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Wang D, Shi Y, Cheng Z, Luo L, Cheng K, Gan S, Liu C, Chen Z, Yang B. A Toxoplasma gondii thioredoxin with cell adhesion and antioxidant function. Front Cell Infect Microbiol 2024; 14:1404120. [PMID: 39211799 PMCID: PMC11358088 DOI: 10.3389/fcimb.2024.1404120] [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: 03/20/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024] Open
Abstract
Background Toxoplasma gondii (T. gondii) is a widespread, zoonotic protozoan intracellular parasite with a complex life cycle, which can cause toxoplasmosis, a potentially serious disease. During the invasion process, T. gondii proteins first bind to the relevant host cell receptors, such as glycosaminoglycan molecule (GAG-binding motif), which is one of the main receptors for parasites or virus to infect host cells. However, research on TGME49_216510 (T. gondii Trx21), a protein from Toxoplasma gondii, is limited. Methods Bioinformatics analysis of the Trx21 protein was performed firstly. And specific primers were then designed using the conserved domain and GAG-binding motif to amplify, express, and purify a fragment of the Trx21 protein. The purified Trx21-GST protein was used for antioxidant and cell adhesion experiments. Simultaneously, mice were immunized with Trx21-His to generate specific polyclonal antibodies for subcellular localization analysis. Results The Trx21 protein, consisting of 774 amino acids, included a transmembrane region, three GAG-binding motifs, and a Thioredoxin-like domain. The recombinant Trx21-His protein had a molecular mass of about 31 kDa, while the Trx21-GST protein had a molecular mass of about 55 kDa, which was analyzed by SDS-PAGE and Western blot. Subcellular localization analysis by IFA revealed that Trx21 is predominantly distributed in the cytoplasm of T. gondii. Furthermore, Trx21 exhibited a protective effect on supercoiled DNA against metal-catalyzed oxidation (MCO) and demonstrated adhesion abilities to Vero cells. Conclusions These results indicate that Trx21 plays an important role in host cell interaction and oxidative damage.
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Affiliation(s)
- Dawei Wang
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, Liaoning, China
- Collaborative Innovation Center for Prevention and Control of Zoonoses, Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Yuyi Shi
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, Liaoning, China
- Collaborative Innovation Center for Prevention and Control of Zoonoses, Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Ziwen Cheng
- Collaborative Innovation Center for Prevention and Control of Zoonoses, Jinzhou Medical University, Jinzhou, Liaoning, China
- College of Basic Medicine, Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Like Luo
- Collaborative Innovation Center for Prevention and Control of Zoonoses, Jinzhou Medical University, Jinzhou, Liaoning, China
- College of Basic Medicine, Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Kuo Cheng
- Collaborative Innovation Center for Prevention and Control of Zoonoses, Jinzhou Medical University, Jinzhou, Liaoning, China
- College of Basic Medicine, Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Shengqi Gan
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, Liaoning, China
- Collaborative Innovation Center for Prevention and Control of Zoonoses, Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Che Liu
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, Liaoning, China
- Collaborative Innovation Center for Prevention and Control of Zoonoses, Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Zeliang Chen
- Collaborative Innovation Center for Prevention and Control of Zoonoses, Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Baoling Yang
- Collaborative Innovation Center for Prevention and Control of Zoonoses, Jinzhou Medical University, Jinzhou, Liaoning, China
- College of Basic Medicine, Jinzhou Medical University, Jinzhou, Liaoning, China
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Lin X, Wang C, Zheng J, Liu M, Li M, Xu H, Dong H. Image Omics Nomogram Based on Incoherent Motion Diffusion-Weighted Imaging in Voxels Predicts ATRX Gene Mutation Status of Brain Glioma Patients. JOURNAL OF IMAGING INFORMATICS IN MEDICINE 2024; 37:1336-1345. [PMID: 38378963 PMCID: PMC11300756 DOI: 10.1007/s10278-024-00984-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/04/2023] [Accepted: 11/14/2023] [Indexed: 02/22/2024]
Abstract
This study aimed to construct an imaging genomics nomogram based on intravoxel incoherent motion diffusion-weighted imaging (IVIM-DWI) to predict the status of the alpha thalassemia/mental retardation syndrome X-linked (ATRX) gene in patients with brain gliomas. We retrospectively analyzed routine MR and IVIM-DWI data from 85 patients with pathologically confirmed brain gliomas from January 2017 to May 2023. The data were divided into a training set (N=61) and a test set (N=24) in a 7:3 ratio. Regions of interest (ROIs) of brain gliomas, including the solid tumor region (rCET), edema region (rE), and necrotic region (rNec), were delineated using 3D-Slicer software and projected onto the D, D*, and f sequences. A total of 1037 features were extracted from each ROI, resulting in 3111 features per patient. Age was incorporated in the calculation of the Radscore, and a clinical-imaging genomics combined model was constructed, from which a nomogram graph was generated. Separate models were built for the D, D*, and f parameters. The AUC value of the D parameter model was 0.97 (95% CI: 0.93-1.00) in the training set and 0.91 (95% CI: 0.79-1.00) in the validation set, which was significantly higher than that of the D* parameter model (0.90, 0.82) and the f parameter model (0.89, 0.91). The imaging genomics nomogram based on IVIM-DWI can effectively predict the ATRX gene status of patients with brain gliomas, with the D parameter showing the highest efficacy.
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Affiliation(s)
- Xueyao Lin
- Department of Radiology, Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo, China
| | - Chaochao Wang
- Department of Radiology, Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo, China
| | - Jingjing Zheng
- Department of Radiology, Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo, China
| | - Mengru Liu
- Department of Radiology, Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo, China
| | - Ming Li
- Department of Radiology, Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo, China
| | - Hongbin Xu
- Department of Radiology, Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo, China
| | - Haibo Dong
- Department of Radiology, Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo, China.
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Richardson TE, Walker JM, Hambardzumyan D, Brem S, Hatanpaa KJ, Viapiano MS, Pai B, Umphlett M, Becher OJ, Snuderl M, McBrayer SK, Abdullah KG, Tsankova NM. Genetic and epigenetic instability as an underlying driver of progression and aggressive behavior in IDH-mutant astrocytoma. Acta Neuropathol 2024; 148:5. [PMID: 39012509 PMCID: PMC11252228 DOI: 10.1007/s00401-024-02761-7] [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: 05/23/2024] [Revised: 06/28/2024] [Accepted: 06/29/2024] [Indexed: 07/17/2024]
Abstract
In recent years, the classification of adult-type diffuse gliomas has undergone a revolution, wherein specific molecular features now represent defining diagnostic criteria of IDH-wild-type glioblastomas, IDH-mutant astrocytomas, and IDH-mutant 1p/19q-codeleted oligodendrogliomas. With the introduction of the 2021 WHO CNS classification, additional molecular alterations are now integrated into the grading of these tumors, given equal weight to traditional histologic features. However, there remains a great deal of heterogeneity in patient outcome even within these established tumor subclassifications that is unexplained by currently codified molecular alterations, particularly in the IDH-mutant astrocytoma category. There is also significant intercellular genetic and epigenetic heterogeneity and plasticity with resulting phenotypic heterogeneity, making these tumors remarkably adaptable and robust, and presenting a significant barrier to the design of effective therapeutics. Herein, we review the mechanisms and consequences of genetic and epigenetic instability, including chromosomal instability (CIN), microsatellite instability (MSI)/mismatch repair (MMR) deficits, and epigenetic instability, in the underlying biology, tumorigenesis, and progression of IDH-mutant astrocytomas. We also discuss the contribution of recent high-resolution transcriptomics studies toward defining tumor heterogeneity with single-cell resolution. While intratumoral heterogeneity is a well-known feature of diffuse gliomas, the contribution of these various processes has only recently been considered as a potential driver of tumor aggressiveness. CIN has an independent, adverse effect on patient survival, similar to the effect of histologic grade and homozygous CDKN2A deletion, while MMR mutation is only associated with poor overall survival in univariate analysis but is highly correlated with higher histologic/molecular grade and other aggressive features. These forms of genomic instability, which may significantly affect the natural progression of these tumors, response to therapy, and ultimately clinical outcome for patients, are potentially measurable features which could aid in diagnosis, grading, prognosis, and development of personalized therapeutics.
