validated as well based on ICGs as a means of facilitating clinical decision-making. The RNA-seq data as well as corresponding clinical data of LGG samples have been retrieved utilizing the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. ICG-defined non-negative matrix factorization (NMF) clustering was performed to categorize patients with LGG into two molecular subtypes with different prognoses, clinical traits, and immune microenvironments. In the TCGA database, a signature integrating 8 genes has been developed utilizing the LASSO Cox method and validated in the GEO database. The signature developed is superior to other well-recognized signatures in terms of predicting the survival probability of patients with LGG. This 8-gene signature was then subsequently applied to categorize patients into high- and low-risk groups, and differences between them in terms of gene alteration frequency were observed. There were remarkable variations in IDH1 (91% and 64%) across low-as well as high-risk groups. Additionally, various analyses like function enrichment, tumor immune microenvironment, and chemotherapy drug sensitivity revealed significant variations across high- and low-risk populations. Overall, this 8-gene signature may function as a useful tool for prognosis and immunotherapy outcome predictions among LGG patients.
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Affiliation(s)
- Yangyang Guo
- Department of Neurosurgery, The First Affiliated Hospital of Ningbo University, Haishu District, Ningbo, 315010, Zhejiang, People's Republic of China
| | - Jingxia Bao
- Department of Breast Surgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
| | - Danfeng Lin
- Department of Breast Surgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
| | - Kai Hong
- Department of Neurosurgery, The First Affiliated Hospital of Ningbo University, Haishu District, Ningbo, 315010, Zhejiang, People's Republic of China
| | - Kenan Cen
- The Affiliated Hospital of Medical School of Ningbo University, Jiangbei District, Ningbo, 315020, Zhejiang, People's Republic of China
| | - Jie Sun
- Department of Neurosurgery, The First Affiliated Hospital of Ningbo University, Haishu District, Ningbo, 315010, Zhejiang, People's Republic of China
| | - Zhepei Wang
- Department of Neurosurgery, The First Affiliated Hospital of Ningbo University, Haishu District, Ningbo, 315010, Zhejiang, People's Republic of China
| | - Zhixuan Wu
- Department of Breast Surgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
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Chen W, Guo S, Wang Y, Shi Y, Guo X, Liu D, Li Y, Wang Y, Xing H, Xia Y, Li J, Wu J, Liang T, Wang H, Liu Q, Jin S, Qu T, Li H, Yang T, Zhang K, Wang Y, Ma W. Novel insight into histological and molecular astrocytoma, IDH-mutant, Grade 4 by the updated WHO classification of central nervous system tumors. Cancer Med 2023; 12:18666-18678. [PMID: 37667984 PMCID: PMC10557904 DOI: 10.1002/cam4.6476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 08/02/2023] [Accepted: 08/14/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND The latest fifth edition of the World Health Organization (WHO) classification of the central nervous system (CNS) tumors (WHO CNS 5 classification) released in 2021 defined astrocytoma, IDH-mutant, Grade 4. However, the understanding of this subtype is still limited. We conducted this study to describe the features of astrocytoma, IDH-mutant, Grade 4 and explored the similarities and differences between histological and molecular subtypes. METHODS Patients who underwent surgery from January 2011 to January 2022, classified as astrocytoma, IDH-mutant, Grade 4 were included in this study. Clinical, radiological, histopathological, molecular pathological, and survival data were collected for analysis. RESULTS Altogether 33 patients with astrocytoma, IDH-mutant, Grade 4 were selected, including 20 with histological and 13 with molecular WHO Grade 4 astrocytoma. Tumor enhancement, intratumoral-necrosis like presentation, larger peritumoral edema, and more explicit tumor margins were frequently observed in histological WHO Grade 4 astrocytoma. Additionally, molecular WHO Grade 4 astrocytoma showed a tendency for relatively longer overall survival, while a statistical significance was not reached (47 vs. 25 months, p = 0.22). TP53, CDK6, and PIK3CA alteration was commonly observed, while PIK3R1 (p = 0.033), Notch1 (p = 0.027), and Mycn (p = 0.027) alterations may affect the overall survival of molecular WHO Grade 4 astrocytomas. CONCLUSIONS Our study scrutinized IDH-mutant, Grade 4 astrocytoma. Therefore, further classification should be considered as the prognosis varied between histological and molecular WHO Grade 4 astrocytomas. Notably, therapies aiming at PIK3R1, Notch 1, and Mycn may be beneficial.
