1
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Tomoszková S, Škarda J, Lipina R. Potential Diagnostic and Clinical Significance of Selected Genetic Alterations in Glioblastoma. Int J Mol Sci 2024; 25:4438. [PMID: 38674026 PMCID: PMC11050250 DOI: 10.3390/ijms25084438] [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: 03/04/2024] [Revised: 04/08/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Glioblastoma is currently considered the most common and, unfortunately, also the most aggressive primary brain tumor, with the highest morbidity and mortality rates. The average survival of patients diagnosed with glioblastoma is 14 months, and only 2% of patients survive 3 years after surgery. Based on our clinical experience and knowledge from extensive clinical studies, survival is mainly related to the molecular biological properties of glioblastoma, which are of interest to the general medical community. Our study examined a total of 71 retrospective studies published from 2016 through 2022 and available on PubMed that deal with mutations of selected genes in the pathophysiology of GBM. In conclusion, we can find other mutations within a given gene group that have different effects on the prognosis and quality of survival of a patient with glioblastoma. These mutations, together with the associated mutations of other genes, as well as intratumoral heterogeneity itself, offer enormous potential for further clinical research and possible application in therapeutic practice.
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Affiliation(s)
- Silvia Tomoszková
- Neurosurgery Clinic, University Hospital Ostrava, 17. listopadu 1790/5, 708 00 Ostrava, Czech Republic;
- Medical Faculty, University of Ostrava, Syllabova 19, 703 00 Ostrava, Czech Republic;
| | - Jozef Škarda
- Medical Faculty, University of Ostrava, Syllabova 19, 703 00 Ostrava, Czech Republic;
- Institute of Molecular and Clinical Pathology and Medical Genetics, University Hospital Ostrava, 17. listopadu 1790/5, 708 00 Ostrava, Czech Republic
| | - Radim Lipina
- Neurosurgery Clinic, University Hospital Ostrava, 17. listopadu 1790/5, 708 00 Ostrava, Czech Republic;
- Medical Faculty, University of Ostrava, Syllabova 19, 703 00 Ostrava, Czech Republic;
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2
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Astarita G, Kelly RS, Lasky-Su J. Metabolomics and lipidomics strategies in modern drug discovery and development. Drug Discov Today 2023; 28:103751. [PMID: 37640150 PMCID: PMC10543515 DOI: 10.1016/j.drudis.2023.103751] [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: 06/27/2023] [Revised: 08/09/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023]
Abstract
Metabolomics and lipidomics have an increasingly pivotal role in drug discovery and development. In the context of drug discovery, monitoring changes in the levels or composition of metabolites and lipids relative to genetic variations yields functional insights, bolstering human genetics and (meta)genomic methodologies. This approach also sheds light on potential novel targets for therapeutic intervention. In the context of drug development, metabolite and lipid biomarkers contribute to enhanced success rates, promising a transformative impact on precision medicine. In this review, we deviate from analytical chemist-focused perspectives, offering an overview tailored to drug discovery. We provide introductory insight into state-of-the-art mass spectrometry (MS)-based metabolomics and lipidomics techniques utilized in drug discovery and development, drawing from the collective expertise of our research teams. We comprehensively outline the application of metabolomics and lipidomics in advancing drug discovery and development, spanning fundamental research, target identification, mechanisms of action, and the exploration of biomarkers.
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Affiliation(s)
- Giuseppe Astarita
- Georgetown University, Washington, DC, USA; Arkuda Therapeutics, Watertown, MA, USA.
| | - Rachel S Kelly
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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3
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Mukherjee AG, Gopalakrishnan AV, Jayaraj R, Ganesan R, Renu K, Vellingiri B, Dey A, Parveen M. Recent advances in understanding brain cancer metabolomics: a review. Med Oncol 2023; 40:220. [PMID: 37402029 DOI: 10.1007/s12032-023-02109-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023]
Abstract
Regardless of the significant progress made in surgical techniques and adjuvant therapies, brain tumors are a major contributor to cancer-related morbidity and mortality in both pediatric and adult populations. Gliomas represent a significant proportion of cerebral neoplasms, exhibiting diverse levels of malignancy. The etiology and mechanisms of resistance of this malignancy are inadequately comprehended, and the optimization of patient diagnosis and prognosis is a challenge due to the diversity of the disease and the restricted availability of therapeutic options. Metabolomics refers to the comprehensive analysis of endogenous and exogenous small molecules, both in a targeted and untargeted manner, that enables the characterization of an individual's phenotype and offers valuable insights into cellular activity, particularly in the context of cancer biology, including brain tumor biology. Metabolomics has garnered attention in current years due to its potential to facilitate comprehension of the dynamic spatiotemporal regulatory network of enzymes and metabolites that enables cancer cells to adapt to their environment and foster the development of tumors. Metabolic changes are widely acknowledged as a significant characteristic for tracking the advancement of diseases, treatment efficacy, and identifying novel molecular targets for successful medical management. Metabolomics has emerged as an exciting area for personalized medicine and drug discovery, utilizing advanced analytical techniques such as nuclear magnetic resonance spectroscopy (MRS) and mass spectrometry (MS) to achieve high-throughput analysis. This review examines and highlights the latest developments in MRS, MS, and other technologies in studying human brain tumor metabolomics.
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Affiliation(s)
- Anirban Goutam Mukherjee
- Department of Biomedical Sciences, School of Bio-Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India
| | - Abilash Valsala Gopalakrishnan
- Department of Biomedical Sciences, School of Bio-Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India.
| | - Rama Jayaraj
- Jindal Institute of Behavioral Sciences (JIBS), Jindal Global Institution of Eminence Deemed to Be University, 28, Sonipat, 131001, India
- Director of Clinical Sciences, Northern Territory Institute of Research and Training, Darwin, NT, 0909, Australia
| | - Raja Ganesan
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea
| | - Kaviyarasi Renu
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Institute of Medical and Technical Sciences, Saveetha Dental College & Hospitals, Saveetha University, Chennai, 600077, Tamil Nadu, India
| | - Balachandar Vellingiri
- Stem cell and Regenerative Medicine/Translational Research, Department of Zoology, School of Basic Sciences, Central University of Punjab (CUPB), Bathinda, 151401, Punjab, India
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata, 700073, West Bengal, India
| | - Mohamudha Parveen
- Faculty of Medicine, University of Texas Rio Grande Valley, Harlingen, USA
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4
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Liu Y, Xu W, Li M, Yang Y, Sun D, Chen L, Li H, Chen L. The regulatory mechanisms and inhibitors of isocitrate dehydrogenase 1 in cancer. Acta Pharm Sin B 2023; 13:1438-1466. [PMID: 37139412 PMCID: PMC10149907 DOI: 10.1016/j.apsb.2022.12.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/07/2022] [Accepted: 11/18/2022] [Indexed: 02/04/2023] Open
Abstract
Reprogramming of energy metabolism is one of the basic characteristics of cancer and has been proved to be an important cancer treatment strategy. Isocitrate dehydrogenases (IDHs) are a class of key proteins in energy metabolism, including IDH1, IDH2, and IDH3, which are involved in the oxidative decarboxylation of isocitrate to yield α-ketoglutarate (α-KG). Mutants of IDH1 or IDH2 can produce d-2-hydroxyglutarate (D-2HG) with α-KG as the substrate, and then mediate the occurrence and development of cancer. At present, no IDH3 mutation has been reported. The results of pan-cancer research showed that IDH1 has a higher mutation frequency and involves more cancer types than IDH2, implying IDH1 as a promising anti-cancer target. Therefore, in this review, we summarized the regulatory mechanisms of IDH1 on cancer from four aspects: metabolic reprogramming, epigenetics, immune microenvironment, and phenotypic changes, which will provide guidance for the understanding of IDH1 and exploring leading-edge targeted treatment strategies. In addition, we also reviewed available IDH1 inhibitors so far. The detailed clinical trial results and diverse structures of preclinical candidates illustrated here will provide a deep insight into the research for the treatment of IDH1-related cancers.
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5
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Huang X, Vafaei S, Li L, Wang Y, Sun J, Gao Y, Zhang J. Identification of necroptosis-related genes as prognostic indicators for lower-grade glioma. Am J Cancer Res 2023; 13:692-708. [PMID: 36895971 PMCID: PMC9989601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 09/21/2022] [Indexed: 03/11/2023] Open
Abstract
The purpose of this research is to develop a predictive model based on necroptosis-related genes to predict the prognosis and survival of lower grade gliomas (LGGs) efficiently. To achieve this goal, we searched for differentially expressed necrotizing apoptosis-related genes using the TCGA and CGGA databases. To construct a prognostic model, LASSO Cox and COX regression analyses were conducted on the differentially expressed genes. In this study, three genes were used to develop a prognostic model of necrotizing apoptosis, and all samples were split into high- and low-risk groups. We observed that patients with a high-risk score had a worse overall survival rate (OS) than those with a low-risk score. In the TCGA and CGGA cohorts, the nomogram plot showed a high capacity to predict overall survival of LGG patients. GSEA analysis revealed that the high-risk group was enriched for inflammatory responses, tumor-related pathways, and pathological processes. Additionally, the high-risk score was associated with invading immune cell expression. In conclusion, our predictive model based on necroptosis-related genes in LGG was shown to be effective in the diagnosis and could predict the prognosis of LGG. In addition, we identified possible targets related to necroptosis-related genes for glioma therapy in this study.
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Affiliation(s)
- Xiaowan Huang
- Department of Laboratory Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine Shanghai 200021, China
| | - Somayeh Vafaei
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences Tehran, Iran
| | - Lingxia Li
- Department of Laboratory Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine Shanghai 200021, China
| | - Yunjiu Wang
- Department of Laboratory Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine Shanghai 200021, China
| | - Jian Sun
- Department of Laboratory Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine Shanghai 200021, China
| | - Yuzhen Gao
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital of Zhejiang University School of Medicine Hangzhou 310016, Zhejiang, China
| | - Jue Zhang
- Department of Laboratory Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine Shanghai 200021, China
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6
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Ni Y, Shen P, Wang X, Liu H, Luo H, Han X. The roles of IDH1 in tumor metabolism and immunity. Future Oncol 2022; 18:3941-3953. [PMID: 36621781 DOI: 10.2217/fon-2022-0583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
IDH1 is a key metabolic enzyme for cellular respiration in the tricarboxylic acid (TCA) cycle that can convert isocitrate into α-ketoglutarate (α-KG) and generate NADPH. The reduction of IDH1 may affect dioxygenase activity and damage the body's detoxification mechanism. Many studies have shown that IDH1 is closely related to the occurrence and development of tumors, and the changes in IDH1 expression levels or gene mutations have appeared in many tumor tissues and produced a series of metabolic and immunity changes at the same time. To better understand the relationship between IDH1 and tumor development, this article reviews the latest advances in IDH1 and tumor metabolism, tumor immunity, IDH1 regulatory mechanisms and IDH1 target inhibitors.
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Affiliation(s)
- Yingqian Ni
- Department of Pharmacology, School of Pharmaceutical Sciences, Shandong University, 44 West Wenhua Road, Jinan, 250012, China
| | - Peibo Shen
- Department of Pharmacology, School of Pharmaceutical Sciences, Shandong University, 44 West Wenhua Road, Jinan, 250012, China
| | - Xingchen Wang
- Department of Pharmacology, School of Pharmaceutical Sciences, Shandong University, 44 West Wenhua Road, Jinan, 250012, China
| | - He Liu
- Department of Pharmacology, School of Pharmaceutical Sciences, Shandong University, 44 West Wenhua Road, Jinan, 250012, China
| | - Huiyuan Luo
- Department of Pharmacology, School of Pharmaceutical Sciences, Shandong University, 44 West Wenhua Road, Jinan, 250012, China
| | - Xiuzhen Han
- Department of Pharmacology, School of Pharmaceutical Sciences, Shandong University, 44 West Wenhua Road, Jinan, 250012, China.,Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Science, Shandong University, China.,Shandong Cancer Hospital and Institute, 440 Jiyan Road, Jinan, 250117, Shandong Province, China
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7
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Obukhova L, Kopytova T, Murach E, Shchelchkova N, Kontorshchikova C, Medyanik I, Orlinskaya N, Grishin A, Kontorshchikov M, Badanina D. Relationship between Glutathione-Dependent Enzymes and the Immunohistochemical Profile of Glial Neoplasms. Biomedicines 2022; 10:biomedicines10102393. [PMID: 36289655 PMCID: PMC9598304 DOI: 10.3390/biomedicines10102393] [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: 08/05/2022] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/25/2022] Open
Abstract
This research aimed to investigate the relationships between the parameters of glutathione metabolism and the immunohistochemical characteristics of glial tumors. Postoperative material from 20 patients with gliomas of different grades of anaplasia was analyzed. Bioinformatic analysis of the interactions between the gliomas’ immunohistochemical markers and their glutathione-dependent enzymes was carried out using the STRING, BioGrid, while Signor databases revealed interactions between such glioma markers as IDH and p53 and the glutathione exchange enzymes (glutathione peroxidase, glutathione reductase, glutathione S-transferase). The most pronounced relationship with glutathione metabolism was demonstrated by the level of the nuclear protein Ki67 as a marker of proliferative activity, and the presence of the IDH1 mutation as one of the key genetic events of gliomagenesis. The glutathione system is an active participant in the body’s antioxidant defense, involving the p53 markers and MGMT promoter methylation. It allows characterization of the gliomal cells’ status at different stages of tumor development.