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Affiliation(s)
- Timothy E Richardson
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA.
| | - Jamie M Walker
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Dolores Hambardzumyan
- Department of Oncological Sciences, The Tisch Cancer Institute, Mount Sinai Icahn School of Medicine, New York, NY, 10029, USA
- Department of Neurosurgery, Mount Sinai Icahn School of Medicine, New York, NY, 10029, USA
| | - Steven Brem
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Glioblastoma Translational Center of Excellence, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kimmo J Hatanpaa
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Mariano S Viapiano
- Department of Neuroscience and Physiology, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Neurosurgery, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
| | - Balagopal Pai
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Melissa Umphlett
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA
| | - Oren J Becher
- Department of Oncological Sciences, The Tisch Cancer Institute, Mount Sinai Icahn School of Medicine, New York, NY, 10029, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Matija Snuderl
- Department of Pathology, New York University Langone Health, New York, NY, 10016, USA
| | - Samuel K McBrayer
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Kalil G Abdullah
- Department of Neurosurgery, University of Pittsburgh School of Medicine, 200 Lothrop St, Pittsburgh, PA, 15213, USA
- Hillman Comprehensive Cancer Center, University of Pittsburgh Medical Center, 5115 Centre Ave, Pittsburgh, PA, 15232, USA
| | - Nadejda M Tsankova
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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Nayarisseri A, Bandaru S, Khan A, Sharma K, Bhrdwaj A, Kaur M, Ghosh D, Chopra I, Panicker A, Kumar A, Saravanan P, Belapurkar P, Mendonça Junior FJB, Singh SK. Epigenetic dysregulation in cancers by isocitrate dehydrogenase 2 (IDH2). ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 141:223-253. [PMID: 38960475 DOI: 10.1016/bs.apcsb.2023.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Recent advances in genome-wide studies have revealed numerous epigenetic regulations brought about by genes involved in cellular metabolism. Isocitrate dehydrogenase (IDH), an essential enzyme, that converts isocitrate into -ketoglutarate (KG) predominantly in the tricarboxylic acid (TCA) cycle, has gained particular importance due to its cardinal role in the metabolic pathway in cells. IDH1, IDH2, and IDH3 are the three isomeric IDH enzymes that have been shown to regulate cellular metabolism. Of particular importance, IDH2 genes are associated with several cancers, including gliomas, oligodendroglioma, and astrocytomas. These mutations lead to the production of oncometabolite D-2-hydroxyglutarate (D-2-HG), which accumulates in cells promoting tumor growth. The enhanced levels of D-2-HG competitively inhibit α-KG dependent enzymes, inhibiting cell TCA cycle, upregulating the cell growth and survival relevant HIF-1α pathway, promoting DNA hypermethylation related epigenetic activity, all of which synergistically contribute to carcinogenesis. The present review discusses epigenetic mechanisms inIDH2 regulation in cells and further its clinical implications.
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Affiliation(s)
- Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India; Bioinformatics Research Laboratory, LeGene Biosciences Pvt Ltd, Indore, Madhya Pradesh, India.
| | - Srinivas Bandaru
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India; Department of Biotechnology, Koneru Lakshmaiah Educational Foundation (KLEF), Green Fields, Vaddeswaram, Andhra Pradesh, India
| | - Arshiya Khan
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India; Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Khushboo Sharma
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India; Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Anushka Bhrdwaj
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India; Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Manmeet Kaur
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Dipannita Ghosh
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Ishita Chopra
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India; School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
| | - Aravind Panicker
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Abhishek Kumar
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India; Department of Biosciences, Acropolis Institute, Indore, Madhya Pradesh, India
| | - Priyadevi Saravanan
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Pranoti Belapurkar
- Department of Biosciences, Acropolis Institute, Indore, Madhya Pradesh, India
| | | | - Sanjeev Kumar Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
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Malik P, Soliman R, Chen YA, Munoz DG, Das S, Bharatha A, Mathur S. Patterns of T2-FLAIR discordance across a cohort of adult-type diffuse gliomas and deviations from the classic T2-FLAIR mismatch sign. Neuroradiology 2024; 66:521-530. [PMID: 38347151 DOI: 10.1007/s00234-024-03297-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/25/2024] [Indexed: 03/14/2024]
Abstract
PURPOSE T2-FLAIR mismatch serves as a highly specific but insensitive marker for IDH-mutant (IDHm) astrocytoma with potential limitations in real-world application. We aimed to assess the utility of a broader definition of T2-FLAIR discordance across a cohort of adult-type diffuse lower-grade gliomas (LrGG) to see if specific patterns emerge and additionally examine factors determining deviation from the classic T2-FLAIR mismatch sign. METHODS Preoperative MRIs of non-enhancing adult-type diffuse LrGGs were reviewed. Relevant demographic, molecular, and MRI data were compared across tumor subgroups. RESULTS Eighty cases satisfied the inclusion criteria. Highest discordance prevalence and > 50% T2-FLAIR discordance volume were noted with IDHm astrocytomas (P < 0.001), while < 25% discordance volume was associated with oligodendrogliomas (P = 0.03) and IDH-wildtype (IDHw) LrGG (P = 0.004). "T2-FLAIR matched pattern" was associated with IDHw LrGG (P < 0.001) and small or minimal areas of discordance with oligodendrogliomas (P = 0.03). Sensitivity and specificity of classic mismatch sign for IDHm astrocytoma were 25.7% and 100%, respectively (P = 0.06). Retained ATRX expression and/or non-canonical IDH mutation (n = 10) emerged as a significant factor associated with absence of classic T2-FLAIR mismatch sign in IDHm astrocytomas (100%, P = 0.02) and instead had minimal discordance or matched pattern (40%, P = 0.04). CONCLUSION T2-FLAIR discordance patterns in adult-type diffuse LrGGs exist on a diverging but distinct spectrum of classic mismatch to T2-FLAIR matched patterns. Specific molecular markers may play a role in deviations from classic mismatch sign.
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Affiliation(s)
- Prateek Malik
- Division of Neuroradiology, Department of Medical Imaging, St. Michael's Hospital, University of Toronto, 30 Bond St., Toronto, ON, M5B 1W8, Canada
| | - Radwa Soliman
- Diagnostic and Interventional Radiology Department, Assiut University, Asyut, Egypt
| | - Yingming Amy Chen
- Division of Neuroradiology, Department of Medical Imaging, St. Michael's Hospital, University of Toronto, 30 Bond St., Toronto, ON, M5B 1W8, Canada
| | - David G Munoz
- Department of Pathology, St. Michael's Hospital, University of Toronto, Toronto, Canada
| | - Sunit Das
- Division of Neurosurgery, St. Michael's Hospital, University of Toronto, Toronto, Canada
| | - Aditya Bharatha
- Division of Neuroradiology, Department of Medical Imaging, St. Michael's Hospital, University of Toronto, 30 Bond St., Toronto, ON, M5B 1W8, Canada
| | - Shobhit Mathur
- Division of Neuroradiology, Department of Medical Imaging, St. Michael's Hospital, University of Toronto, 30 Bond St., Toronto, ON, M5B 1W8, Canada.
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He Y, Duan L, Dong G, Chen F, Li W. Computational pathology-based weakly supervised prediction model for MGMT promoter methylation status in glioblastoma. Front Neurol 2024; 15:1345687. [PMID: 38385046 PMCID: PMC10880091 DOI: 10.3389/fneur.2024.1345687] [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: 12/01/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024] Open
Abstract
Introduction The methylation status of oxygen 6-methylguanine-DNA methyltransferase (MGMT) is closely related to the treatment and prognosis of glioblastoma. However, there are currently some challenges in detecting the methylation status of MGMT promoters. The hematoxylin and eosin (H&E)-stained histopathological slides have always been the gold standard for tumor diagnosis. Methods In this study, based on the TCGA database and H&E-stained Whole slide images (WSI) of Beijing Tiantan Hospital, we constructed a weakly supervised prediction model of MGMT promoter methylation status in glioblastoma by using two Transformer structure models. Results The accuracy scores of this model in the TCGA dataset and our independent dataset were 0.79 (AUC = 0.86) and 0.76 (AUC = 0.83), respectively. Conclusion The model demonstrates effective prediction of MGMT promoter methylation status in glioblastoma and exhibits some degree of generalization capability. At the same time, our study also shows that adding Patches automatic screening module to the computational pathology research framework of glioma can significantly improve the model effect.
