1
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Younesian S, Mohammadi MH, Younesian O, Momeny M, Ghaffari SH, Bashash D. DNA methylation in human diseases. Heliyon 2024; 10:e32366. [PMID: 38933971 PMCID: PMC11200359 DOI: 10.1016/j.heliyon.2024.e32366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Aberrant epigenetic modifications, particularly DNA methylation, play a critical role in the pathogenesis and progression of human diseases. The current review aims to reveal the role of aberrant DNA methylation in the pathogenesis and progression of diseases and to discuss the original data obtained from international research laboratories on this topic. In the review, we mainly summarize the studies exploring the role of aberrant DNA methylation as diagnostic and prognostic biomarkers in a broad range of human diseases, including monogenic epigenetics, autoimmunity, metabolic disorders, hematologic neoplasms, and solid tumors. The last section provides a general overview of the possibility of the DNA methylation machinery from the perspective of pharmaceutic approaches. In conclusion, the study of DNA methylation machinery is a phenomenal intersection that each of its ways can reveal the mysteries of various diseases, introduce new diagnostic and prognostic biomarkers, and propose a new patient-tailored therapeutic approach for diseases.
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Affiliation(s)
- Samareh Younesian
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
| | - Mohammad Hossein Mohammadi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
| | - Ommolbanin Younesian
- School of Medicine, Tonekabon Branch, Islamic Azad University, Tonekabon, 46841-61167 Iran
| | - Majid Momeny
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, 77030 TX, USA
| | - Seyed H. Ghaffari
- Hematology, Oncology and Stem Cell Transplantation Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, 1411713135 Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
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2
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Wu J, Liu N, Chen J, Tao Q, Li Q, Li J, Chen X, Peng C. The Tricarboxylic Acid Cycle Metabolites for Cancer: Friend or Enemy. RESEARCH (WASHINGTON, D.C.) 2024; 7:0351. [PMID: 38867720 PMCID: PMC11168306 DOI: 10.34133/research.0351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 03/18/2024] [Indexed: 06/14/2024]
Abstract
The tricarboxylic acid (TCA) cycle is capable of providing sufficient energy for the physiological activities under aerobic conditions. Although tumor metabolic reprogramming places aerobic glycolysis in a dominant position, the TCA cycle remains indispensable for tumor cells as a hub for the metabolic linkage and interconversion of glucose, lipids, and certain amino acids. TCA intermediates such as citrate, α-ketoglutarate, succinate, and fumarate are altered in tumors, and they regulate the tumor metabolism, signal transduction, and immune environment to affect tumorigenesis and tumor progression. This article provides a comprehensive review of the modifications occurring in tumor cells in relation to the intermediates of the TCA cycle, which affects tumor pathogenesis and current therapeutic strategy for therapy through targeting TCA cycle in cancer cells.
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Affiliation(s)
- Jie Wu
- The Department of Dermatology, Xiangya Hospital,
Central South University, Changsha, Hunan, China
- Furong Labratory, Changsha, Hunan, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital,
Central South University, Changsha, Hunan, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital,
Central South University, Changsha, Hunan, China
| | - Nian Liu
- The Department of Dermatology, Xiangya Hospital,
Central South University, Changsha, Hunan, China
- Furong Labratory, Changsha, Hunan, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital,
Central South University, Changsha, Hunan, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital,
Central South University, Changsha, Hunan, China
| | - Jing Chen
- The Department of Dermatology, Xiangya Hospital,
Central South University, Changsha, Hunan, China
- Furong Labratory, Changsha, Hunan, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital,
Central South University, Changsha, Hunan, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital,
Central South University, Changsha, Hunan, China
| | - Qian Tao
- The Department of Dermatology, Xiangya Hospital,
Central South University, Changsha, Hunan, China
- Furong Labratory, Changsha, Hunan, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital,
Central South University, Changsha, Hunan, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital,
Central South University, Changsha, Hunan, China
| | - Qiuqiu Li
- The Department of Dermatology, Xiangya Hospital,
Central South University, Changsha, Hunan, China
- Furong Labratory, Changsha, Hunan, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital,
Central South University, Changsha, Hunan, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital,
Central South University, Changsha, Hunan, China
| | - Jie Li
- The Department of Dermatology, Xiangya Hospital,
Central South University, Changsha, Hunan, China
- Furong Labratory, Changsha, Hunan, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital,
Central South University, Changsha, Hunan, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital,
Central South University, Changsha, Hunan, China
| | - Xiang Chen
- The Department of Dermatology, Xiangya Hospital,
Central South University, Changsha, Hunan, China
- Furong Labratory, Changsha, Hunan, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital,
Central South University, Changsha, Hunan, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital,
Central South University, Changsha, Hunan, China
| | - Cong Peng
- The Department of Dermatology, Xiangya Hospital,
Central South University, Changsha, Hunan, China
- Furong Labratory, Changsha, Hunan, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital,
Central South University, Changsha, Hunan, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital,
Central South University, Changsha, Hunan, China
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3
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Solomou G, Finch A, Asghar A, Bardella C. Mutant IDH in Gliomas: Role in Cancer and Treatment Options. Cancers (Basel) 2023; 15:cancers15112883. [PMID: 37296846 DOI: 10.3390/cancers15112883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
Altered metabolism is a common feature of many cancers and, in some cases, is a consequence of mutation in metabolic genes, such as the ones involved in the TCA cycle. Isocitrate dehydrogenase (IDH) is mutated in many gliomas and other cancers. Physiologically, IDH converts isocitrate to α-ketoglutarate (α-KG), but when mutated, IDH reduces α-KG to D2-hydroxyglutarate (D2-HG). D2-HG accumulates at elevated levels in IDH mutant tumours, and in the last decade, a massive effort has been made to develop small inhibitors targeting mutant IDH. In this review, we summarise the current knowledge about the cellular and molecular consequences of IDH mutations and the therapeutic approaches developed to target IDH mutant tumours, focusing on gliomas.
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Affiliation(s)
- Georgios Solomou
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Division of Academic Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Alina Finch
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Asim Asghar
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Chiara Bardella
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
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4
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Favre L, Sako N, Tarfi S, Quang VT, Joy C, Dupuy A, Guillerm E, Gaulard P, Wagner‐Ballon O, Pujals A, Sloma I. Evaluation of two new highly multiplexed PCR assays as an alternative to next-generation sequencing for IDH1/2 mutation detection. Mol Oncol 2022; 16:3916-3926. [PMID: 36062346 PMCID: PMC9718115 DOI: 10.1002/1878-0261.13311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/20/2022] [Accepted: 09/02/2022] [Indexed: 12/24/2022] Open
Abstract
IDH1 and IDH2 somatic mutations have been identified in solid tumors and blood malignancies. The development of inhibitors of mutant IDH1 and IDH2 in the past few years has prompted the development of a fast and sensitive assay to detect IDH1R132 , IDH2R140 and IDH2R172 mutations to identify patients eligible for these targeted therapies. This study aimed to compare two new multiplexed PCR assays - an automated quantitative PCR (qPCR) on the PGX platform and a droplet digital PCR (ddPCR) with next-generation sequencing (NGS) for IDH1/2 mutation detection. These assays were evaluated on 102 DNA extracted from patient peripheral blood, bone marrow and formalin-fixed paraffin-embedded tissue samples with mutation allelic frequency ranging from 0.6% to 45.6%. The ddPCR assay had better analytical performances than the PGX assay with 100% specificity, 100% sensitivity and a detection limit down to 0.5% on IDH1R132 , IDH2R140 and IDH2R172 codons, and a high correlation with NGS results. Therefore, the new highly multiplexed ddPCR is a fast and cost-effective assay that meets most clinical needs to identify and follow cancer patients in the era of anti-IDH1/2-targeted therapies.
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Affiliation(s)
- Loetitia Favre
- Department of PathologyAP‐HP, Henri Mondor University HospitalCreteilFrance,Univ Paris Est Creteil, INSERM, IMRBFrance
| | - Nouhoum Sako
- Department of PathologyAP‐HP, Henri Mondor University HospitalCreteilFrance
| | - Sihem Tarfi
- Univ Paris Est Creteil, INSERM, IMRBFrance,Hematology and Immunology DepartmentAP‐HP, Henri Mondor University HospitalCreteilFrance
| | - Violaine Tran Quang
- Univ Paris Est Creteil, INSERM, IMRBFrance,Hematology and Immunology DepartmentAP‐HP, Henri Mondor University HospitalCreteilFrance
| | - Corine Joy
- Hematology and Immunology DepartmentAP‐HP, Henri Mondor University HospitalCreteilFrance
| | | | - Erell Guillerm
- Genetic DepartmentAP‐HP, University Hospital Pitié SalpêtrièreParisFrance
| | - Philippe Gaulard
- Department of PathologyAP‐HP, Henri Mondor University HospitalCreteilFrance,Univ Paris Est Creteil, INSERM, IMRBFrance
| | - Orianne Wagner‐Ballon
- Univ Paris Est Creteil, INSERM, IMRBFrance,Hematology and Immunology DepartmentAP‐HP, Henri Mondor University HospitalCreteilFrance
| | - Anaïs Pujals
- Department of PathologyAP‐HP, Henri Mondor University HospitalCreteilFrance,Univ Paris Est Creteil, INSERM, IMRBFrance
| | - Ivan Sloma
- Univ Paris Est Creteil, INSERM, IMRBFrance,Hematology and Immunology DepartmentAP‐HP, Henri Mondor University HospitalCreteilFrance
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Sarcognato S, Sacchi D, Fabris L, Zanus G, Gringeri E, Niero M, Gallina G, Guido M. Ferroptosis in Intrahepatic Cholangiocarcinoma: IDH1105GGT Single Nucleotide Polymorphism Is Associated With Its Activation and Better Prognosis. Front Med (Lausanne) 2022; 9:886229. [PMID: 35872783 PMCID: PMC9304620 DOI: 10.3389/fmed.2022.886229] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/21/2022] [Indexed: 11/26/2022] Open
Abstract
Objectives Intrahepatic cholangiocarcinoma (ICC) has a dismal prognosis and often demonstrates an anti-apoptotic landscape, which is a key step to chemotherapy resistance. Isocitrate dehydrogenase 1 or 2 (IDH1-2)-mutated ICCs have been described and associated with better prognosis. Ferroptosis is a regulated iron-mediated cell death induced by glutathione peroxidase 4 (GPX4) inhibition, and may be triggered pharmacologically. GPX4 is overexpressed in aggressive cancers, while its expression is inhibited by IDH1R132C mutation in cell lines. We investigated tissue expression of ferroptosis activation markers in ICC and its correlation with clinical-pathological features and IDH1-2 status. Materials and Methods We enrolled 112 patients who underwent hepatic resection or diagnostic liver biopsy for ICC. Immunostaining for transferrin-receptor 1 and GPX4, and Pearls’ stain for iron deposits were performed to evaluate ferroptosis activation. Immunostaining for STAT3 was performed to study pro-inflammatory and anti-apoptotic landscape. Main IDH1-2 mutations were investigated in 90 cases by real-time polymerase chain reaction. Results GPX4 overexpression was seen in 79.5% of cases and related to poor histological prognostic factors (grading and perineural and vascular invasion; p < 0.005 for all) and worse prognosis (OS p = 0.03; DFS p = 0.01). STAT3 was expressed in 95.5% of cases, confirming the inflammation-related anti-apoptotic milieu in ICC, and directly related to GPX4 expression (p < 0.0001). A high STAT3 expression correlated to a worse prognosis (OS p = 0.02; DFS p = 0.001). Nearly 12% of cases showed IDH1105GGT single nucleotide polymorphism, which was never described in ICC up to now, and was related to lower tumor grade (p < 0.0001), longer overall survival (p = 0.04), and lower GPX4 levels (p = 0.001). Conclusion Our study demonstrates for the first time that in most inflammatory ICCs ferroptosis is not active, and its triggering is related to IDH1-2 status. This supports the possible therapeutic role of ferroptosis-inducer drugs in ICC patients, especially in drug-resistant cases.