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8
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Suleman M, Umme-I-Hani S, Salman M, Aljuaid M, Khan A, Iqbal A, Hussain Z, Ali SS, Ali L, Sher H, Waheed Y, Wei DQ. Sequence-structure functional implications and molecular simulation of high deleterious nonsynonymous substitutions in IDH1 revealed the mechanism of drug resistance in glioma. Front Pharmacol 2022; 13:927570. [PMID: 36188571 PMCID: PMC9523485 DOI: 10.3389/fphar.2022.927570] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 07/25/2022] [Indexed: 11/30/2022] Open
Abstract
In the past few years, various somatic point mutations of isocitrate dehydrogenase (IDH) encoding genes (IDH1 and IDH2) have been identified in a broad range of cancers, including glioma. Despite the important function of IDH1 in tumorigenesis and its very polymorphic nature, it is not yet clear how different nsSNPs affect the structure and function of IDH1. In the present study, we employed different machine learning algorithms to screen nsSNPs in the IDH1 gene that are highly deleterious. From a total of 207 SNPs, all of the servers classified 80 mutations as deleterious. Among the 80 deleterious mutations, 14 were reported to be highly destabilizing using structure-based prediction methods. Three highly destabilizing mutations G15E, W92G, and I333S were further subjected to molecular docking and simulation validation. The docking results and molecular simulation analysis further displayed variation in dynamics features. The results from molecular docking and binding free energy demonstrated reduced binding of the drug in contrast to the wild type. This, consequently, shows the impact of these deleterious substitutions on the binding of the small molecule. PCA (principal component analysis) and FEL (free energy landscape) analysis revealed that these mutations had caused different arrangements to bind small molecules than the wild type where the total internal motion is decreased, thus consequently producing minimal binding effects. This study is the first extensive in silico analysis of the IDH1 gene that can narrow down the candidate mutations for further validation and targeting for therapeutic purposes.
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Affiliation(s)
- Muhammad Suleman
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | | | | | - Mohammed Aljuaid
- Department of Health Administration, College of Business Administration, King Saud University, Riyadh, Saudi Arabia
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Henan, China
| | - Arshad Iqbal
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Zahid Hussain
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Syed Shujait Ali
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Liaqat Ali
- Division of Biology, Kansas State University, Manhattan, KS, United States
| | - Hassan Sher
- Centre for Plant Science and Biodiversity, University of Swat, Charbagh, Pakistan
| | - Yasir Waheed
- Office of Research, Innovation and Commercialization, Shaheed Zulfiqar Ali Bhutto Medical University (SZABMU), Islamabad, Pakistan
- *Correspondence: Yasir Waheed, ; Dong-Qing Wei,
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Henan, China
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Peng Cheng Laboratory, Shenzhen, Guangdong, China
- *Correspondence: Yasir Waheed, ; Dong-Qing Wei,
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Obukhova LM, Evdokimov II, Medyanik IA, Orlinskaya NY, Grishin AS, Babintsev VE, Barinov YA, Kontorshchikov MM, Gorshkova TN, Lazukin VF. Prospects for the use of blood elemental status to assess the molecular genetic profile of gliomas. Klin Lab Diagn 2022; 67:497-503. [PMID: 36099457 DOI: 10.51620/0869-2084-2022-67-9-497-503] [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] [Indexed: 06/15/2023]
Abstract
It has been established that blood element homeostasis is related to gliomagenesis which increases the attractiveness of the analysis of its components as a promising preoperative mediated characteristics of the molecular genetic profile of gliomas. The aim of this work is to analyze the relationship between mineral metabolism parameters and immunohistochemical characteristics of glial tumors and evaluate the clinical significance of blood element homeostasis analysis for preoperative assessment of the molecular profile of gliomas. The levels of cancer specific markers MGMT, Ki-67, p-53, IDH1 were determined immunohistochemically using the corresponding antibody clones. Micronutrient levels were analyzed by inductively coupled plasma atomic emission spectrometry recalculating the results per 1 g of protein which was determined by the Lowry method. The data on cancer-specific marker levels obtained in primary brain tumors (20) and in blood plasma of gliomas patients (20) and practically healthy subjects (5) were compared using a number of statistical programs. We found significant differences in the levels of sodium, potassium, zinc and copper depending on the value of the mitotic index Ki-67 and IDH1 isocitrate dehydrogenase gene mutation. For the first time, a significant correlation showing the consistency between the level of glial tumor cancer-specific markers and blood mineral metabolism was observed. The revealed correlations provide new insights into understanding of gliomagenesis mechanisms and can be used as a predictive preoperative assessment of molecular genetic markers of gliomas.
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Affiliation(s)
- Larisa Mikhailovna Obukhova
- Federal State Budgetary Educational Institution of Higher Educational "Privolzhsky Research Medical University" of the Ministry of Health of the Russian Federation
| | - I I Evdokimov
- Federal Budgetary Scientific Institution G.G. Devyatykh Institute of Chemistry High-Purity Chemistry of the Russian Academy of Sciences
| | - I A Medyanik
- Federal State Budgetary Educational Institution of Higher Educational "Privolzhsky Research Medical University" of the Ministry of Health of the Russian Federation
| | - N Yu Orlinskaya
- Federal State Budgetary Educational Institution of Higher Educational "Privolzhsky Research Medical University" of the Ministry of Health of the Russian Federation
| | - A S Grishin
- Federal State Budgetary Educational Institution of Higher Educational "Privolzhsky Research Medical University" of the Ministry of Health of the Russian Federation
| | - V E Babintsev
- Federal State Budgetary Educational Institution of Higher Educational "Privolzhsky Research Medical University" of the Ministry of Health of the Russian Federation
| | - Yu A Barinov
- Federal State Budgetary Educational Institution of Higher Educational "Privolzhsky Research Medical University" of the Ministry of Health of the Russian Federation
| | - M M Kontorshchikov
- Federal State Budgetary Educational Institution of Higher Educational "Privolzhsky Research Medical University" of the Ministry of Health of the Russian Federation
| | - T N Gorshkova
- Federal State-Funded Healthcare Institution "Privolzhsky District Medical Center" of Federal and Biological Agency of Russia
| | - V F Lazukin
- Federal State Budgetary Educational Institution of Higher Educational "Privolzhsky Research Medical University" of the Ministry of Health of the Russian Federation
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10
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The Value of FET PET/CT in Recurrent Glioma with a Different IDH Mutation Status: The Relationship between Imaging and Molecular Biomarkers. Int J Mol Sci 2022; 23:ijms23126787. [PMID: 35743228 PMCID: PMC9224265 DOI: 10.3390/ijms23126787] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 12/04/2022] Open
Abstract
The evaluation of treatment response remains a challenge in glioma cases because the neuro oncological therapy can lead to the development of treatment-related changes (TRC) that mimic true progression (TP). Positron emission tomography (PET) using O-(2-[18F] fluoroethyl-)-L-tyrosine (18F-FET) has been shown to be a useful tool for detecting TRC and TP. We assessed the diagnostic performance of different 18F-FET PET segmentation approaches and different imaging biomarkers for differentiation between late TRC and TP in glioma patients. Isocitrate dehydrogenase (IDH) status was evaluated as a predictor of disease outcome. In our study, the proportion of TRC in IDH wild type (IDHwt) and IDH mutant (IDHm) subgroups was without significant difference. We found that the diagnostic value of static and dynamic biomarkers of 18F-FET PET for discrimination between TRC and TP depends on the IDH mutation status of the tumor. Dynamic 18F-FET PET acquisition proved helpful in the IDH wild type (IDHwt) subgroup, as opposed to the IDH mutant (IDHm) subgroup, providing an early indication to discontinue dynamic imaging in the IDHm subgroup.
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11
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Wang B, Ma Q, Wang X, Guo K, Liu Z, Li G. TGIF1 overexpression promotes glioma progression and worsens patient prognosis. Cancer Med 2022; 11:5113-5128. [PMID: 35569122 PMCID: PMC9761070 DOI: 10.1002/cam4.4822] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 04/16/2022] [Accepted: 04/26/2022] [Indexed: 02/03/2023] Open
Abstract
Transforming growth factor β-induced factor homeobox 1 (TGIF1) reportedly promotes the pathological processes of various malignant tumors. However, few studies have investigated the role of TGIF1 in gliomas. We aimed to explore the relationship between TGIF1 expression and the clinical characteristics of patients with glioma, including their overall survival. A total of thousands transcriptome datapoints were downloaded from public databases to determine the correlations between TGIF1 and various clinicopathological features using the Wilcoxon or Kruskal-Wallis tests. The Kaplan-Meier and Cox statistical methods were used to explore the prognostic significance of TGIF1. Gene set enrichment analysis (GSEA) was used to indirectly identify the pathological mechanisms modulated by TGIF1, and compounds that inhibit its expression were determined using a connectivity map (CMap). TGIF1 was significantly overexpressed in gliomas and was correlated with unfavorable prognostic factors and shorter overall survival. Cox analysis confirmed that TGIF1 expression was a significant predictor of poor prognosis in patients with glioma. GSEA revealed that the signaling pathways associated with TGIF1 expression in glioma included extracellular matrix receptor- and cell cycle-modulating proteins. CMap analysis showed that the small molecules scriptaid, torasemide, dexpropranolol, ipratropium bromide, and harmine were potential negative regulators of TGIF1. Finally, in vitro experiments demonstrated that knockdown of TGIF1 significantly inhibited the proliferation and invasion of glioma cell. Taken together, our study, which is the first to comprehensively analyze TGIF1 in gliomas, revealed it to be a novel oncogene in terms of its association with this disease. As such, TGIF1 may be a potential therapeutic target for individualized treatment of patients with glioma.
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Affiliation(s)
- Baoya Wang
- Department of Clinical Laboratory, Henan Provincial People's HospitalPeople's Hospital of Zhengzhou University, People's, Hospital of Henan UniversityZhengzhouPeople's Republic of China
| | - Qiong Ma
- Department of Clinical Laboratory, Henan Provincial People's HospitalPeople's Hospital of Zhengzhou University, People's, Hospital of Henan UniversityZhengzhouPeople's Republic of China
| | - Xuelin Wang
- Department of Respiratory and Critical Care Medicine, Henan Provincial People's HospitalPeople's Hospital of Zhengzhou University, People's, Hospital of Henan UniversityZhengzhouPeople's Republic of China
| | - Kunshan Guo
- Xuchang Central Hospital of Henan University of Science and TechnologyXuchangPeople's Republic of China
| | - Zhendong Liu
- Department of Surgery of Spine and Spinal CordHenan Provincial People's HospitalZhengzhouPeople's Republic of China
| | - Gang Li
- Department of Clinical Laboratory, Henan Provincial People's HospitalPeople's Hospital of Zhengzhou University, People's, Hospital of Henan UniversityZhengzhouPeople's Republic of China
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12
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Obukhova L, Nikiforova O, Kontorshchikova C, Medyanik I, Orlinskaya N, Grishin A, Kontorshchikov M, Shchelchkova N. Carbohydrate Metabolism Parameters of Adult Glial Neoplasms According to Immunohistochemical Profile. Biomedicines 2022; 10:biomedicines10051007. [PMID: 35625744 PMCID: PMC9138280 DOI: 10.3390/biomedicines10051007] [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: 03/23/2022] [Revised: 04/22/2022] [Accepted: 04/25/2022] [Indexed: 11/16/2022] Open
Abstract
This research aimed to investigate the interrelationship of carbohydrate metabolism parameters and immunohistochemical characteristics of glial tumors. Tumor tissue, peritumoral area, and adjacent noncancerous tissue fragments of 20 patients with gliomas of varying degrees of anaplasia were analyzed. The greatest differences in the carbohydrate metabolism compared to adjacent noncancerous tissues were identified in the tumor tissue: reduction in the levels of lactate and glycogen synthase kinase-3β. Significant differences with adjacent noncancerous tissues for the peritumoral zone were not found. The activity of the carbohydrate metabolism enzymes was different depending on the immunohistochemical glioma profile, especially from Ki 67 level. Bioinformatic analysis of the interactions of immunohistochemical markers of gliomas and carbohydrate metabolism enzymes using the databases of STRING, BioGrid, and Signor revealed the presence of biologically significant interactions with glycogen synthase kinase 3β, hexokinase, glucose-6-phosphate dehydrogenase, and transketolase. The established interconnection of glycolysis with methylation of the promoter of O-6-methylguanine-DNA-methyltransferase (MGMT) of gliomas can be used to increase chemotherapy efficiency.