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Affiliation(s)
- Yongqi He
- Department of Neuro-Oncology, Cancer Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ling Duan
- Department of Neuro-Oncology, Cancer Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Gehong Dong
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Feng Chen
- Department of Neuro-Oncology, Cancer Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wenbin Li
- Department of Neuro-Oncology, Cancer Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
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Tang T, Wang Y, Dai Y, Liu Q, Fan X, Cheng Y, Tang J, Xiao X, Shan Y, Wei P, Zhao G. IDH1 mutation predicts seizure occurrence and prognosis in lower-grade glioma adults. Pathol Res Pract 2024; 254:155165. [PMID: 38286053 DOI: 10.1016/j.prp.2024.155165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 01/21/2024] [Accepted: 01/21/2024] [Indexed: 01/31/2024]
Abstract
Epileptic seizures are frequently the first symptom in glioma patients. However, the causal relationship between glioma and epilepsy is not yet fully understood, as it cannot be explained solely by tumor mass effect or peritumoral factors. In this study, we retrospectively enrolled 320 patients with grade 2-4 glioma who received treatment between January 2019 and July 2022, and explored the biomarkers of seizure occurrence and seizure outcome prediction using univariate and multivariate logistic regression analyses. Our results showed that IDH1 R132H mutation was an independent risk factor for seizure occurrence in lower-grade glioma (LGG) patients (OR = 4.915, 95%CI = 1.713 - 14.103, P = 0.003). Additionally, IDH1 R132H mutation predicted higher seizure-free ratios in LGG patients with intact ATRX expression (OR = 6.793, 95%CI = 1.217 - 37.923, P = 0.029) one year after diagnosis. Therefore, our findings suggest that IDH1 mutation can predict seizure occurrence and control in LGG patients, providing further insights into the relationship between glioma and epilepsy.
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Affiliation(s)
- Ting Tang
- Department of Neurosurgery, Xuanwu Hospital Capital Medical University, Beijing 100053, China
| | - Yihe Wang
- Department of Neurosurgery, Xuanwu Hospital Capital Medical University, Beijing 100053, China
| | - Yang Dai
- Department of Neurosurgery, Xuanwu Hospital Capital Medical University, Beijing 100053, China
| | - Quanlei Liu
- Department of Neurosurgery, Xuanwu Hospital Capital Medical University, Beijing 100053, China
| | - Xiaotong Fan
- Department of Neurosurgery, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Clinical Research Center for Epilepsy, Capital Medical University, Beijing 100053, China
| | - Ye Cheng
- Department of Neurosurgery, Xuanwu Hospital Capital Medical University, Beijing 100053, China
| | - Jie Tang
- Department of Neurosurgery, Xuanwu Hospital Capital Medical University, Beijing 100053, China
| | - Xinru Xiao
- Department of Neurosurgery, Xuanwu Hospital Capital Medical University, Beijing 100053, China
| | - Yongzhi Shan
- Department of Neurosurgery, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Clinical Research Center for Epilepsy, Capital Medical University, Beijing 100053, China
| | - Penghu Wei
- Department of Neurosurgery, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Clinical Research Center for Epilepsy, Capital Medical University, Beijing 100053, China.
| | - Guoguang Zhao
- Department of Neurosurgery, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Clinical Research Center for Epilepsy, Capital Medical University, Beijing 100053, China; Beijing Municipal Geriatric Medical Research Center, Beijing 100053, China.
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Hariharan S, Whitfield BT, Pirozzi CJ, Waitkus MS, Brown MC, Bowie ML, Irvin DM, Roso K, Fuller R, Hostettler J, Dharmaiah S, Gibson EA, Briley A, Mangoli A, Fraley C, Shobande M, Stevenson K, Zhang G, Malgulwar PB, Roberts H, Roskoski M, Spasojevic I, Keir ST, He Y, Castro MG, Huse JT, Ashley DM. Interplay between ATRX and IDH1 mutations governs innate immune responses in diffuse gliomas. Nat Commun 2024; 15:730. [PMID: 38272925 PMCID: PMC10810843 DOI: 10.1038/s41467-024-44932-w] [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: 04/24/2023] [Accepted: 01/10/2024] [Indexed: 01/27/2024] Open
Abstract
Stimulating the innate immune system has been explored as a therapeutic option for the treatment of gliomas. Inactivating mutations in ATRX, defining molecular alterations in IDH-mutant astrocytomas, have been implicated in dysfunctional immune signaling. However, little is known about the interplay between ATRX loss and IDH mutation on innate immunity. To explore this, we generated ATRX-deficient glioma models in the presence and absence of the IDH1R132H mutation. ATRX-deficient glioma cells are sensitive to dsRNA-based innate immune agonism and exhibit impaired lethality and increased T-cell infiltration in vivo. However, the presence of IDH1R132H dampens baseline expression of key innate immune genes and cytokines in a manner restored by genetic and pharmacological IDH1R132H inhibition. IDH1R132H co-expression does not interfere with the ATRX deficiency-mediated sensitivity to dsRNA. Thus, ATRX loss primes cells for recognition of dsRNA, while IDH1R132H reversibly masks this priming. This work reveals innate immunity as a therapeutic vulnerability of astrocytomas.
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Affiliation(s)
- Seethalakshmi Hariharan
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Benjamin T Whitfield
- Departments of Pathology and Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher J Pirozzi
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Matthew S Waitkus
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Michael C Brown
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Michelle L Bowie
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - David M Irvin
- Departments of Pathology and Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kristen Roso
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Rebecca Fuller
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Janell Hostettler
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Sharvari Dharmaiah
- Departments of Pathology and Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Emiley A Gibson
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Aaron Briley
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Avani Mangoli
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Casey Fraley
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Mariah Shobande
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Kevin Stevenson
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Gao Zhang
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Prit Benny Malgulwar
- Departments of Pathology and Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hannah Roberts
- Departments of Pathology and Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Martin Roskoski
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Ivan Spasojevic
- PK/PD Core Laboratory, Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA
- Department of Medicine - Oncology, Duke University Medical Center, Durham, NC, USA
| | - Stephen T Keir
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Yiping He
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Maria G Castro
- Department of Neurosurgery, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - Jason T Huse
- Departments of Pathology and Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - David M Ashley
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA.
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA.
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Malgulwar PB, Danussi C, Dharmaiah S, Johnson W, Singh A, Rai K, Rao A, Huse JT. Sirtuin 2 inhibition modulates chromatin landscapes genome-wide to induce senescence in ATRX-deficient malignant glioma. Neuro Oncol 2024; 26:55-67. [PMID: 37625115 PMCID: PMC10769000 DOI: 10.1093/neuonc/noad155] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Functional inactivation of ATRX characterizes large subgroups of malignant gliomas in adults and children. ATRX deficiency in glioma induces widespread chromatin remodeling, driving transcriptional shifts and oncogenic phenotypes. Effective strategies to therapeutically target these broad epigenomic sequelae remain undeveloped. METHODS We utilized integrated multiomics and the Broad Institute Connectivity Map (CMAP) to identify drug candidates that could potentially revert ATRX-deficient transcriptional changes. We then employed disease-relevant experimental models to evaluate functional phenotypes, coupling these studies with epigenomic profiling to elucidate molecular mechanism(s). RESULTS CMAP analysis and transcriptional/epigenomic profiling implicated the Class III HDAC Sirtuin2 (SIRT2) as a central mediator of ATRX-deficient cellular phenotypes and a driver of unfavorable prognosis in ATRX-deficient glioma. SIRT2 inhibitors reverted Atrx-deficient transcriptional signatures in murine neuroepithelial progenitor cells (mNPCs), impaired cell migration in Atrx/ATRX-deficient mNPCs and human glioma stem cells (GSCs), and increased expression of senescence markers in glioma models. Moreover, SIRT2 inhibition impaired growth and increased senescence in ATRX-deficient GSCs in vivo. These effects were accompanied by genome-wide shifts in enhancer-associated H3K27ac and H4K16ac marks, with the latter in particular demonstrating compelling transcriptional links to SIRT2-dependent phenotypic reversals. Motif analysis of these data identified the transcription factor KLF16 as a mediator of phenotype reversal in Atrx-deficient cells upon SIRT2 inhibition. CONCLUSIONS Our findings indicate that SIRT2 inhibition selectively targets ATRX-deficient gliomas for senescence through global chromatin remodeling, while demonstrating more broadly a viable approach to combat complex epigenetic rewiring in cancer.