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Affiliation(s)
- Samantha Sarcognato
- Department of Pathology, Azienda ULSS2 Marca Trevigiana, Treviso, Italy
- *Correspondence: Samantha Sarcognato,
| | - Diana Sacchi
- Department of Pathology, Azienda ULSS2 Marca Trevigiana, Treviso, Italy
| | - Luca Fabris
- Department of Molecular Medicine – DMM, University of Padova, Padova, Italy
| | - Giacomo Zanus
- 4th Surgery Unit, Azienda ULSS2 Marca Trevigiana, Treviso, Italy
- Department of Surgery, Oncology and Gastroenterology – DISCOG, University of Padova, Padova, Italy
| | - Enrico Gringeri
- Department of Surgery, Oncology and Gastroenterology – DISCOG, University of Padova, Padova, Italy
| | - Monia Niero
- Department of Pathology, Azienda ULSS2 Marca Trevigiana, Treviso, Italy
| | - Giovanna Gallina
- Department of Pathology, Azienda ULSS2 Marca Trevigiana, Treviso, Italy
| | - Maria Guido
- Department of Pathology, Azienda ULSS2 Marca Trevigiana, Treviso, Italy
- Department of Medicine – DIMED, University of Padova, Padova, Italy
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6
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Structure and Function of TET Enzymes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:239-267. [DOI: 10.1007/978-3-031-11454-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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7
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Hvinden IC, Cadoux-Hudson T, Schofield CJ, McCullagh JS. Metabolic adaptations in cancers expressing isocitrate dehydrogenase mutations. Cell Rep Med 2021; 2:100469. [PMID: 35028610 PMCID: PMC8714851 DOI: 10.1016/j.xcrm.2021.100469] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The most frequently mutated metabolic genes in human cancer are those encoding the enzymes isocitrate dehydrogenase 1 (IDH1) and IDH2; these mutations have so far been identified in more than 20 tumor types. Since IDH mutations were first reported in glioma over a decade ago, extensive research has revealed their association with altered cellular processes. Mutations in IDH lead to a change in enzyme function, enabling efficient conversion of 2-oxoglutarate to R-2-hydroxyglutarate (R-2-HG). It is proposed that elevated cellular R-2-HG inhibits enzymes that regulate transcription and metabolism, subsequently affecting nuclear, cytoplasmic, and mitochondrial biochemistry. The significance of these biochemical changes for tumorigenesis and potential for therapeutic exploitation remains unclear. Here we comprehensively review reported direct and indirect metabolic changes linked to IDH mutations and discuss their clinical significance. We also review the metabolic effects of first-generation mutant IDH inhibitors and highlight the potential for combination treatment strategies and new metabolic targets.
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Affiliation(s)
- Ingvild Comfort Hvinden
- Chemistry Research Laboratory, 12 Mansfield Road, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Tom Cadoux-Hudson
- Chemistry Research Laboratory, 12 Mansfield Road, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Christopher J. Schofield
- Chemistry Research Laboratory, 12 Mansfield Road, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
- Ineos Oxford Institute for Antimicrobial Research, 12 Mansfield Road, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - James S.O. McCullagh
- Chemistry Research Laboratory, 12 Mansfield Road, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
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8
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Cadoux-Hudson T, Schofield CJ, McCullagh JS. Isocitrate dehydrogenase gene variants in cancer and their clinical significance. Biochem Soc Trans 2021; 49:2561-2572. [PMID: 34854890 PMCID: PMC8786286 DOI: 10.1042/bst20210277] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/13/2021] [Accepted: 10/18/2021] [Indexed: 11/30/2022]
Abstract
Human isocitrate dehydrogenase (IDH) genes encode for the IDH1, 2 & 3 isoenzymes which catalyse the formation of 2-oxoglutarate from isocitrate and are essential for normal mammalian metabolism. Although mutations in these genes in cancer were long thought to lead to a 'loss of function', combined genomic and metabolomic studies led to the discovery that a common IDH 1 mutation, present in low-grade glioma and acute myeloid leukaemia (AML), yields a variant (R132H) with a striking change of function leading to the production of (2R)-hydroxyglutarate (2HG) which consequently accumulates in large quantities both within and outside cells. Elevated 2HG is proposed to promote tumorigenesis, although the precise mechanism by which it does this remains uncertain. Inhibitors of R132H IDH1, and other subsequently identified cancer-linked 2HG producing IDH variants, are approved for clinical use in the treatment of chemotherapy-resistant AML, though resistance enabled by additional substitutions has emerged. In this review, we provide a current overview of cancer linked IDH mutations focussing on their distribution in different cancer types, the effects of substitution mutations on enzyme activity, the mode of action of recently developed inhibitors, and their relationship with emerging resistance-mediating double mutations.
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Affiliation(s)
- Thomas Cadoux-Hudson
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Institute for Antimicrobial Research, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Institute for Antimicrobial Research, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - James S.O. McCullagh
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Institute for Antimicrobial Research, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
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9
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Ratajczak M, Gaweł D, Godlewska M. Novel Inhibitor-Based Therapies for Thyroid Cancer-An Update. Int J Mol Sci 2021; 22:11829. [PMID: 34769260 PMCID: PMC8584403 DOI: 10.3390/ijms222111829] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 12/16/2022] Open
Abstract
Thyroid cancers (TCs) are the most common tumors of the endocrine system and a constant rise in the number of TC cases has been observed for the past few decades. TCs are one of the most frequent tumors in younger adults, especially in women, therefore early diagnosis and effective therapy are especially important. Ultrasonography examination followed by fine needle biopsy have become the gold standard for diagnosis of TCs, as these strategies allow for early-stage detection and aid accurate qualification for further procedures, including surgical treatment. Despite all the advancements in detection and treatment of TCs, constant mortality levels are still observed. Therefore, a novel generation line of targeted treatment strategies is being developed, including personalized therapies with kinase inhibitors. Recent molecular studies on TCs demonstrate that kinase inhibitor-based therapies might be considered as the most promising. In the past decade, new kinase inhibitors with different mechanisms of action have been reported and approved for clinical trials. This review presents an up-to-date picture of new approaches and challenges of inhibitor-based therapies in treatment of TCs, focusing on the latest findings reported over the past two years.
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Affiliation(s)
- Maciej Ratajczak
- Centre of Postgraduate Medical Education, Department of Endocrinology, Marymoncka 99/103, 01-813 Warsaw, Poland;
| | - Damian Gaweł
- Centre of Postgraduate Medical Education, Department of Immunohematology, Marymoncka 99/103, 01-813 Warsaw, Poland
- Centre of Postgraduate Medical Education, Department of Biochemistry and Molecular Biology, Marymoncka 99/103, 01-813 Warsaw, Poland
| | - Marlena Godlewska
- Centre of Postgraduate Medical Education, Department of Biochemistry and Molecular Biology, Marymoncka 99/103, 01-813 Warsaw, Poland
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10
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Chou FJ, Liu Y, Lang F, Yang C. D-2-Hydroxyglutarate in Glioma Biology. Cells 2021; 10:cells10092345. [PMID: 34571995 PMCID: PMC8464856 DOI: 10.3390/cells10092345] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/04/2021] [Accepted: 09/06/2021] [Indexed: 12/12/2022] Open
Abstract
Isocitrate dehydrogenase (IDH) mutations are common genetic abnormalities in glioma, which result in the accumulation of an "oncometabolite", D-2-hydroxyglutarate (D-2-HG). Abnormally elevated D-2-HG levels result in a distinctive pattern in cancer biology, through competitively inhibiting α-ketoglutarate (α-KG)/Fe(II)-dependent dioxgenases (α-KGDDs). Recent studies have revealed that D-2-HG affects DNA/histone methylation, hypoxia signaling, DNA repair, and redox homeostasis, which impacts the oncogenesis of IDH-mutated cancers. In this review, we will discuss the current understanding of D-2-HG in cancer biology, as well as the emerging opportunities in therapeutics in IDH-mutated glioma.
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11
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Murugan AK, Qasem E, Al-Hindi H, Alzahrani AS. Analysis of ALK, IDH1, IDH2 and MMP8 somatic mutations in differentiated thyroid cancers. Mol Clin Oncol 2021; 15:210. [PMID: 34462665 PMCID: PMC8375036 DOI: 10.3892/mco.2021.2373] [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: 03/11/2020] [Accepted: 07/13/2021] [Indexed: 11/06/2022] Open
Abstract
Anaplastic lymphoma kinase (ALK), isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2) and matrix metalloproteinase 8 (MMP8) gene mutations have been frequently reported in human cancers; however, to the best of our knowledge, they have not been specifically examined in differentiated thyroid cancers (DTCs). Therefore, the present study aimed to determine the somatic mutational frequencies of these genes in DTCs. Mutational analysis of the ALK (exons 23, 24 and 25), IDH1 (exon 4), IDH2 (exon 4), and MMP8 (all exons 1-10) was performed in 126, 271, 271 and 50 DTCs, respectively. All the indicated exons were PCR-amplified and the PCR products were directly sequenced by Sanger sequencing. The present study identified a high frequency (86%; 43/50) of MMP8 single nucleotide polymorphism (SNP) and also found some rare SNPs of this gene (S3C, T32I, L310P and K460T) in DTCs but no somatic mutation in ALK, IDH1, IDH2 and MMP8. Analyses of 414 DTCs from The Cancer Genome Atlas revealed rare ALK (1%) and MMP8 (0.24%) mutations and none in IDH1 and IDH2. Conversely, analyses of 117 aggressive thyroid cancers [84, poorly differentiated thyroid cancer (PDTC); 33, anaplastic thyroid cancer (ATC)] from the Memorial Sloan Kettering Cancer Center cohort revealed ALK mutations in 3% of ATCs and fusions in 3.6% of PDTCs. IDH1 mutation was identified in 1.25% of PDTCs but not in ATC. IDH2 mutation was identified in 3% of ATCs but not in PDTC. The present study demonstrated that these genes are less frequently mutated in DTCs, but common in ATCs and PDTCs. It suggests that these genes serve a role in a small portion of DTCs and a more important role in ATCs and PDTCs and may serve as potential therapeutic targets in these subsets.
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Affiliation(s)
- Avaniyapuram Kannan Murugan
- Division of Molecular Endocrinology, Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Ebtesam Qasem
- Division of Molecular Endocrinology, Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Hindi Al-Hindi
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Ali S Alzahrani
- Division of Molecular Endocrinology, Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia.,Department of Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
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12
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Carneiro TNR, Bim LV, Buzatto VC, Galdeno V, Asprino PF, Lee EA, Galante PAF, Cerutti JM. Evidence of Cooperation between Hippo Pathway and RAS Mutation in Thyroid Carcinomas. Cancers (Basel) 2021; 13:2306. [PMID: 34065786 PMCID: PMC8151534 DOI: 10.3390/cancers13102306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/30/2021] [Accepted: 04/06/2021] [Indexed: 12/30/2022] Open
Abstract
Thyroid cancer incidences have been steadily increasing worldwide and are projected to become the fourth leading cancer diagnosis by 2030. Improved diagnosis and prognosis predictions for this type of cancer depend on understanding its genetic bases and disease biology. RAS mutations have been found in a wide range of thyroid tumors, from benign to aggressive thyroid carcinomas. Based on that and in vivo studies, it has been suggested that RAS cooperates with other driver mutations to induce tumorigenesis. This study aims to identify genetic alterations or pathways that cooperate with the RAS mutation in the pathogenesis of thyroid cancer. From a cohort of 120 thyroid carcinomas, 11 RAS-mutated samples were identified. The samples were subjected to RNA-Sequencing analyses. The mutation analysis in our eleven RAS-positive cases uncovered that four genes that belong to the Hippo pathway were mutated. The gene expression analysis revealed that this pathway was dysregulated in the RAS-positive samples. We additionally explored the mutational status and expression profiling of 60 RAS-positive papillary thyroid carcinomas (PTC) from The Cancer Genome Atlas (TCGA) cohort. Altogether, the mutational landscape and pathway enrichment analysis (gene set enrichment analysis (GSEA) and Kyoto Encyclopedia of Genes and Genome (KEGG)) detected the Hippo pathway as dysregulated in RAS-positive thyroid carcinomas. Finally, we suggest a crosstalk between the Hippo and other signaling pathways, such as Wnt and BMP.
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Affiliation(s)
- Thaise Nayane Ribeiro Carneiro
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Pedro de Toledo 669, 11 Andar, São Paulo, SP 04039-032, Brazil; (T.N.R.C.); (L.V.B.)
| | - Larissa Valdemarin Bim
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Pedro de Toledo 669, 11 Andar, São Paulo, SP 04039-032, Brazil; (T.N.R.C.); (L.V.B.)
| | - Vanessa Candiotti Buzatto
- Centro de Oncologia Molecular, Hospital Sírio-libanês, Rua Professor Daher Cutait 69, Bela Vista, São Paulo, SP 01308-060, Brazil; (V.C.B.); (V.G.); (P.F.A.); (P.A.F.G.)
| | - Vanessa Galdeno
- Centro de Oncologia Molecular, Hospital Sírio-libanês, Rua Professor Daher Cutait 69, Bela Vista, São Paulo, SP 01308-060, Brazil; (V.C.B.); (V.G.); (P.F.A.); (P.A.F.G.)
| | - Paula Fontes Asprino
- Centro de Oncologia Molecular, Hospital Sírio-libanês, Rua Professor Daher Cutait 69, Bela Vista, São Paulo, SP 01308-060, Brazil; (V.C.B.); (V.G.); (P.F.A.); (P.A.F.G.)
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Boston Children’s Hospital and Harvard Medical School, 3 Blackfan Circle, CLS (Center for Life Science) Building 15th Floor, Office 15020 | Lab 15072, Boston, MA 02115, USA;
| | - Pedro Alexandre Favoretto Galante
- Centro de Oncologia Molecular, Hospital Sírio-libanês, Rua Professor Daher Cutait 69, Bela Vista, São Paulo, SP 01308-060, Brazil; (V.C.B.); (V.G.); (P.F.A.); (P.A.F.G.)
| | - Janete Maria Cerutti
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Pedro de Toledo 669, 11 Andar, São Paulo, SP 04039-032, Brazil; (T.N.R.C.); (L.V.B.)
