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Kaiser L, Quach S, Zounek AJ, Wiestler B, Zatcepin A, Holzgreve A, Bollenbacher A, Bartos LM, Ruf VC, Böning G, Thon N, Herms J, Riemenschneider MJ, Stöcklein S, Brendel M, Rupprecht R, Tonn JC, Bartenstein P, von Baumgarten L, Ziegler S, Albert NL. Enhancing predictability of IDH mutation status in glioma patients at initial diagnosis: a comparative analysis of radiomics from MRI, [ 18F]FET PET, and TSPO PET. Eur J Nucl Med Mol Imaging 2024; 51:2371-2381. [PMID: 38396261 PMCID: PMC11178656 DOI: 10.1007/s00259-024-06654-5] [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: 10/13/2023] [Accepted: 02/10/2024] [Indexed: 02/25/2024]
Abstract
PURPOSE According to the World Health Organization classification for tumors of the central nervous system, mutation status of the isocitrate dehydrogenase (IDH) genes has become a major diagnostic discriminator for gliomas. Therefore, imaging-based prediction of IDH mutation status is of high interest for individual patient management. We compared and evaluated the diagnostic value of radiomics derived from dual positron emission tomography (PET) and magnetic resonance imaging (MRI) data to predict the IDH mutation status non-invasively. METHODS Eighty-seven glioma patients at initial diagnosis who underwent PET targeting the translocator protein (TSPO) using [18F]GE-180, dynamic amino acid PET using [18F]FET, and T1-/T2-weighted MRI scans were examined. In addition to calculating tumor-to-background ratio (TBR) images for all modalities, parametric images quantifying dynamic [18F]FET PET information were generated. Radiomic features were extracted from TBR and parametric images. The area under the receiver operating characteristic curve (AUC) was employed to assess the performance of logistic regression (LR) classifiers. To report robust estimates, nested cross-validation with five folds and 50 repeats was applied. RESULTS TBRGE-180 features extracted from TSPO-positive volumes had the highest predictive power among TBR images (AUC 0.88, with age as co-factor 0.94). Dynamic [18F]FET PET reached a similarly high performance (0.94, with age 0.96). The highest LR coefficients in multimodal analyses included TBRGE-180 features, parameters from kinetic and early static [18F]FET PET images, age, and the features from TBRT2 images such as the kurtosis (0.97). CONCLUSION The findings suggest that incorporating TBRGE-180 features along with kinetic information from dynamic [18F]FET PET, kurtosis from TBRT2, and age can yield very high predictability of IDH mutation status, thus potentially improving early patient management.
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Affiliation(s)
- Lena Kaiser
- Department of Nuclear Medicine, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany.
| | - S Quach
- Department of Neurosurgery, University Hospital, LMU Munich, 81377, Munich, Germany
| | - A J Zounek
- Department of Nuclear Medicine, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - B Wiestler
- Department of Neuroradiology, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
- Bavarian Cancer Research Center (BZKF), 91054, Erlangen, Germany
| | - A Zatcepin
- Department of Nuclear Medicine, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), 81377, Munich, Germany
| | - A Holzgreve
- Department of Nuclear Medicine, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - A Bollenbacher
- Department of Nuclear Medicine, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - L M Bartos
- Department of Nuclear Medicine, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - V C Ruf
- Center for Neuropathology and Prion Research, Faculty of Medicine, LMU Munich, Munich, Germany
| | - G Böning
- Department of Nuclear Medicine, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - N Thon
- Department of Neurosurgery, University Hospital, LMU Munich, 81377, Munich, Germany
| | - J Herms
- Center for Neuropathology and Prion Research, Faculty of Medicine, LMU Munich, Munich, Germany
| | - M J Riemenschneider
- Department of Neuropathology, University Hospital Regensburg, 93053, Regensburg, Germany
- Bavarian Cancer Research Center (BZKF), 91054, Erlangen, Germany
| | - S Stöcklein
- Department of Radiology, University Hospital, LMU Munich, 81377, Munich, Germany
| | - M Brendel
- Department of Nuclear Medicine, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), 81377, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), 81377, Munich, Germany
| | - R Rupprecht
- Department of Psychiatry and Psychotherapy, University of Regensburg, 93053, Regensburg, Germany
| | - J C Tonn
- Department of Neurosurgery, University Hospital, LMU Munich, 81377, Munich, Germany
- Bavarian Cancer Research Center (BZKF), 91054, Erlangen, Germany
| | - P Bartenstein
- Department of Nuclear Medicine, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - L von Baumgarten
- Department of Neurosurgery, University Hospital, LMU Munich, 81377, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Bavarian Cancer Research Center (BZKF), 91054, Erlangen, Germany
| | - S Ziegler
- Department of Nuclear Medicine, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - N L Albert
- Department of Nuclear Medicine, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Bavarian Cancer Research Center (BZKF), 91054, Erlangen, Germany
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Liu S, Wang Y, Duan L, Cui D, Deng K, Dong Z, Wei S. Whole transcriptome sequencing identifies a competitive endogenous RNA network that regulates the immunity of bladder cancer. Heliyon 2024; 10:e29344. [PMID: 38681584 PMCID: PMC11053192 DOI: 10.1016/j.heliyon.2024.e29344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 05/01/2024] Open
Abstract
Several types of non-coding RNAs such as circRNAs, lncRNAs, and miRNAs have been identified to regulate mRNAs through the mechanism known as the competitive endogenous RNA (ceRNA) network. To explore the role of the ceRNA regulatory network in the immune microenvironment of bladder cancer, whole-transcriptome sequencing of bladder tumor and its peritumoral tissues from 38 bladder cancer patients, with a total of 63 samples, was performed to screen differentially expressed circ-, lnc-, mi-, and mRNAs to construct a circ/lnc-mi-mRNA regulatory network with pruning algorithms. We excavated a key immune-related gene BDNF to build the final ceRNA network as hsa-miR-107 sponged by hsa-circ-000211, AC108488.1, and LINC00163. Finally, a meta-analysis of 7 public datasets demonstrated that low expression of BDNF and high expression of hsa-miR-107 were associated with longer survival. Our study identified a ceRNA regulatory network as a potentially new prognostic marker and molecular therapeutic target of bladder cancer.