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Affiliation(s)
- Prit Benny Malgulwar
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Carla Danussi
- Sanofi, Research and Development, Cambridge, Massachusetts, USA
| | - Sharvari Dharmaiah
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - William Johnson
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Anand Singh
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kunal Rai
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Arvind Rao
- Departments of Biostatistics, Computational Medicine and Bioinformatics, and Radiation Oncology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jason T Huse
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Qian H, Ji R, Shen C, Wei Y, Sheng C, Ni Q, Pan J, Chi Y, You H, Miao Y, Shi M, Huang X, Shen A. ATRX is a predictive marker for endocrinotherapy and chemotherapy resistance in HER2-/HR+ breast cancer through the regulation of the AR, GLI3 and GATA2 transcriptional network. Aging (Albany NY) 2023; 15:14996-15024. [PMID: 38126976 PMCID: PMC10781474 DOI: 10.18632/aging.205327] [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: 11/04/2022] [Accepted: 11/01/2023] [Indexed: 12/23/2023]
Abstract
Drug resistance in breast cancer (BC) is a clinical challenge. Exploring the mechanism and identifying a precise predictive biomarker for the drug resistance in BC is critical. Three first-line drug (paclitaxel, doxorubicin and tamoxifen) resistance datasets in BC from GEO were merged to obtain 1,461 differentially expressed genes for weighted correlation network analysis, resulting in identifying ATRX as the hub gene. ATRX is a chromatin remodelling protein, therefore, ATRX-associated transcription factors were explored, thereby identifying the network of AR, GLI3 and GATA2. GO and KEGG analyses revealed immunity, transcriptional regulation and endocrinotherapy/chemotherapy resistance were enriched. Moreover, CIBERSORT revealed immunity regulation was inhibited in the resistance group. ssGSEA showed a significantly lower immune status in the ATRX-Low group compared to the ATRX-High group. Furthermore, the peaks of H3K9me3 ChIP-seq on the four genes were higher in normal tissues than in BC tissues. Notably, the frequency of ATRX mutation was higher than BRCA in BC. Moreover, depressed ATRX revealed worse overall survival and disease-free survival in the human epidermal growth factor receptor 2 (HER2)-/hormone receptor (HR)+ BC. Additionally, depressed ATRX predicted poor results for patients who underwent endocrinotherapy or chemotherapy in the HER2-/HR+ BC subgroup. A nomogram based on ATRX, TILs and ER exhibited a significantly accurate survival prediction ability. Importantly, overexpression of ATRX significantly inhibited the IC50 of the three first-line drugs on MCF-7 cell. Thus, ATRX is an efficient predictive biomarker for endocrinotherapy and chemotherapy resistance in HER2-/HR+ BC and acts by suppressing the AR, GLI3 and GATA2 transcriptional network.
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Affiliation(s)
- Hongyan Qian
- Cancer Research Center Nantong, Nantong Tumor Hospital, Affiliated Tumor Hospital of Nantong University, Nantong 226361, China
| | - Rui Ji
- Department of Gynecology Oncology, Nantong Tumor Hospital, Affiliated Tumor Hospital of Nantong University, Nantong 226361, China
| | - Cheng Shen
- Department of Computer Science and Engineering, Tandon School of Engineering, New York University, Brooklyn, NY 11201, USA
| | - Yinze Wei
- Department of Pathology, Affiliated Tumor Hospital of Nantong University, Nantong 226361, China
| | - Chenyi Sheng
- Department of Breast Surgery, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Qichao Ni
- Department of Breast Surgery, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Jing Pan
- School of Medicine, Nantong University, Nantong 226001, China
| | - Yifan Chi
- School of Medicine, Nantong University, Nantong 226001, China
| | - Huan You
- School of Medicine, Nantong University, Nantong 226001, China
| | - Ying Miao
- School of Medicine, Nantong University, Nantong 226001, China
| | - Minxin Shi
- Department of Surgery, Affiliated Tumor Hospital of Nantong University, Nantong 226361, China
| | - Xianghua Huang
- Department of Surgery, Affiliated Tumor Hospital of Nantong University, Nantong 226361, China
| | - Aiguo Shen
- Cancer Research Center Nantong, Nantong Tumor Hospital, Affiliated Tumor Hospital of Nantong University, Nantong 226361, China
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Hu Y, Shen F, Yang X, Han T, Long Z, Wen J, Huang J, Shen J, Guo Q. Single-cell sequencing technology applied to epigenetics for the study of tumor heterogeneity. Clin Epigenetics 2023; 15:161. [PMID: 37821906 PMCID: PMC10568863 DOI: 10.1186/s13148-023-01574-x] [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: 07/16/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Previous studies have traditionally attributed the initiation of cancer cells to genetic mutations, considering them as the fundamental drivers of carcinogenesis. However, recent research has shed light on the crucial role of epigenomic alterations in various cell types present within the tumor microenvironment, suggesting their potential contribution to tumor formation and progression. Despite these significant findings, the progress in understanding the epigenetic mechanisms regulating tumor heterogeneity has been impeded over the past few years due to the lack of appropriate technical tools and methodologies. RESULTS The emergence of single-cell sequencing has enhanced our understanding of the epigenetic mechanisms governing tumor heterogeneity by revealing the distinct epigenetic layers of individual cells (chromatin accessibility, DNA/RNA methylation, histone modifications, nucleosome localization) and the diverse omics (transcriptomics, genomics, multi-omics) at the single-cell level. These technologies provide us with new insights into the molecular basis of intratumoral heterogeneity and help uncover key molecular events and driving mechanisms in tumor development. CONCLUSION This paper provides a comprehensive review of the emerging analytical and experimental approaches of single-cell sequencing in various omics, focusing specifically on epigenomics. These approaches have the potential to capture and integrate multiple dimensions of individual cancer cells, thereby revealing tumor heterogeneity and epigenetic features. Additionally, this paper outlines the future trends of these technologies and their current technical limitations.
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Affiliation(s)
- Yuhua Hu
- Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, Jiangsu, China
- Graduate School, Dalian Medical University, Dalian, 116044, Liaoning, China
| | - Feng Shen
- Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, Jiangsu, China
- Department of Neurosurgery, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, Jiangsu, China
| | - Xi Yang
- Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Tingting Han
- Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, Jiangsu, China
- Graduate School, Dalian Medical University, Dalian, 116044, Liaoning, China
| | - Zhuowen Long
- Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, Jiangsu, China
| | - Jiale Wen
- Graduate School, Dalian Medical University, Dalian, 116044, Liaoning, China
- Department of Cardiology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, Jiangsu, China
| | - Junxing Huang
- Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, Jiangsu, China.
| | - Jiangfeng Shen
- Department of Thoracic Surgery, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, Jiangsu, China.
| | - Qing Guo
- Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, Jiangsu, China.
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12
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Cao W, Sun P, Luo S, Zeng Z, Xiao C, Yu W, Lei S. An immune signature to predict the prognosis of ATRX-wildtype glioma patients and guide immune checkpoint blockade therapy. Aging (Albany NY) 2023; 15:10453-10472. [PMID: 37812190 PMCID: PMC10599764 DOI: 10.18632/aging.205088] [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: 05/01/2023] [Accepted: 08/21/2023] [Indexed: 10/10/2023]
Abstract
Immune and stromal cells contribute to glioma progression by infiltrating the tumor microenvironment. We used clinical characteristics, RNA sequencing data and the ESTIMATE algorithm to obtain stromal and immune scores for alpha thalassemia retardation syndrome X-linked (ATRX)-mutation-type (ATRX-mt) and ATRX-wildtype (ATRX-wt) glioma tissues from The Cancer Genome Atlas. To identify specific immune biomarkers of glioma, we compared the gene expression profiles of ATRX-wt glioma tissues with high vs. low immune/stromal scores, and discovered 162 differentially expressed genes. The protein-protein interaction network based on these results contained 80 interacting genes, of which seven (HOXA5, PTPN2, WT1, HOXD10, POSTN, ADAMDEC1 and MYBPH) were identified as key prognostic genes via LASSO and Cox regression analyses. A risk model constructed using the expression of these seven genes could predict survival for ATRX-wt glioma patients, but was ineffective for ATRX-mt patients. T cells and macrophages were more prevalent in low-risk than in high-risk glioma tissues. Immune checkpoint blockade treatment was highly beneficial for patients with low risk scores. High-risk gliomas were predicted to be more sensitive to rapamycin, dasatinib, 5-fluorouracil and gemcitabine. Thus, our model can be used for the diagnosis, prognostic prediction and treatment planning of ATRX-wt glioma patients.
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Affiliation(s)
- Wenpeng Cao
- Department of Anatomy, Key Laboratory of Human Brain bank for Functions and Diseases of Department of Education of Guizhou, Guizhou Medical University, Guiyang 550009, Guizhou, China
| | - Ping Sun
- Department of Neurosurgery, The Second People Hospital of Guiyang, Guiyang 550009, Guizhou, China
| | - Shipeng Luo
- Department of Anatomy, Key Laboratory of Human Brain bank for Functions and Diseases of Department of Education of Guizhou, Guizhou Medical University, Guiyang 550009, Guizhou, China
| | - Zhirui Zeng
- Department of Physiology, School of Basic Medicine, Guizhou Medical University, Guiyang 550009, Guizhou, China
| | - Chaolun Xiao
- Department of Anatomy, Key Laboratory of Human Brain bank for Functions and Diseases of Department of Education of Guizhou, Guizhou Medical University, Guiyang 550009, Guizhou, China
| | - Wenfeng Yu
- Department of Anatomy, Key Laboratory of Human Brain bank for Functions and Diseases of Department of Education of Guizhou, Guizhou Medical University, Guiyang 550009, Guizhou, China
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, School of Basic Medicine, Guizhou Medical University, Guiyang 550009, Guizhou, China
- Key Laboratory of Medical Molecular Biology, School of Basic Medicine, Guizhou Medical University, Guiyang 550009, Guizhou, China
| | - Shan Lei
- Department of Physiology, School of Basic Medicine, Guizhou Medical University, Guiyang 550009, Guizhou, China
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Gao MY, Wang JQ, He J, Gao R, Zhang Y, Li X. Single-Cell RNA-Sequencing in Astrocyte Development, Heterogeneity, and Disease. Cell Mol Neurobiol 2023; 43:3449-3464. [PMID: 37552355 DOI: 10.1007/s10571-023-01397-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 07/29/2023] [Indexed: 08/09/2023]
Abstract
Astrocytes are the most plentiful cell type in the central nervous system (CNS) and perform complicated functions in health and disease. It is obvious that different astrocyte subpopulations, or activation states, are relevant with specific genomic programs and functions. In recent years, the emergence of new technologies such as single-cell RNA sequencing (scRNA-seq) has made substantial advance in the characterization of astrocyte heterogeneity, astrocyte developmental trajectory, and its role in CNS diseases which has had a significant impact on neuroscience. In this review, we present an overview of astrocyte development, heterogeneity, and its essential role in the physiological and pathological environments of the CNS. We focused on the critical role of single-cell sequencing in revealing astrocyte development, heterogeneity, and its role in different CNS diseases.