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13
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Kang DH, Jeong DJ, Ahn TS, Lee HY, Kim HJ, Bae SB, Kim HJ, Lee MS, Kwon HY, Baek MJ. Expression of AMP-activated protein kinase/ten-eleven translocation 2 and their clinical relevance in colorectal cancer. Oncol Lett 2021; 21:164. [PMID: 33552282 PMCID: PMC7798087 DOI: 10.3892/ol.2021.12425] [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: 08/22/2019] [Accepted: 11/26/2020] [Indexed: 01/10/2023] Open
Abstract
Inactivation of the ten-eleven translocation (TET) family members and catalyzation of 5-methylcytosine (5-mC) into 5-hydroxymethylcytosine (5-hmC) is associated with cancer initiation and progression. AMP-activated protein kinase (AMPK) is an enzyme that stabilizes TET2; however, the clinical relevance of AMPK and TET2 expression levels is currently unclear. Therefore, the present study aimed to investigate the clinical implications of AMPK/TET2 expression levels in colorectal cancer (CRC). Immunohistochemistry was used to retrospectively examine the expression levels of AMPK and TET2 in paraffin-embedded specimens obtained from 343 patients with CRC. The results demonstrated that AMPK and TET2 were highly expressed in CRC samples. No significant association was observed between the expression levels of TET2 and patient clinicopathological characteristics (age, tumor location, lymphatic, vascular and perineural invasion, Tumor-Node-Metastasis stages and differentiation); however, patients with low expression levels of TET2 more frequently presented with distant metastasis. By contrast, the expression levels of AMPK were significantly associated with lymph node and distant metastases. The survival analysis results revealed that high expression levels of TET2 were an independent predictor of favorable prognosis compared with low TET2 levels. However, no significant differences in overall survival were observed between patients with high and low expression levels of AMPK. These results described the clinical significance of AMPK/TET2 in CRC. The results of the multivariate analysis demonstrated that high expression levels of TET2 were a predictor of a favorable prognosis, whereas AMPK was not a significant factor for determining patient prognosis; therefore, further functional analysis of AMPK/TET2 expression in CRC is needed.
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Affiliation(s)
- Dong Hyun Kang
- Division of Colon and Rectal Surgery, Department of Surgery, College of Medicine, Soonchunhyang University Cheonan Hospital, Cheonan, Chungcheongnam-do 31151, Republic of Korea
| | - Dong Jun Jeong
- Soonchunhyang Medical Science Research Institute, College of Medicine, Soonchunhyang University Cheonan Hospital, Cheonan, Chungcheongnam-do 31151, Republic of Korea.,Department of Pathology, College of Medicine, Soonchunhyang University Cheonan Hospital, Cheonan, Chungcheongnam-do 31151, Republic of Korea
| | - Tae Sung Ahn
- Division of Colon and Rectal Surgery, Department of Surgery, College of Medicine, Soonchunhyang University Cheonan Hospital, Cheonan, Chungcheongnam-do 31151, Republic of Korea
| | - Hyun Yong Lee
- Division of Colon and Rectal Surgery, Department of Surgery, College of Medicine, Soonchunhyang University Cheonan Hospital, Cheonan, Chungcheongnam-do 31151, Republic of Korea
| | - Han Jo Kim
- Department of Oncology, College of Medicine, Soonchunhyang University Cheonan Hospital, Cheonan, Chungcheongnam-do 31151, Republic of Korea
| | - Sang Byung Bae
- Department of Oncology, College of Medicine, Soonchunhyang University Cheonan Hospital, Cheonan, Chungcheongnam-do 31151, Republic of Korea
| | - Hyeong Joo Kim
- Soonchunhyang Medical Science Research Institute, College of Medicine, Soonchunhyang University Cheonan Hospital, Cheonan, Chungcheongnam-do 31151, Republic of Korea
| | - Moon Soo Lee
- Division of Gastrointestinal Surgery, Department of Surgery, College of Medicine, Soonchunhyang University Cheonan Hospital, Cheonan, Chungcheongnam-do 31151, Republic of Korea
| | - Hyog Young Kwon
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, Cheonan, Chungcheongnam-do 31151, Republic of Korea
| | - Moo-Jun Baek
- Division of Colon and Rectal Surgery, Department of Surgery, College of Medicine, Soonchunhyang University Cheonan Hospital, Cheonan, Chungcheongnam-do 31151, Republic of Korea
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Oishi N, Vuong HG, Mochizuki K, Kondo T. Loss of 5-Hydroxymethylcytosine is an Epigenetic Hallmark of Thyroid Carcinomas with TERT Promoter Mutations. Endocr Pathol 2020; 31:359-366. [PMID: 33058026 DOI: 10.1007/s12022-020-09652-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/25/2020] [Indexed: 12/19/2022]
Abstract
Epigenetic dysregulation is a hallmark of cancer, and aberrant methylation of cytosine residues plays a crucial role in abnormal gene expression in cancer cells. Recent studies demonstrate that 5-hydroxymethylcytosine (5-hmC) generated through 5-methylcytosine (5-mC) oxidation is significantly depleted in various cancers. However, whether 5-hmC levels change during the stepwise progression of thyroid carcinoma and the mechanisms underlying this effect remain unknown. The aims of this study were (i) to assess 5-hmC levels in normal and cancerous thyroid tissues, and (ii) identify clinicopathologic and genetic factors associated with the dysregulated hydroxymethylation of cytosine. Enzyme-linked immunosorbent assay (ELISA) showed that 5-hmC was significantly reduced in TERT promoter-mutated papillary thyroid carcinomas (PTCs) and anaplastic thyroid carcinomas (ATCs), while there was no significant difference in 5-hmC levels between TERT promoter-wild-type PTCs and normal thyroid tissues. Results of semi-quantitative analysis of 5-hmC through immunohistochemistry correlated well with those of ELISA and confirmed the loss of 5-hmC in tumor cells. Immunohistochemistry confirmed lower 5-hmC positivity in TERT promoter-mutated PTCs (n = 10) and ATCs (n = 4) than in normal thyroid tissues (n = 8) and TERT promoter-wild-type PTCs (n = 63). Tumor size (> 1 cm) and advanced stage were associated with decreased global 5-hmC in PTCs, while age, gross extrathyroidal invasion, node metastasis, and BRAF mutation were not. Collectively, these findings demonstrated that loss of 5-hmC is an epigenetic hallmark of thyroid carcinomas with TERT promoter mutation, indicating that TERT promoter-mutated thyroid carcinoma has a distinct molecular profile.
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Affiliation(s)
- Naoki Oishi
- Faculty of Medicine, Department of Pathology, University of Yamanashi, 1110 Shimokato, 409-3898, Chuo, Yamanashi, Japan.
| | - Huy Gia Vuong
- Faculty of Medicine, Department of Pathology, University of Yamanashi, 1110 Shimokato, 409-3898, Chuo, Yamanashi, Japan
| | - Kunio Mochizuki
- Faculty of Medicine, Department of Pathology, University of Yamanashi, 1110 Shimokato, 409-3898, Chuo, Yamanashi, Japan
| | - Tetsuo Kondo
- Faculty of Medicine, Department of Pathology, University of Yamanashi, 1110 Shimokato, 409-3898, Chuo, Yamanashi, Japan
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Molecular Alterations in Thyroid Cancer: From Bench to Clinical Practice. Genes (Basel) 2019; 10:genes10090709. [PMID: 31540307 PMCID: PMC6771012 DOI: 10.3390/genes10090709] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/26/2019] [Accepted: 09/10/2019] [Indexed: 12/11/2022] Open
Abstract
Thyroid cancer comprises different clinical and histological entities. Whereas differentiated (DTCs) malignancies are sensitive to radioiodine therapy, anaplastic (ATCs) and medullary (MTCs) tumors do not uptake radioactive iodine and display aggressive features associated with a poor prognosis. Moreover, in a majority of DTCs, disease evolution leads to the progressive loss of iodine sensitivity. Hence, iodine-refractory DTCs, along with ATCs and MTCs, require alternative treatments reflective of their different tumor biology. In the last decade, the molecular mechanisms promoting thyroid cancer development and progression have been extensively studied. This has led to a better understanding of the genomic landscape, displayed by thyroid malignancies, and to the identification of novel therapeutic targets. Indeed, several pharmacological compounds have been developed for iodine-refractory tumors, with four multi-target tyrosine kinase inhibitors already available for DTCs (sorafenib and lenvatinib) and MTCs (cabozantib and vandetanib), and a plethora of drugs currently being evaluated in clinical trials. In this review, we will describe the genomic alterations and biological processes intertwined with thyroid cancer development, also providing a thorough overview of targeted drugs already tested or under investigation for these tumors. Furthermore, given the existing preclinical evidence, we will briefly discuss the potential role of immunotherapy as an additional therapeutic strategy for the treatment of thyroid cancer.
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16
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Pekova B, Dvorakova S, Sykorova V, Vacinova G, Vaclavikova E, Moravcova J, Katra R, Vlcek P, Sykorova P, Kodetova D, Vcelak J, Bendlova B. Somatic genetic alterations in a large cohort of pediatric thyroid nodules. Endocr Connect 2019; 8:796-805. [PMID: 31085772 PMCID: PMC6590202 DOI: 10.1530/ec-19-0069] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 05/14/2019] [Indexed: 01/09/2023]
Abstract
There is a rise in the incidence of thyroid nodules in pediatric patients. Most of them are benign tissues, but part of them can cause papillary thyroid cancer (PTC). The aim of this study was to detect the mutations in commonly investigated genes as well as in novel PTC-causing genes in thyroid nodules and to correlate the found mutations with clinical and pathological data. The cohort of 113 pediatric samples consisted of 30 benign lesions and 83 PTCs. DNA from samples was used for next-generation sequencing to identify mutations in the following genes: HRAS, KRAS, NRAS, BRAF, IDH1, CHEK2, PPM1D, EIF1AX, EZH1 and for capillary sequencing in case of the TERT promoter. RNA was used for real-time PCR to detect RET/PTC1 and RET/PTC3 rearrangements. Total detection rate of mutations was 5/30 in benign tissues and 35/83 in PTCs. Mutations in RAS genes (HRAS G13R, KRAS G12D, KRAS Q61R, NRAS Q61R) were detected in benign lesions and HRAS Q61R and NRAS Q61K mutations in PTCs. The RET/PTC rearrangement was identified in 18/83 of PTCs and was significantly associated with higher frequency of local and distant metastases. The BRAF V600E mutation was identified in 15/83 of PTCs and significantly correlated with higher age of patients and classical variant of PTC. Germline variants in the genes IDH1, CHEK2 and PPM1D were found. In conclusion, RET/PTC rearrangements and BRAF mutations were associated with different clinical and histopathological features of pediatric PTC. RAS mutations were detected with high frequency in patients with benign nodules; thus, our results suggest that these patients should be followed up intensively.
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Affiliation(s)
- Barbora Pekova
- Department of Molecular Endocrinology, Institute of Endocrinology, Prague 1, Czech Republic
- Correspondence should be addressed to B Pekova:
| | - Sarka Dvorakova
- Department of Molecular Endocrinology, Institute of Endocrinology, Prague 1, Czech Republic
| | - Vlasta Sykorova
- Department of Molecular Endocrinology, Institute of Endocrinology, Prague 1, Czech Republic
| | - Gabriela Vacinova
- Department of Molecular Endocrinology, Institute of Endocrinology, Prague 1, Czech Republic
| | - Eliska Vaclavikova
- Department of Molecular Endocrinology, Institute of Endocrinology, Prague 1, Czech Republic
| | - Jitka Moravcova
- Department of Molecular Endocrinology, Institute of Endocrinology, Prague 1, Czech Republic
| | - Rami Katra
- Department of Ear, Nose and Throat, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague 5, Czech Republic
| | - Petr Vlcek
- Department of Nuclear Medicine and Endocrinology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague 5, Czech Republic
| | - Pavla Sykorova
- Department of Nuclear Medicine and Endocrinology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague 5, Czech Republic
| | - Daniela Kodetova
- Department of Pathology and Molecular Medicine, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague 5, Czech Republic
| | - Josef Vcelak
- Department of Molecular Endocrinology, Institute of Endocrinology, Prague 1, Czech Republic
| | - Bela Bendlova
- Department of Molecular Endocrinology, Institute of Endocrinology, Prague 1, Czech Republic
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17
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The significance of gene mutations across eight major cancer types. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2019; 781:88-99. [PMID: 31416581 DOI: 10.1016/j.mrrev.2019.04.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 04/11/2019] [Accepted: 04/30/2019] [Indexed: 12/12/2022]
Abstract
Mutations occur spontaneously, which can be induced by either chemicals (e.g. benzene) or biological factors (e.g. virus). Not all mutations cause noticeable changes in cellular functions. However, mutation in key cellular genes leads to developmental disorders. It is one of the main ways in which proto-oncogenes can be changed into their oncogenic state. The progressive accumulation of multiple mutations throughout life leads to cancer. In the past few decades, extensive research on cancer biology has discovered many genes and pathways having role in cancer development. In this review, we tried to summarize the current knowledge of mutational effect on different cancer types and its consequences in brief for future reference and guidance of researchers in cancer biology.