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Affiliation(s)
- Sanhe Liu
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China
- Department of Urology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430079, China
- Division of Infection and Immunity, Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, CF14 4XN, United Kingdom
| | - Yiqi Wang
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China
- Center for Neurological Disease Research, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, China
| | - Liqun Duan
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China
- Department of Radiation Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430079, China
| | - Diansheng Cui
- Department of Urology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430079, China
| | - Kangli Deng
- Department of Urology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430079, China
| | - Zhiqiang Dong
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China
- Center for Neurological Disease Research, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, China
| | - Shaozhong Wei
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China
- Department of Urology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430079, China
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Luo S, Liu Z, Chang H, Cheng X, Qian R, Gao Y, Hou C. Potential value of expression of receptor accessory protein 4 for evaluating the prognosis of lower-grade glioma patients. Aging (Albany NY) 2024; 16:6188-6211. [PMID: 38552216 PMCID: PMC11042925 DOI: 10.18632/aging.205695] [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: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 04/23/2024]
Abstract
BACKGROUND REEP4 is involved in the regulation of the biological process of mitosis. Lower grade glioma (LGG), as a malignant tumor, is accompanied by abnormalities in mitosis, but there have been no reports of REEP4 so far. METHODS We collected transcriptome data, DNA methylation data and the clinical characteristics of thousands of patients with LGG. Various big data analysis methods and molecular biology experiments were employed to reveal the impact of REEP4 on the pathological process of LGG. RESULTS It was found that the expression of REEP4 was significantly elevated and negatively regulated by its methylation site. Therefore, both the high expression of REEP4 and low methylation state of cg16311504 showed that the patients are correlated with lower patient survival rate. In addition, high REEP4 expression participates in the regulation of various cancer-related cellular signaling pathways, such as the cell cycle, MAPK signaling pathway, NOD-like receptor signaling pathway, etc. More importantly, the level of immune cell infiltration significantly increased in the high expression group of REEP4 in the LGG tumor microenvironment and REEP4 has a high positive correlation with PD-L1 and other immune checkpoints. CONCLUSIONS In brief, this study is the first to introduce REEP4 in malignant tumors, which can be used as an independent risk factor that participates in the malignant process of LGG. More importantly, REEP4 has the potential to become a new star in the field of anti-tumor treatment.
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Affiliation(s)
- Shuping Luo
- Department of Colorectal Surgery, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, China
| | - Zhendong Liu
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Zhengzhou 450003, Henan, China
| | - Haigang Chang
- Department of Neurosurgery, The First Affiliated Hospital of Xinxiang Medical University, Weihui, Henan, China
| | - Xingbo Cheng
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Zhengzhou 450003, Henan, China
| | - Rongjun Qian
- Department of Neurosurgery, Henan Provincial People’s Hospital, People’s Hospital of Henan University, People’s Hospital of Zhengzhou University, Zhengzhou 450003, Henan, China
| | - Yanzheng Gao
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Zhengzhou 450003, Henan, China
| | - Chaofeng Hou
- Department of Colorectal Surgery, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, China
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Ahmad O, Ahmad T, Pfister SM. IDH mutation, glioma immunogenicity, and therapeutic challenge of primary mismatch repair deficient IDH-mutant astrocytoma PMMRDIA: a systematic review. Mol Oncol 2024. [PMID: 38339779 DOI: 10.1002/1878-0261.13598] [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: 09/27/2023] [Revised: 12/28/2023] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
In 2021, Suwala et al. described Primary Mismatch Repair Deficient IDH-mutant Astrocytoma (PMMRDIA) as a distinct group of gliomas. In unsupervised clustering, PMMRDIA forms distinct cluster, separate from other IDH-mutant gliomas, including IDH-mutant gliomas with secondary mismatch repair (MMR) deficiency. In the published cohort, three patients received treatment with an immune checkpoint blocker (ICB), yet none exhibited a response, which aligns with existing knowledge about the decreased immunogenicity of IDH-mutant gliomas in comparison to IDH-wildtype. In the case of PMMRDIA, the inherent resistance to the standard-of-care temozolomide caused by MMR deficiency is an additional challenge. It is known that a gain-of-function mutation of IDH1/2 genes produces the oncometabolite R-2-hydroxyglutarate (R-2-HG), which increases DNA and histone methylation contributing to the characteristic glioma-associated CpG island methylator phenotype (G-CIMP). While other factors could be involved in remodeling the tumor microenvironment (TME) of IDH-mutant gliomas, this systematic review emphasizes the role of R-2-HG and the subsequent G-CIMP in immune suppression. This highlights a potential actionable pathway to enhance the response of ICB, which might be relevant for addressing the unmet therapeutic challenge of PMMRDIA.