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13
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Zhang J, Xiao X, Guo Q, Wei Z, Hua W. Identification of Four Metabolic Subtypes of Glioma Based on Glycolysis-Cholesterol Synthesis Genes. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:9448144. [PMID: 35242216 PMCID: PMC8886743 DOI: 10.1155/2022/9448144] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/06/2022] [Accepted: 01/17/2022] [Indexed: 12/21/2022]
Abstract
Based on alterations in gene expression associated with the production of glycolysis and cholesterol, this research classified glioma into prognostic metabolic subgroups. In this study, data from the CGGA325 and The Cancer Genome Atlas (TCGA) datasets were utilized to extract single nucleotide variants (SNVs), RNA-seq expression data, copy number variation data, short insertions and deletions (InDel) mutation data, and clinical follow-up information from glioma patients. Glioma metabolic subtypes were classified using the ConsensusClusterPlus algorithm. This study determined four metabolic subgroups (glycolytic, cholesterogenic, quiescent, and mixed). Cholesterogenic patients had a higher survival chance. Genome-wide investigation revealed that inappropriate amplification of MYC and TERT was associated with improper cholesterol anabolic metabolism. In glioma metabolic subtypes, the mRNA levels of mitochondrial pyruvate carriers 1 and 2 (MPC1/2) presented deletion and amplification, respectively. Differentially upregulated genes in the glycolysis group were related to pathways, including IL-17, HIF-1, and TNF signaling pathways and carbon metabolism. Downregulated genes in the glycolysis group were enriched in terpenoid backbone biosynthesis, nitrogen metabolism, butanoate metabolism, and fatty acid metabolism pathway. Cox analysis of univariate and multivariate survival showed that risks of glycolysis subtypes were significantly higher than other subtypes. Those results were validated in the CGGA325 dataset. The current findings greatly contribute to a comprehensive understanding of glioma and personalized treatment.
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Affiliation(s)
- Jinsen Zhang
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
- Neurosurgical Institute of Fudan University, Shanghai 200040, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai 200040, China
- Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Shanghai 200040, China
| | - Xing Xiao
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
- Neurosurgical Institute of Fudan University, Shanghai 200040, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai 200040, China
- Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Shanghai 200040, China
| | - Qinglong Guo
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
- Neurosurgical Institute of Fudan University, Shanghai 200040, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai 200040, China
- Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Shanghai 200040, China
| | - Zixuan Wei
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Wei Hua
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
- Neurosurgical Institute of Fudan University, Shanghai 200040, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai 200040, China
- Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Shanghai 200040, China
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14
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Metabolic Features of Brain Function with Relevance to Clinical Features of Alzheimer and Parkinson Diseases. Molecules 2022; 27:molecules27030951. [PMID: 35164216 PMCID: PMC8839962 DOI: 10.3390/molecules27030951] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 12/04/2022] Open
Abstract
Brain metabolism is comprised in Alzheimer’s disease (AD) and Parkinson’s disease (PD). Since the brain primarily relies on metabolism of glucose, ketone bodies, and amino acids, aspects of these metabolic processes in these disorders—and particularly how these altered metabolic processes are related to oxidative and/or nitrosative stress and the resulting damaged targets—are reviewed in this paper. Greater understanding of the decreased functions in brain metabolism in AD and PD is posited to lead to potentially important therapeutic strategies to address both of these disorders, which cause relatively long-lasting decreased quality of life in patients.
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15
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Dai L, Li Z, Liang W, Hu W, Zhou S, Yang Z, Tao Y, Hou X, Xing Z, Mao J, Shi Z, Wang X. SOCS proteins and their roles in the development of glioblastoma. Oncol Lett 2021; 23:5. [PMID: 34820004 PMCID: PMC8607235 DOI: 10.3892/ol.2021.13123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/11/2021] [Indexed: 12/13/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most common type of primary brain tumor in adults. GBM is characterized by a high degree of malignancy and aggressiveness, as well as high morbidity and mortality rates. GBM is currently treatable via surgical resection, chemotherapy and radiotherapy, but the prognosis of patients with GBM is poor. The suppressor of cytokine signaling (SOCS) protein family comprises eight members, including SOCS1-SOCS7 and cytokine-inducible SH2-containing protein. SOCS proteins regulate the biogenesis of GBM via the JAK/STAT and NF-κB signaling pathways. Driven by NF-κB, the expression of SOCS proteins can serve as a negative regulator of the JAK/STAT signaling pathway and exerts a potential inhibitory effect on GBM. In GBM, E3 ubiquitin ligase is involved in the regulation of cellular functions, such as the receptor tyrosine kinase (RTK) survival signal, in which SOCS proteins negatively regulate RTK signaling, and kinase overexpression or mutation can lead to the development of malignancies. Moreover, SOCS proteins affect the proliferation and differentiation of GBM cells by regulating the tumor microenvironment. SOCS proteins also serve specific roles in GBM of different grades and different isocitrate dehydrogenase mutation status. The aim of the present review was to describe the biogenesis and function of the SOCS protein family, the roles of SOCS proteins in the microenvironment of GBM, as well as the role of this protein family and E3 ubiquitin ligases in GBM. Furthermore, the role of SOCS proteins as diagnostic and prognostic markers in GBM and their potential role as GBM therapeutics were explored.
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Affiliation(s)
- Lirui Dai
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Science and Technology of Henan Province, Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan 450052, P.R. China
| | - Zian Li
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Science and Technology of Henan Province, Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan 450052, P.R. China
| | - Wulong Liang
- Department of Science and Technology of Henan Province, Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan 450052, P.R. China
| | - Weihua Hu
- Department of Science and Technology of Henan Province, Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan 450052, P.R. China
| | - Shaolong Zhou
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Science and Technology of Henan Province, Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan 450052, P.R. China
| | - Zhuo Yang
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Science and Technology of Henan Province, Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan 450052, P.R. China
| | - Yiran Tao
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Science and Technology of Henan Province, Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan 450052, P.R. China
| | - Xuelei Hou
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Science and Technology of Henan Province, Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan 450052, P.R. China
| | - Zhe Xing
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Science and Technology of Henan Province, Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan 450052, P.R. China
| | - Jianchao Mao
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Science and Technology of Henan Province, Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan 450052, P.R. China
| | - Zimin Shi
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Science and Technology of Henan Province, Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan 450052, P.R. China
| | - Xinjun Wang
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Science and Technology of Henan Province, Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan 450052, P.R. China
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16
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Jin FQ, Jin L, Wang YL. Downregulation of STOX1 is a novel prognostic biomarker for glioma patients. Open Life Sci 2021; 16:1164-1174. [PMID: 34722888 PMCID: PMC8546287 DOI: 10.1515/biol-2021-0119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 09/18/2021] [Accepted: 10/01/2021] [Indexed: 12/31/2022] Open
Abstract
Storkhead box 1 (STOX1) is a winged helix transcription factor structurally and functionally related to the forkhead family of transcription factors. Recent studies have highlighted its role in the central nervous system and revealed hints in the development of glioma. However, the expression profiles of STOX1, its association with clinicopathological characteristics, and potential functions in glioma remain unknown. In this study, we analyzed three publicly available datasets including CGGA, TCGA, and Rembrandt and revealed a grade-dependent reduction in STOX1 expression in glioma (P < 0.001). Chi-square test demonstrated that low STOX1 expression was significantly associated with older age at initial diagnosis (P < 0.001), less IDH1 mutation (P < 0.001), and advanced WHO grade (P < 0.001). Moreover, multivariate Cox regression analysis showed that STOX1 expression may serve as a novel independent prognostic biomarker in glioma patients. Bioinformatic functional analysis (GSEA) predicted that STOX1 was related to many key cancer pathways including P53 signaling pathway (P < 0.01), DNA replication (P < 0.05), homologous recombination (P < 0.05), and Wnt signaling pathway (P < 0.05). Taken together, these findings suggested that STOX1 may be used as a novel predictive molecular biomarker for glioma grading and overall patient survival. Further investigations on the functional roles and therapeutic value of STOX1 in glioma are warranted.
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Affiliation(s)
- Fei-qin Jin
- Department of Radiology, People’s Hospital of Gaoxin District, Suzhou, 215129, Jiangsu, China
| | - Lei Jin
- Department of Neurosurgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510000, Guangdong, China
- Department of Surgery, Division of Neurosurgery, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong, China
| | - Yan-ling Wang
- Department of Radiology, People’s Hospital of Gaoxin District, Suzhou, 215129, Jiangsu, China
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17
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Lin W, Ou G, Zhao W. Mutational profiling of low-grade gliomas identifies prognosis and immunotherapy-related biomarkers and tumour immune microenvironment characteristics. J Cell Mol Med 2021; 25:10111-10125. [PMID: 34597473 PMCID: PMC8572778 DOI: 10.1111/jcmm.16947] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/08/2021] [Accepted: 09/11/2021] [Indexed: 02/05/2023] Open
Abstract
Low-grade glioma (LGG) is a heterogeneous tumour with the median survival rate less than 10 years. Therefore, it is urgent to develop efficient immunotherapy strategies of LGG. In this study, we analysed mutation profiles based on the data of 510 LGG patients from the Cancer Genome Atlas (TCGA) database and investigated the prognostic value of mutated genes and evaluate their immune infiltration. Tumor Immune Dysfunction and Exclusion (TIDE) algorithm was used to indicate the characteristics of gliomas that respond to immune checkpoint blockade (ICB) therapy. Univariate and multivariate cox regression analysis was performed to identify indicators to construct the nomogram model. 485 (95.47%) of 508 LGG samples showed gene mutation, and 9 mutated genes were significantly related to overall survival (OS), among which 6 mutated genes were significantly correlated with OS between mutation and wildtypes. Immune infiltration and immune score analyses revealed that these six mutated genes were significantly associated with tumour immune microenvironment in LGG. The response of LGG with different characteristics to ICB was evaluated by TIDE algorithm. Finally, CIC gene was screened through both univariate and multivariate Cox regression analyses, and the nomogram model was established to determine the potential prognostic value of CIC in LGG. Our study provides comprehensive analysis of mutated genes in LGG, supporting modulation of mutated genes in the management of LGG.
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Affiliation(s)
- Wen‐wen Lin
- Center for NeuroscienceShantou University Medical CollegeShantouGuangdongChina
| | - Guan‐yong Ou
- Center for NeuroscienceShantou University Medical CollegeShantouGuangdongChina
| | - Wei‐jiang Zhao
- Center for NeuroscienceShantou University Medical CollegeShantouGuangdongChina
- Cell biology department, Wuxi School of MedicineJiangnan UniversityWuxi, JiangsuChina
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18
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Pinto GP, Hendrikse NM, Stourac J, Damborsky J, Bednar D. Virtual screening of potential anticancer drugs based on microbial products. Semin Cancer Biol 2021; 86:1207-1217. [PMID: 34298109 DOI: 10.1016/j.semcancer.2021.07.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 07/14/2021] [Accepted: 07/18/2021] [Indexed: 01/20/2023]
Abstract
The development of microbial products for cancer treatment has been in the spotlight in recent years. In order to accelerate the lengthy and expensive drug development process, in silico screening tools are systematically employed, especially during the initial discovery phase. Moreover, considering the steadily increasing number of molecules approved by authorities for commercial use, there is a demand for faster methods to repurpose such drugs. Here we present a review on virtual screening web tools, such as publicly available databases of molecular targets and libraries of ligands, with the aim to facilitate the discovery of potential anticancer drugs based on microbial products. We provide an entry-level step-by-step description of the workflow for virtual screening of microbial metabolites with known protein targets, as well as two practical examples using freely available web tools. The first case presents a virtual screening study of drugs developed from microbial products using Caver Web, a web tool that performs docking along a tunnel. The second case comprises a comparative analysis between a wild type isocitrate dehydrogenase 1 and a mutant that results in cancer, using the recently developed web tool PredictSNPOnco. In summary, this review provides the basic and essential background information necessary for virtual screening experiments, which may accelerate the discovery of novel anticancer drugs.
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Affiliation(s)
- Gaspar P Pinto
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, Brno, 625 00, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, Brno, 656 91, Czech Republic
| | - Natalie M Hendrikse
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, Brno, 625 00, Czech Republic
| | - Jan Stourac
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, Brno, 625 00, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, Brno, 656 91, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, Brno, 625 00, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, Brno, 656 91, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, Brno, 625 00, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, Brno, 656 91, Czech Republic.