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18
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SPINT2 is hypermethylated in both IDH1 mutated and wild-type glioblastomas, and exerts tumor suppression via reduction of c-Met activation. J Neurooncol 2019; 142:423-434. [PMID: 30838489 DOI: 10.1007/s11060-019-03126-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 02/09/2019] [Indexed: 02/07/2023]
Abstract
PURPOSE Both IDH1-mutated and wild-type gliomas abundantly display aberrant CpG island hypermethylation. However, the potential role of hypermethylation in promoting gliomas, especially the most aggressive form, glioblastoma (GBM), remains poorly understood. METHODS We analyzed RRBS-generated methylation profiles for 11 IDH1WT gliomas (including 7 GBMs), 24 IDH1MUT gliomas (including 6 GBMs), and 5 normal brain samples and employed TCGA GBM methylation profiles as a validation set. Upon classification of differentially methylated CpG islands by IDH1 status, we used integrated analysis of methylation and gene expression to identify SPINT2 as a top cancer related gene. To explore functional consequences of SPINT2 methylation in GBM, we validated SPINT2 methylation status using targeted bisulfite sequencing in a large cohort of GBM samples. We assessed DNA methylation-mediated SPINT2 gene regulation using 5-aza-2'-deoxycytidine treatment, DNMT1 knockdown and luciferase reporter assays. We conducted functional analyses of SPINT2 in GBM cell lines in vitro and in vivo. RESULTS We identified SPINT2 as a candidate tumor-suppressor gene within a group of CpG islands (designated GT-CMG) that are hypermethylated in both IDH1MUT and IDH1WT gliomas but not in normal brain. We established that SPINT2 downregulation results from promoter hypermethylation, and that restoration of SPINT2 expression reduces c-Met activation and tumorigenic properties of GBM cells. CONCLUSIONS We defined a previously under-recognized group of coordinately methylated CpG islands common to both IDH1WT and IDH1MUT gliomas (GT-CMG). Within GT-CMG, we identified SPINT2 as a top cancer-related candidate and demonstrated that SPINT2 suppressed GBM via down-regulation of c-Met activation.
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Khatami F, Payab M, Sarvari M, Gilany K, Larijani B, Arjmand B, Tavangar SM. Oncometabolites as biomarkers in thyroid cancer: a systematic review. Cancer Manag Res 2019; 11:1829-1841. [PMID: 30881111 PMCID: PMC6395057 DOI: 10.2147/cmar.s188661] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Introduction Thyroid cancer (TC) is an important common endocrine malignancy, and its incidence has increased in the past decades. The current TC diagnosis and classification tools are fine-needle aspiration (FNA) and histological examination following thyroidectomy. The metabolite profile alterations of thyroid cells (oncometabolites) can be considered for current TC diagnosis and management protocols. Methods This systematic review focuses on metabolite alterations within the plasma, FNA specimens, and tissue of malignant TC contrary to benign, goiter, or healthy TC samples. A systematic search of MEDLINE (PubMed), Scopus, Embase, and Web of Science databases was conducted, and the final 31 studies investigating metabolite biomarkers of TC were included. Results A total of 15 targeted studies and 16 untargeted studies revealed several potential metabolite signatures of TC such as glucose, fructose, galactose, mannose, 2-keto-d-gluconic acid and rhamnose, malonic acid and inosine, cholesterol and arachidonic acid, glycosylation (immunoglobulin G [IgG] Fc-glycosylation), outer mitochondrial membrane 20 (TOMM20), monocarboxylate transporter 4 (MCT4), choline, choline derivatives, myo-/scyllo-inositol, lactate, fatty acids, several amino acids, cell membrane phospholipids, estrogen metabolites such as 16 alpha-OH E1/2-OH E1 and catechol estrogens (2-OH E1), and purine and pyrimidine metabolites, which were suggested as the TC oncometabolite. Conclusion Citrate was suggested as the first most significant biomarker and lactate as the second one. Further research is needed to confirm these biomarkers as the TC diagnostic oncometabolite.
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Affiliation(s)
- Fatemeh Khatami
- Chronic Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran,
| | - Moloud Payab
- Obesity and Eating Habits Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoumeh Sarvari
- Metabolomics and Genomics Research Center, Endocrinology and Metabolomics Molecular Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Kambiz Gilany
- Metabolomics and Genomics Research Center, Endocrinology and Metabolomics Molecular Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.,Reproductive Biotechnology Research Center, Avicenna Research Institute, Academic Center for Education, Culture and Research (ACECR), Tehran, Iran.,Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, Acercr, Tehran, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Babak Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran,
| | - Seyed Mohammad Tavangar
- Chronic Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran, .,Department of Pathology, Dr. Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran,
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20
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Kaushik AK, DeBerardinis RJ. Applications of metabolomics to study cancer metabolism. Biochim Biophys Acta Rev Cancer 2018; 1870:2-14. [PMID: 29702206 PMCID: PMC6193562 DOI: 10.1016/j.bbcan.2018.04.009] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 04/20/2018] [Indexed: 12/13/2022]
Abstract
Reprogrammed metabolism supports tumor growth and provides a potential source of therapeutic targets and disease biomarkers. Mass spectrometry-based metabolomics has emerged as a broadly informative technique for profiling metabolic features associated with specific oncogenotypes, disease progression, therapeutic liabilities and other clinically relevant aspects of tumor biology. In this review, we introduce the applications of metabolomics to study deregulated metabolism and metabolic vulnerabilities in cancer. We provide examples of studies that used metabolomics to discover novel metabolic regulatory mechanisms, including processes that link metabolic alterations with gene expression, protein function, and other aspects of systems biology. Finally, we discuss emerging applications of metabolomics for in vivo isotope tracing and metabolite imaging, both of which hold promise to advance our understanding of the role of metabolic reprogramming in cancer.
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Affiliation(s)
- Akash K Kaushik
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX 75390-8502, United States
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX 75390-8502, United States.
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21
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Kennedy S, Rice M, Toomey S, Horgan N, Hennessey BT, Larkin A. An insight into the molecular genetics of a uveal melanoma patient cohort. J Cancer Res Clin Oncol 2018; 144:1861-1868. [DOI: 10.1007/s00432-018-2705-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 07/05/2018] [Indexed: 12/26/2022]
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22
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Gao Y, de Wit M, Struys EA, van der Linde HCZ, Salomons GS, Lamfers MLM, Willemsen R, Sillevis Smitt PAE, French PJ. IDH1-mutated transgenic zebrafish lines: An in-vivo model for drug screening and functional analysis. PLoS One 2018; 13:e0199737. [PMID: 29953513 PMCID: PMC6023169 DOI: 10.1371/journal.pone.0199737] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/13/2018] [Indexed: 01/04/2023] Open
Abstract
Introduction The gene encoding isocitrate dehydrogenase 1 (IDH1) is frequently mutated in several tumor types including gliomas. The most prevalent mutation in gliomas is a missense mutation leading to a substitution of arginine with histidine at the residue 132 (R132H). Wild type IDH1 catalyzes oxidative decarboxylation of isocitrate to α-ketoglutarate (α-KG) whereas mutant IDH1 converts α-KG into D2-hydroxyglutarate (D2HG). Unfortunately, there are few in vivo model systems for IDH-mutated tumors to study the effects of IDH1 mutations in tumor development. We have therefore created transgenic zebrafish lines that express various IDH1 mutants. Materials and methods IDH1 mutations (IDH1R132H, IDH1R132C and loss-of-function mutation IDH1G70D), IDH1wildtype or eGFP were cloned into constructs with several brain-specific promoters (Nestin, Gfap or Gata2). These constructs were injected into fertilized zebrafish eggs at the one-cell stage. Results In total more than ten transgenic zebrafish lines expressing various brain-specific IDH1 mutations were created. A significant increase in the level of D2HG was observed in all transgenic lines expressing IDH1R132C or IDH1R132H, but not in any of the lines expressing IDH1wildtype, IDH1G70D or eGFP. No differences in 5-hydroxymethyl cytosine and mature collagen IV levels were observed between wildtype and mutant IDH1 transgenic fish. To our surprise, we failed to identify any strong phenotype, despite increased levels of the oncometabolite D2HG. No tumors were observed, even when backcrossing with tp53-mutant fish which suggests that additional transforming events are required for tumor formation. Elevated D2HG levels could be lowered by treatment of the transgenic zebrafish with an inhibitor of mutant IDH1 activity. Conclusions We have generated a transgenic zebrafish model system for mutations in IDH1 that can be used for functional analysis and drug screening. Our model systems help understand the biology of IDH1 mutations and its role in tumor formation.
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Affiliation(s)
- Ya Gao
- Department of Neurology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Maurice de Wit
- Department of Neurology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Eduard A. Struys
- Department of Clinical Chemistry, VU University Medical Center, Amsterdam, the Netherlands
| | | | - Gajja S. Salomons
- Department of Clinical Chemistry, VU University Medical Center, Amsterdam, the Netherlands
| | | | - Rob Willemsen
- Department of Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - Pim J. French
- Department of Neurology, Erasmus Medical Center, Rotterdam, the Netherlands
- * E-mail:
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Li T, Cox CD, Ozer BH, Nguyen NT, Nguyen HN, Lai TJ, Li S, Liu F, Kornblum HI, Liau LM, Nghiemphu PL, Cloughesy TF, Lai A. D-2-Hydroxyglutarate Is Necessary and Sufficient for Isocitrate Dehydrogenase 1 Mutant-Induced MIR148A Promoter Methylation. Mol Cancer Res 2018; 16:947-960. [PMID: 29545476 DOI: 10.1158/1541-7786.mcr-17-0367] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 01/13/2018] [Accepted: 02/20/2018] [Indexed: 12/14/2022]
Abstract
Mutant isocitrate dehydrogenase (IDH) 1/2 converts α-ketoglutarate (α-KG) to D-2 hydroxyglutarate (D-2-HG), a putative oncometabolite that can inhibit α-KG-dependent enzymes, including ten-eleven translocation methylcytosine dioxygenase (TET) DNA demethylases. We recently established that miRNAs are components of the IDH1 mutant-associated glioma CpG island methylator phenotype (G-CIMP) and specifically identified MIR148A as a tumor-suppressive miRNA within G-CIMP. However, the precise mechanism by which mutant IDH induces hypermethylation of MIR148A and other G-CIMP promoters remains to be elucidated. In this study, we demonstrate that treatment with exogenous D-2-HG induces MIR148A promoter methylation and transcriptional silencing in human embryonic kidney 293T (293T) cells and primary normal human astrocytes. Conversely, we show that the development of MIR148A promoter methylation in mutant IDH1-overexpressing 293T cells is abrogated via treatment with C227, an inhibitor of mutant IDH1 generation of D-2-HG. Using dot blot assays for global assessment of 5-hydroxymethylcytosine (5-hmC), we show that D-2-HG treatment reduces 5-hmC levels, whereas C227 treatment increases 5-hmC levels, strongly suggesting TET inhibition by D-2-HG. Moreover, we show that withdrawal of D-2-HG treatment reverses methylation with an associated increase in MIR148A transcript levels and transient generation of 5-hmC. We also demonstrate that RNA polymerase II binds endogenously to the predicted promoter region of MIR148A, validating the hypothesis that its transcription is driven by an independent promoter.Implications: Establishment of D-2-HG as a necessary and sufficient intermediate by which mutant IDH1 induces CpG island methylation of MIR148A will help with understanding the efficacy of selective mutant IDH1 inhibitors in the clinic. Mol Cancer Res; 16(6); 947-60. ©2018 AACR.
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Affiliation(s)
- Tie Li
- Neuro-Oncology Program, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Christopher D Cox
- Neuro-Oncology Program, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Byram H Ozer
- Neuro-Oncology Program, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Nhung T Nguyen
- Neuro-Oncology Program, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - HuyTram N Nguyen
- Neuro-Oncology Program, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Thomas J Lai
- Neuro-Oncology Program, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Sichen Li
- Neuro-Oncology Program, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Fei Liu
- Neuro-Oncology Program, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Harley I Kornblum
- Department of Pediatrics, Psychiatry and Biobehavioral Sciences, Pediatric Neurology, Semel Institute for Neuroscience and Human Behavior, Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Linda M Liau
- Department of Neurosurgery, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Phioanh L Nghiemphu
- Neuro-Oncology Program, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Timothy F Cloughesy
- Neuro-Oncology Program, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Albert Lai
- Neuro-Oncology Program, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.
