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He Z, Peng Y, Wang D, Yang C, Zhou C, Gong B, Song S, Wang Y. Single-cell transcriptomic analysis identifies downregulated phosphodiesterase 8B as a novel oncogene in IDH-mutant glioma. Front Immunol 2024; 15:1427200. [PMID: 38989284 PMCID: PMC11233524 DOI: 10.3389/fimmu.2024.1427200] [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: 05/03/2024] [Accepted: 06/04/2024] [Indexed: 07/12/2024] Open
Abstract
Introduction Glioma, a prevalent and deadly brain tumor, is marked by significant cellular heterogeneity and metabolic alterations. However, the comprehensive cell-of-origin and metabolic landscape in high-grade (Glioblastoma Multiforme, WHO grade IV) and low-grade (Oligoastrocytoma, WHO grade II) gliomas remains elusive. Methods In this study, we undertook single-cell transcriptome sequencing of these glioma grades to elucidate their cellular and metabolic distinctions. Following the identification of cell types, we compared metabolic pathway activities and gene expressions between high-grade and low-grade gliomas. Results Notably, astrocytes and oligodendrocyte progenitor cells (OPCs) exhibited the most substantial differences in both metabolic pathways and gene expression, indicative of their distinct origins. The comprehensive analysis identified the most altered metabolic pathways (MCPs) and genes across all cell types, which were further validated against TCGA and CGGA datasets for clinical relevance. Discussion Crucially, the metabolic enzyme phosphodiesterase 8B (PDE8B) was found to be exclusively expressed and progressively downregulated in astrocytes and OPCs in higher-grade gliomas. This decreased expression identifies PDE8B as a metabolism-related oncogene in IDH-mutant glioma, marking its dual role as both a protective marker for glioma grading and prognosis and as a facilitator in glioma progression.
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Affiliation(s)
- Zongze He
- Department of Neurosurgery, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Yu Peng
- Department of Academic Journal, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Duo Wang
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Chen Yang
- Department of Neurosurgery, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Chengzhi Zhou
- Department of Neurosurgery, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Bo Gong
- Department of Health Management, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- The Key Laboratory for Human Disease Gene Study of Sichuan Province and Institute of Laboratory Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Siyuan Song
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
| | - Yi Wang
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- Clinical Immunology Translational Medicine Key Laboratory of Sichuan Province, Center of Organ Transplantation, Sichuan Academy of Medical Science and Sichuan Provincial People’s Hospital, Chengdu, China
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Wang H, Zhu X, Zhao F, Guo P, Li J, Du J, Shan G, Li Y, Li J. Integrative analysis of single-cell and bulk RNA-sequencing data revealed disulfidptosis genes-based molecular subtypes and a prognostic signature in lung adenocarcinoma. Aging (Albany NY) 2024; 16:2753-2773. [PMID: 38319721 PMCID: PMC10911368 DOI: 10.18632/aging.205509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 11/02/2023] [Indexed: 02/07/2024]
Abstract
BACKGROUND Disulfidoptosis is an unconventional form of programmed cell death that distinguishes itself from well-established cell death pathways like ferroptosis, pyroptosis, and necroptosis. METHODS Initially, we conducted a single-cell analysis of the GSE131907 dataset from the GEO database to identify disulfidoptosis-related genes (DRGs). We utilized differentially expressed DRGs to classify TCGA samples with an unsupervised clustering algorithm. Prognostic models were built using Cox regression and LASSO regression. RESULTS Two DRG-related clusters (C1 and C2) were identified based on the DEGs from single-cell sequencing data analysis. In comparison to C1, C2 exhibited significantly worse overall prognosis, along with lower expression levels of immune checkpoint genes (ICGs) and chemoradiotherapy sensitivity-related genes (CRSGs). Furthermore, C2 displayed a notable enrichment in metabolic pathways and cell cycle-associated mechanisms. C2 was also linked to the development and spread of tumors. We created a prognostic risk model known as the DRG score, which relies on the expression levels of five DRGs. Patients were categorized into high-risk and low-risk groups depending on their DRG score, with the former group being linked to a poorer prognosis and higher TMB score. Moreover, the DRG score displayed significant correlations with CRSGs, ICGs, the tumor immune dysfunction and exclusion (TIDE) score, and chemotherapeutic sensitivity. Subsequently, we identified a significant correlation between the DRG score and monocyte macrophages. Additionally, crucial DRGs were additionally validated using qRT-PCR. CONCLUSIONS Our new DRG score can predict the immune landscape and prognosis of LUAD, serving as a reference for immunotherapy and chemotherapy.