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19
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Rajmohan KS, Sugur HS, Shwetha SD, Pandey P, Arivazhagan A, Santosh V. Alpha Internexin: A Surrogate Marker for 1p/19q Codeletion and Prognostic Marker in Anaplastic (WHO grade III) Gliomas. Neurol India 2021; 68:832-837. [PMID: 32859823 DOI: 10.4103/0028-3886.293453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background The WHO 2016 classification of diffuse gliomas has incorporated molecular markers isocitrate dehydrogenase (IDH) gene mutations (IDHmut) and codeletion of chromosomal arms 1p and 19q (1p/19q codeletion) as tumor defining entities. The diagnosis of diffuse oligodendrogliomas (ODG) and anaplastic oligodendroglioma (AO) mandatorily requires the demonstration of IDH1 and/or IDH2 mutations along with 1p/19q codeletion, whereas the 1p/19q noncodeleted diffuse gliomas are labeled as astrocytomas. The current methodologies for assessing 1p/19q codeletion status are expensive and not widely available. Studies have proposed alpha internexin (INA) expression on immunohistochemistry (IHC) as a surrogate marker for 1p/19q codeletion and a good prognostic marker in gliomas. Materials and Methods In this study, we performed IHC for INA expression on the retrospective cohort of anaplastic gliomas (AGs) from our previously published study. Results INA positivity on IHC showed a significant positive correlation with 1p/19q codeletion (P < 0.001) with a Spearman's rank correlation coefficient (Rho) of 0.804, sensitivity of 87.5%, specificity of 93.0%, and a diagnostic odds ratio of 93:1 in AGs. Similar to the 1p/19q codeletion status, INA positivity showed a positive correlation with IDHmut (P = 0.002) and a negative correlation with α-thalassemia mental retardation X-linked protein (ATRX) loss of expression (P < 0.001). On univariate survival analysis, INA positivity was associated with significantly prolonged overall survival (OS) and recurrent free survival (RFS) in AGs (P < 0.001). Furthermore, within AO, INA positivity significantly improved RFS (P = 0.022) with OS trending towards significance (P = 0.094). Conclusions INA expression on IHC could serve as a potential surrogate marker for 1p/19q, and highlights its prognostic value in AO and AGs.
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Affiliation(s)
- K S Rajmohan
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | - Harsha S Sugur
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | - S D Shwetha
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | - Paritosh Pandey
- Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | - Arimappamagan Arivazhagan
- Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | - Vani Santosh
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
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20
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Zhang W, Liu Z, Liu B, Jiang M, Yan S, Han X, Shen H, Na M, Wang Y, Ren Z, Liu B, Jiang Z, Gao Y, Lin Z. GNG5 is a novel oncogene associated with cell migration, proliferation, and poor prognosis in glioma. Cancer Cell Int 2021; 21:297. [PMID: 34098960 PMCID: PMC8186147 DOI: 10.1186/s12935-021-01935-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 04/13/2021] [Indexed: 12/16/2022] Open
Abstract
Background Although many biomarkers have been reported for detecting glioma, the prognosis for the disease remains poor, and therefore, new biomarkers need to be identified. GNG5, which is part of the G-protein family, has been associated with different malignant tumors, though the role of GNG5 in glioma has not been studied. Therefore, we aimed to identify the relationship between GNG5 and glioma prognosis and identify a new biomarker for the diagnosis and treatment of gliomas. Methods We used data on more than a thousand gliomas from multiple databases and clinical data to determine the expression of GNG5 in glioma. Based on clinical data and CGGA database, we identified the correlation between GNG5 and multiple molecular and clinical features and prognosis using various analytical methods. Co-expression analysis and GSEA were performed to detect GNG5-related genes in glioma and possible signaling pathways involved. ESTIMATE, ssGSEA, and TIMER were used to detect the relationship between GNG5 and the immune microenvironment. Functional experiments were performed to explore the function of GNG5 in glioma cells. Results GNG5 is highly expressed in gliomas, and its expression level is positively correlated with pathological grade, histological type, age, and tumor recurrence and negatively correlated with isocitrate dehydrogenase mutation, 1p/19 co-deletion, and chemotherapy. Moreover, GNG5 as an independent risk factor was negatively correlated with the overall survival time. GSEA revealed the potential signaling pathways involved in GNG5 function in gliomas, including cell adhesion molecules signaling pathway. The ssGSEA, ESTIMATE, and TIMER based analysis indicated a correlation between GNG5 expression and various immune cells in glioma. In vivo and in vitro experiments showed that GNG5 could participate in glioma cell proliferation and migration. Conclusions Based on the large data platform and the use of different databases to corroborate results obtained using various datasets, as well as in vitro and in vivo experiments, our study reveals for the first time that GNG5, as an oncogene, is overexpressed in gliomas and can inhibit the proliferation and migration of glioma cells and lead to poor prognosis of patients. Thus, GNG5 is a potential novel biomarker for the clinical diagnosis and treatment of gliomas. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-01935-7.
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Affiliation(s)
- Wang Zhang
- Department of Neurosurgery, The First Affiliate Hospital of Harbin Medical University, 23 Youzheng Street, Nangang District, Harbin, 150001, China.,Department of Orthopaedics, Department of Microbiome Laboratory, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, School of Clinical Medicine, Henan University, No. 7, Weiwu Road, Jinshui District, Zhengzhou, 450003, Henan, China
| | - Zhendong Liu
- Department of Orthopaedics, Department of Microbiome Laboratory, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, School of Clinical Medicine, Henan University, No. 7, Weiwu Road, Jinshui District, Zhengzhou, 450003, Henan, China
| | - Binchao Liu
- Department of Neurosurgery of Xing, Tai People's Hospital, Xing Tai, China
| | - Miaomiao Jiang
- Department of the Pathology, The First Affiliate Hospital of Harbin Medical University, Harbin, China
| | - Shi Yan
- Department of Neurosurgery, The First Affiliate Hospital of Harbin Medical University, 23 Youzheng Street, Nangang District, Harbin, 150001, China
| | - Xian Han
- Department of Neurosurgery, The First Affiliate Hospital of Harbin Medical University, 23 Youzheng Street, Nangang District, Harbin, 150001, China
| | - Hong Shen
- Department of Neurosurgery, The First Affiliate Hospital of Harbin Medical University, 23 Youzheng Street, Nangang District, Harbin, 150001, China
| | - Meng Na
- Department of Neurosurgery, The First Affiliate Hospital of Harbin Medical University, 23 Youzheng Street, Nangang District, Harbin, 150001, China
| | - Yanbiao Wang
- Department of Orthopaedics, Department of Microbiome Laboratory, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, School of Clinical Medicine, Henan University, No. 7, Weiwu Road, Jinshui District, Zhengzhou, 450003, Henan, China
| | - Zhishuai Ren
- Department of Orthopaedics, Department of Microbiome Laboratory, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, School of Clinical Medicine, Henan University, No. 7, Weiwu Road, Jinshui District, Zhengzhou, 450003, Henan, China
| | - Binfeng Liu
- Department of Orthopaedics, Department of Microbiome Laboratory, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, School of Clinical Medicine, Henan University, No. 7, Weiwu Road, Jinshui District, Zhengzhou, 450003, Henan, China
| | - Zhenfeng Jiang
- Department of Neurosurgery, The First Affiliate Hospital of Harbin Medical University, 23 Youzheng Street, Nangang District, Harbin, 150001, China
| | - Yanzheng Gao
- Department of Orthopaedics, Department of Microbiome Laboratory, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, School of Clinical Medicine, Henan University, No. 7, Weiwu Road, Jinshui District, Zhengzhou, 450003, Henan, China.
| | - Zhiguo Lin
- Department of Neurosurgery, The First Affiliate Hospital of Harbin Medical University, 23 Youzheng Street, Nangang District, Harbin, 150001, China.
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21
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Thomas TM, Miyaguchi K, Edwards LA, Wang H, Wollebo H, Aiguo L, Murali R, Wang Y, Braas D, Michael JS, Andres AM, Zhang M, Khalili K, Gottlieb RA, Perez JM, Yu JS. Elevated Asparagine Biosynthesis Drives Brain Tumor Stem Cell Metabolic Plasticity and Resistance to Oxidative Stress. Mol Cancer Res 2021; 19:1375-1388. [PMID: 33863814 DOI: 10.1158/1541-7786.mcr-20-0086] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 02/26/2021] [Accepted: 04/14/2021] [Indexed: 12/12/2022]
Abstract
Asparagine synthetase (ASNS) is a gene on the long arm of chromosome 7 that is copy-number amplified in the majority of glioblastomas. ASNS copy-number amplification is associated with a significantly decreased survival. Using patient-derived glioma stem cells (GSC), we showed that significant metabolic alterations occur in gliomas when perturbing the expression of ASNS, which is not merely restricted to amino acid homeostasis. ASNS-high GSCs maintained a slower basal metabolic profile yet readily shifted to a greatly increased capacity for glycolysis and oxidative phosphorylation when needed. This led ASNS-high cells to a greater ability to proliferate and spread into brain tissue. Finally, we demonstrate that these changes confer resistance to cellular stress, notably oxidative stress, through adaptive redox homeostasis that led to radiotherapy resistance. Furthermore, ASNS overexpression led to modifications of the one-carbon metabolism to promote a more antioxidant tumor environment revealing a metabolic vulnerability that may be therapeutically exploited. IMPLICATIONS: This study reveals a new role for ASNS in metabolic control and redox homeostasis in glioma stem cells and proposes a new treatment strategy that attempts to exploit one vulnerable metabolic node within the larger multilayered tumor network.
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Affiliation(s)
- Tom M Thomas
- Department of Neurosurgery, Maxine-Dunitz Neurosurgical Institute, Cedars Sinai Medical Center, Los Angeles, California
| | - Ken Miyaguchi
- Department of Neurosurgery, Maxine-Dunitz Neurosurgical Institute, Cedars Sinai Medical Center, Los Angeles, California
| | - Lincoln A Edwards
- Department of Neurosurgery, Maxine-Dunitz Neurosurgical Institute, Cedars Sinai Medical Center, Los Angeles, California
| | - Hongqiang Wang
- Department of Neurosurgery, Maxine-Dunitz Neurosurgical Institute, Cedars Sinai Medical Center, Los Angeles, California
| | - Hassen Wollebo
- Department of Neuroscience, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Li Aiguo
- Neuro-Oncology Branch, National Cancer Institute, Bethesda, Maryland
| | - Ramachandran Murali
- Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles, California
| | - Yizhou Wang
- Genomics Core, Cedars Sinai Medical Center, Los Angeles, California
| | - Daniel Braas
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, California
| | - Justin S Michael
- Department of Neurosurgery, Maxine-Dunitz Neurosurgical Institute, Cedars Sinai Medical Center, Los Angeles, California
| | - Allen M Andres
- Mitochondria and Metabolism Core, Cedars Sinai Medical Center, Los Angeles, California
| | - Miqin Zhang
- Department of Materials Science and Engineering, University of Washington, Seattle, Washington
| | - Kamel Khalili
- Department of Neuroscience, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Roberta A Gottlieb
- Mitochondria and Metabolism Core, Cedars Sinai Medical Center, Los Angeles, California
| | - J Manuel Perez
- Department of Neurosurgery, and Biomedical Imaging Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - John S Yu
- Department of Neurosurgery, Maxine-Dunitz Neurosurgical Institute, Cedars Sinai Medical Center, Los Angeles, California.
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22
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Favorable role of IDH1/2 mutations aided with MGMT promoter gene methylation in the outcome of patients with malignant glioma. Future Sci OA 2020; 7:FSO663. [PMID: 33552543 PMCID: PMC7849969 DOI: 10.2144/fsoa-2020-0057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Aim The implications of molecular biomarkers IDH1/2 mutations and MGMT gene promoter methylation were evaluated for prognostic outcome of glioma patients. Materials & methods Glioma cases were analyzed for IDH1/2 mutations and MGMT promoter methylation by DNA sequencing and methylation-specific PCR, respectively. Results Mutations found in IDH1/2 genes totaled 63.4% (N = 40) wherein IDH1 mutations were significantly associated with oligidendrioglioma (p = 0.005) and astrocytoma (p = 0.0002). IDH1 mutants presented more, 60.5% in MGMT promoter-methylated cases (p = 0.03). IDH1 mutant cases had better survival for glioblastoma and oligodendrioglioma (log-rank p = 0.01). Multivariate analysis confirmed better survival in MGMT methylation carriers (hazard ratio [HR]: 0.59; p = 0.031). Combination of both biomarkers showed better prognosis on temozolomide (p < 0.05). Conclusion IDH1/2 mutations proved independent prognostic factors in glioma and associated with MGMT methylation for better survival.
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23
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Balaji E V, Kumar N, Satarker S, Nampoothiri M. Zinc as a plausible epigenetic modulator of glioblastoma multiforme. Eur J Pharmacol 2020; 887:173549. [PMID: 32926916 DOI: 10.1016/j.ejphar.2020.173549] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/26/2020] [Accepted: 09/09/2020] [Indexed: 01/04/2023]
Abstract
Glioblastoma Multiforme (GBM) is an aggressive brain tumor (WHO grade 4 astrocytoma) with unknown causes and is associated with a reduced life expectancy. The available treatment options namely radiotherapy, surgery and chemotherapy have failed to improve life expectancy. Out of the various therapeutic approaches, epigenetic therapy is one of the most studied. Epigenetic therapy is involved in the effective treatment of GBM by inhibiting DNA methyltransferase, histone deacetylation and non-coding RNA. It also promotes the expression of the tumor suppressor gene and is involved in the suppression of the oncogene. Various targets are being studied to implement proper epigenetic regulation to control GBM effectively. Zinc is one of the micronutrients which is considered to maintain epigenetic regulation by promoting the proper DNA folding, protecting genetic material from the oxidative damage and controlling the enzyme activation involved in the epigenetic regulation. Here, we are discussing the importance of zinc in regulating the epigenetic modifications and assessing its role in glioblastoma research. The discussion also highlights the importance of artificial intelligence using epigenetics for envisaging the glioma progression, diagnosis and its management.