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Affiliation(s)
- Olfat Ahmad
- Division of Pediatric Neurooncology, Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
- University of Oxford, Oxford, UK
- King Hussein Cancer Center (KHCC), Amman, Jordan
| | - Tahani Ahmad
- Department of Pediatric Neuroradiology, IWK Health Center, Halifax, Canada
- Dalhousie University, Halifax, Canada
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
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Garcia‐Mora J, Parker RL, Cecere T, Robertson JL, Rossmeisl JH. The T2-FLAIR mismatch sign as an imaging biomarker for oligodendrogliomas in dogs. J Vet Intern Med 2023; 37:1447-1454. [PMID: 37246729 PMCID: PMC10365042 DOI: 10.1111/jvim.16749] [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: 02/14/2023] [Accepted: 05/09/2023] [Indexed: 05/30/2023] Open
Abstract
BACKGROUND In humans, the T2-weighted (T2W)-fluid-attenuated inversion recovery (FLAIR) mismatch sign (T2FMM) is a specific imaging biomarker for the isocitrate dehydrogenase 1 (IDH1)-mutated, 1p/19q non-codeleted low-grade astrocytomas (LGA). The T2FMM is characterized by a homogeneous hyperintense T2W signal and a hypointense signal with a hyperintense peripheral rim on FLAIR sequences. In gliomas in dogs, the T2FMM has not been described. HYPOTHESES/OBJECTIVES In dogs with focal intra-axial brain lesions, T2FMM will discriminate gliomas from other lesions. The T2FMM will be associated with the LGA phenotype and presence of microcysts on histopathology. Interobserver agreement for T2FMM magnetic resonance imaging (MRI) features will be high. ANIMALS One hundred eighty-six dogs with histopathologically diagnosed focal intra-axial lesions on brain MRI including oligodendrogliomas (n = 90), astrocytomas (n = 47), undefined gliomas (n = 9), cerebrovascular accidents (n = 33), and inflammatory lesions (n = 7). METHODS Two blinded raters evaluated the 186 MRI studies and identified cases with the T2FMM. Histopathologic and immunohistochemical slides of T2FMM cases were evaluated for morphologic features and IDH1-mutations and compared to cases without the T2FMM. Gene expression analyses were performed on a subset of oligodendrogliomas (n = 10) with and without T2FMM. RESULTS The T2FMM was identified in 14/186 (8%) of MRI studies, and all dogs with T2FMM had oligodendrogliomas (n = 12 low-grade [LGO], n = 2 high-grade [HGO]; P < .001). Microcystic change was significantly associated with the T2FMM (P < .00001). In oligodendrogliomas with T2FMM, IDH1-mutations or specific differentially expressed genes were not identified. CONCLUSION AND CLINICAL IMPORTANCE The T2FMM can be readily identified on routinely obtained MRI sequences. It is a specific biomarker for oligodendroglioma in dogs, and was significantly associated with non-enhancing LGO.
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Affiliation(s)
- Josefa Garcia‐Mora
- Department of Small Animal Clinical Sciences and Animal Cancer Care and Research CenterVirginia‐Maryland College of Veterinary Medicine, Virginia TechBlacksburgVirginiaUSA
- Veterinary and Comparative Neuro‐Oncology Laboratory, Virginia‐Maryland College of Veterinary Medicine, Virginia TechBlacksburgVirginiaUSA
| | - Rell L. Parker
- Department of Small Animal Clinical Sciences and Animal Cancer Care and Research CenterVirginia‐Maryland College of Veterinary Medicine, Virginia TechBlacksburgVirginiaUSA
| | - Thomas Cecere
- Department of Biomedical Sciences & PathobiologyVirginia‐Maryland College of Veterinary Medicine, Virginia TechBlacksburgVirginiaUSA
| | - John L. Robertson
- Veterinary and Comparative Neuro‐Oncology Laboratory, Virginia‐Maryland College of Veterinary Medicine, Virginia TechBlacksburgVirginiaUSA
- School of Biomedical Engineering and Sciences, Virginia Tech‐Wake Forest UniversityBlacksburgVirginiaUSA
- Comprehensive Cancer Center and Brain Tumor Center of Excellence, Wake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - John H. Rossmeisl
- Department of Small Animal Clinical Sciences and Animal Cancer Care and Research CenterVirginia‐Maryland College of Veterinary Medicine, Virginia TechBlacksburgVirginiaUSA
- Veterinary and Comparative Neuro‐Oncology Laboratory, Virginia‐Maryland College of Veterinary Medicine, Virginia TechBlacksburgVirginiaUSA
- School of Biomedical Engineering and Sciences, Virginia Tech‐Wake Forest UniversityBlacksburgVirginiaUSA
- Comprehensive Cancer Center and Brain Tumor Center of Excellence, Wake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
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Zhu J, Shi L, Su Y. Aquaporin-4 as a New Potential Molecular Biomarker for Prognosis of Low-Grade Glioma: Comprehensive Analysis Based on Online Platforms. World Neurosurg 2023; 175:e713-e722. [PMID: 37037365 DOI: 10.1016/j.wneu.2023.04.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/12/2023]
Abstract
OBJECTIVE Aquaporin-4 (AQP4) is a significant factor in transcellular and transepithelial water movement, and abnormal expression of AQP4 has been detected in many types of tumors. The purpose of this study was to explore its role in low-grade gliomas (LGG) using freely available online bioinformatics tools. METHODS OncoLnc database was used to analyze Cox coefficients and compare AQP4 expression between various types of tumors; Tumor Immune Estimation Resource database and Gene Expression Profiling Interactive Analysis were used to compare gene expression between LGG and normal tissues; University of California Santa Cruz Xena browser generated Kaplan-Meier survival curves in the LGG cohort in The Cancer Genome Atlas and subgroups; LinkedOmics database screened the most relevant genes based on Pearson correlation coefficient; Gene Ontology Biological Process and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were performed through gene set enrichment analysis to explore possible molecular mechanisms. RESULTS LGG had higher AQP4 expression compared with normal tissues and ranked first among 21 different types of cancer (P < 0.05). The oligodendroglioma group had the lowest AQP4 expression and the longest overall survival (OS) (P < 0.05). LGG with astrocytoma, isocitrate dehydrogenase mutation, or 1p/19q codeletion had lower AQP4 expression and longer OS (P < 0.001). LGG with lower AQP4 expression, without 1p/19q codeletion, without chemotherapy, and with or without radiation therapy had longer OS (P < 0.05). AQP4 and coexpressed genes were involved in complex biological processes in LGG, including regulation of neurotransmitter level, peroxisome proliferator-activated receptor signaling pathway, cell adhesion molecules, and others. CONCLUSIONS AQP4 is a prognostic marker in LGG and its subgroups. Patients with lower AQP4 expression may have longer OS.