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Affiliation(s)
- Haixia Wang
- Department of Radiation Oncology, The Fifth Clinical Medical College of Henan University of Chinese Medicine, Zhengzhou People’s Hospital, Zhengzhou 450003, China
| | - Xuemei Zhu
- Department of Ultrasound, Jurong Hospital Affiliated to Jiangsu University, Zhenjiang 212000, China
| | - Fangchao Zhao
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang 050000, China
| | - Pengfei Guo
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang 050000, China
| | - Jing Li
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang 050000, China
| | - Jingfang Du
- Department of Clinical Medicine, Hebei University of Engineering, Handan 056002, China
| | - Guoyong Shan
- Department of Radiation Oncology, The Fifth Clinical Medical College of Henan University of Chinese Medicine, Zhengzhou People’s Hospital, Zhengzhou 450003, China
| | - Yishuai Li
- Department of Thoracic Surgery, Hebei Chest Hospital, Shijiazhuang 050000, China
| | - Juan Li
- School of Nursing, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian 271000, China
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Gallus M, Kwok D, Lakshmanachetty S, Yamamichi A, Okada H. Immunotherapy Approaches in Isocitrate-Dehydrogenase-Mutant Low-Grade Glioma. Cancers (Basel) 2023; 15:3726. [PMID: 37509387 PMCID: PMC10378701 DOI: 10.3390/cancers15143726] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/17/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Low-grade gliomas (LGGs) are slow-growing tumors in the central nervous system (CNS). Patients characteristically show the onset of seizures or neurological deficits due to the predominant LGG location in high-functional brain areas. As a molecular hallmark, LGGs display mutations in the isocitrate dehydrogenase (IDH) enzymes, resulting in an altered cellular energy metabolism and the production of the oncometabolite D-2-hydroxyglutarate. Despite the remarkable progress in improving the extent of resection and adjuvant radiotherapy and chemotherapy, LGG remains incurable, and secondary malignant transformation is often observed. Therefore, novel therapeutic approaches are urgently needed. In recent years, immunotherapeutic strategies have led to tremendous success in various cancer types, but the effect of immunotherapy against glioma has been limited due to several challenges, such as tumor heterogeneity and the immunologically "cold" tumor microenvironment. Nevertheless, recent preclinical and clinical findings from immunotherapy trials are encouraging and offer a glimmer of hope for treating IDH-mutant LGG patients. Here, we aim to review the lessons learned from trials involving vaccines, T-cell therapies, and IDH-mutant inhibitors and discuss future approaches to enhance the efficacy of immunotherapies in IDH-mutant LGG.
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Affiliation(s)
- Marco Gallus
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
- Department of Neurosurgery, University Hospital Muenster, 48149 Muenster, Germany
| | - Darwin Kwok
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
| | | | - Akane Yamamichi
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
| | - Hideho Okada
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, CA 94143, USA
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Shen N, Chen S, Liu D, Min X, Tan Q. Cuproptosis-related classification and personalized treatment in lower-grade gliomas to prompt precise oncology. J Gene Med 2023; 25:e3486. [PMID: 36814111 DOI: 10.1002/jgm.3486] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/07/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Cuproptosis is implicated in regulating tricarboxylic acid cycle and associated with tumor therapeutic sensitivity, patient outcomes and tumorigenesis. However, the classification and prognostic effect of cuproptosis-associated genes (CAGs), the relationship between cuproptosis and tumor microenvironment (TME) and the treatment of lower-grade glioma (LrGG) remain enigmatic. METHODS The genetic and transcriptional alterations, prognostic value and classification related to cuproptosis were systematically analyzed. Subtypes of cuproptosis and cuproptosis score (Cuscore) were constructed and further confirmed by two external cohorts. The relationships between cuproptosis and TME, prognosis, and treatment response were also evaluated. RESULTS Four clusters were identified based on cuproptosis-associated genes. The associations between cuproptosis-associated clusters and clinical features, prognosis, immune cell infiltration, and chemotherapy sensitivity were observed. The Cuscore is an independent prognostic indicator in LrGG patients. The nomogram is constructed according to Cuscore and clinical characteristics, and has good predictive ability and calibration. Patients with high Cuscore had a worse prognosis and advanced performance. A higher Cuscore also indicated a higher stromal score, abundant immune infiltration, and increased tumor mutation burden. A high Cuscore was remarkably related to immune checkpoint inhibitors, immunotherapy response and immune phenotype. CONCLUSIONS This study demonstrates the clinical effect of CAGs, and suggests that cuproptosis could be a potential therapeutic target in LrGG.