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24
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Acquaviva G, Visani M, de Biase D, Marucci G, Franceschi E, Tosoni A, Brandes AA, Rhoden KJ, Pession A, Tallini G. Prevalence of the single-nucleotide polymorphism rs11554137 (IDH1 105GGT) in brain tumors of a cohort of Italian patients. Sci Rep 2018; 8:4459. [PMID: 29535392 PMCID: PMC5849696 DOI: 10.1038/s41598-018-22222-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
IDH mutational status is required for proper diagnosis according to the WHO criteria revised in 2016. The single nucleotide polymorphism (SNP) rs11554137 (IDH1105GGT) at codon 105 of IDH1 has been reported in patients with several tumor types, including those with glioma. The aim of this study is to investigate the prevalence of IDH1105GGT in a cohort of brain tumors, and its association with clinicopathologic features and IDH1 and IDH2 missense mutations. Exon 4 of IDH1 and IDH2 was analyzed in a series of brain tumors classified according to current WHO criteria. DNA from control individuals was analyzed to infer the prevalence of IDH1105GGT in the reference population. Analysis was performed using next generation sequencing. IDH1105GGT was three times more frequent in patients with tumors (44/293 cases, 15.0%) vs. population controls (6/109, 5.5%) (p = 0.0102). IDH1105GGT was more frequent in grade III tumors (26.1%) compared to grade II (10.9%, p = 0.038) and grade IV tumors (13.7%, p = 0.041). IDH1 105GGT was more frequent in grade II and III tumors without an IDH tumor missense mutation (43.8%) than in those with (11.5%, p = 0.005). The IDH1105GGT SNP likely represents an important genetic marker, worthy of additional investigation to better understand the clinical and biological features of IDH-WT infiltrating gliomas.
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Affiliation(s)
- Giorgia Acquaviva
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, Bologna, Italy
| | - Michela Visani
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, Bologna, Italy
| | - Dario de Biase
- Department of Pharmacy and Biotechnology (Dipartimento di Farmacia e Biotecnologie) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna, Bologna, Italy.
| | - Gianluca Marucci
- Anatomic Pathology Unit, AUSL of Bologna, Bologna, Italy (currently at Department of Neuropathology, IRCCS Foundation Carlo Besta Neurological Institute, Milan, Italy
| | - Enrico Franceschi
- Department of Oncology, AUSL Bologna - IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Alicia Tosoni
- Department of Oncology, AUSL Bologna - IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Alba A Brandes
- Department of Oncology, AUSL Bologna - IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Kerry J Rhoden
- Medical Genetics Unit, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Annalisa Pession
- Department of Pharmacy and Biotechnology (Dipartimento di Farmacia e Biotecnologie) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna, Bologna, Italy
| | - Giovanni Tallini
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, Bologna, Italy
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25
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Moraes L, Galrão ALR, Rubió I, Cerutti JM. Transcriptional regulation of the potential tumor suppressor ABI3 gene in thyroid carcinomas: interplay between methylation and NKX2-1 availability. Oncotarget 2018; 7:25960-70. [PMID: 27036019 PMCID: PMC5041957 DOI: 10.18632/oncotarget.8416] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 03/12/2016] [Indexed: 12/05/2022] Open
Abstract
We previously reported that ABI3 expression was decreased in thyroid cancer tissues and that ectopic expression of ABI3 in a follicular thyroid carcinoma cell line delayed cell cycle progression and inhibited cell proliferation, invasion, migration and tumor formation in athymic mice. These data indicated that ABI3 is a tumor suppressor gene; however the mechanism through which ABI3 is silenced in thyroid carcinomas is unknown. We here show that treatment of four follicular thyroid carcinoma cell lines with 5-aza-dC induced demethylation of a specific region of the ABI3 promoter and restored ABI3 expression. In contrast, 5-aza-dC treatment did not restore ABI3 expression in a non-thyroid cell line, suggesting a tissue-specific regulation. We additionally show that 8 CpG sites located within the ABI3 promoter are hypermethylated in most thyroid carcinoma samples and the degree of methylation correlated with ABI3 expression. Narrowing the region to specific CpG sites, the CpG4-6 sites showed the largest difference between benign and malignant lesions. In silico analysis revealed that these CpG sites flank a canonical binding site for NKX2-1, a thyroid specific transcriptional factor. Analysis of thyroid samples shows a correlation between NKX2-1 and ABI3 expression. In vitro assays demonstrate that NKX2-1 was required for ABI3 expression. Luciferase assay further confirmed the promoter activity of this region, which was increased when the cells were co-transfected with NKX2-1. Our study shows that the transcriptional silencing of ABI3 in cancer cells occurs via methylation and uncovered a previously unrecognized role for NKX2-1 in the regulation of ABI3.
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Affiliation(s)
- Lais Moraes
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, SP, Brazil
| | - Ana Luiza R Galrão
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, SP, Brazil
| | - Ileana Rubió
- Department of Biological Sciences, Universidade Federal de São Paulo, SP, Brazil
| | - Janete M Cerutti
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, SP, Brazil
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26
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Smeets E, Lynch AG, Prekovic S, Van den Broeck T, Moris L, Helsen C, Joniau S, Claessens F, Massie CE. The role of TET-mediated DNA hydroxymethylation in prostate cancer. Mol Cell Endocrinol 2018; 462:41-55. [PMID: 28870782 DOI: 10.1016/j.mce.2017.08.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 06/30/2017] [Accepted: 08/31/2017] [Indexed: 10/18/2022]
Abstract
Ten-eleven translocation (TET) proteins are recently characterized dioxygenases that regulate demethylation by oxidizing 5-methylcytosine to 5-hydroxymethylcytosine and further derivatives. The recent finding that 5hmC is also a stable and independent epigenetic modification indicates that these proteins play an important role in diverse physiological and pathological processes such as neural and tumor development. Both the genomic distribution of (hydroxy)methylation and the expression and activity of TET proteins are dysregulated in a wide range of cancers including prostate cancer. Up to now it is still unknown how changes in TET and 5(h)mC profiles are related to the pathogenesis of prostate cancer. In this review, we explore recent advances in the current understanding of how TET expression and function are regulated in development and cancer. Furthermore, we look at the impact on 5hmC in prostate cancer and the potential underlying mechanisms. Finally, we tried to summarize the latest techniques for detecting and quantifying global and locus-specific 5hmC levels of genomic DNA.
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Affiliation(s)
- E Smeets
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
| | - A G Lynch
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - S Prekovic
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - T Van den Broeck
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium; Department of Urology, University Hospitals Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - L Moris
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium; Department of Urology, University Hospitals Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - C Helsen
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - S Joniau
- Department of Urology, University Hospitals Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - F Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - C E Massie
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
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27
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Murugan AK, Munirajan AK, Alzahrani AS. Long noncoding RNAs: emerging players in thyroid cancer pathogenesis. Endocr Relat Cancer 2018; 25:R59-R82. [PMID: 29146581 DOI: 10.1530/erc-17-0188] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 11/16/2017] [Indexed: 12/18/2022]
Abstract
Thyroid cancer continues to be the most common malignancy of endocrine glands. The incidence of thyroid cancer has risen significantly over the past 4 decades and has emerged as a major health issue. In recent years, significant progress has been achieved in our understanding of the molecular mechanisms of thyroid carcinogenesis, resulting in significant diagnostic, prognostic and therapeutic implications; yet, it has not reached a satisfactory level. Identifying novel molecular therapeutic targets and molecules for diagnosis and prognosis is expected to advance the overall management of this common malignancy. Long noncoding RNAs (lncRNAs) are implicated in the regulation of various key cellular genes involved in cell differentiation, proliferation, cell cycle, apoptosis, migration and invasion mainly through modulation of gene expression. Recent studies have established that lncRNAs are deregulated in thyroid cancer. In this review, we discuss extensively the tumor-suppressive (for example, LINC00271, MEG3, NAMA, PTCSC1/2/3, etc.) and oncogenic (for example, ANRIL, FAL1, H19, PVT1, etc.) roles of various lncRNAs and their possible disease associations implicated in thyroid carcinogenesis. We briefly summarize the strategies and mechanisms of lncRNA-targeting agents. We also describe the potential role of lncRNAs as prospective novel therapeutic targets, and diagnostic and prognostic markers in thyroid cancer.
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Affiliation(s)
- Avaniyapuram Kannan Murugan
- Division of Molecular EndocrinologyDepartment of Molecular Oncology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Arasambattu Kannan Munirajan
- Department of GeneticsDr ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, India
| | - Ali S Alzahrani
- Division of Molecular EndocrinologyDepartment of Molecular Oncology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
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28
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Muscat AM, Wong NC, Drummond KJ, Algar EM, Khasraw M, Verhaak R, Field K, Rosenthal MA, Ashley DM. The evolutionary pattern of mutations in glioblastoma reveals therapy-mediated selection. Oncotarget 2017; 9:7844-7858. [PMID: 29487696 PMCID: PMC5814263 DOI: 10.18632/oncotarget.23541] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/05/2017] [Indexed: 01/08/2023] Open
Abstract
Glioblastoma presents as a heterogeneous disease with poor prognosis despite the use of multimodal therapy. Analysis of genomic DNA changes between initial diagnosis and recurrence in response to standard treatment protocols would enhance understanding of disease progression and better inform new treatment strategies. A cohort of 21 patients with primary glioblastoma were examined between diagnosis and first recurrence. This study presented a rare opportunity to characterize molecular alterations in tumors observed in three patients who received no therapeutic intervention, other than surgery, offering a unique control. We focused this study by comparing the dynamic mutation profiles between the primary tumors and their matched recurrent counterparts. Molecular profiling of tumors was performed using multiplexed targeted deep sequencing of 409 well characterized cancer-associated genes, achieving a mean read depth of 1272 x. Three levels of evidence suggested an evolutionary pattern consistent with a response to therapy-mediated selection pressures exists in treated patients: 1) variant burden was reduced in recurrent tumors, 2) neutral evolutionary dynamics apparent in untreated tumors shifted toward a non-neutral mode of evolution in treated patients at recurrence, and 3) the recurrent tumor of one patient displayed an increased mutation rate attributable to a temozolomide-associated hypermutator phenotype. Our observations suggest that current treatment modalities are likely to fail in achieving long term remission with the majority of relapse samples containing distinct mutations when compared to primary diagnostic samples.
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Affiliation(s)
- Andrea M Muscat
- School of Medicine, Deakin University, Geelong, Victoria, Australia.,Cancer Services, Barwon Health, Geelong, Victoria, Australia
| | - Nicholas C Wong
- Department of Pediatrics, The University of Melbourne, Parkville, Victoria, Australia.,Monash Bioinformatics Platform, Monash University, Clayton, Victoria, Australia
| | - Katharine J Drummond
- Department of Neurosurgery, The Royal Melbourne Hospital, Parkville, Victoria, Australia.,Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Parkville, Victoria, Australia
| | - Elizabeth M Algar
- Center for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Mustafa Khasraw
- School of Medicine, Deakin University, Geelong, Victoria, Australia.,Cancer Services, Barwon Health, Geelong, Victoria, Australia.,NHMRC Clinical Trials Center, University of Sydney, Sydney, New South Wales, Australia
| | - Roel Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Kathryn Field
- Department of Neurosurgery, The Royal Melbourne Hospital, Parkville, Victoria, Australia.,Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Parkville, Victoria, Australia
| | - Mark A Rosenthal
- Department of Medical Oncology, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
| | - David M Ashley
- School of Medicine, Deakin University, Geelong, Victoria, Australia.,Cancer Services, Barwon Health, Geelong, Victoria, Australia
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29
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Visani M, Acquaviva G, Marucci G, Paccapelo A, Mura A, Franceschi E, Grifoni D, Pession A, Tallini G, Brandes AA, de Biase D. Non-canonical IDH1 and IDH2 mutations: a clonal and relevant event in an Italian cohort of gliomas classified according to the 2016 World Health Organization (WHO) criteria. J Neurooncol 2017; 135:245-254. [PMID: 28748342 DOI: 10.1007/s11060-017-2571-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/13/2017] [Indexed: 02/05/2023]
Abstract
According to the 2016 World Health Organization (WHO) classification of tumors of the central nervous system, assessment of exon 4 mutations in isocitrate dehydrogenase 1 or 2 genes (IDH1 or IDH2) is an essential step in the characterization of gliomas. The p.R132H mutation is the most frequent alteration in IDH genes, however other non-canonical IDH mutations can be identified. The aim of this study is to investigate in depth the prevalence of non-R132H IDH ("non-canonical") mutations in brain tumors classified according to the 2016 WHO scheme and their clonal distribution in neoplastic cells. A total of 288 consecutive cases of brain gliomas (grade II-IV) were analyzed for exon 4 IDH1 and IDH2 mutations. IDH1 and IDH2 analysis was performed using next generation sequencing. Non-canonical IDH mutations were identified in 13/52 (25.0%) grade II gliomas (astrocytomas: 8/31, 25.8%; oligodendrogliomas: 5/21, 23.8%) and in 5/40 (12.5%) grade III gliomas (astrocytomas: 3/25, 12.0%; oligodendrogliomas: 2/15, 13.3%). They were not identified in 196 grade IV gliomas (192 glioblastomas, 4 gliosarcomas). In the large majority (>80%) of tumors IDH mutations, both IDH1-R132H and the non-canonical ones, were present in the large majority (>80%) of neoplastic cells. Our data highlight the importance of investigating not only the IDH1-R132H mutation but also the non-canonical ones. These mutations are clonally distributed, with proportions of mutated neoplastic cells overlapping with those of p.R132H, a finding consistent with their driver role in gliomagenesis.