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Affiliation(s)
- Jin Zhu
- Department of Neurosurgery, Beijing Jishuitan Hospital, Xicheng District, Beijing, China
| | - Liang Shi
- Department of Neurosurgery, Beijing Jishuitan Hospital, Xicheng District, Beijing, China
| | - Yibing Su
- Department of Neurosurgery, Beijing Jishuitan Hospital, Xicheng District, Beijing, China.
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Liu B, Guan Y, Wang M, Han Y, Wang W, Wang Y, Wu P. ABRACL as a potential prognostic biomarker and correlates with immune infiltration in low-grade gliomas. INTERDISCIPLINARY NEUROSURGERY 2022. [DOI: 10.1016/j.inat.2022.101618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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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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Wang LC, Wang YL, He B, Zheng YJ, Yu HC, Liu ZY, Fan RR, Zan X, Liang RC, Wu ZP, Tang X, Wang GQ, Xu JG, Zhou LX. Expression and clinical significance of VISTA, B7-H3, and PD-L1 in glioma. Clin Immunol 2022; 245:109178. [DOI: 10.1016/j.clim.2022.109178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/15/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022]
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Xu W, Nie C, Lv H, Chen B, Wang J, Wang S, Zhao J, He Y, Chen X. Molecular subtypes based on Wnt-signaling gene expression predict prognosis and tumor microenvironment in hepatocellular carcinoma. Front Immunol 2022; 13:1010554. [PMID: 36275697 PMCID: PMC9582750 DOI: 10.3389/fimmu.2022.1010554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Based on increasing research evidence, hepatocellular carcinoma (HCC) is heterogeneous, and genetic profiling has led to the identification of multiple subtypes of this disease. To advance our knowledge and the ability to use individualized medicine in the treatment of HCC, it is essential to perform a complete and methodical characterization of various molecular subtypes. The canonical Wnt/β-catenin pathway is an evolutionarily conserved complicated signaling mechanism that plays a role in carcinogenesis and progression of HCC. In this study, we acquired RNA sequencing, somatic mutation, and clinical data from 701 patients from The Cancer Genome Atlas and Gene Expression Omnibus databases and stratified patients into two subgroups: WNT-high and WNT-low. In general, the WNT-high subtype is associated with an immunosuppressive microenvironment, poor prognosis, cancer-related pathways, and a low response to immune checkpoint therapy. We also found that WNT3 is negatively linked to CD8+ T-cell infiltration using multiple immunofluorescence assays. Finally, we developed a WNT-related prognostic model to predict the survival time of patients with HCC. In summary, we developed a new classification scheme for HCC based on Wnt signaling signatures. This classification produced substantial clinical effects, both in terms of assessing patient prognosis and immunotherapy administered to patients with HCC.
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Affiliation(s)
- Weifeng Xu
- Department of Medical Oncology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, China
| | - Caiyun Nie
- Department of Medical Oncology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Huifang Lv
- Department of Medical Oncology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - BeiBei Chen
- Department of Medical Oncology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Jianzheng Wang
- Department of Medical Oncology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Saiqi Wang
- Department of Medical Oncology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Jing Zhao
- Department of Medical Oncology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Yunduan He
- Department of Medical Oncology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Xiaobing Chen
- Department of Medical Oncology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, China
- *Correspondence: Xiaobing Chen,
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Tang F, Pan Z, Wang Y, Lan T, Wang M, Li F, Quan W, Liu Z, Wang Z, Li Z. Advances in the Immunotherapeutic Potential of Isocitrate Dehydrogenase Mutations in Glioma. Neurosci Bull 2022; 38:1069-1084. [PMID: 35670952 PMCID: PMC9468211 DOI: 10.1007/s12264-022-00866-1] [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: 11/22/2021] [Accepted: 02/16/2022] [Indexed: 11/26/2022] Open
Abstract
Isocitrate dehydrogenase (IDH) is an essential metabolic enzyme in the tricarboxylic acid cycle (TAC). The high mutation frequency of the IDH gene plays a complicated role in gliomas. In addition to affecting gliomas directly, mutations in IDH can also alter their immune microenvironment and can change immune-cell function in direct and indirect ways. IDH mutations mediate immune-cell infiltration and function by modulating immune-checkpoint gene expression and chemokine secretion. In addition, IDH mutation-derived D2-hydroxyglutarate can be absorbed by surrounding immune cells, also affecting their functioning. In this review, we summarize current knowledge about the effects of IDH mutations as well as other gene mutations on the immune microenvironment of gliomas. We also describe recent preclinical and clinical data related to IDH-mutant inhibitors for the treatment of gliomas. Finally, we discuss different types of immunotherapy and the immunotherapeutic potential of IDH mutations in gliomas.