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Affiliation(s)
- Nanxi Shen
- Department of Radiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shu Chen
- United Imaging Intelligence, Shanghai, China
| | - Dong Liu
- Department of Radiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiangde Min
- Department of Radiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qinghai Tan
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Zhang Y, Yu B, Tian Y, Ren P, Lyu B, Fu L, Chen H, Li J, Gong S. A novel risk score model based on fourteen chromatin regulators-based genes for predicting overall survival of patients with lower-grade gliomas. Front Genet 2022; 13:957059. [PMID: 36246611 PMCID: PMC9554745 DOI: 10.3389/fgene.2022.957059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/31/2022] [Indexed: 12/02/2022] Open
Abstract
Background: Low grade gliomas(LGGs) present vexatious management issues for neurosurgeons. Chromatin regulators (CRs) are emerging as a focus of tumor research due to their pivotal role in tumorigenesis and progression. Hence, the goal of the current work was to unveil the function and value of CRs in patients with LGGs. Methods: RNA-Sequencing and corresponding clinical data were extracted from The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA) database. A single-cell RNA-seq dataset was sourced from the Gene Expression Omnibus (GEO) database. Altogether 870 CRs were retrieved from the published articles in top academic journals. The least absolute shrinkage and selection operator (LASSO) algorithm and Cox regression analysis were applied to construct the prognostic risk model. Patients were then assigned into high- and low-risk groups based on the median risk score. The Kaplan–Meier (K-M) survival curve and receiver operating characteristic curve (ROC) were performed to assess the prognostic value. Sequentially, functional enrichment, tumor immune microenvironment, tumor mutation burden, drug prediction, single cell analysis and so on were analyzed to further explore the value of CR-based signature. Finally, the expression of signature genes were validated by immunohistochemistry (IHC) and quantitative real-time PCR (qRT-PCR). Results: We successfully constructed and validated a 14 CRs-based model for predicting the prognosis of patients with LGGs. Moreover, we also found 14 CRs-based model was an independent prognostic factor. Functional analysis revealed that the differentially expressed genes were mainly enriched in tumor and immune related pathways. Subsequently, our research uncovered that LGGs patients with higher risk scores exhibited a higher TMB and were less likely to be responsive to immunotherapy. Meanwhile, the results of drug analysis offered several potential drug candidates. Furthermore, tSNE plots highlighting the magnitude of expression of the genes of interest in the cells from the scRNA-seq assay. Ultimately, transcription expression of six representative signature genes at the mRNA level was consistent with their protein expression changes. Conclusion: Our findings provided a reliable biomarker for predicting the prognosis, which is expected to offer new insight into LGGs management and would hopefully become a promising target for future research.
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Affiliation(s)
- Yongfeng Zhang
- Department of Neurourgery, The Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Beibei Yu
- Department of Neurourgery, The Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Yunze Tian
- Department of Neurourgery, The Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Pengyu Ren
- Department of Neurourgery, The Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Boqiang Lyu
- Department of Neurourgery, The Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Longhui Fu
- Department of Neurourgery, The Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Huangtao Chen
- Department of Neurourgery, The Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
| | - Jianzhong Li
- Department of Thoracic Surgery, The Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
- *Correspondence: Jianzhong Li, ; Shouping Gong,
| | - Shouping Gong
- Department of Neurourgery, The Second Affiliated Hospital of Xi’an Jiao Tong University, Xi’an, China
- *Correspondence: Jianzhong Li, ; Shouping Gong,
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Wang R, Zhao L, Wang S, Zhao X, Liang C, Wang P, Li D. Regulatory pattern of abnormal promoter CpG island methylation in the glioblastoma multiforme classification. Front Genet 2022; 13:989985. [PMID: 36199581 PMCID: PMC9527345 DOI: 10.3389/fgene.2022.989985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/30/2022] [Indexed: 11/15/2022] Open
Abstract
Glioblastoma (GBM) is characterized by extensive genetic and phenotypic heterogeneity. However, it remains unexplored primarily how CpG island methylation abnormalities in promoter mediate glioblastoma typing. First, we presented a multi-omics scale map between glioblastoma sample clusters constructed based on promoter CpG island (PCGI) methylation-driven genes, using datasets including methylation profiles, expression profiles, and single-cell sequencing data from multiple highly annotated public clinical cohorts. Second, we identified differences in the tumor microenvironment between the two glioblastoma sample clusters and resolved key signaling pathways between cell clusters at the single-cell level based on comprehensive comparative analyses to investigate the reasons for survival differences between two of these clusters. Finally, we developed a diagnostic map and a prediction model for glioblastoma, and compared theoretical differences of drug sensitivity between two glioblastoma sample clusters. In summary, this study established a classification system for dissecting promoter CpG island methylation heterogeneity in glioblastoma and provides a new perspective for the diagnosis and treatment of glioblastoma.