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Affiliation(s)
- Wenlin Chen
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Siying Guo
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- Eight‐year Medical Doctor ProgramChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Yaning Wang
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Yixin Shi
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- Eight‐year Medical Doctor ProgramChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Xiaopeng Guo
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- China Anti‐Cancer Association Specialty Committee of GliomaBeijingChina
| | - Delin Liu
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- Eight‐year Medical Doctor ProgramChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Yilin Li
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- 4+4 Medical Doctor ProgramChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Yuekun Wang
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Hao Xing
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Yu Xia
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- Eight‐year Medical Doctor ProgramChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Junlin Li
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- Eight‐year Medical Doctor ProgramChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Jiaming Wu
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- Eight‐year Medical Doctor ProgramChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Tingyu Liang
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Hai Wang
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Qianshu Liu
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- Eight‐year Medical Doctor ProgramChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Shanmu Jin
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- 4+4 Medical Doctor ProgramChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Tian Qu
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- Eight‐year Medical Doctor ProgramChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Huanzhang Li
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- Eight‐year Medical Doctor ProgramChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Tianrui Yang
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- Eight‐year Medical Doctor ProgramChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Kun Zhang
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- Eight‐year Medical Doctor ProgramChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Yu Wang
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- China Anti‐Cancer Association Specialty Committee of GliomaBeijingChina
| | - Wenbin Ma
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- China Anti‐Cancer Association Specialty Committee of GliomaBeijingChina
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A Composite Bioinformatic Analysis to Explore Endoplasmic Reticulum Stress-Related Prognostic Marker and Potential Pathogenic Mechanisms in Glioma by Integrating Multiomics Data. JOURNAL OF ONCOLOGY 2022; 2022:9886044. [PMID: 36245971 PMCID: PMC9553508 DOI: 10.1155/2022/9886044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/18/2022] [Accepted: 08/14/2022] [Indexed: 11/18/2022]
Abstract
In recent years, abnormal endoplasmic reticulum stress (ERS) response, as an important regulator of immunity, may play a vital role in the occurrence, development, and treatment of glioma. Weighted correlation network analysis (WGCNA) based on six glioma datasets was used to screen eight prognostic-related differentially expressed ERS-related genes (PR-DE-ERSGs) and to construct a prognostic model. BMP2 and HEY2 were identified as protective factors (HR < 1), and NUP107, DRAM1, F2R, PXDN, RNF19A, and SCG5 were identified as risk factors for glioma (HR > 1). QRT-PCR further supported significantly higher DRAM1 and lower SCG5 relative mRNA expression in gliomas. Our model has demonstrated excellent performance in predicting the prognosis of glioma patients from numerous datasets. In addition, the model shows good stability in multiple tests. Our model also shows broad clinical promise in predicting drug treatment effects. More immune cells/processes in the high-risk population with poor prognosis illustrate the importance of the tumor immunosuppressive environment in glioma. The potential role of the HEY2-based competitive endogenous RNA (ceRNA) regulatory network in glioma was validated and revealed the possible important role of glycolysis in glioma ERS. IDH1 and TP53 mutations with better prognosis were strongly associated with the risk score and PR-DE-ERSGs expression in the model. mDNAsi was also closely related to the risk score and clinical characteristics.