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Affiliation(s)
- Meng-Yuan Gao
- A National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
| | - Jia-Qi Wang
- A National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
| | - Jin He
- A National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
| | - Rui Gao
- A National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
| | - Yuan Zhang
- A National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
| | - Xing Li
- A National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China.
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14
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Chen Y, Pan Y, Gao H, Yi Y, Qin S, Ma F, Zhou X, Guan M. Mechanistic insights into super-enhancer-driven genes as prognostic signatures in patients with glioblastoma. J Cancer Res Clin Oncol 2023; 149:12315-12332. [PMID: 37432454 DOI: 10.1007/s00432-023-05121-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/04/2023] [Indexed: 07/12/2023]
Abstract
BACKGROUND Glioblastoma (GBM) is one of the most common malignant brain tumors in adults and is characterized by high aggressiveness and rapid progression, poor treatment, high recurrence rate, and poor prognosis. Although super-enhancer (SE)-driven genes haven been recognized as prognostic markers for several cancers, whether it can be served as effective prognostic markers for patients with GBM has not been evaluated. METHODS We first combined histone modification data with transcriptome data to identify SE-driven genes associated with prognosis in patients with GBM. Second, we developed a SE-driven differentially expressed genes (SEDEGs) risk score prognostic model by univariate Cox analysis, KM survival analysis, multivariate Cox analysis and least absolute shrinkage and selection operator (LASSO) regression. Its reliability in predicting was verified by two external data sets. Third, through mutation analysis, immune infiltration, we explored the molecular mechanisms of prognostic genes. Next, Genomics of Drug Sensitivity in Cancer (GDSC) and the Connectivity Map (cMap) database were employed to assess different sensitivities to chemotherapeutic agents and small-molecule drug candidates between high- and low-risk patients. Finally, SEanalysis database was chosen to identify SE-driven transcription factors (TFs) regulating prognostic markers which will reveal a potential SE-driven transcriptional regulatory network. RESULTS First, we developed a 11-gene risk score prognostic model (NCF2, MTHFS, DUSP6, G6PC3, HOXB2, EN2, DLEU1, LBH, ZEB1-AS1, LINC01265, and AGAP2-AS1) selected from 1,154 SEDEGs, which is not only an independent prognostic factor for patients, but also can effectively predict the survival rate of patients. The model can effectively predict 1-, 2- and 3-year survival of patients and was validated in external Chinese Glioma Genome Atlas (CGGA) and Gene Expression Omnibus (GEO) datasets. Second, the risk score was positively correlated with the infiltration of regulatory T cell, CD4 memory activated T cell, activated NK cell, neutrophil, resting mast cell, M0 macrophage, and memory B cell. Third, we found that high-risk patients showed higher sensitivity than low-risk patients to both 27 chemotherapeutic agents and 4 small-molecule drug candidates which might benefit further precision therapy for GBM patients. Finally, 13 potential SE-driven TFs imply how SE regulates GBM patient's prognosis. CONCLUSION The SEDEG risk model not only helps to elucidate the impact of SEs on the course of GBM, but also provides a bright future for prognosis determination and choice of treatment for GBM patients.
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Affiliation(s)
- Youran Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, Jiangsu, China
| | - Yi Pan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, Jiangsu, China
| | - Hanyu Gao
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, Jiangsu, China
| | - Yunmeng Yi
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, Jiangsu, China
| | - Shijie Qin
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, Jiangsu, China
| | - Fei Ma
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, Jiangsu, China
| | - Xue Zhou
- School of Chemistry and Biological Engineering, Nanjing Normal University Taizhou College, Taizhou, 225300, China.
| | - Miao Guan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, Jiangsu, China.
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15
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Hariharan S, Whitfield BT, Pirozzi CJ, Waitkus MS, Brown MC, Bowie ML, Irvin DM, Roso K, Fuller R, Hostettler J, Dharmaiah S, Gibson EA, Briley A, Mangoli A, Fraley C, Shobande M, Stevenson K, Zhang G, Malgulwar PB, Roberts H, Roskoski M, Spasojevic I, Keir ST, He Y, Castro MG, Huse JT, Ashley DM. Interplay between ATRX and IDH1 mutations governs innate immune responses in diffuse gliomas. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.20.537594. [PMID: 37131619 PMCID: PMC10153255 DOI: 10.1101/2023.04.20.537594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Stimulating the innate immune system has been explored as a therapeutic option for the treatment of gliomas. Inactivating mutations in ATRX , defining molecular alterations in IDH -mutant astrocytomas, have been implicated in dysfunctional immune signaling. However, little is known about the interplay between ATRX loss and IDH mutation on innate immunity. To explore this, we generated ATRX knockout glioma models in the presence and absence of the IDH1 R 132 H mutation. ATRX-deficient glioma cells were sensitive to dsRNA-based innate immune agonism and exhibited impaired lethality and increased T-cell infiltration in vivo . However, the presence of IDH1 R 132 H dampened baseline expression of key innate immune genes and cytokines in a manner restored by genetic and pharmacological IDH1 R132H inhibition. IDH1 R132H co-expression did not interfere with the ATRX KO-mediated sensitivity to dsRNA. Thus, ATRX loss primes cells for recognition of dsRNA, while IDH1 R132H reversibly masks this priming. This work reveals innate immunity as a therapeutic vulnerability of astrocytoma.
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Wei Y, Li G, Feng J, Wu F, Zhao Z, Bao Z, Zhang W, Su X, Li J, Qi X, Duan Z, Zhang Y, Vega SF, Jakola AS, Sun Y, Carén H, Jiang T, Fan X. Stalled oligodendrocyte differentiation in IDH-mutant gliomas. Genome Med 2023; 15:24. [PMID: 37055795 PMCID: PMC10103394 DOI: 10.1186/s13073-023-01175-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 03/28/2023] [Indexed: 04/15/2023] Open
Abstract
BACKGROUND Roughly 50% of adult gliomas harbor isocitrate dehydrogenase (IDH) mutations. According to the 2021 WHO classification guideline, these gliomas are diagnosed as astrocytomas, harboring no 1p19q co-deletion, or oligodendrogliomas, harboring 1p19q co-deletion. Recent studies report that IDH-mutant gliomas share a common developmental hierarchy. However, the neural lineages and differentiation stages in IDH-mutant gliomas remain inadequately characterized. METHODS Using bulk transcriptomes and single-cell transcriptomes, we identified genes enriched in IDH-mutant gliomas with or without 1p19q co-deletion, we also assessed the expression pattern of stage-specific signatures and key regulators of oligodendrocyte lineage differentiation. We compared the expression of oligodendrocyte lineage stage-specific markers between quiescent and proliferating malignant single cells. The gene expression profiles were validated using RNAscope analysis and myelin staining and were further substantiated using data of DNA methylation and single-cell ATAC-seq. As a control, we assessed the expression pattern of astrocyte lineage markers. RESULTS Genes concordantly enriched in both subtypes of IDH-mutant gliomas are upregulated in oligodendrocyte progenitor cells (OPC). Signatures of early stages of oligodendrocyte lineage and key regulators of OPC specification and maintenance are enriched in all IDH-mutant gliomas. In contrast, signature of myelin-forming oligodendrocytes, myelination regulators, and myelin components are significantly down-regulated or absent in IDH-mutant gliomas. Further, single-cell transcriptomes of IDH-mutant gliomas are similar to OPC and differentiation-committed oligodendrocyte progenitors, but not to myelinating oligodendrocyte. Most IDH-mutant glioma cells are quiescent; quiescent cells and proliferating cells resemble the same differentiation stage of oligodendrocyte lineage. Mirroring the gene expression profiles along the oligodendrocyte lineage, analyses of DNA methylation and single-cell ATAC-seq data demonstrate that genes of myelination regulators and myelin components are hypermethylated and show inaccessible chromatin status, whereas regulators of OPC specification and maintenance are hypomethylated and show open chromatin status. Markers of astrocyte precursors are not enriched in IDH-mutant gliomas. CONCLUSIONS Our studies show that despite differences in clinical manifestation and genomic alterations, all IDH-mutant gliomas resemble early stages of oligodendrocyte lineage and are stalled in oligodendrocyte differentiation due to blocked myelination program. These findings provide a framework to accommodate biological features and therapy development for IDH-mutant gliomas.