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Affiliation(s)
- Rendong Wang
- School of Biomedical Engineering, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical, Capital Medical University, Beijing, China
| | - Lei Zhao
- Department of Anesthesiology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Shijia Wang
- School of Biomedical Engineering, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical, Capital Medical University, Beijing, China
| | - Xiaoxiao Zhao
- School of Biomedical Engineering, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical, Capital Medical University, Beijing, China
| | - Chuanyu Liang
- Department of Anesthesiology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Pei Wang
- Department of Anesthesiology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Dongguo Li
- School of Biomedical Engineering, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical, Capital Medical University, Beijing, China
- *Correspondence: Dongguo Li,
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Bao JH, Lu WC, Duan H, Ye YQ, Li JB, Liao WT, Li YC, Sun YP. Identification of a novel cuproptosis-related gene signature and integrative analyses in patients with lower-grade gliomas. Front Immunol 2022; 13:933973. [PMID: 36045691 PMCID: PMC9420977 DOI: 10.3389/fimmu.2022.933973] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 07/22/2022] [Indexed: 12/20/2022] Open
Abstract
Background Cuproptosis is a newly discovered unique non-apoptotic programmed cell death distinguished from known death mechanisms like ferroptosis, pyroptosis, and necroptosis. However, the prognostic value of cuproptosis and the correlation between cuproptosis and the tumor microenvironment (TME) in lower-grade gliomas (LGGs) remain unknown. Methods In this study, we systematically investigated the genetic and transcriptional variation, prognostic value, and expression patterns of cuproptosis-related genes (CRGs). The CRG score was applied to quantify the cuproptosis subtypes. We then evaluated their values in the TME, prognostic prediction, and therapeutic responses in LGG. Lastly, we collected five paired LGG and matched normal adjacent tissue samples from Sun Yat-sen University Cancer Center (SYSUCC) to verify the expression of signature genes by quantitative real-time PCR (qRT-PCR) and Western blotting (WB). Results Two distinct cuproptosis-related clusters were identified using consensus unsupervised clustering analysis. The correlation between multilayer CRG alterations with clinical characteristics, prognosis, and TME cell infiltration were observed. Then, a well-performed cuproptosis-related risk model (CRG score) was developed to predict LGG patients' prognosis, which was evaluated and validated in two external cohorts. We classified patients into high- and low-risk groups according to the CRG score and found that patients in the low-risk group showed significantly higher survival possibilities than those in the high-risk group (P<0.001). A high CRG score implies higher TME scores, more significant TME cell infiltration, and increased mutation burden. Meanwhile, the CRG score was significantly correlated with the cancer stem cell index, chemoradiotherapy sensitivity-related genes and immune checkpoint genes, and chemotherapeutic sensitivity, indicating the association with CRGs and treatment responses. Univariate and multivariate Cox regression analyses revealed that the CRG score was an independent prognostic predictor for LGG patients. Subsequently, a highly accurate predictive model was established for facilitating the clinical application of the CRG score, showing good predictive ability and calibration. Additionally, crucial CRGs were further validated by qRT-PCR and WB. Conclusion Collectively, we demonstrated a comprehensive overview of CRG profiles in LGG and established a novel risk model for LGG patients' therapy status and prognosis. Our findings highlight the potential clinical implications of CRGs, suggesting that cuproptosis may be the potential therapeutic target for patients with LGG.