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Affiliation(s)
- Vignesh Balaji E
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Nitesh Kumar
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Sairaj Satarker
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Madhavan Nampoothiri
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India.
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24
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Zhang P, Xia Q, Liu L, Li S, Dong L. Current Opinion on Molecular Characterization for GBM Classification in Guiding Clinical Diagnosis, Prognosis, and Therapy. Front Mol Biosci 2020; 7:562798. [PMID: 33102518 PMCID: PMC7506064 DOI: 10.3389/fmolb.2020.562798] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/18/2020] [Indexed: 12/11/2022] Open
Abstract
Glioblastoma (GBM) is highly invasive and the deadliest brain tumor in adults. It is characterized by inter-tumor and intra-tumor heterogeneity, short patient survival, and lack of effective treatment. Prognosis and therapy selection is driven by molecular data from gene transcription, genetic alterations and DNA methylation. The four GBM molecular subtypes are proneural, neural, classical, and mesenchymal. More effective personalized therapy heavily depends on higher resolution molecular subtype signatures, combined with gene therapy, immunotherapy and organoid technology. In this review, we summarize the principal GBM molecular classifications that guide diagnosis, prognosis, and therapeutic recommendations.
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Affiliation(s)
- Pei Zhang
- School of Life Sciences, Beijing Institute of Technology, Beijing, China
| | - Qin Xia
- School of Life Sciences, Beijing Institute of Technology, Beijing, China
| | - Liqun Liu
- School of Life Sciences, Beijing Institute of Technology, Beijing, China
| | - Shouwei Li
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Lei Dong
- School of Life Sciences, Beijing Institute of Technology, Beijing, China
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25
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Li X, Fan W, Yao A, Song H, Ge Y, Yan M, Shan Y, Zhang C, Li P, Jia L. Downregulation of reelin predicts poor prognosis for glioma. Biomark Med 2020; 14:651-663. [PMID: 32613843 DOI: 10.2217/bmm-2019-0609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aim: In the present study, we studied the relationship between RELN and prognosis in glioma. Materials & methods: Expression profiles and methylation data of RELN were obtained from bioinformatic datasets. Correlations between RELN and clinicopathological features and overall survival were respectively assessed using chi-square test and Kaplan-Meier analysis. Results: RELN was downregulated in glioma, and its downregulation correlated well with glioma malignancy and overall survival. Meanwhile, hypermethylation of RELN was significantly correlated with low RELN expression. Additionally, gene set enrichment analysis demonstrated that low expression of RELN correlated with many key cancer pathways, possibly highlighting the importance of RELN in carcinogenesis of brain. Conclusion: RELN may serve as a potential prognostic marker and promising target molecule for new therapy of glioma.
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Affiliation(s)
- Xueli Li
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Wange Fan
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Anhui Yao
- Department of Neurosurgery, The General Hospital of PLA, Beijing, China.,Department of Neurosurgery, 988th Hospital of Chinese People's Liberation Army, Zhengzhou, Henan Province, PR China
| | - Huiling Song
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Yunxiao Ge
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Mengyao Yan
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Yubo Shan
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Chujie Zhang
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Pu Li
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Liyun Jia
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, China
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26
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Shen X, Wu S, Zhang J, Li M, Xu F, Wang A, Lei Y, Zhu G. Wild‑type IDH1 affects cell migration by modulating the PI3K/AKT/mTOR pathway in primary glioblastoma cells. Mol Med Rep 2020; 22:1949-1957. [PMID: 32705169 PMCID: PMC7411459 DOI: 10.3892/mmr.2020.11250] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 05/18/2020] [Indexed: 12/15/2022] Open
Abstract
Glioblastoma (GBM) is the most common type of brain cancer and has the highest mortality. Dysregulated expression of wild-type isocitrate dehydrogenase 1 (IDH1) has been demonstrated to promote the progression of primary GBM without accumulating D-2-hydroxyglutarate, which differs from IDH1 mutation-related mechanisms of tumorigenesis. Previous studies have revealed several roles of wild-type IDH1 in primary GBM, involving proliferation and apoptosis. However, the function of IDH1 in cell migration has not been investigated. In the current study, the results of bioinformatics analysis revealed that IDH1 expression was significantly upregulated in patients with primary GBM. Wound healing and Transwell assays demonstrated that IDH1 overexpression promoted cell migration in primary GBM cells and that IDH1 knockdown hindered this process. Furthermore, α-ketoglutarate (α-KG), which is the main product of IDH1-catalyzed reactions, was significantly decreased by IDH1 knockdown and upregulated by IDH1 overexpression. α-KG treatment significantly increased the migration of primary GBM cells. Additionally, RNA sequence analysis of patients with primary GBM reported significant alterations in the expression of phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT)/mammalian target of rapamycin (mTOR) pathway-regulated genes, including Myc, Snail family transcriptional repressor 2 and Twist-related protein 1, which are primarily cell migration regulatory factors. Western blotting revealed that the overexpression or knockdown of IDH1 promoted or inhibited the PI3K/AKT/mTOR pathway, respectively. α-KG treatment of primary GBM cells also promoted the PI3K/AKT/mTOR pathway. Furthermore, IDH1-overexpressing and α-KG-treated U87 cells were incubated with rapamycin, an mTOR-specific inhibitor, and the results revealed that rapamycin treatment reversed the increased cell migration caused by IDH1 overexpression and α-KG treatment. The results indicated that IDH1 regulated the migration of primary GBM cells by altering α-KG levels and that the function of the IDH1/α-KG axis may rely on PI3K/AKT/mTOR pathway regulation.
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Affiliation(s)
- Xiaopeng Shen
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, P.R. China
| | - Shen Wu
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, P.R. China
| | - Jingyi Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, P.R. China
| | - Meng Li
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, P.R. China
| | - Feng Xu
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, P.R. China
| | - Ao Wang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, P.R. China
| | - Yang Lei
- Department of Inspection, Wuhu Center for Disease Control and Prevention, Wuhu, Anhui 241000, P.R. China
| | - Guoping Zhu
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, P.R. China
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Abstract
Glioma is the most malignant primary brain cancer which frequently occurred in adults. In recent years, long-non coding RNAs (lncRNAs) have been demonstrated to play pivotal roles in human cancers. However, the role of most lncRNAs in gliomagenesis has not been probed. Presently, through TCGA, a novel lncRNA LINC01198 was found to be up-regulated and associated with clinical outcomes in glioblastoma multiforme (GBM). In our study, LINC01198 was proved to be up-regulated in glioma cell lines, and silenced LINC01198 curbed glioma cell proliferation and accelerated cell apoptosis. Importantly, we corroborated that LINC01198 activated the PI3 K/AKT pathway to aggravate glioma progression by targeting PIK3 CA and PTEN. Subsequently, LINC01198 was validated to localize in both cytoplasm and nucleus of glioma cells. Through mechanistic exploration, we illustrated that LINC01198 increased PIK3CA expression by sponging miR-129-5p in the cytoplasm. Furthermore, PTEN was transcriptionally repressed by REST/RCOR1/HDAC2 complex. More importantly, LINC01198 accelerated the assembly of REST/RCOR1/HDAC2 complex and recruited such complex to PTEN promoter so as to impair PTEN expression in glioma. Finally, we further verified that LINC01198 hindered glioma tumour growth in vivo through AKT-dependent manner. Jointly, LINC01198 activates PI3 K/AKT signalling to exert oncogenic function in gliomagenesis by regulating PIK3CA and PTEN, which highlights a new approach for glioma treatment.
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Affiliation(s)
- Yuan Xie
- Department of Neurosurgery, The Second Affiliated Hospital of Chongqing Medical University , Chongqing, China
| | - Yuan Cheng
- Department of Neurosurgery, The Second Affiliated Hospital of Chongqing Medical University , Chongqing, China
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28
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Liao Y, Zhang B, Zhang T, Zhang Y, Wang F. LncRNA GATA6-AS Promotes Cancer Cell Proliferation and Inhibits Apoptosis in Glioma by Downregulating lncRNA TUG1. Cancer Biother Radiopharm 2020; 34:660-665. [PMID: 31809214 DOI: 10.1089/cbr.2019.2830] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background: Long noncoding RNA (lncRNA) GATA6-AS regulates the growth of endothelial cells, indicating its involvement in human diseases. The present study aimed to investigate the roles of GATA6-AS in glioma. Results: GATA6-AS was significantly upregulated in glioma. GATA6-AS levels in plasma was positively and significantly correlated with its expression levels in glioma tissues. TUG1 was significantly downregulated in glioma and was inversely correlated with GATA6-AS. GATA6-AS overexpression led to TUG1 downregulation, whereas TUG1 overexpression failed to significantly affect GATA6-AS. GATA6-AS overexpression promoted glioma cell proliferation and inhibited apoptosis, TUG1 overexpression inhibited cell proliferation and attenuated the effects of GATA6-AS overexpression. Conclusions: Therefore, lncRNA GATA6-AS affects cell proliferation and apoptosis and regulates TUG1 expression in glioma.
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Affiliation(s)
- Yuzhi Liao
- Department of Neurosurgery, PLA Rocket Force General Hospital, Beijing, P.R. China
| | - Baozhong Zhang
- Department of Neurosurgery, PLA Rocket Force General Hospital, Beijing, P.R. China
| | - Ting Zhang
- Department of Neurosurgery, PLA Rocket Force General Hospital, Beijing, P.R. China
| | - Yiming Zhang
- Department of Neurosurgery, PLA Rocket Force General Hospital, Beijing, P.R. China
| | - Fei Wang
- Department of Neurosurgery, PLA Rocket Force General Hospital, Beijing, P.R. China
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29
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Guo X, Park JE, Gallart-Palau X, Sze SK. Oxidative Damage to the TCA Cycle Enzyme MDH1 Dysregulates Bioenergetic Enzymatic Activity in the Aged Murine Brain. J Proteome Res 2020; 19:1706-1717. [DOI: 10.1021/acs.jproteome.9b00861] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Xue Guo
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Jung Eun Park
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Xavier Gallart-Palau
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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30
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Zhao YY, Wan QS, Hao Z, Zhu HX, Xing ZL, Li MH. Clinical nomogram for predicting the survival of patients with cerebral anaplastic gliomas. Medicine (Baltimore) 2020; 99:e19416. [PMID: 32150092 PMCID: PMC7478695 DOI: 10.1097/md.0000000000019416] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The present study aimed to develop an effective nomogram for predicting the overall survival (OS) of patients with cerebral anaplastic glioma (AG).This study included 1939 patients diagnosed with AG between 1973 and 2013 who were identified using the Surveillance, Epidemiology, and End Results database. A multivariate Cox regression analysis revealed that age, histology, tumor site, marital status, radiotherapy, and surgery were independent prognostic factors and, thus, these factors were selected to build a clinical nomogram. Harrell's concordance index (C-index) and a calibration curve were formulated to evaluate the discrimination and calibration of the nomogram using bootstrapping.A nomogram was developed to predict 5- and 9-year OS rates based on 6 independent prognostic factors identified in the training set: age, tumor site, marital status, histology, radiotherapy, and surgery (P < .05). The Harrell's concordance index values of the training and validation sets were 0.776 (0.759-0.793) and 0.766 (0.739-0.792), respectively. The calibration curve exhibited good consistency with the actual observation curve in both sets.Although the prognostic value of the World Health Organization (WHO) classification has been validated, we developed a novel nomogram based on readily available clinical variables in terms of demographic data, therapeutic modalities, and tumor characteristics to predict the survival of AG patients. When used in combination with the WHO classification system, this clinical nomogram can aid clinicians in making individualized predictions of AG patient survival and improving treatment strategies.
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Affiliation(s)
| | - Qin-Si Wan
- Department of gastroenterology, the First Affiliated Hospital of Nanchang University, Nanchang, China
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31
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Valdebenito S, D'Amico D, Eugenin E. Novel approaches for glioblastoma treatment: Focus on tumor heterogeneity, treatment resistance, and computational tools. Cancer Rep (Hoboken) 2019; 2:e1220. [PMID: 32729241 PMCID: PMC7941428 DOI: 10.1002/cnr2.1220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 06/05/2019] [Accepted: 07/02/2019] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Glioblastoma (GBM) is a highly aggressive primary brain tumor. Currently, the suggested line of action is the surgical resection followed by radiotherapy and treatment with the adjuvant temozolomide, a DNA alkylating agent. However, the ability of tumor cells to deeply infiltrate the surrounding tissue makes complete resection quite impossible, and, in consequence, the probability of tumor recurrence is high, and the prognosis is not positive. GBM is highly heterogeneous and adapts to treatment in most individuals. Nevertheless, these mechanisms of adaption are unknown. RECENT FINDINGS In this review, we will discuss the recent discoveries in molecular and cellular heterogeneity, mechanisms of therapeutic resistance, and new technological approaches to identify new treatments for GBM. The combination of biology and computer resources allow the use of algorithms to apply artificial intelligence and machine learning approaches to identify potential therapeutic pathways and to identify new drug candidates. CONCLUSION These new approaches will generate a better understanding of GBM pathogenesis and will result in novel treatments to reduce or block the devastating consequences of brain cancers.