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Affiliation(s)
- Yanfei Wei
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, School of Life Sciences, and Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences, Beijing Normal University, Beijing, China
| | - Guanzhang Li
- Beijing Neurosurgical Institute, Beijing, 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Jing Feng
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, School of Life Sciences, and Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences, Beijing Normal University, Beijing, China
| | - Fan Wu
- Beijing Neurosurgical Institute, Beijing, 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Zheng Zhao
- Beijing Neurosurgical Institute, Beijing, 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Zhaoshi Bao
- Beijing Neurosurgical Institute, Beijing, 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Wei Zhang
- Beijing Neurosurgical Institute, Beijing, 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Xiaodong Su
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jiuyi Li
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
| | - Xueling Qi
- Department of Pathology, San Bo Brain Hospital, Capital Medical University, Beijing, 100093, China
| | - Zejun Duan
- Department of Pathology, San Bo Brain Hospital, Capital Medical University, Beijing, 100093, China
| | - Yunqiu Zhang
- Center of Growth Metabolism & Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Sandra Ferreyra Vega
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 41390, Sweden
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 41390, Gothenburg, Sweden
| | - Asgeir Store Jakola
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 41390, Sweden
- Department of Neurosurgery, Sahlgrenska University Hospital, Gothenburg, 41390, Sweden
| | - Yingyu Sun
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, School of Life Sciences, and Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences, Beijing Normal University, Beijing, China
| | - Helena Carén
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 41390, Gothenburg, Sweden.
| | - Tao Jiang
- Beijing Neurosurgical Institute, Beijing, 100070, China.
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China.
- Chinese Glioma Genome Atlas Network (CGGA), Beijing, 100070, China.
| | - Xiaolong Fan
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, School of Life Sciences, and Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences, Beijing Normal University, Beijing, China.
- Chinese Glioma Genome Atlas Network (CGGA), Beijing, 100070, China.
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17
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Pang Y, Chen X, Ji T, Cheng M, Wang R, Zhang C, Liu M, Zhang J, Zhong C. The Chromatin Remodeler ATRX: Role and Mechanism in Biology and Cancer. Cancers (Basel) 2023; 15:cancers15082228. [PMID: 37190157 DOI: 10.3390/cancers15082228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/30/2023] [Accepted: 04/06/2023] [Indexed: 05/17/2023] Open
Abstract
The alpha-thalassemia mental retardation X-linked (ATRX) syndrome protein is a chromatin remodeling protein that primarily promotes the deposit of H3.3 histone variants in the telomere area. ATRX mutations not only cause ATRX syndrome but also influence development and promote cancer. The primary molecular characteristics of ATRX, including its molecular structures and normal and malignant biological roles, are reviewed in this article. We discuss the role of ATRX in its interactions with the histone variant H3.3, chromatin remodeling, DNA damage response, replication stress, and cancers, particularly gliomas, neuroblastomas, and pancreatic neuroendocrine tumors. ATRX is implicated in several important cellular processes and serves a crucial function in regulating gene expression and genomic integrity throughout embryogenesis. However, the nature of its involvement in the growth and development of cancer remains unknown. As mechanistic and molecular investigations on ATRX disclose its essential functions in cancer, customized therapies targeting ATRX will become accessible.
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Affiliation(s)
- Ying Pang
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai 200120, China
| | - Xu Chen
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai 200120, China
| | - Tongjie Ji
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai 200120, China
| | - Meng Cheng
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai 200120, China
| | - Rui Wang
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai 200120, China
| | - Chunyu Zhang
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai 200120, China
| | - Min Liu
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai 200120, China
| | - Jing Zhang
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai 200120, China
- Institute for Advanced Study, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Chunlong Zhong
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai 200120, China
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18
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Malgulwar PB, Danussi C, Dharmaiah S, Johnson WE, Rao A, Huse JT. Sirtuin 2 inhibition modulates chromatin landscapes genome-wide to induce senescence in ATRX-deficient malignant glioma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523324. [PMID: 36711727 PMCID: PMC9882017 DOI: 10.1101/2023.01.09.523324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Inactivating mutations in ATRX characterize large subgroups of malignant gliomas in adults and children. ATRX deficiency in glioma induces widespread chromatin remodeling, driving transcriptional shifts and oncogenic phenotypes. Effective strategies to therapeutically target these broad epigenomic sequelae remain undeveloped. We utilized integrated mulit-omics and the Broad Institute Connectivity Map (CMAP) to identify drug candidates that could potentially revert ATRX-deficient transcriptional changes. We then employed disease-relevant experimental models to evaluate functional phenotypes, coupling these studies with epigenomic profiling to elucidate molecular mechanim(s). CMAP analysis and transcriptional/epigenomic profiling implicated the Class III HDAC Sirtuin2 (Sirt2) as a central mediator of ATRX-deficient cellular phenotypes and a driver of unfavorable prognosis in ATRX-deficient glioma. Sirt2 inhibitors reverted Atrx-deficient transcriptional signatures in murine neuroprogenitor cells (mNPCs) and impaired cell migration in Atrx/ATRX-deficient mNPCs and human glioma stem cells (GSCs). While effects on cellular proliferation in these contexts were more modest, markers of senescence significantly increased, suggesting that Sirt2 inhibition promotes terminal differentiation in ATRX-deficient glioma. These phenotypic effects were accompanied by genome-wide shifts in enhancer-associated H3K27ac and H4K16ac marks, with the latter in particular demonstrating compelling transcriptional links to Sirt2-dependent phenotypic reversals. Motif analysis of these data identified the transcription factor KLF16 as a mediator of phenotype reversal in Atrx-deficient cells upon Sirt2 inhibition. Finally, Sirt2 inhibition impaired growth and increased senescence in ATRX-deficient GSCs in vivo . Our findings indicate that Sirt2 inhibition selectively targets ATRX-deficient gliomas through global chromatin remodeling, while demonstrating more broadly a viable approach to combat complex epigenetic rewiring in cancer. One Sentence Summary Our study demonstrates that SIRT2 inhibition promotes senescence in ATRX-deficient glioma model systems through global epigenomic remodeling, impacting key downstream transcriptional profiles.
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19
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Sussman JH, Xu J, Amankulor N, Tan K. Dissecting the tumor microenvironment of epigenetically driven gliomas: Opportunities for single-cell and spatial multiomics. Neurooncol Adv 2023; 5:vdad101. [PMID: 37706202 PMCID: PMC10496944 DOI: 10.1093/noajnl/vdad101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023] Open
Abstract
Malignant gliomas are incurable brain neoplasms with dismal prognoses and near-universal fatality, with minimal therapeutic progress despite billions of dollars invested in research and clinical trials over the last 2 decades. Many glioma studies have utilized disparate histologic and genomic platforms to characterize the stunning genomic, transcriptomic, and immunologic heterogeneity found in gliomas. Single-cell and spatial omics technologies enable unprecedented characterization of heterogeneity in solid malignancies and provide a granular annotation of transcriptional, epigenetic, and microenvironmental states with limited resected tissue. Heterogeneity in gliomas may be defined, at the broadest levels, by tumors ostensibly driven by epigenetic alterations (IDH- and histone-mutant) versus non-epigenetic tumors (IDH-wild type). Epigenetically driven tumors are defined by remarkable transcriptional programs, immunologically distinct microenvironments, and incompletely understood topography (unique cellular neighborhoods and cell-cell interactions). Thus, these tumors are the ideal substrate for single-cell multiomic technologies to disentangle the complex intra-tumoral features, including differentiation trajectories, tumor-immune cell interactions, and chromatin dysregulation. The current review summarizes the applications of single-cell multiomics to existing datasets of epigenetically driven glioma. More importantly, we discuss future capabilities and applications of novel multiomic strategies to answer outstanding questions, enable the development of potent therapeutic strategies, and improve personalized diagnostics and treatment via digital pathology.