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Affiliation(s)
- Jia-hao Bao
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Wei-cheng Lu
- State Key Laboratory of Oncology in Southern China, Department of Anesthesiology, Sun Yat-sen University Cancer Center, Collaborative Innovation for Cancer Medicine, Guangzhou, China
| | - Hao Duan
- Department of Neurosurgery/Neuro-oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Ya-qi Ye
- State Key Laboratory of Oncology in Southern China, Department of Anesthesiology, Sun Yat-sen University Cancer Center, Collaborative Innovation for Cancer Medicine, Guangzhou, China
| | - Jiang-bo Li
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Wen-ting Liao
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China,*Correspondence: Yang-peng Sun, ; Yong-chun Li, ; Wen-ting Liao,
| | - Yong-chun Li
- State Key Laboratory of Oncology in Southern China, Department of Anesthesiology, Sun Yat-sen University Cancer Center, Collaborative Innovation for Cancer Medicine, Guangzhou, China,*Correspondence: Yang-peng Sun, ; Yong-chun Li, ; Wen-ting Liao,
| | - Yang-peng Sun
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China,*Correspondence: Yang-peng Sun, ; Yong-chun Li, ; Wen-ting Liao,
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Li G, Wu Z, Gu J, Zhu Y, Zhang T, Wang F, Huang K, Gu C, Xu K, Zhan R, Shen J. Metabolic Signature-Based Subtypes May Pave Novel Ways for Low-Grade Glioma Prognosis and Therapy. Front Cell Dev Biol 2021; 9:755776. [PMID: 34888308 PMCID: PMC8650219 DOI: 10.3389/fcell.2021.755776] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/09/2021] [Indexed: 12/19/2022] Open
Abstract
Metabolic signatures are frequently observed in cancer and are starting to be recognized as important regulators for tumor progression and therapy. Because metabolism genes are involved in tumor initiation and progression, little is known about the metabolic genomic profiles in low-grade glioma (LGG). Here, we applied bioinformatics analysis to determine the metabolic characteristics of patients with LGG from the Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA). We also performed the ConsensusClusterPlus, the CIBERSORT algorithm, the Estimate software, the R package "GSVA," and TIDE to comprehensively describe and compare the characteristic difference between three metabolic subtypes. The R package WGCNA helped us to identify co-expression modules with associated metabolic subtypes. We found that LGG patients were classified into three subtypes based on 113 metabolic characteristics. MC1 patients had poor prognoses and MC3 patients obtained longer survival times. The different metabolic subtypes had different metabolic and immune characteristics, and may have different response patterns to immunotherapy. Based on the metabolic subtype, different patterns were exhibited that reflected the characteristics of each subtype. We also identified eight potential genetic markers associated with the characteristic index of metabolic subtypes. In conclusion, a comprehensive understanding of metabolism associated characteristics and classifications may improve clinical outcomes for LGG.
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Affiliation(s)
- Ganglei Li
- Department of Neurosurgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Zhanxiong Wu
- School of Electronic Information, Hangzhou Dianzi University, Hangzhou, China
| | - Jun Gu
- Department of Neurosurgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yu Zhu
- Department of Neurosurgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Tiesong Zhang
- Department of Neurosurgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Feng Wang
- Department of Neurosurgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Kaiyuan Huang
- Department of Neurosurgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Chenjie Gu
- Department of Neurosurgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Kangli Xu
- Department of Neurosurgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Renya Zhan
- Department of Neurosurgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jian Shen
- Department of Neurosurgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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Hicks WH, Bird CE, Traylor JI, Shi DD, El Ahmadieh TY, Richardson TE, McBrayer SK, Abdullah KG. Contemporary Mouse Models in Glioma Research. Cells 2021; 10:cells10030712. [PMID: 33806933 PMCID: PMC8004772 DOI: 10.3390/cells10030712] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/20/2021] [Accepted: 03/20/2021] [Indexed: 02/07/2023] Open
Abstract
Despite advances in understanding of the molecular pathogenesis of glioma, outcomes remain dismal. Developing successful treatments for glioma requires faithful in vivo disease modeling and rigorous preclinical testing. Murine models, including xenograft, syngeneic, and genetically engineered models, are used to study glioma-genesis, identify methods of tumor progression, and test novel treatment strategies. Since the discovery of highly recurrent isocitrate dehydrogenase (IDH) mutations in lower-grade gliomas, there is increasing emphasis on effective modeling of IDH mutant brain tumors. Improvements in preclinical models that capture the phenotypic and molecular heterogeneity of gliomas are critical for the development of effective new therapies. Herein, we explore the current status, advancements, and challenges with contemporary murine glioma models.