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Affiliation(s)
- Feng Tang
- Brain Glioma Center and Department of Neurosurgery, Wuhan University Zhongnan Hospital, Wuhan, 430071, China
| | - Zhiyong Pan
- Brain Glioma Center and Department of Neurosurgery, Wuhan University Zhongnan Hospital, Wuhan, 430071, China
| | - Yi Wang
- Department of Physiology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China
| | - Tian Lan
- Brain Glioma Center and Department of Neurosurgery, Wuhan University Zhongnan Hospital, Wuhan, 430071, China
| | - Mengyue Wang
- Department of Physiology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China
| | - Fengping Li
- Brain Glioma Center and Department of Neurosurgery, Wuhan University Zhongnan Hospital, Wuhan, 430071, China
| | - Wei Quan
- Brain Glioma Center and Department of Neurosurgery, Wuhan University Zhongnan Hospital, Wuhan, 430071, China
| | - Zhenyuan Liu
- Brain Glioma Center and Department of Neurosurgery, Wuhan University Zhongnan Hospital, Wuhan, 430071, China
| | - Zefen Wang
- Department of Physiology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China.
| | - Zhiqiang Li
- Brain Glioma Center and Department of Neurosurgery, Wuhan University Zhongnan Hospital, Wuhan, 430071, China.
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12
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Ye Z, Zhang S, Cai J, Ye L, Gao L, Wang Y, Tong S, Sun Q, Wu Y, Xiong X, Chen Q. Development and validation of cuproptosis-associated prognostic signatures in WHO 2/3 glioma. Front Oncol 2022; 12:967159. [PMID: 36059638 PMCID: PMC9434124 DOI: 10.3389/fonc.2022.967159] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
WHO 2/3 glioma is a common intracranial tumor that seriously affects the quality of life and survival time of patients. Previous studies have shown that the tricarboxylic acid (TCA) cycle is closely related to the occurrence and development of glioma, while recent studies have shown that cuproptosis, a novel programmed death pathway, is closely related to the inhibition of the TCA cycle. In our study, eight of ten cuproptosis-related genes (CRGs) were found to be differentially expressed between normal and WHO 2/3 glioma tissues. Through the LASSO algorithm, the cuproptosis-associated risk signatures (CARSs) were constructed, which can effectively predict the prognosis of WHO 2/3 glioma patients and are closely related to clinicopathological features. We analyzed the relationship between risk score and immune cell infiltration through Xcell, ssGSEA, TIMER database, and immune checkpoint molecules. In addition, the relationship between risk score and chemotherapeutic drug sensitivity was also investigated. The prognosis-related independent risk factors FDX1 and CDKN2A identified from CARSs are considered potential prognostic biomarkers for WHO 2/3 glioma. The clinical prognosis model based on cuproptosis is expected to provide an effective reference for the diagnosis and treatment of clinical WHO 2/3 glioma patients.
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Affiliation(s)
- Zhang Ye
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Shenqi Zhang
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jiayang Cai
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Liguo Ye
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Lun Gao
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yixuan Wang
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Shiao Tong
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Qian Sun
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yu Wu
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xiaoxing Xiong
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
- *Correspondence: Xiaoxing Xiong, ; Qianxue Chen,
| | - Qianxue Chen
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
- *Correspondence: Xiaoxing Xiong, ; Qianxue Chen,
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13
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Long Q, Yuan Y, Li M. RNA-SSNV: A Reliable Somatic Single Nucleotide Variant Identification Framework for Bulk RNA-Seq Data. Front Genet 2022; 13:865313. [PMID: 35846154 PMCID: PMC9279659 DOI: 10.3389/fgene.2022.865313] [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: 01/29/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
The usage of expressed somatic mutations may have a unique advantage in identifying active cancer driver mutations. However, accurately calling mutations from RNA-seq data is difficult due to confounding factors such as RNA-editing, reverse transcription, and gap alignment. In the present study, we proposed a framework (named RNA-SSNV, https://github.com/pmglab/RNA-SSNV) to call somatic single nucleotide variants (SSNV) from tumor bulk RNA-seq data. Based on a comprehensive multi-filtering strategy and a machine-learning classification model trained with comprehensively curated features, RNA-SSNV achieved the best precision–recall rate (0.880–0.884) in a testing dataset and robustly retained 0.94 AUC for the precision–recall curve in three validation adult-based TCGA (The Cancer Genome Atlas) datasets. We further showed that the somatic mutations called by RNA-SSNV tended to have a higher functional impact and therapeutic power in known driver genes. Furthermore, VAF (variant allele fraction) analysis revealed that subclonal harboring expressed mutations had evolutional selection advantage and RNA had higher detection power to rescue DNA-omitted mutations. In sum, RNA-SSNV will be a useful approach to accurately call expressed somatic mutations for a more insightful analysis of cancer drive genes and carcinogenic mechanisms.
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Affiliation(s)
- Qihan Long
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Center for Precision Medicine, Sun Yat-Sen University, Guangzhou, China
- Center for Disease Genome Research, Sun Yat-Sen University, Guangzhou, China
| | - Yangyang Yuan
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Center for Precision Medicine, Sun Yat-Sen University, Guangzhou, China
- Center for Disease Genome Research, Sun Yat-Sen University, Guangzhou, China
| | - Miaoxin Li
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Center for Precision Medicine, Sun Yat-Sen University, Guangzhou, China
- Center for Disease Genome Research, Sun Yat-Sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Key Laboratory of Tropical Disease Control (SYSU), Ministry of Education, Guangzhou, China
- *Correspondence: Miaoxin Li,
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14
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A Novel Classification Model for Lower-Grade Glioma Patients Based on Pyroptosis-Related Genes. Brain Sci 2022; 12:brainsci12060700. [PMID: 35741587 PMCID: PMC9221219 DOI: 10.3390/brainsci12060700] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/13/2022] [Accepted: 05/23/2022] [Indexed: 02/06/2023] Open
Abstract
Recent studies demonstrated that pyroptosis plays a crucial role in shaping the tumor-immune microenvironment. However, the influence of pyroptosis on lower-grade glioma regarding immunotherapy and targeted therapy is still unknown. This study analyzed the variations of 33 pyroptosis-related genes in lower-grade glioma and normal tissues. Our study found considerable genetic and expression alterations in heterogeneity among lower-grade gliomas and normal brain tissues. There are two pyroptosis phenotypes in lower-grade glioma, and they exhibited differences in cell infiltration characteristics and clinical characters. Then, a PyroScore model using the lasso-cox method was constructed to measure the level of pyroptosis in each patient. PyroScore can refine the lower-grade glioma patients with a stratified prognosis and a distinct tumor immune microenvironment. Pyscore may also be an effective factor in predicting potential therapeutic benefits. In silico analysis showed that patients with a lower PyroScore are expected to be more sensitive to targeted therapy and immunotherapy. These findings may enhance our understanding of pyroptosis in lower-grade glioma and might help optimize risk stratification for the survival and personalized management of lower-grade glioma patients.