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Affiliation(s)
- Michela Visani
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, Bologna, Italy
| | - Giorgia Acquaviva
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, Bologna, Italy
| | - Gianluca Marucci
- Anatomic Pathology Unit, AUSL of Bologna, Via Altura 3, 40139, Bologna, Italy
- Department of Neuropathology, IRCCS Foundation Carlo Besta Neurological Institute, Milan, Italy
| | - Alexandro Paccapelo
- Department of Oncology, AUSL Bologna - IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Antonella Mura
- Department of Oncology, AUSL Bologna - IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Enrico Franceschi
- Department of Oncology, AUSL Bologna - IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Daniela Grifoni
- Department of Pharmacy and Biotechnology (Dipartimento di Farmacia e Biotecnologie) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna, Bologna, Italy
| | - Annalisa Pession
- Department of Pharmacy and Biotechnology (Dipartimento di Farmacia e Biotecnologie) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna, Bologna, Italy
| | - Giovanni Tallini
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, Bologna, Italy.
- Anatomia Patologica, ASL Bologna, Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale, Scuola di Medicina e Chirurgia, Università di Bologna, Via Altura 3, 40139, Bologna, Italy.
| | - Alba A Brandes
- Department of Oncology, AUSL Bologna - IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Dario de Biase
- Department of Pharmacy and Biotechnology (Dipartimento di Farmacia e Biotecnologie) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna, Bologna, Italy
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30
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Molinaro E, Romei C, Biagini A, Sabini E, Agate L, Mazzeo S, Materazzi G, Sellari-Franceschini S, Ribechini A, Torregrossa L, Basolo F, Vitti P, Elisei R. Anaplastic thyroid carcinoma: from clinicopathology to genetics and advanced therapies. Nat Rev Endocrinol 2017; 13:644-660. [PMID: 28707679 DOI: 10.1038/nrendo.2017.76] [Citation(s) in RCA: 265] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Anaplastic thyroid carcinoma (ATC) is a rare malignancy, accounting for 1-2% of all thyroid cancers. Although rare, ATC accounts for the majority of deaths from thyroid carcinoma. ATC often originates in a pre-existing thyroid cancer lesion, as suggested by the simultaneous presence of areas of differentiated or poorly differentiated thyroid carcinoma. ATC is characterized by the accumulation of several oncogenic alterations, and studies have shown that an increased number of oncogenic alterations equates to an increased level of dedifferentiation and aggressiveness. The clinical management of ATC requires a multidisciplinary approach; according to recent American Thyroid Association guidelines, surgery, radiotherapy and/or chemotherapy should be considered. In addition to conventional therapies, novel molecular targeted therapies are the most promising emerging treatment modalities. These drugs are often multiple receptor tyrosine kinase inhibitors, several of which have been tested in clinical trials with encouraging results so far. Accordingly, clinical trials are ongoing to evaluate the safety, efficacy and effectiveness of these new agents. This Review describes the updated clinical and pathological features of ATC and provides insight into the molecular biology of this disease. The most recent literature regarding conventional, newly available and future therapies for ATC is also discussed.
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Affiliation(s)
- Eleonora Molinaro
- Endocrine Unit, Department of Clinical and Experimental Medicine, University Hospital of Pisa
| | - Cristina Romei
- Endocrine Unit, Department of Clinical and Experimental Medicine, University Hospital of Pisa
| | - Agnese Biagini
- Endocrine Unit, Department of Clinical and Experimental Medicine, University Hospital of Pisa
| | - Elena Sabini
- Endocrine Unit, Department of Clinical and Experimental Medicine, University Hospital of Pisa
| | - Laura Agate
- Endocrine Unit, Department of Clinical and Experimental Medicine, University Hospital of Pisa
| | - Salvatore Mazzeo
- Diagnostic and Interventional Radiology Department of Translational Research and New Technologies in Medicine and Surgery, University Hospital of Pisa
| | - Gabriele Materazzi
- Division of Endocrine Surgery, Department of Surgical Pathology, University Hospital of Pisa
| | | | | | - Liborio Torregrossa
- Department of Surgical, Medical and Molecular Pathology, University Hospital of Pisa, Via Paradisa 2, 56124 Pisa, Italy
| | - Fulvio Basolo
- Department of Surgical, Medical and Molecular Pathology, University Hospital of Pisa, Via Paradisa 2, 56124 Pisa, Italy
| | - Paolo Vitti
- Endocrine Unit, Department of Clinical and Experimental Medicine, University Hospital of Pisa
| | - Rossella Elisei
- Endocrine Unit, Department of Clinical and Experimental Medicine, University Hospital of Pisa
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31
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Yi HS, Chang JY, Kim KS, Shong M. Oncogenes, mitochondrial metabolism, and quality control in differentiated thyroid cancer. Korean J Intern Med 2017; 32:780-789. [PMID: 28823142 PMCID: PMC5583459 DOI: 10.3904/kjim.2016.420] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 03/07/2017] [Indexed: 02/02/2023] Open
Abstract
Thyroid cancer is one of the most common malignancies of endocrine organs, and its incidence rate has increased steadily over the past several decades. Most differentiated thyroid tumors derived from thyroid epithelial cells exhibit slow-growing cancers, and patients with these tumors can achieve a good prognosis with surgical removal and radioiodine treatment. However, a small proportion of patients present with advanced thyroid cancer and are unusually resistant to current drug treatment modalities. Thyroid tumorigenesis is a complex process that is regulated by the activation of oncogenes, inactivation of tumor suppressors, and alterations in programmed cell death. Mitochondria play an essential role during tumor formation, progression, and metastasis of thyroid cancer. Recent studies have successfully observed the mitochondrial etiology of thyroid carcinogenesis. This review focuses on the recent progress in understanding the molecular mechanisms of thyroid cancer relating to altered mitochondrial metabolism.
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Affiliation(s)
- Hyon-Seung Yi
- Research Center for Endocrine and Metabolic Diseases, Chungnam National University School of Medicine, Daejeon, Korea
| | - Joon Young Chang
- Research Center for Endocrine and Metabolic Diseases, Chungnam National University School of Medicine, Daejeon, Korea
- Department of Medical Science, Chungnam National University School of Medicine, Daejeon, Korea
| | - Koon Soon Kim
- Research Center for Endocrine and Metabolic Diseases, Chungnam National University School of Medicine, Daejeon, Korea
| | - Minho Shong
- Research Center for Endocrine and Metabolic Diseases, Chungnam National University School of Medicine, Daejeon, Korea
- Correspondence to Minho Shong, M.D. Research Center for Endocrine and Metabolic Diseases, Chungnam National University School of Medicine, 266 Munhwa-ro, Jung-gu, Daejeon 35015, Korea Tel: +82-42-280-6994 Fax: +82-42-280-7995 E-mail:
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32
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Abstract
OPINION STATEMENT Radioiodine refractory differentiated thyroid cancer (RAI-R DTC) is a challenging malignancy with limited prognosis and treatment options. Recently, clinical trials with targeted therapies have advanced the outlook of these patients, and inhibition of the vascular endothelial growth factor (VEGF) axis has led to the approval of small-molecule tyrosine kinase inhibitors (TKIs) for first-line treatment of radioiodine refractory disease. In addition to approved therapies (sorafenib and lenvatinib), other multi-targeted tyrosine kinase inhibitors that are commercially available have been recognized as viable treatment options for RAI-R DTC. Our preference is to initially use lenvatinib, given the dramatic progression-free survival (PFS) improvement versus placebo, with the caveat that 24 mg daily is not often tolerated and lower doses often used. In patients with BRAF V600E mutation, BRAF inhibitors are now considered for treatment, especially if patients are at high risk from antiangiogenic therapy. Research is continuing to evolve in identifying mechanisms related to radioiodine refractoriness, and trials are evaluating therapeutic molecules to overcome this resistance. Clinical care of patients with RAI-R DTC requires careful consideration of both patient and disease characteristics. Many patients with asymptomatic and indolent disease can be followed for years without treatment while others with high volume or rapidly progressive disease merit early intervention.
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Anderson NM, Mucka P, Kern JG, Feng H. The emerging role and targetability of the TCA cycle in cancer metabolism. Protein Cell 2017; 9:216-237. [PMID: 28748451 PMCID: PMC5818369 DOI: 10.1007/s13238-017-0451-1] [Citation(s) in RCA: 299] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 06/26/2017] [Indexed: 02/08/2023] Open
Abstract
The tricarboxylic acid (TCA) cycle is a central route for oxidative phosphorylation in cells, and fulfills their bioenergetic, biosynthetic, and redox balance requirements. Despite early dogma that cancer cells bypass the TCA cycle and primarily utilize aerobic glycolysis, emerging evidence demonstrates that certain cancer cells, especially those with deregulated oncogene and tumor suppressor expression, rely heavily on the TCA cycle for energy production and macromolecule synthesis. As the field progresses, the importance of aberrant TCA cycle function in tumorigenesis and the potentials of applying small molecule inhibitors to perturb the enhanced cycle function for cancer treatment start to evolve. In this review, we summarize current knowledge about the fuels feeding the cycle, effects of oncogenes and tumor suppressors on fuel and cycle usage, common genetic alterations and deregulation of cycle enzymes, and potential therapeutic opportunities for targeting the TCA cycle in cancer cells. With the application of advanced technology and in vivo model organism studies, it is our hope that studies of this previously overlooked biochemical hub will provide fresh insights into cancer metabolism and tumorigenesis, subsequently revealing vulnerabilities for therapeutic interventions in various cancer types.
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Affiliation(s)
- Nicole M Anderson
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, 19104-6160, USA.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Patrick Mucka
- Departments of Pharmacology and Medicine, The Center for Cancer Research, Section of Hematology and Medical Oncology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Joseph G Kern
- Program in Biomedical Sciences, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Hui Feng
- Departments of Pharmacology and Medicine, The Center for Cancer Research, Section of Hematology and Medical Oncology, Boston University School of Medicine, Boston, MA, 02118, USA.
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Yin X, Xu Y. Structure and Function of TET Enzymes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 945:275-302. [PMID: 27826843 DOI: 10.1007/978-3-319-43624-1_12] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Mammalian DNA methylation mainly occurs at the carbon-C5 position of cytosine (5mC). TET enzymes were discovered to successively oxidize 5mC to 5-hydromethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). TET enzymes and oxidized 5mC derivatives play important roles in various biological and pathological processes, including regulation of DNA demethylation, gene transcription, embryonic development, and oncogenesis. In this chapter, we will discuss the discovery of TET-mediated 5mC oxidation and the structure, function, and regulation of TET enzymes.
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Affiliation(s)
- Xiaotong Yin
- Fudan University Shanghai Cancer Center, Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
- Key Laboratory of Molecular Medicine, Ministry of Education, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China.
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Avellaneda Matteo D, Grunseth AJ, Gonzalez ER, Anselmo SL, Kennedy MA, Moman P, Scott DA, Hoang A, Sohl CD. Molecular mechanisms of isocitrate dehydrogenase 1 (IDH1) mutations identified in tumors: The role of size and hydrophobicity at residue 132 on catalytic efficiency. J Biol Chem 2017; 292:7971-7983. [PMID: 28330869 DOI: 10.1074/jbc.m117.776179] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/16/2017] [Indexed: 12/12/2022] Open
Abstract
Isocitrate dehydrogenase 1 (IDH1) catalyzes the reversible NADP+-dependent conversion of isocitrate (ICT) to α-ketoglutarate (αKG) in the cytosol and peroxisomes. Mutations in IDH1 have been implicated in >80% of lower grade gliomas and secondary glioblastomas and primarily affect residue 132, which helps coordinate substrate binding. However, other mutations found in the active site have also been identified in tumors. IDH1 mutations typically result in a loss of catalytic activity, but many also can catalyze a new reaction, the NADPH-dependent reduction of αKG to d-2-hydroxyglutarate (D2HG). D2HG is a proposed oncometabolite that can competitively inhibit αKG-dependent enzymes. Some kinetic parameters have been reported for several IDH1 mutations, and there is evidence that mutant IDH1 enzymes vary widely in their ability to produce D2HG. We report that most IDH1 mutations identified in tumors are severely deficient in catalyzing the normal oxidation reaction, but that D2HG production efficiency varies among mutant enzymes up to ∼640-fold. Common IDH1 mutations have moderate catalytic efficiencies for D2HG production, whereas rarer mutations exhibit either very low or very high efficiencies. We then designed a series of experimental IDH1 mutants to understand the features that support D2HG production. We show that this new catalytic activity observed in tumors is supported by mutations at residue 132 that have a smaller van der Waals volume and are more hydrophobic. We report that one mutation can support both the normal and neomorphic reactions. These studies illuminate catalytic features of mutations found in the majority of patients with lower grade gliomas.
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Affiliation(s)
- Diego Avellaneda Matteo
- From the Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182 and
| | - Adam J Grunseth
- From the Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182 and
| | - Eric R Gonzalez
- From the Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182 and
| | - Stacy L Anselmo
- From the Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182 and
| | - Madison A Kennedy
- From the Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182 and
| | - Precious Moman
- From the Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182 and
| | - David A Scott
- the Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - An Hoang
- From the Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182 and
| | - Christal D Sohl
- From the Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182 and
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Abstract
In the past few years, it has become clear that mutations in epigenetic regulatory genes are common in human cancers. Therapeutic strategies are now being developed to target cancers with mutations in these genes using specific chemical inhibitors. In addition, a complementary approach based on the concept of synthetic lethality, which allows exploitation of loss-of-function mutations in cancers that are not targetable by conventional methods, has gained traction. Both of these approaches are now being tested in several clinical trials. In this Review, we present recent advances in epigenetic drug discovery and development, and suggest possible future avenues of investigation to drive progress in this area.