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Affiliation(s)
- William H. Hicks
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA; (W.H.H.); (C.E.B.); (J.I.T.); (T.Y.E.A.)
| | - Cylaina E. Bird
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA; (W.H.H.); (C.E.B.); (J.I.T.); (T.Y.E.A.)
| | - Jeffrey I. Traylor
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA; (W.H.H.); (C.E.B.); (J.I.T.); (T.Y.E.A.)
| | - Diana D. Shi
- Department of Radiation Oncology, Brigham and Women’s Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA;
| | - Tarek Y. El Ahmadieh
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA; (W.H.H.); (C.E.B.); (J.I.T.); (T.Y.E.A.)
| | - Timothy E. Richardson
- Department of Pathology, Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, TX 75229, USA;
| | - Samuel K. McBrayer
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harrold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
- Correspondence: (S.K.M.); (K.G.A.)
| | - Kalil G. Abdullah
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA; (W.H.H.); (C.E.B.); (J.I.T.); (T.Y.E.A.)
- Harrold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
- Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
- Correspondence: (S.K.M.); (K.G.A.)
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Hajj GNM, Nunes PBC, Roffe M. Genome-wide translation patterns in gliomas: An integrative view. Cell Signal 2020; 79:109883. [PMID: 33321181 DOI: 10.1016/j.cellsig.2020.109883] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 12/01/2020] [Accepted: 12/11/2020] [Indexed: 02/06/2023]
Abstract
Gliomas are the most frequent tumors of the central nervous system (CNS) and include the highly malignant glioblastoma (GBM). Characteristically, gliomas have translational control deregulation related to overactivation of signaling pathways such as PI3K/AKT/mTORC1 and Ras/ERK1/2. Thus, mRNA translation appears to play a dominant role in glioma gene expression patterns. The, analysis of genome-wide translated transcripts, together known as the translatome, may reveal important information for understanding gene expression patterns in gliomas. This review provides a brief overview of translational control mechanisms altered in gliomas with a focus on the current knowledge related to the translatomes of glioma cells and murine glioma models. We present an integrative meta-analysis of selected glioma translatome data with the aim of identifying recurrent patterns of gene expression preferentially regulated at the level of translation and obtaining clues regarding the pathological significance of these alterations. Re-analysis of several translatome datasets was performed to compare the translatomes of glioma models with those of their non-tumor counterparts and to document glioma cell responses to radiotherapy and MNK modulation. The role of recurrently altered genes in the context of translational control and tumorigenesis are discussed.
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Affiliation(s)
- Glaucia Noeli Maroso Hajj
- International Research Institute, A.C.Camargo Cancer Center, Rua Taguá, 440, São Paulo ZIP Code: 01508-010, Brazil; National Institute of Oncogenomics and Innovation, Brazil.
| | - Paula Borzino Cordeiro Nunes
- International Research Institute, A.C.Camargo Cancer Center, Rua Taguá, 440, São Paulo ZIP Code: 01508-010, Brazil
| | - Martin Roffe
- International Research Institute, A.C.Camargo Cancer Center, Rua Taguá, 440, São Paulo ZIP Code: 01508-010, Brazil; National Institute of Oncogenomics and Innovation, Brazil.