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8
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Fan X, Nie X, Huang J, Zhang L, Wang X, Lu M. A Composite Bioinformatic Analysis to Explore Endoplasmic Reticulum Stress-Related Prognostic Marker and Potential Pathogenic Mechanisms in Glioma by Integrating Multiomics Data. JOURNAL OF ONCOLOGY 2022. [DOI: https:/doi.org/10.1155/2022/9886044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
In recent years, abnormal endoplasmic reticulum stress (ERS) response, as an important regulator of immunity, may play a vital role in the occurrence, development, and treatment of glioma. Weighted correlation network analysis (WGCNA) based on six glioma datasets was used to screen eight prognostic-related differentially expressed ERS-related genes (PR-DE-ERSGs) and to construct a prognostic model. BMP2 and HEY2 were identified as protective factors (HR < 1), and NUP107, DRAM1, F2R, PXDN, RNF19A, and SCG5 were identified as risk factors for glioma (HR > 1). QRT-PCR further supported significantly higher DRAM1 and lower SCG5 relative mRNA expression in gliomas. Our model has demonstrated excellent performance in predicting the prognosis of glioma patients from numerous datasets. In addition, the model shows good stability in multiple tests. Our model also shows broad clinical promise in predicting drug treatment effects. More immune cells/processes in the high-risk population with poor prognosis illustrate the importance of the tumor immunosuppressive environment in glioma. The potential role of the HEY2-based competitive endogenous RNA (ceRNA) regulatory network in glioma was validated and revealed the possible important role of glycolysis in glioma ERS. IDH1 and TP53 mutations with better prognosis were strongly associated with the risk score and PR-DE-ERSGs expression in the model. mDNAsi was also closely related to the risk score and clinical characteristics.
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Affiliation(s)
- Xin Fan
- Department of Emergency, Shangrao Hospital Affiliated to Nanchang University, Shangrao People’s Hospital, Shangrao 334000, China
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Nanchang University, Nanchang 330000, China
| | - Xiyi Nie
- Department of Neurosurgery, Yichun Hospital Affiliated to Nanchang University, Yichun People’s Hospital, Yichun 334000, China
| | - Junwen Huang
- The First Clinical Medical College of Nanchang University, Nanchang 330000, China
| | - Lingling Zhang
- School of Stomatology, Nanchang University, Nanchang 330000, China
| | - Xifu Wang
- Department of Emergency, Shangrao Hospital Affiliated to Nanchang University, Shangrao People’s Hospital, Shangrao 334000, China
| | - Min Lu
- Department of Emergency, Shangrao Hospital Affiliated to Nanchang University, Shangrao People’s Hospital, Shangrao 334000, China
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9
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Fan X, Nie X, Huang J, Zhang L, Wang X, Lu M. A Composite Bioinformatic Analysis to Explore Endoplasmic Reticulum Stress-Related Prognostic Marker and Potential Pathogenic Mechanisms in Glioma by Integrating Multiomics Data. JOURNAL OF ONCOLOGY 2022. [DOI: doi.org/10.1155/2022/9886044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
In recent years, abnormal endoplasmic reticulum stress (ERS) response, as an important regulator of immunity, may play a vital role in the occurrence, development, and treatment of glioma. Weighted correlation network analysis (WGCNA) based on six glioma datasets was used to screen eight prognostic-related differentially expressed ERS-related genes (PR-DE-ERSGs) and to construct a prognostic model. BMP2 and HEY2 were identified as protective factors (HR < 1), and NUP107, DRAM1, F2R, PXDN, RNF19A, and SCG5 were identified as risk factors for glioma (HR > 1). QRT-PCR further supported significantly higher DRAM1 and lower SCG5 relative mRNA expression in gliomas. Our model has demonstrated excellent performance in predicting the prognosis of glioma patients from numerous datasets. In addition, the model shows good stability in multiple tests. Our model also shows broad clinical promise in predicting drug treatment effects. More immune cells/processes in the high-risk population with poor prognosis illustrate the importance of the tumor immunosuppressive environment in glioma. The potential role of the HEY2-based competitive endogenous RNA (ceRNA) regulatory network in glioma was validated and revealed the possible important role of glycolysis in glioma ERS. IDH1 and TP53 mutations with better prognosis were strongly associated with the risk score and PR-DE-ERSGs expression in the model. mDNAsi was also closely related to the risk score and clinical characteristics.