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Affiliation(s)
- Silvana Valdebenito
- Department of Neuroscience, Cell Biology, and AnatomyUniversity of Texas Medical Branch (UTMB)GalvestonTexas
| | - Daniela D'Amico
- Department of Neuroscience, Cell Biology, and AnatomyUniversity of Texas Medical Branch (UTMB)GalvestonTexas
- Department of Biomedicine and Clinic NeuroscienceUniversity of PalermoPalermoItaly
| | - Eliseo Eugenin
- Department of Neuroscience, Cell Biology, and AnatomyUniversity of Texas Medical Branch (UTMB)GalvestonTexas
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32
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Sukswai N, Khoury JD. Immunohistochemistry Innovations for Diagnosis and Tissue-Based Biomarker Detection. Curr Hematol Malig Rep 2019; 14:368-375. [DOI: 10.1007/s11899-019-00533-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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33
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Ye J, Zhu J, Chen H, Qian J, Zhang L, Wan Z, Chen F, Sun S, Li W, Luo C. A novel lncRNA-LINC01116 regulates tumorigenesis of glioma by targeting VEGFA. Int J Cancer 2019; 146:248-261. [PMID: 31144303 DOI: 10.1002/ijc.32483] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 04/16/2019] [Accepted: 05/07/2019] [Indexed: 12/19/2022]
Abstract
Brain glioma is the most common malignant tumor of the central nervous system, and one of the leading causes of death in patients with intracranial tumors. The clinical outcome of glioma is usually poor due to abundant vascularity, fast growth and susceptibility of invasion to normal brain tissues. Our microarray study showed that lncRNA-LINC01116 was significantly upregulated in glioma tissues and played an important role in cell proliferation, cycle, migration, invasion and angiogenesis. In addition, vascular endothelial growth factor (VEGFA) may be the major target genes in the downstream of lncRNA-LINC01116. Dual luciferase assay showed that LINC01116 and VEGFA both contained a miR-31-5p binding site, and LINC01116 could regulate the expression of VEGFA through competitive absorption of miR-31-5p. RNA immunoprecipitation indicated that LINC01116 and VEGFA were present in the miR-31-5p-RISC complex, and biotinylated miR-31-5p pull-down assay suggested that there was a competitive relationship between LINC01116 and VEGFA to bind with miR-31-5p. Collectively, our study has identified a novel lncRNA-LINC01116 and clarified the role and mechanism of LINC01116 in the tumorigenesis of glioma. LINC01116 may prove to be a potential target for the clinical diagnosis and treatment of glioma.
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Affiliation(s)
- Jingliang Ye
- Department of Neurosurgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Neurosurgery, 72 Group Military Hospital of CPLA, Huzhou, China
| | - Junle Zhu
- Department of Neurosurgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Huairui Chen
- Department of Neurosurgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jun Qian
- Department of Neurosurgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lei Zhang
- Department of Neurosurgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhiping Wan
- Department of Neurosurgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Feng Chen
- Department of Neurosurgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shuhan Sun
- Department of Medical Genetics, Second Military Medical University, Shanghai, China
| | - Wen Li
- Center of Reproductive Medicine, Shanghai Changzheng Hospital, Shanghai, China
| | - Chun Luo
- Department of Neurosurgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
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34
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Low VDAC1 Expression Is Associated with an Aggressive Phenotype and Reduced Overall Patient Survival in Cholangiocellular Carcinoma. Cells 2019; 8:cells8060539. [PMID: 31167495 PMCID: PMC6627691 DOI: 10.3390/cells8060539] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/03/2019] [Accepted: 06/04/2019] [Indexed: 12/16/2022] Open
Abstract
Cancer cells frequently exhibit dysfunctional oxidative phosphorylation (OXPHOS) and a concomitant increase in glycolytic flux. We investigated the expression of OXPHOS complex subunits and mitochondrial mass in 34 human cholangiocellular carcinomas (CCCs) and adjacent normal tissue by using tissue microarrays. In the tumor periphery, all OXPHOS complexes were reduced except complex I. In addition, significantly lower levels of complex IV were found at the tumor center (p < 0.0001). Mitochondrial mass, as indicated by VDAC1 expression, was significantly increased in CCCs compared to corresponding normal tissue (p < 0.0001). VDAC1 levels were inversely correlated with UICC (Union Internationale Contre le Cancer) cancer stage classification (p = 0.0065). Furthermore, significantly lower VDAC1 was present in patients with lymph node involvement (p = 0.02). Consistent with this, patients whose carcinomas expressed VDAC1 at low to moderate levels had significantly reduced survival compared to high expressors (p < 0.05). Therefore, low mitochondrial mass is associated with more aggressive CCC. These metabolic features are indicative of a Warburg phenotype in CCCs. This metabolic signature has potential therapeutic implications because tumors with low mitochondrial function may be targeted by metabolic therapies such as a high-fat, low-carbohydrate ketogenic diet.
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35
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Xi X, Chu Y, Liu N, Wang Q, Yin Z, Lu Y, Chen Y. Joint bioinformatics analysis of underlying potential functions of hsa-let-7b-5p and core genes in human glioma. J Transl Med 2019; 17:129. [PMID: 30995921 PMCID: PMC6471881 DOI: 10.1186/s12967-019-1882-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 04/11/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Glioma accounts for a large proportion of cancer, and an effective treatment for this disease is still lacking because of the absence of specific driver molecules. Current challenges in the treatment of glioma are the accurate and timely diagnosis of brain glioma and targeted treatment plans. To investigate the diagnostic biomarkers and prospective role of miRNAs in the tumorigenesis and progression of glioma, we analyzed the expression of miRNAs and key genes in glioma based on The Cancer Genome Atlas database. METHODS Of the 701 cases that were downloaded, five were normal and 696 were glioma. Then, 1626 differentially expressed genes were identified, and 173 aberrantly expressed miRNAs were calculated by edgeR. GO and KEGG pathway enrichment analyses were performed using Cytoscape software. A coexpression network was built by weighted correlation network analysis (WGCNA). A cell scratch test and transwell, cell apoptosis and cell cycle assays were performed to validate the function of hsa-let-7b-5p. RESULTS Based on crosstalk genes in the KEGG, PPI network, and WGCNA analyses, PLK1, CCNA2, cyclin B2 (CCNB2), and AURKA were screened as candidate diagnostic marker genes. The survival analysis revealed that high mRNA expression of PLK1, CCNA2, and AURKA was significantly associated with poor overall survival. Furthermore, hsa-let-7b-5p was identified as a core miRNA in the regulation of candidate genes involved in glioma development. We confirmed that hsa-let-7b-5p could inhibit the migration, invasion, and cell cycle of glioma cells. CONCLUSIONS This study provides four potential biomarkers for the diagnosis of glioma, offers a potential explanation of its pathogenesis, and proposes hsa-let-7b-5p as a therapeutic target.
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Affiliation(s)
- Xiaonan Xi
- College of Pharmacy, Nankai University, Tianjin, 300350 People’s Republic of China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350 People’s Republic of China
| | - Yahui Chu
- College of Pharmacy, Nankai University, Tianjin, 300350 People’s Republic of China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350 People’s Republic of China
| | - Ning Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350 People’s Republic of China
| | - Qianqian Wang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350 People’s Republic of China
| | - Zheng Yin
- College of Pharmacy, Nankai University, Tianjin, 300350 People’s Republic of China
| | - Yaxin Lu
- College of Pharmacy, Nankai University, Tianjin, 300350 People’s Republic of China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350 People’s Republic of China
| | - Yue Chen
- College of Pharmacy, Nankai University, Tianjin, 300350 People’s Republic of China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350 People’s Republic of China
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36
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Menon H, Ramapriyan R, Cushman TR, Verma V, Kim HH, Schoenhals JE, Atalar C, Selek U, Chun SG, Chang JY, Barsoumian HB, Nguyen QN, Altan M, Cortez MA, Hahn SM, Welsh JW. Role of Radiation Therapy in Modulation of the Tumor Stroma and Microenvironment. Front Immunol 2019; 10:193. [PMID: 30828330 PMCID: PMC6384252 DOI: 10.3389/fimmu.2019.00193] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/23/2019] [Indexed: 12/22/2022] Open
Abstract
In recent decades, there has been substantial growth in our understanding of the immune system and its role in tumor growth and overall survival. A central finding has been the cross-talk between tumor cells and the surrounding environment or stroma. This tumor stroma, comprised of various cells, and extracellular matrix (ECM), has been shown to aid in suppressing host immune responses against tumor cells. Through immunosuppressive cytokine secretion, metabolic alterations, and other mechanisms, the tumor stroma provides a complex network of safeguards for tumor proliferation. With recent advances in more effective, localized treatment, radiation therapy (XRT) has allowed for strategies that can effectively alter and ablate tumor stromal tissue. This includes promoting immunogenic cell death through tumor antigen release to increasing immune cell trafficking, XRT has a unique advantage against the tumoral immune evasion mechanisms that are orchestrated by stromal cells. Current studies are underway to elucidate pathways within the tumor stroma as potential targets for immunotherapy and chemoradiation. This review summarizes the effects of tumor stroma in tumor immune evasion, explains how XRT may help overcome these effects, with potential combinatorial approaches for future treatment modalities.
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Affiliation(s)
- Hari Menon
- Departments of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Rishab Ramapriyan
- Departments of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Taylor R. Cushman
- Departments of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Vivek Verma
- Department of Radiation Oncology, Allegheny General Hospital, Pittsburgh, PA, United States
| | - Hans H. Kim
- Department of Radiation Medicine, School of Medicine, Oregon Health and Sciences University, Portland, OR, United States
| | | | - Cemre Atalar
- Departments of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ugur Selek
- Department of Radiation Oncology, School of Medicine, Koç University, Istanbul, Turkey
| | - Stephen G. Chun
- Departments of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Joe Y. Chang
- Departments of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Hampartsoum B. Barsoumian
- Departments of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Quynh-Nhu Nguyen
- Departments of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Mehmet Altan
- Thoracic/Head and Neck Medical Oncology, Houston, TX, United States
| | - Maria A. Cortez
- Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Stephen M. Hahn
- Departments of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - James W. Welsh
- Departments of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
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Domblides C, Lartigue L, Faustin B. Control of the Antitumor Immune Response by Cancer Metabolism. Cells 2019; 8:cells8020104. [PMID: 30708988 PMCID: PMC6406288 DOI: 10.3390/cells8020104] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 12/12/2022] Open
Abstract
The metabolic reprogramming of tumor cells and immune escape are two major hallmarks of cancer cells. The metabolic changes that occur during tumorigenesis, enabling survival and proliferation, are described for both solid and hematological malignancies. Concurrently, tumor cells have deployed mechanisms to escape immune cell recognition and destruction. Additionally, therapeutic blocking of tumor-mediated immunosuppression has proven to have an unprecedented positive impact in clinical oncology. Increased evidence suggests that cancer metabolism not only plays a crucial role in cancer signaling for sustaining tumorigenesis and survival, but also has wider implications in the regulation of antitumor immune signaling through both the release of signaling molecules and the expression of immune membrane ligands. Here, we review these molecular events to highlight the contribution of cancer cell metabolic reprogramming on the shaping of the antitumor immune response.
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Affiliation(s)
- Charlotte Domblides
- Bordeaux University, CNRS, UMR 5164, ImmunoConcEpT, 33000 Bordeaux, France.
- Department of Medical Oncology, Hôpital Saint-André, Bordeaux University Hospital-CHU, 33000 Bordeaux, France.
| | - Lydia Lartigue
- Curematch, Inc., 6440 Lusk Bvld, San Diego, CA 92121, USA.
| | - Benjamin Faustin
- Bordeaux University, CNRS, UMR 5164, ImmunoConcEpT, 33000 Bordeaux, France.
- Cellomet, CGFB, 146 Rue léo Saignat, F-33000 Bordeaux, France.
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Malta TM, de Souza CF, Sabedot TS, Silva TC, Mosella MS, Kalkanis SN, Snyder J, Castro AVB, Noushmehr H. Glioma CpG island methylator phenotype (G-CIMP): biological and clinical implications. Neuro Oncol 2019; 20:608-620. [PMID: 29036500 DOI: 10.1093/neuonc/nox183] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Gliomas are a heterogeneous group of brain tumors with distinct biological and clinical properties. Despite advances in surgical techniques and clinical regimens, treatment of high-grade glioma remains challenging and carries dismal rates of therapeutic success and overall survival. Challenges include the molecular complexity of gliomas, as well as inconsistencies in histopathological grading, resulting in an inaccurate prediction of disease progression and failure in the use of standard therapy. The updated 2016 World Health Organization (WHO) classification of tumors of the central nervous system reflects a refinement of tumor diagnostics by integrating the genotypic and phenotypic features, thereby narrowing the defined subgroups. The new classification recommends molecular diagnosis of isocitrate dehydrogenase (IDH) mutational status in gliomas. IDH-mutant gliomas manifest the cytosine-phosphate-guanine (CpG) island methylator phenotype (G-CIMP). Notably, the recent identification of clinically relevant subsets of G-CIMP tumors (G-CIMP-high and G-CIMP-low) provides a further refinement in glioma classification that is independent of grade and histology. This scheme may be useful for predicting patient outcome and may be translated into effective therapeutic strategies tailored to each patient. In this review, we highlight the evolution of our understanding of the G-CIMP subsets and how recent advances in characterizing the genome and epigenome of gliomas may influence future basic and translational research.