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11
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Subramanian S, Scheufele K, Mehl M, Biros G. WHERE DID THE TUMOR START? AN INVERSE SOLVER WITH SPARSE LOCALIZATION FOR TUMOR GROWTH MODELS. INVERSE PROBLEMS 2020; 36:045006. [PMID: 33746330 PMCID: PMC7971430 DOI: 10.1088/1361-6420/ab649c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
We present a numerical scheme for solving an inverse problem for parameter estimation in tumor growth models for glioblastomas, a form of aggressive primary brain tumor. The growth model is a reaction-diffusion partial differential equation (PDE) for the tumor concentration. We use a PDE-constrained optimization formulation for the inverse problem. The unknown parameters are the reaction coefficient (proliferation), the diffusion coefficient (infiltration), and the initial condition field for the tumor PDE. Segmentation of Magnetic Resonance Imaging (MRI) scans drive the inverse problem where segmented tumor regions serve as partial observations of the tumor concentration. Like most cases in clinical practice, we use data from a single time snapshot. Moreover, the precise time relative to the initiation of the tumor is unknown, which poses an additional difficulty for inversion. We perform a frozen-coefficient spectral analysis and show that the inverse problem is severely ill-posed. We introduce a biophysically motivated regularization on the structure and magnitude of the tumor initial condition. In particular, we assume that the tumor starts at a few locations (enforced with a sparsity constraint on the initial condition of the tumor) and that the initial condition magnitude in the maximum norm is equal to one. We solve the resulting optimization problem using an inexact quasi-Newton method combined with a compressive sampling algorithm for the sparsity constraint. Our implementation uses PETSc and AccFFT libraries. We conduct numerical experiments on synthetic and clinical images to highlight the improved performance of our solver over a previously existing solver that uses standard two-norm regularization for the calibration parameters. The existing solver is unable to localize the initial condition. Our new solver can localize the initial condition and recover infiltration and proliferation. In clinical datasets (for which the ground truth is unknown), our solver results in qualitatively different solutions compared to the two-norm regularized solver.
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Affiliation(s)
- Shashank Subramanian
- Oden Institute for Computational Engineering and Sciences, University of Texas at Austin, 201 E. 24th Street, Austin, Texas, USA
| | - Klaudius Scheufele
- Institute for Parallel and Distributed Systems, Universität Stuttgart, Universitatsstraßë38, Stuttgart, Germany
| | - Miriam Mehl
- Institute for Parallel and Distributed Systems, Universität Stuttgart, Universitatsstraßë38, Stuttgart, Germany
| | - George Biros
- Oden Institute for Computational Engineering and Sciences, University of Texas at Austin, 201 E. 24th Street, Austin, Texas, USA
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12
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Naert T, Dimitrakopoulou D, Tulkens D, Demuynck S, Carron M, Noelanders R, Eeckhout L, Van Isterdael G, Deforce D, Vanhove C, Van Dorpe J, Creytens D, Vleminckx K. RBL1 (p107) functions as tumor suppressor in glioblastoma and small-cell pancreatic neuroendocrine carcinoma in Xenopus tropicalis. Oncogene 2020; 39:2692-2706. [PMID: 32001819 DOI: 10.1038/s41388-020-1173-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 01/13/2020] [Accepted: 01/20/2020] [Indexed: 11/09/2022]
Abstract
Alterations of the retinoblastoma and/or the p53 signaling network are associated with specific cancers such as high-grade astrocytoma/glioblastoma, small-cell lung cancer (SCLC), choroid plexus tumors, and small-cell pancreatic neuroendocrine carcinoma (SC-PaNEC). However, the intricate functional redundancy between RB1 and the related pocket proteins RBL1/p107 and RBL2/p130 in suppressing tumorigenesis remains poorly understood. Here we performed lineage-restricted parallel inactivation of rb1 and rbl1 by multiplex CRISPR/Cas9 genome editing in the true diploid Xenopus tropicalis to gain insight into this in vivo redundancy. We show that while rb1 inactivation is sufficient to induce choroid plexus papilloma, combined rb1 and rbl1 inactivation is required and sufficient to drive SC-PaNEC, retinoblastoma and astrocytoma. Further, using a novel Li-Fraumeni syndrome-mimicking tp53 mutant X. tropicalis line, we demonstrate increased malignancy of rb1/rbl1-mutant glioma towards glioblastoma upon concomitant inactivation of tp53. Interestingly, although clinical SC-PaNEC samples are characterized by abnormal p53 expression or localization, in the current experimental models, the tp53 status had little effect on the establishment and growth of SC-PaNEC, but may rather be essential for maintaining chromosomal stability. SCLC was only rarely observed in our experimental setup, indicating requirement of additional or alternative oncogenic insults. In conclusion, we used CRISPR/Cas9 to delineate the tumor suppressor properties of Rbl1, generating new insights in the functional redundancy within the retinoblastoma protein family in suppressing neuroendocrine pancreatic cancer and glioma/glioblastoma.
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Affiliation(s)
- Thomas Naert
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Dionysia Dimitrakopoulou
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Dieter Tulkens
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Suzan Demuynck
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Marjolein Carron
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Rivka Noelanders
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Liza Eeckhout
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | | | - Dieter Deforce
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Christian Vanhove
- Cancer Research Institute Ghent, Ghent, Belgium
- Infinity lab, Ghent University Hospital, Ghent, Belgium
| | - Jo Van Dorpe
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Pathology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - David Creytens
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Pathology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Kris Vleminckx
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
- Cancer Research Institute Ghent, Ghent, Belgium.