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Affiliation(s)
- Xin Fan
- Department of Emergency, Shangrao Hospital Affiliated to Nanchang University, Shangrao People’s Hospital, Shangrao 334000, China
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Nanchang University, Nanchang 330000, China
| | - Xiyi Nie
- Department of Neurosurgery, Yichun Hospital Affiliated to Nanchang University, Yichun People’s Hospital, Yichun 334000, China
| | - Junwen Huang
- The First Clinical Medical College of Nanchang University, Nanchang 330000, China
| | - Lingling Zhang
- School of Stomatology, Nanchang University, Nanchang 330000, China
| | - Xifu Wang
- Department of Emergency, Shangrao Hospital Affiliated to Nanchang University, Shangrao People’s Hospital, Shangrao 334000, China
| | - Min Lu
- Department of Emergency, Shangrao Hospital Affiliated to Nanchang University, Shangrao People’s Hospital, Shangrao 334000, China
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Dong J, Zhao H, Wang F, Jin J, Ji H, Yan X, Wang N, Zhang J, Hu S. Ferroptosis-Related Gene Contributes to Immunity, Stemness and Predicts Prognosis in Glioblastoma Multiforme. Front Neurol 2022; 13:829926. [PMID: 35359663 PMCID: PMC8960280 DOI: 10.3389/fneur.2022.829926] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/31/2022] [Indexed: 12/22/2022] Open
Abstract
Ferroptosis, a recently discovered regulated programmed cell death, is associated with tumorigenesis and progression in glioblastoma. Based on widely recognized ferroptosis-related genes (FRGs), the regulation of ferroptosis patterns and corresponding characteristics of immune infiltration of 516 GBM samples with GSE13041, TCGA-GBM, and CGGA-325 were comprehensively analyzed. Here, we revealed the expression, mutations, and CNV of FRGs in GBM. We identified three distinct regulation patterns of ferroptosis and found the hub genes of immunity and stemness among DEGs in three patterns. A prognostic model was constructed based on five FRGs and verified at the mRNA and protein level. The risk score can not only predict the prognosis but also the degree of immune infiltration and ICB responsiveness by functional annotation. The overall assessment of FRGs in GBM patients will guide the direction of improved research and develop new prognostic prediction tools.
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Affiliation(s)
- Jiawei Dong
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Hongtao Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Fang Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Jiaqi Jin
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Hang Ji
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Xiuwei Yan
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Nan Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Jiheng Zhang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Shaoshan Hu
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
- *Correspondence: Shaoshan Hu
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Huang LE. Impact of CDKN2A/B Homozygous Deletion on the Prognosis and Biology of IDH-Mutant Glioma. Biomedicines 2022; 10:biomedicines10020246. [PMID: 35203456 PMCID: PMC8869746 DOI: 10.3390/biomedicines10020246] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 12/13/2022] Open
Abstract
Although hotspot mutations in isocitrate dehydrogenase (IDH) genes are associated with favorable clinical outcomes in glioma, CDKN2A/B homozygous deletion has been identified as an independent predicator of poor prognosis. Accordingly, the 2021 edition of the World Health Organization (WHO) classification of tumors of the central nervous system (CNS) has adopted this molecular feature by upgrading IDH-mutant astrocytoma to CNS WHO grade IV, even in the absence of glioblastoma-specific histological features—necrosis and microvascular proliferation. This new entity of IDH-mutant astrocytoma not only signifies an exception to the generally favorable outcome of IDH-mutant glioma, but also brings into question whether, and, if so, how, CDKN2A/B homozygous deletion overrides the anti-tumor activity of IDH mutation by promoting the proliferation of stem/neural progenitor-like cells. Understanding the mechanism by which IDH mutation requires intact tumor-suppressor genes for conferring favorable outcome may improve therapeutics.
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Affiliation(s)
- L. Eric Huang
- Department of Neurosurgery, Clinical Neurosciences Center, University of Utah, Salt Lake City, UT 84132, USA;
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
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