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Affiliation(s)
- Jonathan H Sussman
- Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Medical Scientist Training Program, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jason Xu
- Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Medical Scientist Training Program, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nduka Amankulor
- Department of Neurosurgery, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Kai Tan
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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20
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Wang Y, Wang G, Zheng H, Liu J, Ma G, Huang G, Song Q, Du J. Distinct gene mutation profiles among multiple and single primary lung adenocarcinoma. Front Oncol 2022; 12. [PMID: 36531058 PMCID: PMC9755731 DOI: 10.3389/fonc.2022.1014997] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023] Open
Abstract
With the development of technologies, multiple primary lung cancer (MPLC) has been detected more frequently. Although large-scale genomics studies have made significant progress, the aberrant gene mutation in MPLC is largely unclear. In this study, 141 and 44 lesions from single and multiple primary lung adenocarcinoma (SP- and MP-LUAD) were analyzed. DNA and RNA were extracted from formalin-fixed, paraffin-embedded tumor tissue and sequenced by using the next-generation sequencing-based YuanSu450TM gene panel. We systematically analyzed the clinical features and gene mutations of these lesions, and found that there were six genes differently mutated in MP-LUAD and SP-LUAD lesions, including RBM10, CDK4, ATRX, NTRK1, PREX2, SS18. Data from the cBioPortal database indicated that mutation of these genes was related to some clinical characteristics, such as TMB, tumor type, et al. Besides, heterogeneity analysis suggested that different lesions could be tracked back to monophyletic relationships. We compared the mutation landscape of MP-LUAD and SP-LUAD and identified six differentially mutated genes (RBM10, CDK4, ATRX, NTRK1, PREX2, SS18), and certain SNV loci in TP53 and EGFR which might play key roles in lineage decomposition in multifocal samples. These findings may provide insight into personalized prognosis prediction and new therapies for MP-LUAD patients.
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21
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Richard Q, Laurenge A, Mallat M, Sanson M, Castro-Vega LJ. New insights into the Immune TME of adult-type diffuse gliomas. Curr Opin Neurol 2022; 35:794-802. [PMID: 36226710 PMCID: PMC9671594 DOI: 10.1097/wco.0000000000001112] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
PURPOSE OF REVIEW Adult-type diffuse gliomas are highly heterogeneous tumors. Bulk transcriptome analyses suggested that the composition of the tumor microenvironment (TME) corresponds to genetic and clinical features. In this review, we highlight novel findings on the intratumoral heterogeneity of IDH-wildtype and IDH-mutant gliomas characterized at single-cell resolution, and emphasize the mechanisms shaping the immune TME and therapeutic implications. RECENT FINDINGS Emergent evidence indicates that in addition to genetic drivers, epigenetic mechanisms and microenvironmental factors influence the glioma subtypes. Interactions between glioma and immune cells contribute to immune evasion, particularly in aggressive tumors. Spatial and temporal heterogeneity of malignant and immune cell subpopulations is high in recurrent gliomas. IDH-wildtype and IDH-mutant tumors display distinctive changes in their myeloid and lymphoid compartments, and D-2HG produced by IDH-mutant cells impacts the immune TME. SUMMARY The comprehensive dissection of the intratumoral ecosystem of human gliomas using single-cell and spatial transcriptomic approaches advances our understanding of the mechanisms underlying the immunosuppressed state of the TME, supports the prognostic value of tumor-associated macrophages and microglial cells, and sheds light on novel therapeutic options.
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Affiliation(s)
- Quentin Richard
- Paris Brain Institute (ICM), Hôpital Pitié-Salpêtrière, Inserm U 1127, CNRS UMR 7225, Sorbonne Université, Genetics and Development of Brain Tumors Team
| | - Alice Laurenge
- Paris Brain Institute (ICM), Hôpital Pitié-Salpêtrière, Inserm U 1127, CNRS UMR 7225, Sorbonne Université, Genetics and Development of Brain Tumors Team
| | - Michel Mallat
- Paris Brain Institute (ICM), Hôpital Pitié-Salpêtrière, Inserm U 1127, CNRS UMR 7225, Sorbonne Université, Genetics and Development of Brain Tumors Team
| | - Marc Sanson
- Paris Brain Institute (ICM), Hôpital Pitié-Salpêtrière, Inserm U 1127, CNRS UMR 7225, Sorbonne Université, Genetics and Development of Brain Tumors Team
- Department of Neurology 2, Pitié-Salpêtrière Hospital
- Onconeurotek Tumor Bank, Paris, France
| | - Luis Jaime Castro-Vega
- Paris Brain Institute (ICM), Hôpital Pitié-Salpêtrière, Inserm U 1127, CNRS UMR 7225, Sorbonne Université, Genetics and Development of Brain Tumors Team
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22
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Chen HM, Nikolic A, Singhal D, Gallo M. Roles of Chromatin Remodelling and Molecular Heterogeneity in Therapy Resistance in Glioblastoma. Cancers (Basel) 2022; 14:4942. [PMID: 36230865 PMCID: PMC9563350 DOI: 10.3390/cancers14194942] [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: 09/15/2022] [Revised: 09/29/2022] [Accepted: 10/07/2022] [Indexed: 11/16/2022] Open
Abstract
Cancer stem cells (CSCs) represent a therapy-resistant reservoir in glioblastoma (GBM). It is now becoming clear that epigenetic and chromatin remodelling programs link the stemlike behaviour of CSCs to their treatment resistance. New evidence indicates that the epigenome of GBM cells is shaped by intrinsic and extrinsic factors, including their genetic makeup, their interactions and communication with other neoplastic and non-neoplastic cells, including immune cells, and their metabolic niche. In this review, we explore how all these factors contribute to epigenomic heterogeneity in a tumour and the selection of therapy-resistant cells. Lastly, we discuss current and emerging experimental platforms aimed at precisely understanding the epigenetic mechanisms of therapy resistance that ultimately lead to tumour relapse. Given the growing arsenal of drugs that target epigenetic enzymes, our review addresses promising preclinical and clinical applications of epidrugs to treat GBM, and possible mechanisms of resistance that need to be overcome.
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Affiliation(s)
- Huey-Miin Chen
- Arnie Charbonneau Cancer Institute, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Ana Nikolic
- Arnie Charbonneau Cancer Institute, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Divya Singhal
- Arnie Charbonneau Cancer Institute, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Marco Gallo
- Arnie Charbonneau Cancer Institute, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
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23
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Gonzalez Castro LN, Liu I, Filbin M. Characterizing the biology of primary brain tumors and their microenvironment via single-cell profiling methods. Neuro Oncol 2022; 25:234-247. [PMID: 36197833 PMCID: PMC9925698 DOI: 10.1093/neuonc/noac211] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genomic and transcriptional heterogeneity is prevalent among the most common and aggressive primary brain tumors in children and adults. Over the past 20 years, advances in bioengineering, biochemistry and bioinformatics have enabled the development of an array of techniques to study tumor biology at single-cell resolution. The application of these techniques to study primary brain tumors has helped advance our understanding of their intra-tumoral heterogeneity and uncover new insights regarding their co-option of developmental programs and signaling from their microenvironment to promote tumor proliferation and invasion. These insights are currently being harnessed to develop new therapeutic approaches. Here we provide an overview of current single-cell techniques and discuss relevant biology and therapeutic insights uncovered by their application to primary brain tumors in children and adults.
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Affiliation(s)
- L Nicolas Gonzalez Castro
- Corresponding Author: L. Nicolas Gonzalez Castro, MD, PhD, Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA ()
| | | | - Mariella Filbin
- Pediatric Neuro-Oncology Program, Dana-Farber/Boston Children’s and Blood Disorders Center, Boston, MA, USA
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24
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Johnson AL, Laterra J, Lopez-Bertoni H. Exploring glioblastoma stem cell heterogeneity: Immune microenvironment modulation and therapeutic opportunities. Front Oncol 2022; 12:995498. [PMID: 36212415 PMCID: PMC9532940 DOI: 10.3389/fonc.2022.995498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/02/2022] [Indexed: 11/29/2022] Open
Abstract
Despite its growing use in cancer treatment, immunotherapy has been virtually ineffective in clinical trials for gliomas. The inherently cold tumor immune microenvironment (TIME) in gliomas, characterized by a high ratio of pro-tumor to anti-tumor immune cell infiltrates, acts as a seemingly insurmountable barrier to immunotherapy. Glioma stem cells (GSCs) within these tumors are key contributors to this cold TIME, often functioning indirectly through activation and recruitment of pro-tumor immune cell types. Furthermore, drivers of GSC plasticity and heterogeneity (e.g., reprogramming transcription factors, epigenetic modifications) are associated with induction of immunosuppressive cell states. Recent studies have identified GSC-intrinsic mechanisms, including functional mimicry of immune suppressive cell types, as key determinants of anti-tumor immune escape. In this review, we cover recent advancements in our understanding of GSC-intrinsic mechanisms that modulate GSC-TIME interactions and discuss cutting-edge techniques and bioinformatics platforms available to study immune modulation at high cellular resolution with exploration of both malignant (i.e., GSC) and non-malignant (i.e., immune) cell fractions. Finally, we provide insight into the therapeutic opportunities for targeting immunomodulatory GSC-intrinsic mechanisms to potentiate immunotherapy response in gliomas.