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Li J, Lu J, He Y, Wu Y, Wu Y, Song X, Jiang Y, Tang M, Weng X, Yi W, Luo X, Sun L, Bode AM, Cao Y. A new functional IDH2 genetic variant is associated with the risk of lung cancer. Mol Carcinog 2016; 56:1082-1087. [PMID: 27649069 DOI: 10.1002/mc.22573] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 09/06/2016] [Accepted: 09/16/2016] [Indexed: 12/20/2022]
Abstract
Recently, mutations in isocitrate dehydrogenase 1/2 (IDH1/2) were discovered in 70% of low-grade glioma and secondary glioblastoma multiforme. The discovery of an oncogenic function and the identification of onco-metabolites of IDH1/2 support new roles for metabolism in cancer. For example, some evidence indicates that IDH2 might also exhibit oncogenic functions by promoting cellular metabolism and cancer cell growth. We examined the association between IDH2 rs11540478 and lung cancer risk in 262 lung cancer patient cases and 602 healthy control subjects and also investigated the biological function of rs11540478 in vivo. We found that a higher risk was observed in lung cancer patient carriers of rs11540478 TT and CT compared with CC carriers (OR = 1.44; 95%CI = 1.04-2.00; P = 0.03). The frequency of IDH2 rs11540478 TT and CT carriers was decreased in healthy individuals between the ages of 50-77 compared to those aged 30-49 (OR = 0.67; 95%CI = 0.47-0.96; P = 0.03). Functional analysis showed the effect of rs11540478 on IDH2 expression and lung cancer cell viability, with higher IDH2 expression and cell viability among T allele compared with C allele. IDH2 mRNA was higher in peripheral blood lymphocytes from lung cancer patients compared to healthy subjects. Herein, for the first time we identified IDH2 rs11540478 as a new susceptibility locus for lung cancer. The effect of rs11540478 on mRNA expression of IDH2 and lung cancer cell viability might provide new insight for the genetic basis of lung cancer. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Jiangjiang Li
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, China.,Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha, China
| | - Jingchen Lu
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, China.,Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha, China.,Department of Medical Oncology, Xiangya Hospital, Central South University, Changsha, China
| | - Ya He
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, China.,Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha, China
| | - Yong Wu
- Department of Medicine Clinical Laboratory, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Yuan Wu
- Department of Medicine Clinical Laboratory, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Xin Song
- Cancer Biotherapy Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, China
| | - Yuee Jiang
- Department of Clinical Laboratory, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Min Tang
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, China.,Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha, China
| | - Xinxian Weng
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, China.,Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha, China
| | - Wei Yi
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, China.,Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha, China
| | - Xiangjian Luo
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, China.,Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha, China
| | - Lunquan Sun
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, China.,Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Ya Cao
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, China.,Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha, China
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Carvalheira G, Nozima BH, Cerutti JM. microRNA-106b-mediated down-regulation of C1orf24 expression induces apoptosis and suppresses invasion of thyroid cancer. Oncotarget 2016; 6:28357-70. [PMID: 26317551 PMCID: PMC4695065 DOI: 10.18632/oncotarget.4947] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 07/02/2015] [Indexed: 01/10/2023] Open
Abstract
We previously showed that C1orf24 expression is increased in thyroid carcinomas. Nonetheless, the mechanism underlying C1orf24 deregulation is not fully understood. It has been widely demonstrated that microRNAs are involved in post-transcriptional gene regulation in several diseases, including cancer. Using in silico prediction approach, five microRNAs that bind to the 3'-untranslated region (3'-UTR) of C1orf24 were identified. The expression of two selected microRNAs (miR-17-5p, miR-106b) and the expression of C1orf24 were tested in 48 benign and malignant thyroid lesions and in five thyroid carcinoma cell lines. miR-106b was down-regulated in thyroid cancer specimens and thyroid carcinoma cell lines, while C1orf24 expression was markedly increased. To demonstrate that miR-106b reduces C1orf24 expression, follicular (WRO) and papillary (TPC1) thyroid carcinoma cell lines were transiently transfected with miR-106b mimic. Ectopic expression of the miR-106b mimic significantly inhibits C1orf24 mRNA and protein expression in both WRO and TPC1 cells. Dual-luciferase report assays demonstrated that miR-106b directly targets C1orf24 by binding its 3'-UTR. Moreover, miR-106b-mediated down-regulation of C1orf24 expression increased apoptosis and inhibited migration. We additionally demonstrated that siRNA against C1orf24 significantly decreased its expression, inhibited cell migration and cell cycle progression while induced apoptosis. In summary, our findings not only provide new insights into molecular mechanism associated with C1orf24 overexpression in thyroid carcinomas but also show that C1orf24 might increase proliferation and cell migration. Thus, decreasing C1orf24 levels, by restoring miR-106b function, may have therapeutic implications.
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Affiliation(s)
- Gianna Carvalheira
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, SP, Brazil
| | - Bruno Heidi Nozima
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, SP, Brazil
| | - Janete Maria Cerutti
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Universidade Federal de São Paulo, SP, Brazil
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Jeon MJ, Chun SM, Kim D, Kwon H, Jang EK, Kim TY, Kim WB, Shong YK, Jang SJ, Song DE, Kim WG. Genomic Alterations of Anaplastic Thyroid Carcinoma Detected by Targeted Massive Parallel Sequencing in a BRAF(V600E) Mutation-Prevalent Area. Thyroid 2016; 26:683-90. [PMID: 26980298 DOI: 10.1089/thy.2015.0506] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
BACKGROUND Anaplastic thyroid carcinoma (ATC), the most aggressive type of thyroid cancer, has no effective therapy. Due to its dismal prognosis, it is vital to understand the genetic alterations of ATC and identify effective molecular targets. Targeted next-generation sequencing was performed to investigate the mutational profile of ATC using a massive parallel sequencing approach. METHODS DNA from formalin-fixed, paraffin-embedded archival samples of 11 ATCs and normal matched pairs were used. A total of 48 genetic alterations were identified by targeted exome sequencing. These alterations were validated by mass spectrometric genotyping and direct Sanger sequencing. RESULTS The most commonly mutated gene was BRAF, identified in 10 samples (91%), all showing the V600E point mutation. A KRAS point mutation was observed in the one sample (9%) without the BRAF(V600E) mutation. All 11 ATCs harbored BRAF or RAS mutations, reflecting the possibility that differentiated thyroid carcinomas progress to ATCs after the accumulation of mutations. A loss of function mutation of TP53 was observed in eight samples (73%), a PIK3CA mutation was observed in two samples (18%), and a frameshift mutation of PTEN was observed in one sample (9%). Twenty-eight novel mutated genes were found that had not previously been associated with ATC. Of these, loss of function mutations of NF2, KMT2D, and PKHD1 were repeatedly seen in three samples (27%), two samples (18%), and two samples (18%), respectively. Using direct Sanger sequencing, two samples (18%) were also found with a RASAL1 mutation. KMT2D and RASAL1 mutations were significantly associated with shorter ATC patient survival. CONCLUSIONS This comprehensive analysis of ATCs using targeted massive parallel sequencing identified several novel mutations in ATCs, such as loss of function mutations of NF2 or KMT2D. Future studies are needed to confirm the role of these novel mutations as independent drivers of ATC development.
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Affiliation(s)
- Min Ji Jeon
- 1 Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine , Seoul, Korea
| | - Sung-Min Chun
- 2 Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine , Seoul, Korea
| | - Deokhoon Kim
- 3 Center for Cancer Genome Discovery, Asan Institute for Life Science , Seoul, Korea
| | - Hyemi Kwon
- 1 Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine , Seoul, Korea
| | - Eun Kyung Jang
- 1 Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine , Seoul, Korea
| | - Tae Yong Kim
- 1 Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine , Seoul, Korea
| | - Won Bae Kim
- 1 Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine , Seoul, Korea
| | - Young Kee Shong
- 1 Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine , Seoul, Korea
| | - Se Jin Jang
- 2 Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine , Seoul, Korea
| | - Dong Eun Song
- 2 Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine , Seoul, Korea
| | - Won Gu Kim
- 1 Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine , Seoul, Korea
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Ding N, Che L, Li XL, Liu Y, Jiang LJ, Fan B, Tao JY, Chen X, Ji JF. Oncogenic potential of IDH1R132C mutant in cholangiocarcinoma development in mice. World J Gastroenterol 2016; 22:2071-2080. [PMID: 26877611 PMCID: PMC4726679 DOI: 10.3748/wjg.v22.i6.2071] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 08/04/2015] [Accepted: 09/02/2015] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate whether IDH1R132C mutant in combination with loss of p53 and activated Notch signaling promotes intrahepatic cholangiocarcinoma (ICC) development.
METHODS: We applied hydrodynamic injection and sleeping beauty mediated somatic integration to induce loss of p53 (via shP53), activation of Notch [via intracellular domain of Notch1 (NICD)] and/or overexpression of IDH1R132C mutant together with the sleeping beauty transposase into the mouse liver. Specifically, we co-expressed shP53 and NICD (shP53/NICD, n = 4), shP53 and IDH1R132C (shP53/IDH1R132C, n = 3), NICD and IDH1R132C (NICD/IDH1R132C, n = 4), as well as NICD, shP53 and IDH1R132C (NICD/shP53/IDH1R132C, n = 9) in mice. Mice were monitored for liver tumor development and euthanized at various time points. Liver histology was analyzed by hematoxylin and eosin staining. Molecular features of NICD/shP53/IDH1R132C ICC tumor cells were characterized by Myc tag, Flag tag, Ki-67, p-Erk and p-AKT immunohistochemical staining. Desmoplastic reaction in tumor tissues was studied by Picro-Sirius red staining.
RESULTS: We found that co-expression of shP53/NICD, shP53/IDH1R132C or NICD/IDH1R132C did not lead to liver tumor formation. In striking contrast, co-expression of NICD/shP53/IDH1R132C resulted in ICC development in mice (P < 0.01). The tumors could be identified as early as 12 wk post hydrodynamic injection. Tumors rapidly progressed, and by 18 wk post hydrodynamic injection, multiple cystic lesions could be identified on the liver surface. NICD/shP53/IDH1R132C liver tumors shared multiple histological features of human ICCs, including hyperplasia of irregular glands. Importantly, all tumor cells were positive for the biliary epithelial cell marker cytokeratin 19. Extensive collagen fibers could be visualized in tumor tissues using Sirus red staining, duplicating the desmoplastic reaction observed in human ICC. Tumors were highly proliferative and expressed ectopically injected genes. Together these studies supported that NICD/shP53/IDH1R132C liver tumors were indeed ICCs. Finally, no p-AKT or p-ERK positive staining was observed, suggesting that NICD/shP53/IDH1R132C driven ICC development was independent of AKT/mTOR and Ras/MAPK signaling cascades.
CONCLUSION: We have generated a simple, non-germline murine ICC model with activated Notch, loss of p53 and IDH1R132C mutant. The study supported the oncogenic potential of IDH1R132C.
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A holistic view of cancer bioenergetics: mitochondrial function and respiration play fundamental roles in the development and progression of diverse tumors. Clin Transl Med 2016; 5:3. [PMID: 26812134 PMCID: PMC4728164 DOI: 10.1186/s40169-016-0082-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/11/2016] [Indexed: 02/01/2023] Open
Abstract
Since Otto Warburg made the first observation that tumor cells exhibit altered metabolism and bioenergetics in the 1920s, many scientists have tried to further the understanding of tumor bioenergetics. Particularly, in the past decade, the application of the state-of the-art metabolomics and genomics technologies has revealed the remarkable plasticity of tumor metabolism and bioenergetics. Firstly, a wide array of tumor cells have been shown to be able to use not only glucose, but also glutamine for generating cellular energy, reducing power, and metabolic building blocks for biosynthesis. Secondly, many types of cancer cells generate most of their cellular energy via mitochondrial respiration and oxidative phosphorylation. Glutamine is the preferred substrate for oxidative phosphorylation in tumor cells. Thirdly, tumor cells exhibit remarkable versatility in using bioenergetics substrates. Notably, tumor cells can use metabolic substrates donated by stromal cells for cellular energy generation via oxidative phosphorylation. Further, it has been shown that mitochondrial transfer is a critical mechanism for tumor cells with defective mitochondria to restore oxidative phosphorylation. The restoration is necessary for tumor cells to gain tumorigenic and metastatic potential. It is also worth noting that heme is essential for the biogenesis and proper functioning of mitochondrial respiratory chain complexes. Hence, it is not surprising that recent experimental data showed that heme flux and function are elevated in non-small cell lung cancer (NSCLC) cells and that elevated heme function promotes intensified oxygen consumption, thereby fueling tumor cell proliferation and function. Finally, emerging evidence increasingly suggests that clonal evolution and tumor genetic heterogeneity contribute to bioenergetic versatility of tumor cells, as well as tumor recurrence and drug resistance. Although mutations are found only in several metabolic enzymes in tumors, diverse mutations in signaling pathways and networks can cause changes in the expression and activity of metabolic enzymes, which likely enable tumor cells to gain their bioenergetic versatility. A better understanding of tumor bioenergetics should provide a more holistic approach to investigate cancer biology and therapeutics. This review therefore attempts to comprehensively consider and summarize the experimental data supporting our latest view of cancer bioenergetics.