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Affiliation(s)
- Tathiane M Malta
- Department of Neurosurgery, Henry Ford Hospital, Detroit, Michigan, USA.,Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Camila F de Souza
- Department of Neurosurgery, Henry Ford Hospital, Detroit, Michigan, USA.,Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Thais S Sabedot
- Department of Neurosurgery, Henry Ford Hospital, Detroit, Michigan, USA.,Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Tiago C Silva
- Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Maritza S Mosella
- Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Steven N Kalkanis
- Department of Neurosurgery, Henry Ford Hospital, Detroit, Michigan, USA
| | - James Snyder
- Department of Neurosurgery, Henry Ford Hospital, Detroit, Michigan, USA.,Department of Neurology, Henry Ford Hospital, Detroit, Michigan, USA
| | | | - Houtan Noushmehr
- Department of Neurosurgery, Henry Ford Hospital, Detroit, Michigan, USA.,Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, São Paulo, Brazil
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Jeanquartier F, Jean-Quartier C, Holzinger A. Use case driven evaluation of open databases for pediatric cancer research. BioData Min 2019; 12:2. [PMID: 30675185 PMCID: PMC6334395 DOI: 10.1186/s13040-018-0190-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 12/05/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND A plethora of Web resources are available offering information on clinical, pre-clinical, genomic and theoretical aspects of cancer, including not only the comprehensive cancer projects as ICGC and TCGA, but also less-known and more specialized projects on pediatric diseases such as PCGP. However, in case of data on childhood cancer there is very little information openly available. Several web-based resources and tools offer general biomedical data which are not purpose-built, for neither pediatric nor cancer analysis. Additionally, many Web resources on cancer focus on incidence data and statistical social characteristics as well as self-regulating communities. METHODS We summarize those resources which are open and are considered to support scientific fundamental research, while we address our comparison to 11 identified pediatric cancer-specific resources (5 tools, 6 databases). The evaluation consists of 5 use cases on the example of brain tumor research and covers user-defined search scenarios as well as data mining tasks, also examining interactive visual analysis features. RESULTS Web resources differ in terms of information quantity and presentation. Pedican lists an abundance of entries with few selection features. PeCan and PedcBioPortal include visual analysis tools while the latter integrates published and new consortia-based data. UCSC Xena Browser offers an in-depth analysis of genomic data. ICGC data portal provides various features for data analysis and an option to submit own data. Its focus lies on adult Pan-Cancer projects. Pediatric Pan-Cancer datasets are being integrated into PeCan and PedcBioPortal. Comparing information on prominent mutations within glioma discloses well-known, unknown, possible, as well as inapplicable biomarkers. This summary further emphasizes the varying data allocation. Tested tools show advantages and disadvantages, depending on the respective use case scenario, providing inhomogeneous data quantity and information specifics. CONCLUSIONS Web resources on specific pediatric cancers are less abundant and less-known compared to those offering adult cancer research data. Meanwhile, current efforts of ongoing pediatric data collection and Pan-Cancer projects indicate future opportunities for childhood cancer research, that is greatly needed for both fundamental as well as clinical research.
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Affiliation(s)
- Fleur Jeanquartier
- Institute of Interactive Systems and Data Science, Graz University of Technology, Graz, Austria
- Holzinger Group HCI-KDD, Institute for Medical Informatics, Statistics and Documentation, Medical University Graz, Auenbruggerplatz 2/V, Graz, 8036 Austria
| | - Claire Jean-Quartier
- Holzinger Group HCI-KDD, Institute for Medical Informatics, Statistics and Documentation, Medical University Graz, Auenbruggerplatz 2/V, Graz, 8036 Austria
| | - Andreas Holzinger
- Institute of Interactive Systems and Data Science, Graz University of Technology, Graz, Austria
- Holzinger Group HCI-KDD, Institute for Medical Informatics, Statistics and Documentation, Medical University Graz, Auenbruggerplatz 2/V, Graz, 8036 Austria
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Youn A, Kim KI, Rabadan R, Tycko B, Shen Y, Wang S. A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes. BMC Med Genomics 2018; 11:98. [PMID: 30400878 PMCID: PMC6218985 DOI: 10.1186/s12920-018-0425-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 10/19/2018] [Indexed: 01/08/2023] Open
Abstract
Background Recent large-scale cancer sequencing studies have discovered many novel cancer driver genes (CDGs) in human cancers. Some studies also suggest that CDG mutations contribute to cancer-associated epigenomic and transcriptomic alterations across many cancer types. Here we aim to improve our understanding of the connections between CDG mutations and altered cancer cell epigenomes and transcriptomes on pan-cancer level and how these connections contribute to the known association between epigenome and transcriptome. Method Using multi-omics data including somatic mutation, DNA methylation, and gene expression data of 20 cancer types from The Cancer Genome Atlas (TCGA) project, we conducted a pan-cancer analysis to identify CDGs, when mutated, have strong associations with genome-wide methylation or expression changes across cancer types, which we refer as methylation driver genes (MDGs) or expression driver genes (EDGs), respectively. Results We identified 32 MDGs, among which, eight are known chromatin modification or remodeling genes. Many of the remaining 24 MDGs are connected to chromatin regulators through either regulating their transcription or physically interacting with them as potential co-factors. We identified 29 EDGs, 26 of which are also MDGs. Further investigation on target genes’ promoters methylation and expression alteration patterns of these 26 overlapping driver genes shows that hyper-methylation of target genes’ promoters are significantly associated with down-regulation of the same target genes and hypo-methylation of target genes’ promoters are significantly associated with up-regulation of the same target genes. Conclusion This finding suggests a pivotal role for genetically driven changes in chromatin remodeling in shaping DNA methylation and gene expression patterns during tumor development. Electronic supplementary material The online version of this article (10.1186/s12920-018-0425-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ahrim Youn
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, New York, USA.,The Jackson Laboratory For Genomic Medicine, Farmington, Connecticut, USA
| | - Kyung In Kim
- The Jackson Laboratory For Genomic Medicine, Farmington, Connecticut, USA
| | - Raul Rabadan
- Department of System Biology, Columbia University, New York, New York, USA.,Department of Biomedical Informatics, Columbia University, New York, New York, USA
| | - Benjamin Tycko
- Division of Genetics & Epigenetics, Hackensack University Medical Center, Hackensack, New Jersey, USA
| | - Yufeng Shen
- Department of System Biology, Columbia University, New York, New York, USA.,Department of Biomedical Informatics, Columbia University, New York, New York, USA.,Columbia Genome Center, Columbia University, New York, New York, USA
| | - Shuang Wang
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, New York, USA.
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Abstract
OBJECTIVES To identify the tumors included in the WHO classification of low-grade gliomas, and review the importance of molecular biomarkers and their implication for treatment, prognosis, and outcomes. DATA SOURCES Published research, clinical guidelines, educational articles in oncology journals, and Web-based resources. CONCLUSION Molecular neuropathology has influenced the reclassification of low-grade gliomas and, as such, has provided patient-specific treatments with improving outcomes. IMPLICATIONS FOR NURSING PRACTICE Nurses play a key role in patient education and communication with the patient's interdisciplinary care team. Understanding the molecular neuropathology that determine treatment recommendations and in turn recognizing and identifying complications provides improved patient/caregiver satisfaction and outcomes.
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Avellaneda Matteo D, Wells GA, Luna LA, Grunseth AJ, Zagnitko O, Scott DA, Hoang A, Luthra A, Swairjo MA, Schiffer JM, Sohl CD. Inhibitor potency varies widely among tumor-relevant human isocitrate dehydrogenase 1 mutants. Biochem J 2018; 475:3221-3238. [PMID: 30249606 PMCID: PMC6422176 DOI: 10.1042/bcj20180424] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/14/2018] [Accepted: 09/18/2018] [Indexed: 01/15/2023]
Abstract
Mutations in isocitrate dehydrogenase 1 (IDH1) drive most low-grade gliomas and secondary glioblastomas and many chondrosarcomas and acute myeloid leukemia cases. Most tumor-relevant IDH1 mutations are deficient in the normal oxidization of isocitrate to α-ketoglutarate (αKG), but gain the neomorphic activity of reducing αKG to D-2-hydroxyglutarate (D2HG), which drives tumorigenesis. We found previously that IDH1 mutants exhibit one of two reactivities: deficient αKG and moderate D2HG production (including commonly observed R132H and R132C) or moderate αKG and high D2HG production (R132Q). Here, we identify a third type of reactivity, deficient αKG and high D2HG production (R132L). We show that R132Q IDH1 has unique structural features and distinct reactivities towards mutant IDH1 inhibitors. Biochemical and cell-based assays demonstrate that while most tumor-relevant mutations were effectively inhibited by mutant IDH1 inhibitors, R132Q IDH1 had up to a 16 300-fold increase in IC50 versus R132H IDH1. Only compounds that inhibited wild-type (WT) IDH1 were effective against R132Q. This suggests that patients with a R132Q mutation may have a poor response to mutant IDH1 therapies. Molecular dynamics simulations revealed that near the NADP+/NADPH-binding site in R132Q IDH1, a pair of α-helices switches between conformations that are more wild-type-like or more mutant-like, highlighting mechanisms for preserved WT activity. Dihedral angle changes in the dimer interface and buried surface area charges highlight possible mechanisms for loss of inhibitor affinity against R132Q. This work provides a platform for predicting a patient's therapeutic response and identifies a potential resistance mutation that may arise upon treatment with mutant IDH inhibitors.
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Affiliation(s)
| | - Grace A Wells
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, U.S.A
| | - Lucas A Luna
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, U.S.A
| | - Adam J Grunseth
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, U.S.A
| | - Olga Zagnitko
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, U.S.A
| | - David A Scott
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, U.S.A
| | - An Hoang
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, U.S.A
| | - Amit Luthra
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, U.S.A
| | - Manal A Swairjo
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, U.S.A
| | | | - Christal D Sohl
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, U.S.A.
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S AS, Goutham R N A, Mohan S S. In silico screening of cancer-associated mutations in the HSA domain of BRG1 and its role in affecting the Arp-HSA sub-complex of SWI/SNF. Comput Biol Chem 2018; 77:109-115. [PMID: 30286321 DOI: 10.1016/j.compbiolchem.2018.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 06/24/2018] [Accepted: 07/03/2018] [Indexed: 11/30/2022]
Abstract
SWI/SNF (SWItch/Sucrose Non-Fermentable) complexes regulate the gene expression programs by remodeling the nucleosome architecture of the chromatin functional elements. These large multi-component complexes comprise eight or more subunits and are conserved from yeast to human. Noticeably, nuclear actin and actin-related proteins (Arps) are an integral part of these complexes and are known to directly interact with the helicase-SANT-associated (HSA) domain of ATPase subunit. Recently, SWI/SNF subunits are gaining importance because of the prevalence of cancer-causing mutations associated with them. The functional characterization of the mutations in the SWI/SNF subunits is important for understanding their role in tumorigenesis and identifying potential therapeutic strategies. To study the actin-related complex of human SWI/SNF and the cancer-associated mutations interfering Arp assembly with the ATPase subunit, we modelled the structure of the β-actin-BAF53A-HSA complex based on the yeast Arp-HSA complex (PDB ID: 4I6M). Seven deleterious mutations in the HSA domain of BRG1 were identified based on the functional screening of cancer-associated mutations in the COSMIC database. Detailed structural analysis of the six mutations (R466H, R469W, Y489C, K502N, R513Q and R521P) based on molecular dynamics (MD) simulations reveal the distinct effect of each mutation in destabilizing the structure of the Arp-HSA complex. Predominantly we could notice the long-range effect of the HSA mutations in influencing the dynamics of the Arp subunits.
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Affiliation(s)
- Alagu Sankareswaran S
- School of Chemical & Biotechnology, Sastra Deemed University, Tirumalaisamudram, Thanjavur, 613401, India
| | - Arun Goutham R N
- School of Chemical & Biotechnology, Sastra Deemed University, Tirumalaisamudram, Thanjavur, 613401, India
| | - Suma Mohan S
- School of Chemical & Biotechnology, Sastra Deemed University, Tirumalaisamudram, Thanjavur, 613401, India.