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Affiliation(s)
- Amanda L. Johnson
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, MD, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - John Laterra
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, MD, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- *Correspondence: John Laterra, ; Hernando Lopez-Bertoni,
| | - Hernando Lopez-Bertoni
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, MD, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- *Correspondence: John Laterra, ; Hernando Lopez-Bertoni,
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25
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Inhibitory Effect of miR-339-5p on Glioma through PTP4A1/HMGB1 Pathway. DISEASE MARKERS 2022; 2022:2231195. [PMID: 35872698 PMCID: PMC9307383 DOI: 10.1155/2022/2231195] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/12/2022] [Accepted: 06/18/2022] [Indexed: 12/29/2022]
Abstract
Objective Finding miR-339-5p inhibitory functions in glioma through PTP4A1/HMGB1 pathway. Methods From May 2020 to August 2021, 20 glioblastoma and para cancer tissues were chosen for qRT-PCR analysis. The miR-NC, miR-con, miR-339-5PMIMIC, and miR-con + groups were transfected into human glioma U251 cells. The capacity of cell vascular-like structure construction was found by simulating angiogenesis, and the ability of cell movement was examined by cell scratching. The twofold luciferase reporter gene method determined that miR-339-5p targets PTP4A1, and the protein expression levels of PTP4A1 and HMGB1 were examined using Western blot. Results MiR-339-5P expression was substantially lower in cancer samples than noncancer samples (P < 0.05). PTP4A1 expression in cancer samples was higher than in healthy controls (P < 0.05). The miR-339-5p group produced significantly less vascular-like structures than the NC and miR-con groups (P < 0.05). The miR-339-5p group lowered the invasive index and migratory rate of U251 cells (P < 0.05). PTP4A1 inhibited the luciferase activity of the pTP4A1-WT reporter gene (P < 0.05) but not the PTP4A1-MUT (P > 0.05). The miR-339-5p group had lower protein levels of PTP4A1 and HMGB1 than the NC and miR-con groups (P < 0.05). The development of vascular-like structures was substantially more significant in the miR-con +PTP4A1 group than in the miR-con and miR-339-5p +PTP4A1 groups (P < 0.05). In terms of migration and invasion index, there was a substantial difference between the miR-339-5p +PTP4A1 and the miR-con +PTP4A1 groups (P < 0.05). The miR-con +PTP4A1 group had a greater migration rate and invasive index than the miR-con and miR-339-5p +PTP4A1 groups (P < 0.05). Conclusion MiR-339-5P inhibits angiogenic mimicry, migration, and invasion of brain glioma U251 cells by inhibiting the PTP4A1/HMGB1 signal pathway.
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26
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Yuan Y, Yang B, Qi Z, Han Z, Cai J, Song J. KDELR1 Is an Independent Prognostic Predictor and Correlates With Immunity in Glioma. Front Oncol 2022; 12:783721. [PMID: 35814367 PMCID: PMC9263977 DOI: 10.3389/fonc.2022.783721] [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: 09/26/2021] [Accepted: 05/23/2022] [Indexed: 11/20/2022] Open
Abstract
Background Gliomas are the most malignant central nervous system tumors. With the development of sequencing technology, more potential biomarkers related to the treatment, prognosis, and molecular classification of glioma have been identified. Here, we intend to investigate the potential biological function and clinical value of a new biomarker in glioma. Methods KDELR1 expression data and the corresponding clinical information were downloaded from public databases and then preprocessed using R language. Correlation, Kaplan–Meier survival, and Cox regression analyses were performed to explore the clinical significance of KDELR1 in glioma patients. Furthermore, the immune infiltration and microenvironment parameters were evaluated via TIMER and CIBERSORT. Immunohistochemistry was conducted to confirm the KDELR1 expression and its correlation with immunity infiltration and prognosis. Results KDELR1 was upregulated in glioma samples compared with normal brain tissues, and its expression was significantly correlated with age, the World Health Organization (WHO) grade, recurrence, necrosis, microvascular proliferation, molecular classification, isocitrate dehydrogenase (IDH) mutation, and 1p/19q codeletion status. In addition, survival analysis showed that glioma patients with KDELR1 overexpression had shorter overall survival (OS) and disease-free survival times, and Cox regression analysis revealed that KDELR1 acted as an independent prognostic factor of OS in glioma patients. Gene set enrichment analysis indicated a significant enrichment of metabolism-associated pathways. KDELR1 expression was positively associated with immune infiltration (including infiltration by CD8+ T cells, CD4+ T cells, macrophages, and so on) and microenvironment parameters (including stromal, immune, and ESTIMATE scores) in gliomas. The expression of KDELR1 and its correlation with the tumor grade and prognosis were confirmed by immunohistochemistry in clinical samples (n = 119, P < 0.05). Conclusions Taken together, these findings suggest that KDELR1 is correlated with the tumor grade, molecular classifications, and immune infiltration; highlighting that KDELR1 is a novel and promising biomarker for molecular classification, treatment, and prognostic assessment may further indicate the treating effect of immune therapy.
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Affiliation(s)
- Yifan Yuan
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders, Shanghai, China
- Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, School of Basic Medical Sciences and Institutes of Brain Science, Fudan University, Shanghai, China
| | - Biao Yang
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders, Shanghai, China
- Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, School of Basic Medical Sciences and Institutes of Brain Science, Fudan University, Shanghai, China
| | - Zengxin Qi
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders, Shanghai, China
- Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, School of Basic Medical Sciences and Institutes of Brain Science, Fudan University, Shanghai, China
| | - Zhenyuan Han
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, China
| | - Jiajun Cai
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders, Shanghai, China
- Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, School of Basic Medical Sciences and Institutes of Brain Science, Fudan University, Shanghai, China
- *Correspondence: Jianping Song, ; Jiajun Cai,
| | - Jianping Song
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders, Shanghai, China
- Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, School of Basic Medical Sciences and Institutes of Brain Science, Fudan University, Shanghai, China
- Neurosurgical Institute of Fudan University, Shanghai, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China
- *Correspondence: Jianping Song, ; Jiajun Cai,
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27
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Yan D, Li W, Liu Q, Yang K. Advances in Immune Microenvironment and Immunotherapy of Isocitrate Dehydrogenase Mutated Glioma. Front Immunol 2022; 13:914618. [PMID: 35769466 PMCID: PMC9234270 DOI: 10.3389/fimmu.2022.914618] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/16/2022] [Indexed: 11/21/2022] Open
Abstract
The tumor immune microenvironment and immunotherapy have become current important tumor research concerns. The unique immune microenvironment plays a crucial role in the malignant progression of isocitrate dehydrogenase (IDH) mutant gliomas. IDH mutations in glioma can inhibit tumor-associated immune system evasion of NK cell immune surveillance. Meanwhile, mutant IDH can inhibit classical and alternative complement pathways and directly inhibit T-cell responses by metabolizing isocitrate to D-2-Hydroxyglutaric acid (2-HG). IDH has shown clinically relevant efficacy as a potential target for immunotherapy. This article intends to summarize the research progress in the immunosuppressive microenvironment and immunotherapy of IDH-mutant glioma in recent years in an attempt to provide new ideas for the study of occurrence, progression, and treatment of IDH-mutant glioma.
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Affiliation(s)
- Dongming Yan
- Department of Neurosurgery, The First Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Weicheng Li
- Department of Neurosurgery, The First Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Qibing Liu
- Department of Pharmacology, School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou, China
- Department of Pharmacy, The First Affiliated Hospital of Hainan Medical University, Haikou, China
- *Correspondence: Qibing Liu, ; Kun Yang,
| | - Kun Yang
- Department of Neurosurgery, The First Affiliated Hospital of Hainan Medical University, Haikou, China
- *Correspondence: Qibing Liu, ; Kun Yang,
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Diaz AA. Loss of ATRX suppresses anti-tumor immunity. Neuro Oncol 2022; 24:901-902. [PMID: 35235678 PMCID: PMC9159454 DOI: 10.1093/neuonc/noac059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Aaron A Diaz
- Corresponding Author: Aaron Diaz, PhD, Department of Neurological Surgery, University of California, San Francisco, 1450 3rd Street, San Francisco, CA 94158, USA ()
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