- Center for Medical Genetics, Ghent University, Ghent, Belgium.
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13
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Hou PS, hAilín DÓ, Vogel T, Hanashima C. Transcription and Beyond: Delineating FOXG1 Function in Cortical Development and Disorders. Front Cell Neurosci 2020; 14:35. [PMID: 32158381 PMCID: PMC7052011 DOI: 10.3389/fncel.2020.00035] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 02/04/2020] [Indexed: 11/13/2022] Open
Abstract
Forkhead Box G1 (FOXG1) is a member of the Forkhead family of genes with non-redundant roles in brain development, where alteration of this gene's expression significantly affects the formation and function of the mammalian cerebral cortex. FOXG1 haploinsufficiency in humans is associated with prominent differences in brain size and impaired intellectual development noticeable in early childhood, while homozygous mutations are typically fatal. As such, FOXG1 has been implicated in a wide spectrum of congenital brain disorders, including the congenital variant of Rett syndrome, infantile spasms, microcephaly, autism spectrum disorder (ASD) and schizophrenia. Recent technological advances have yielded greater insight into phenotypic variations observed in FOXG1 syndrome, molecular mechanisms underlying pathogenesis of the disease, and multifaceted roles of FOXG1 expression. In this review, we explore the emerging mechanisms of FOXG1 in a range of transcriptional to posttranscriptional events in order to evolve our current view of how a single transcription factor governs the assembly of an elaborate cortical circuit responsible for higher cognitive functions and neurological disorders.
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Affiliation(s)
- Pei-Shan Hou
- Laboratory for Developmental Biology, Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, Tokyo, Japan.,Institute of Anatomy and Cell Biology, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Darren Ó hAilín
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Medical Faculty, University of Freiburg, Freiburg, Germany
| | - Tanja Vogel
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Medical Faculty, University of Freiburg, Freiburg, Germany.,Center for Basics in NeuroModulation (NeuroModul Basics), Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Carina Hanashima
- Laboratory for Developmental Biology, Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, Tokyo, Japan.,Department of Integrative Bioscience and Biomedical Engineering, Graduate School of Advanced Science and Engineering, Waseda University Center for Advanced Biomedical Sciences, Tokyo, Japan
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14
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Shao F, Liu C. Revisit the Candidacy of Brain Cell Types as the Cell(s) of Origin for Human High-Grade Glioma. Front Mol Neurosci 2018. [PMID: 29515370 PMCID: PMC5826356 DOI: 10.3389/fnmol.2018.00048] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
High-grade glioma, particularly, glioblastoma, is the most aggressive cancer of the central nervous system (CNS) in adults. Due to its heterogeneous nature, glioblastoma almost inevitably relapses after surgical resection and radio-/chemotherapy, and is thus highly lethal and associated with a dismal prognosis. Identifying the cell of origin has been considered an important aspect in understanding tumor heterogeneity, thereby holding great promise in designing novel therapeutic strategies for glioblastoma. Taking advantage of genetic lineage-tracing techniques, performed mainly on genetically engineered mouse models (GEMMs), multiple cell types in the CNS have been suggested as potential cells of origin for glioblastoma, among which adult neural stem cells (NSCs) and oligodendrocyte precursor cells (OPCs) are the major candidates. However, it remains highly debated whether these cell types are equally capable of transforming in patients, given that in the human brain, some cell types divide so slowly, therefore may never have a chance to transform. With the recent advances in studying adult NSCs and OPCs, particularly from the perspective of comparative biology, we now realize that notable differences exist among mammalian species. These differences have critical impacts on shaping our understanding of the cell of origin of glioma in humans. In this perspective, we update the current progress in this field and clarify some misconceptions with inputs from important findings about the biology of adult NSCs and OPCs. We propose to re-evaluate the cellular origin candidacy of these cells, with an emphasis on comparative studies between animal models and humans.
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Affiliation(s)
- Fangjie Shao
- Department of Pathology and Pathophysiology, Zhejiang University School of Medicine, Hangzhou, China
| | - Chong Liu
- Department of Pathology and Pathophysiology, Zhejiang University School of Medicine, Hangzhou, China
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