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DeWitt JC, Jordan JT, Frosch MP, Samore WR, Iafrate AJ, Louis DN, Lennerz JK. Cost-effectiveness of IDH testing in diffuse gliomas according to the 2016 WHO classification of tumors of the central nervous system recommendations. Neuro Oncol 2018; 19:1640-1650. [PMID: 29016871 DOI: 10.1093/neuonc/nox120] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Background Due to the decreasing prevalence of IDH1 mutations in older patients, the 2016 World Health Organization (WHO) classification of brain tumors proposed not to perform sequencing for isocitrate dehydrogenase (IDH) in glioblastoma patients ≥55 years old. We present a cost-effectiveness analysis to estimate the financial impact of these guidelines. Methods From 2010 to 2015 we performed 1023 IDH tests in gliomas, amounting to ~$1.09 million in direct laboratory test costs. Samples were tested using R132H-specific immunohistochemistry, DNA sequencing validated for detection of noncanonical IDH1/2 mutations, or both methods. Results In cases tested by DNA sequencing, the fraction of non-R132H mutations was 5.4%, which included only 2 high-grade gliomas in patients ≥55 years (0.9%). When remodeling the optimal age cutoff in our patient population using 5-year age-binning, we found a 10-times higher pretest probability for the presence of a noncanonical IDH1 mutation in the setting of a negative IDH1-R132H immunohistochemistry result in patients <55 years. Applying the independently confirmed age cutoff of 55 years to glioblastoma patients (64%) would result in $403200 saved (43%). By not performing sequencing in patients ≥55 years, the turn-around time to final integrated neuropathological diagnosis is reduced by 53%, allowing these patients to gain earlier benefits from personalized genomic medicine. Conclusion The negligible prevalence of noncanonical IDH mutations in glioblastoma patients ≥55 years argues against universal IDH sequencing in this population. We predict that adoption of this age-based sequencing cutoff recommendation from the 2016 WHO guidelines will result in significant cost and time savings throughout the global health care system.
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Affiliation(s)
- John C DeWitt
- Department of Pathology; Department of Neurology, Division of Neuro-Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Justin T Jordan
- Department of Pathology; Department of Neurology, Division of Neuro-Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Matthew P Frosch
- Department of Pathology; Department of Neurology, Division of Neuro-Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Wesley R Samore
- Department of Pathology; Department of Neurology, Division of Neuro-Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - A John Iafrate
- Department of Pathology; Department of Neurology, Division of Neuro-Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - David N Louis
- Department of Pathology; Department of Neurology, Division of Neuro-Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jochen K Lennerz
- Department of Pathology; Department of Neurology, Division of Neuro-Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
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45
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Zhao Q, Manning JR, Sutton J, Costales A, Sendzik M, Shafer CM, Levell JR, Liu G, Caferro T, Cho YS, Palermo M, Chenail G, Dooley J, Villalba B, Farsidjani A, Chen J, Dodd S, Gould T, Liang G, Slocum K, Pu M, Firestone B, Growney J, Heimbach T, Pagliarini R. Optimization of 3-Pyrimidin-4-yl-oxazolidin-2-ones as Orally Bioavailable and Brain Penetrant Mutant IDH1 Inhibitors. ACS Med Chem Lett 2018; 9:746-751. [PMID: 30034612 DOI: 10.1021/acsmedchemlett.8b00182] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 06/11/2018] [Indexed: 12/11/2022] Open
Abstract
Mutant isocitrate dehydrogenase 1 (IDH1) is an attractive therapeutic target for the treatment of various cancers such as AML, glioma, and glioblastoma. We have evaluated 3-pyrimidin-4-yl-oxazolidin-2-ones as mutant IDH1 inhibitors that bind to an allosteric, induced pocket of IDH1R132H. This Letter describes SAR exploration focused on improving both the in vitro and in vivo metabolic stability of the compounds, leading to the identification of 19 as a potent and selective mutant IDH1 inhibitor that has demonstrated brain penetration and excellent oral bioavailability in rodents. In a preclinical patient-derived IDH1 mutant xenograft tumor model study, 19 efficiently inhibited the production of the biomarker 2-HG.
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Affiliation(s)
- Qian Zhao
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - James R. Manning
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - James Sutton
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Abran Costales
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Martin Sendzik
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Cynthia M. Shafer
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Julian R. Levell
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Gang Liu
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Thomas Caferro
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Young Shin Cho
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Mark Palermo
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Gregg Chenail
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Julia Dooley
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Brian Villalba
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ali Farsidjani
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jinyun Chen
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Stephanie Dodd
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ty Gould
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Guiqing Liang
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Kelly Slocum
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Minying Pu
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Brant Firestone
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Joseph Growney
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Tycho Heimbach
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Raymond Pagliarini
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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Lee SC. Diffuse Gliomas for Nonneuropathologists: The New Integrated Molecular Diagnostics. Arch Pathol Lab Med 2018; 142:804-814. [PMID: 29775073 DOI: 10.5858/arpa.2017-0449-ra] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Diffuse gliomas comprise the bulk of "brain cancer" in adults. The recent update to the 4th edition of the World Health Organization's classification of tumors of the central nervous system reflects an unprecedented change in the landscape of the diagnosis and management of diffuse gliomas that will affect all those involved in the management and care of patients. Of the recently discovered gene alterations, mutations in the Krebs cycle enzymes isocitrate dehydrogenases (IDHs) 1 and 2 have fundamentally changed the way the gliomas are understood and classified. Incorporating information on a few genetic parameters (IDH, ATRX and/or p53, and chromosome 1p19q codeletion), a relatively straightforward diagnostic algorithm has been generated with robust and reproducible results that correlate with patients' survival far better than relying on conventional histology alone. Evidence also supports the conclusion that the vast majority of diffuse gliomas without IDH mutations (IDH-wild-type astrocytomas) behave like IDH-wild-type glioblastomas ("molecular GBM"). Together, these changes reflect a big shift in the practice of diagnostic neuropathology in which tumor risk stratification aligns better with molecular information than histology/grading. The purpose of this review is to provide the readers with a brief synopsis of the changes in the 2016 World Health Organization update with an emphasis on diffuse gliomas and to summarize key gene abnormalities on which these classifications are based. Practical points involved in day-to-day diagnostic workup are also discussed, along with a comparison of the various diagnostic tests, including immunohistochemistry, with an emphasis on targeted next-generation sequencing panel technology as a future universal approach.
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Affiliation(s)
- Sunhee C Lee
- From the Department of Pathology, Albert Einstein College of Medicine, and the Department of Neuropathology, Montefiore Medical Center, Bronx, New York
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Migration/Invasion of Malignant Gliomas and Implications for Therapeutic Treatment. Int J Mol Sci 2018; 19:ijms19041115. [PMID: 29642503 PMCID: PMC5979613 DOI: 10.3390/ijms19041115] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 03/22/2018] [Accepted: 04/03/2018] [Indexed: 02/07/2023] Open
Abstract
Malignant tumors of the central nervous system (CNS) are among cancers with the poorest prognosis, indicated by their association with tumors of high-level morbidity and mortality. Gliomas, the most common primary CNS tumors that arise from neuroglial stem or progenitor cells, have estimated annual incidence of 6.6 per 100,000 individuals in the USA, and 3.5 per 100,000 individuals in Taiwan. Tumor invasion and metastasis are the major contributors to the deaths in cancer patients. Therapeutic goals including cancer stem cells (CSC), phenotypic shifts, EZH2/AXL/TGF-β axis activation, miRNAs and exosomes are relevant to GBM metastasis to develop novel targeted therapeutics for GBM and other brain cancers. Herein, we highlight tumor metastasis in our understanding of gliomas, and illustrate novel exosome therapeutic approaches in glioma, thereby paving the way towards innovative therapies in neuro-oncology.
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Li J, Huang J, Huang F, Jin Q, Zhu H, Wang X, Chen M. Decreased expression of IDH1-R132H correlates with poor survival in gastrointestinal cancer. Oncotarget 2018; 7:73638-73650. [PMID: 27655638 PMCID: PMC5342004 DOI: 10.18632/oncotarget.12039] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 08/25/2016] [Indexed: 12/20/2022] Open
Abstract
Isocitrate dehydrogenase (IDH1) is an NADP-dependent enzyme that catalyzes the decarboxylation of isocitrate to alpha-ketoglutarate. The IDH1-R132H mutation predicts a better clinical outcome for glioma patients, and the expression of IDH1-R132H correlates with a favorable outcome in patients with brain tumors. Here, we investigated IDH1-R132H expression in both gastric (n=526) and colorectal (n=399) tissues by performing immunohistochemistry analyses on tissue microarrays. We also tested whether IDH1-R132H expression correlated with various clinical parameters. In both gastric and colorectal cancer, expression of IDH1-R132H was associated with tumor stage. Patients with low IDH1-R132H expression had a poor overall survival. Our data indicate that IDH1-R132H expression could be used as a predictive marker of prognosis for patients with gastrointestinal cancer.
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Affiliation(s)
- Jieying Li
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Jianfei Huang
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Fang Huang
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Qing Jin
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Huijun Zhu
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Xudong Wang
- Department of Laboratory Medicine & Department of Clinical Tissue Bank, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Meng Chen
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NC, USA
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Folguera-Blasco N, Cuyàs E, Menéndez JA, Alarcón T. Epigenetic regulation of cell fate reprogramming in aging and disease: A predictive computational model. PLoS Comput Biol 2018; 14:e1006052. [PMID: 29543808 PMCID: PMC5871006 DOI: 10.1371/journal.pcbi.1006052] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 03/27/2018] [Accepted: 02/21/2018] [Indexed: 01/12/2023] Open
Abstract
Understanding the control of epigenetic regulation is key to explain and modify the aging process. Because histone-modifying enzymes are sensitive to shifts in availability of cofactors (e.g. metabolites), cellular epigenetic states may be tied to changing conditions associated with cofactor variability. The aim of this study is to analyse the relationships between cofactor fluctuations, epigenetic landscapes, and cell state transitions. Using Approximate Bayesian Computation, we generate an ensemble of epigenetic regulation (ER) systems whose heterogeneity reflects variability in cofactor pools used by histone modifiers. The heterogeneity of epigenetic metabolites, which operates as regulator of the kinetic parameters promoting/preventing histone modifications, stochastically drives phenotypic variability. The ensemble of ER configurations reveals the occurrence of distinct epi-states within the ensemble. Whereas resilient states maintain large epigenetic barriers refractory to reprogramming cellular identity, plastic states lower these barriers, and increase the sensitivity to reprogramming. Moreover, fine-tuning of cofactor levels redirects plastic epigenetic states to re-enter epigenetic resilience, and vice versa. Our ensemble model agrees with a model of metabolism-responsive loss of epigenetic resilience as a cellular aging mechanism. Our findings support the notion that cellular aging, and its reversal, might result from stochastic translation of metabolic inputs into resilient/plastic cell states via ER systems.
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Affiliation(s)
- Núria Folguera-Blasco
- Centre de Recerca Matemàtica, Edifici C, Campus de Bellaterra, Bellaterra (Barcelona), Spain
- Departament de Matemàtiques, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Elisabet Cuyàs
- Molecular Oncology Group, Girona Biomedical Research Institute (IDIBGI), Girona, Spain
- MetaboStem, Barcelona, Spain
| | - Javier A. Menéndez
- Molecular Oncology Group, Girona Biomedical Research Institute (IDIBGI), Girona, Spain
- MetaboStem, Barcelona, Spain
- ProCURE (Program Against Cancer Therapeutic Resistance), Metabolism and Cancer Group, Catalan Institute of Oncology, Girona, Spain
| | - Tomás Alarcón
- Centre de Recerca Matemàtica, Edifici C, Campus de Bellaterra, Bellaterra (Barcelona), Spain
- Departament de Matemàtiques, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
- ICREA, Pg. Lluís Companys 23, Barcelona, Spain
- Barcelona Graduate School of Mathematics (BGSMath), Barcelona, Spain
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Validation of a multi-omics strategy for prioritizing personalized candidate driver genes. Oncotarget 2018; 7:38440-38450. [PMID: 27469031 PMCID: PMC5122402 DOI: 10.18632/oncotarget.9540] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 05/08/2016] [Indexed: 01/13/2023] Open
Abstract
Significant heterogeneity between different tumors prevents the discovery of cancer driver genes, especially in a patient-specific manner. We previously prioritized five personalized candidate mutation-driver genes in a hyper-mutated hepatocellular carcinoma patient using a multi-omics strategy. However, the roles of the prioritized driver genes and patient-specific mutations in hepatocarcinogenesis are unclear. We investigated the impact of the tumor-mutated allele on structure-function relationship of the encoded protein and assessed both loss- and gain-of-function of these genes and mutations on hepatoma cell behaviors in vitro. The prioritized mutation-driver genes act as tumor suppressor genes and inhibit cell proliferation and migration. In addition, the loss-of-function effect of the patient-specific mutations promoted cell proliferation and migration. Of note, the HNF1A S247T mutation significantly reduced the HNF1A transcriptional activity for hepatocyte nuclear factor 4 alpha (HNF4A) but did not disrupt nuclear localization of HNF1A. The results provide evidence for supporting the validity of our proposed multi-omics strategy, which supplies a new avenue for prioritizing mutation-drivers towards personalized cancer therapy.
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