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Zhang P, Liu G, Hu J, Chen S, Wang B, Peng P, Yu X, Guo D. Tenascin-C can Serve as an Indicator for the Immunosuppressive Microenvironment of Diffuse Low-Grade Gliomas. Front Immunol 2022; 13:824586. [PMID: 35371015 PMCID: PMC8966496 DOI: 10.3389/fimmu.2022.824586] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/25/2022] [Indexed: 12/15/2022] Open
Abstract
Purpose The development and progression of glioma are associated with the tumor immune microenvironment. Diffuse low-grade gliomas (LGGs) with higher immunosuppressive microenvironment tend to have a poorer prognosis. The study aimed to find a biological marker that can reflect the tumor immune microenvironment status and predict prognosis of LGGs. Methods The target gene tenascin-C (TNC) was obtained by screening the Chinese Glioma Genome Atlas (CGGA) and the Cancer Genome Atlas (TCGA) databases. Then samples of LGGs were collected for experimental verification with immunohistochemistry, immunofluorescence, immunoblotting, quantitative real-time PCR. ELISA was employed to determine the content of TNC in serum and examine its relationship with the tumor immune microenvironment. Eventually, the sensitivity of immunotherapy was predicted on the basis of the content of TNC in LGGs. Results In the high-TNC subgroup, the infiltration of immunosuppressive cells was increased (MDSC: r=0.4721, Treg: r=0.3154, etc.), and immune effector cells were decreased [NKT, γδT, etc. (p<0.05)], immunosuppressive factors were elevated [TGF-β, IL10, etc. (p<0.05)], immunostimulatory factors, such as NKG2D, dropped (p<0.05), hypoxia scores increased (p<0.001), and less benefit from immunotherapy (p<0.05). Serum TNC level could be used to assess the status of tumor immune microenvironment in patients with grade II (AUC=0.8571; 95% CI: 0.6541-1.06) and grade III (AUC=0.8333; 95% CI: 0.6334-1.033) glioma. Conclusions Our data suggested that TNC could serve as an indicator for the immunosuppressive microenvironment status and the prognosis of LGGs. Moreover, it could also act as a predictor for the effect of immunotherapy on LGG patients.
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Affiliation(s)
- Po Zhang
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guohao Liu
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jinyang Hu
- Department of Neurosurgery, The People's Hospital of China Three Gorges University, Yichang, China
| | - Sui Chen
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Baofeng Wang
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peng Peng
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xingjiang Yu
- Department of Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dongsheng Guo
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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16
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Zhao M, Li X, Chen Y, Wang S. MD2 Is a Potential Biomarker Associated with Immune Cell Infiltration in Gliomas. Front Oncol 2022; 12:854598. [PMID: 35372062 PMCID: PMC8968038 DOI: 10.3389/fonc.2022.854598] [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: 01/14/2022] [Accepted: 02/23/2022] [Indexed: 11/30/2022] Open
Abstract
Background Glioma is the most common primary malignant tumor in the central nervous system. Myeloid differentiation protein 2 (MD2) acts as a coreceptor of toll-like receptor 4 (TLR4) to mediate innate immune response. However, the actual roles of MD2 in the regulation of progression and immune cell infiltration in gliomas remain largely unclear. This study aims to explore whether MD2 could be an independent prognostic factor through the mediation of immune cell infiltration in gliomas. Methods The mRNA expression and DNA methylation differential analyses of MD2 were performed using CGGA, TCGA and Rembrandt databases and survival analyses were performed using Kaplan-Meier plotter. Univariate and multivariate Cox regression was applied to analyze the prognostic value of MD2 and nomograms were constructed to evaluate the clinical value of MD2. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were utilized to analyze MD2-related signal pathways. Furthermore, correlations between MD2 and immune cell infiltration were calculated by TIMER and CIBERSOPT. The correlation between MD2 expression and the infiltrations of macrophages and neutrophils was experimentally verified by the knockdown of MD2 expression using small interfering RNA (siRNA) in glioma cells. Results We found that MD2 was overexpressed and associated with a poor prognosis in gliomas. Meanwhile, higher expression of MD2 could be a result of lower DNA methylation of MD2 gene in gliomas. In addition, univariate and multivariate Cox regression analysis indicated that MD2 could be an independent prognostic factor for gliomas. Further functional enrichment analysis revealed that the functions of MD2 were closely related to immune responses. Moreover, the expression level of MD2 was strongly correlated with the infiltration and polarization of pro-tumor phenotype of tumor-associated macrophages and tumor-associated neutrophils in gliomas. Conclusions These findings have provided strong evidence that MD2 could be served as a valuable immune-related biomarker to diagnose and predict the progression of gliomas.
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Affiliation(s)
| | | | - Yijun Chen
- *Correspondence: Shuzhen Wang, ; Yijun Chen,
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17
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Identification of Potential Immune Checkpoint Inhibitor Targets in Gliomas via Bioinformatic Analyses. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1734847. [PMID: 35198632 PMCID: PMC8860561 DOI: 10.1155/2022/1734847] [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: 09/06/2021] [Revised: 12/23/2021] [Accepted: 01/29/2022] [Indexed: 02/07/2023]
Abstract
Background. Glioma is a common tumor originating from the glial cells of the brain. Immune checkpoint inhibitors can potentially be used to treat gliomas, although no drug is currently approved. Methods. The expression levels of the immune checkpoint genes in glioma and normal tissues, and their correlation with the IDH mutation status and complete 1p/19q codeletion, were analyzed using The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA) databases. Survival analyses were conducted using the CGGA database. Protein-protein interaction and functional enrichment analyses were performed via the STRING database using GO, KEGG, and Reactome pathways. The correlation between the immune checkpoints and the immune cell infiltration was determined using the TISIDB and TIMER databases. Results. HAVCR2 was overexpressed in the gliomas compared to normal brain tissues, as well as in the high-grade glioma patients and significantly downregulated in IDH mutant or 1p/19q codeletion patients. Overexpression of HAVCR2 was associated with poor survival in tumor grades II, III, and IV and was the most correlated with immune infiltration of B and T cells. Conclusion. HAVCR2 can be a potential therapeutic target for cancer immunotherapy for glioma patients.
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Gonzalez N, Asad AS, Gómez Escalante J, Peña Agudelo JA, Nicola Candia AJ, García Fallit M, Seilicovich A, Candolfi M. Potential of IDH mutations as immunotherapeutic targets in gliomas: a review and meta-analysis. Expert Opin Ther Targets 2021; 25:1045-1060. [PMID: 34904924 DOI: 10.1080/14728222.2021.2017422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Gliomas are stratified by the presence of a hotspot mutation in the enzyme isocitrate dehydrogenase genes (IDH1/2). While mutated IDH (mIDH) correlates with better prognosis, the role of this mutation in antitumor immunity and the response to immunotherapy is not completely understood. Understanding the relationship between the genetic features of these tumors and the tumor immune microenvironment (TIME) may help to develop appropriate therapeutic strategies. AREAS COVERED In this review we discussed the available literature related to the potential role of IDH mutations as an immunotherapeutic target in gliomas and profiled the immune transcriptome of glioma biopsies. We aimed to shed light on the role of mIDH on the immunological landscape of the different subtypes of gliomas, taking into account the most recent WHO classification of tumors of the central nervous system (CNS). We also discussed different immunotherapeutic approaches to target mIDH tumors and to overcome their immunosuppressive microenvironment. EXPERT OPINION Data presented here indicates that the TIME not only differs in association with IDH mutation status, but also within glioma subtypes, suggesting that the cellular context affects the overall effect of this genetic lesion. Thus, specific therapeutic combinations may help patients diagnosed with different glioma subtypes.
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Affiliation(s)
- Nazareno Gonzalez
- Instituto de Investigaciones Biomédicas (Inbiomed, Uba-conicet), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Antonela S Asad
- Instituto de Investigaciones Biomédicas (Inbiomed, Uba-conicet), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - José Gómez Escalante
- Unidad Funcional de Neurooncologia y Banco de Tumores, Instituto de Oncología Ángel H. Roffo, Buenos Aires, Argentina
| | - Jorge A Peña Agudelo
- Instituto de Investigaciones Biomédicas (Inbiomed, Uba-conicet), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alejandro J Nicola Candia
- Instituto de Investigaciones Biomédicas (Inbiomed, Uba-conicet), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Matías García Fallit
- Instituto de Investigaciones Biomédicas (Inbiomed, Uba-conicet), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina.,Departamento de Química Biológica, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Adriana Seilicovich
- Instituto de Investigaciones Biomédicas (Inbiomed, Uba-conicet), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina.,Departamento de Biología Celular e Histología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Marianela Candolfi
- Instituto de Investigaciones Biomédicas (Inbiomed, Uba-conicet), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
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Singh O, Pratt D, Aldape K. Immune cell deconvolution of bulk DNA methylation data reveals an association with methylation class, key somatic alterations, and cell state in glial/glioneuronal tumors. Acta Neuropathol Commun 2021; 9:148. [PMID: 34496929 PMCID: PMC8425010 DOI: 10.1186/s40478-021-01249-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 08/23/2021] [Indexed: 02/08/2023] Open
Abstract
It is recognized that the tumor microenvironment (TME) plays a critical role in the biology of cancer. To better understand the role of immune cell components in CNS tumors, we applied a deconvolution approach to bulk DNA methylation array data in a large set of newly profiled samples (n = 741) as well as samples from external data sources (n = 3311) of methylation-defined glial and glioneuronal tumors. Using the cell-type proportion data as input, we used dimensionality reduction to visualize sample-wise patterns that emerge from the cell type proportion estimations. In IDH-wildtype glioblastomas (n = 2,072), we identified distinct tumor clusters based on immune cell proportion and demonstrated an association with oncogenic alterations such as EGFR amplification and CDKN2A/B homozygous deletion. We also investigated the immune cluster-specific distribution of four malignant cellular states (AC-like, OPC-like, MES-like and NPC-like) in the IDH-wildtype cohort. We identified two major immune-based subgroups of IDH-mutant gliomas, which largely aligned with 1p/19q co-deletion status. Non-codeleted gliomas showed distinct proportions of a key genomic aberration (CDKN2A/B loss) among immune cell-based groups. We also observed significant positive correlations between monocyte proportion and expression of PD-L1 and PD-L2 (R = 0.54 and 0.68, respectively). Overall, the findings highlight specific roles of the TME in biology and classification of CNS tumors, where specific immune cell admixtures correlate with tumor types and genomic alterations.
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20
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Lv L, Zhang Y, Zhao Y, Wei Q, Zhao Y, Yi Q. Effects of 1p/19q Codeletion on Immune Phenotype in Low Grade Glioma. Front Cell Neurosci 2021; 15:704344. [PMID: 34335194 PMCID: PMC8322528 DOI: 10.3389/fncel.2021.704344] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 06/23/2021] [Indexed: 01/05/2023] Open
Abstract
Background: Chromosome 1p/19q codeletion is one of the most important genetic alterations for low grade gliomas (LGGs), and patients with 1p/19q codeletion have significantly prolonged survival compared to those without the codeletion. And the tumor immune microenvironment also plays a vital role in the tumor progression and prognosis. However, the effect of 1p/19q codeletion on the tumor immune microenvironment in LGGs is unclear. Methods: Immune cell infiltration of 281 LGGs from The Cancer Genome Atlas (TCGA) and 543 LGGs from the Chinese Glioma Genome Atlas (CGGA) were analyzed for immune cell infiltration through three bioinformatics tools: ESTIMATE algorithm, TIMER, and xCell. The infiltrating level of immune cells and expression of immune checkpoint genes were compared between different groups classified by 1p/19q codeletion and IDH (isocitrate dehydrogenase) mutation status. The differential biological processes and signaling pathways were evaluated through Gene Set Enrichment Analysis (GSEA). Correlations were analyzed using Spearman correlation. Results: 1p/19q codeletion was associated with immune-related biological processes in LGGs. The infiltrating level of multiple kinds of immune cells and expression of immune checkpoint genes were significantly lower in 1p/19q codeletion LGGs compared to 1p/19q non-codeletion cohorts. There are 127 immune-related genes on chromosome 1p or 19q, such as TGFB1, JAK1, and CSF1. The mRNA expression of these genes was positively correlated with their DNA copy number. These genes are distributed in multiple immune categories, such as chemokines/cytokines, TGF-β family members, and TNF family members, regulating immune cell infiltration and expression of the immune checkpoint genes in tumors. Conclusion: Our results indicated that 1p/19q codeletion status is closely associated with the immunosuppressive microenvironment in LGGs. LGGs with 1p/19q codeletion display less immune cell infiltration and lower expression of immune checkpoint genes than 1p/19q non-codeletion cases. Mechanistically, this may be, at least in part, due to the deletion of copy number of immune-related genes in LGGs with 1p/19q codeletion. Our findings may be relevant to investigate immune evasion in LGGs and contribute to the design of immunotherapeutic strategies for patients with LGGs.
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Affiliation(s)
- Lei Lv
- Anhui Cancer Hospital, West Branch of the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yuliu Zhang
- Department of Thoracic Surgery, Dingyuan County General Hospital of Chuzhou City in Anhui, Anhui, China
| | - Yujia Zhao
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Qinqin Wei
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Ye Zhao
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Qiyi Yi
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
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21
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Wang X, Wang L, Xu W, Wang X, Ke D, Lin J, Lin W, Bai X. Classification of Osteosarcoma Based on Immunogenomic Profiling. Front Cell Dev Biol 2021; 9:696878. [PMID: 34336848 PMCID: PMC8323066 DOI: 10.3389/fcell.2021.696878] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 06/14/2021] [Indexed: 01/01/2023] Open
Abstract
Accumulating evidence has supported that osteosarcoma is heterogeneous, and several subtypes have been identified based on genomic profiling. Immunotherapy is revolutionizing cancer treatment and is a promising therapeutic strategy. In contrast, few studies have identified osteosarcoma classification based on immune biosignatures, which offer the optimal stratification of individuals befitting immunotherapy. Here, we classified osteosarcoma into two clusters: immunity high and immunity low using the single-sample gene-set enrichment analysis and unsupervised hierarchical clustering. Immunity_H subtype was associated with high immune cells infiltration, a favorable prognosis, benefit to immunotherapy, high human leukocyte antigen gene expression, and activated immune signal pathway indicating an immune-hot phenotype. On the contrary, the Immunity_L subtype was correlated with low immune cell infiltration, poor prognosis, and cancer-related pathway, indicating an immune-cold phenotype. We also identified TYROBP as a key immunoregulatory gene associated with CD8+ T cell infiltration by multiplex immunohistochemistry. Finally, we established an immune-related prognostic model that predicted the survival time of osteosarcoma. In conclusion, we established a new classification system of osteosarcoma based on immune signatures and identified TYROBP as a key immunoregulatory gene. This stratification had significant clinical outcomes for estimating prognosis, as well as the immunotherapy of osteosarcoma patients.
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Affiliation(s)
- Xinwen Wang
- The Third Affiliated Hospital of Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, Guangzhou, China
| | - Liangming Wang
- Department of Orthopedics, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Weifeng Xu
- Department of Medical Oncology, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
| | - Xinwu Wang
- Department of Orthopedics, The First Hospital of Putian City, Putian, China
| | - Dianshan Ke
- Department of Orthopedics, Jiangmen People's Hospital, Jiangmen, China
| | - Jinluan Lin
- Department of Orthopedics, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Wanzun Lin
- Department of Radiation Oncology, Shanghai Proton and Heavy Ion Center, Fudan University Cancer Hospital, Shanghai, China
| | - Xiaochun Bai
- The Third Affiliated Hospital of Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, Guangzhou, China
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