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42
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Gruber JJ, Colevas AD. Differentiated thyroid cancer: focus on emerging treatments for radioactive iodine-refractory patients. Oncologist 2015; 20:113-26. [PMID: 25616432 PMCID: PMC4319630 DOI: 10.1634/theoncologist.2014-0313] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 12/01/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The treatment of differentiated thyroid cancer refractory to radioactive iodine (RAI) had been hampered by few effective therapies. Recently, tyrosine kinase inhibitors (TKIs) have shown activity in this disease. Clinical guidance on the use of these agents in RAI-refractory thyroid cancer is warranted. MATERIALS AND METHODS Molecular mutations found in RAI-refractory thyroid cancer are summarized. Recent phase II and III clinical trial data for TKIs axitinib, lenvatinib, motesanib, pazopanib, sorafenib, sunitinib, and vandetinib are reviewed including efficacy and side effect profiles. Molecular targets and potencies of these agents are compared. Inhibitors of BRAF, mammalian target of rapamycin, and MEK are considered. RESULTS Routine testing for molecular alterations prior to therapy is not yet recommended. TKIs produce progression-free survival of approximately 1 year (range: 7.7-19.6 months) and partial response rates of up to 50% by Response Evaluation Criteria in Solid Tumors. Pazopanib and lenvatinib are the most active agents. The majority of patients experienced tumor shrinkage with TKIs. Common adverse toxicities affect dermatologic, gastrointestinal, and cardiovascular systems. CONCLUSION Multiple TKIs have activity in RAI-refractory differentiated thyroid cancer. Selection of a targeted agent should depend on disease trajectory, side effect profile, and goals of therapy.
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Affiliation(s)
- Joshua J Gruber
- Stanford Cancer Center, Stanford University Medical Center, Stanford, California, USA
| | - A Dimitrios Colevas
- Stanford Cancer Center, Stanford University Medical Center, Stanford, California, USA
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43
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Scourzic L, Mouly E, Bernard OA. TET proteins and the control of cytosine demethylation in cancer. Genome Med 2015; 7:9. [PMID: 25632305 PMCID: PMC4308928 DOI: 10.1186/s13073-015-0134-6] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The discovery that ten-eleven translocation (TET) proteins are α-ketoglutarate-dependent dioxygenases involved in the conversion of 5-methylcytosines (5-mC) to 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine and 5-carboxycytosine has revealed new pathways in the cytosine methylation and demethylation process. The description of inactivating mutations in TET2 suggests that cellular transformation is in part caused by the deregulation of this 5-mC conversion. The direct and indirect deregulation of methylation control through mutations in DNA methyltransferase and isocitrate dehydrogenase (IDH) genes, respectively, along with the importance of cytosine methylation in the control of normal and malignant cellular differentiation have provided a conceptual framework for understanding the early steps in cancer development. Here, we review recent advances in our understanding of the cytosine methylation cycle and its implication in cellular transformation, with an emphasis on TET enzymes and 5-hmC. Ongoing clinical trials targeting the activity of mutated IDH enzymes provide a proof of principle that DNA methylation is targetable, and will trigger further therapeutic applications aimed at controlling both early and late stages of cancer development.
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Affiliation(s)
- Laurianne Scourzic
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité 1170, équipe labellisée Ligue Contre le Cancer, 94805 Villejuif, France ; Institut Gustave Roussy, 94805 Villejuif, France ; University Paris 11 Sud, 91405 Orsay, France
| | - Enguerran Mouly
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité 1170, équipe labellisée Ligue Contre le Cancer, 94805 Villejuif, France ; Institut Gustave Roussy, 94805 Villejuif, France ; University Paris 11 Sud, 91405 Orsay, France
| | - Olivier A Bernard
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité 1170, équipe labellisée Ligue Contre le Cancer, 94805 Villejuif, France ; Institut Gustave Roussy, 94805 Villejuif, France ; University Paris 11 Sud, 91405 Orsay, France
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44
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Kroeze LI, van der Reijden BA, Jansen JH. 5-Hydroxymethylcytosine: An epigenetic mark frequently deregulated in cancer. Biochim Biophys Acta Rev Cancer 2015; 1855:144-54. [PMID: 25579174 DOI: 10.1016/j.bbcan.2015.01.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 01/02/2015] [Accepted: 01/04/2015] [Indexed: 12/26/2022]
Abstract
The epigenetic mark 5-hydroxymethylcytosine (5hmC) has gained interest since 2009, when it was discovered that Ten-Eleven-Translocation (TET) proteins catalyze the conversion of 5-methylcytosine (5mC) into 5hmC. This conversion appears to be an intermediate step in the active DNA demethylation pathway. Factors that regulate DNA hydroxymethylation are frequently affected in cancer, leading to deregulated 5hmC levels. In this review, we will discuss the regulation of DNA hydroxymethylation, defects in this pathway in cancer, and novel therapies that may correct deregulated (hydroxy)methylation of DNA.
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Affiliation(s)
- Leonie I Kroeze
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center and Radboud Institute for Molecular Life Sciences, PO Box 9101, 6500 HB Nijmegen, The Netherlands.
| | - Bert A van der Reijden
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center and Radboud Institute for Molecular Life Sciences, PO Box 9101, 6500 HB Nijmegen, The Netherlands.
| | - Joop H Jansen
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center and Radboud Institute for Molecular Life Sciences, PO Box 9101, 6500 HB Nijmegen, The Netherlands.
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45
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Le Mercier M, D'Haene N, De Nève N, Blanchard O, Degand C, Rorive S, Salmon I. Next-generation sequencing improves the diagnosis of thyroid FNA specimens with indeterminate cytology. Histopathology 2014; 66:215-24. [PMID: 24834793 DOI: 10.1111/his.12461] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 05/14/2014] [Indexed: 01/21/2023]
Abstract
AIMS The assessment of thyroid nodules is a common clinical challenge. Fine-needle aspiration (FNA) is the standard pre-operative tool for thyroid nodule diagnosis. However, up to 30% of the samples are classified as indeterminate. This often leads to unnecessary surgery. In this study, we evaluated the added value of next-generation sequencing (NGS) for helping in the diagnosis of FNA samples. METHODS AND RESULTS We analysed retrospectively 34 indeterminate FNA samples for which surgical resection was performed. DNA was obtained from cell blocks or from stained smears and subjected to NGS to analyse mutations in 50 genes. Mutations in BRAF, NRAS, KRAS and PTEN, that are known to be involved in thyroid cancer biology, were detected in seven FNA samples. The presence of a mutation in these genes was a strong indicator of cancer because five (71%) of the mutation-positive FNA samples had a malignant diagnosis after surgery. Moreover, there was only an 8% cancer risk in nodules with an indeterminate cytological diagnosis but with a negative molecular test. CONCLUSION This study demonstrates that thyroid FNA can be analysed successfully by NGS. The detection of mutations known to be involved in thyroid cancer improves the sensitivity of thyroid FNA diagnosis.
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Affiliation(s)
- Marie Le Mercier
- Department of Pathology, Erasme University Hospital, Université Libre de Bruxelles (ULB), Brussels, Belgium
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46
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Corver WE, van Wezel T, Molenaar K, Schrumpf M, van den Akker B, van Eijk R, Ruano Neto D, Oosting J, Morreau H. Near-haploidization significantly associates with oncocytic adrenocortical, thyroid, and parathyroid tumors but not with mitochondrial DNA mutations. Genes Chromosomes Cancer 2014; 53:833-44. [DOI: 10.1002/gcc.22194] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Accepted: 05/28/2014] [Indexed: 01/06/2023] Open
Affiliation(s)
- Willem E. Corver
- Department of Pathology; Leiden University Medical Center; RC Leiden Netherlands
| | - Tom van Wezel
- Department of Pathology; Leiden University Medical Center; RC Leiden Netherlands
| | - Kees Molenaar
- Department of Pathology; Leiden University Medical Center; RC Leiden Netherlands
| | - Melanie Schrumpf
- Department of Pathology; Leiden University Medical Center; RC Leiden Netherlands
| | - Brendy van den Akker
- Department of Pathology; Leiden University Medical Center; RC Leiden Netherlands
| | - Ronald van Eijk
- Department of Pathology; Leiden University Medical Center; RC Leiden Netherlands
| | - Dina Ruano Neto
- Department of Pathology; Leiden University Medical Center; RC Leiden Netherlands
| | - Jan Oosting
- Department of Pathology; Leiden University Medical Center; RC Leiden Netherlands
| | - Hans Morreau
- Department of Pathology; Leiden University Medical Center; RC Leiden Netherlands
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IDH1/IDH2 but not TP53 mutations predict prognosis in Bulgarian glioblastoma patients. BIOMED RESEARCH INTERNATIONAL 2014; 2014:654727. [PMID: 24868540 PMCID: PMC4017788 DOI: 10.1155/2014/654727] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 03/29/2014] [Indexed: 01/26/2023]
Abstract
Mutations in genes encoding isocitrate dehydrogenase isoforms 1 (IDH1) and 2 (IDH2) have been associated with good prognosis for patients with brain neoplasias and have been commonly found together with mutated TP53 gene. To determine the prevalence of IDH1, IDH2, and TP53 mutations and their impact on overall survival 106 glioblastoma patients were analysed. IDH1 mutations were detected in 13 and IDH2 mutation in one patient. Two homozygous samples with R132H mutation in IDH1 gene and a novel aberration K129R in IDH2 gene were found. Sixty-four percent of IDH1/IDH2 mutated tumours harboured also a mutation in TP53 gene. Genetic aberrations in TP53 were present in 37 patients. Statistical analysis of the impact of the studied factors on the overall survival showed that the mutations in IDH1/IDH2, but not the ones in TP53, were associated with longer survival. Also, the impact of age on prognosis was confirmed. This is the first comprehensive study on glioblastomas in Bulgaria. Our results suggest that IDH1/IDH2 but not TP53 mutations together with other prognostic factors such as age might be applied in clinical practice for prediction of outcome in patients with glioblastomas.
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48
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Vu-Phan D, Koenig RJ. Genetics and epigenetics of sporadic thyroid cancer. Mol Cell Endocrinol 2014; 386:55-66. [PMID: 23933154 PMCID: PMC3867574 DOI: 10.1016/j.mce.2013.07.030] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 07/31/2013] [Accepted: 07/31/2013] [Indexed: 12/23/2022]
Abstract
Thyroid carcinoma is the most common endocrine malignancy, and although the disease generally has an excellent prognosis, therapeutic options are limited for patients not cured by surgery and radioiodine. Thyroid carcinomas commonly contain one of a small number of recurrent genetic mutations. The identification and study of these mutations has led to a deeper understanding of the pathophysiology of this disease and is providing new approaches to diagnosis and therapy. Papillary thyroid carcinomas usually contain an activating mutation in the RAS cascade, most commonly in BRAF and less commonly in RAS itself or through gene fusions that activate RET. A chromosomal translocation that results in production of a PAX8-PPARG fusion protein is found in follicular carcinomas. Anaplastic carcinomas may contain some of the above changes as well as additional mutations. Therapies that are targeted to these mutations are being used in patient care and clinical trials.
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Affiliation(s)
- Dang Vu-Phan
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, MI, USA.
| | - Ronald J Koenig
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, MI, USA.
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49
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Cruz GR, Dias Oliveira I, Moraes L, Del Giudice Paniago M, de Seixas Alves MT, Capellano AM, Saba-Silva N, Cavalheiro S, Cerutti JM, Toledo SRC. Analysis of KIAA1549-BRAF fusion gene expression and IDH1/IDH2 mutations in low grade pediatric astrocytomas. J Neurooncol 2014; 117:235-42. [PMID: 24532263 DOI: 10.1007/s11060-014-1398-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 01/31/2014] [Indexed: 11/30/2022]
Abstract
Low-grade astrocytomas comprise about 30 % of the central nervous system tumors in children. Several investigations have searched a correlation between the BRAF gene fusions alterations and mutations at IDH1 and IDH2 genes in low grade pediatric astrocytomas. This study identified the expression of KIAA1549-BRAF fusion gene and BRAF V600E mutation, mutations at exon 4 of the IDH1 and IDH2 genes in samples of pilocytic astrocytomas (PA) and grade-II astrocytomas (A-II) pediatric patients. The correlation between these alterations and the clinical profile of the patients was also evaluated. Eighty-two samples of low-grade astrocytomas (65 PA and 17 A-II) were analyzed by PCR and sequencing for each of the targets identified. We identified the KIAA1549-BRAF fusion transcript in 45 % of the samples. BRAF V600E and BRAFins598T mutations were detected in 7 and 1 % of the samples, respectively. Mutations in the R132/R172 residues of the IDH1/IDH2 genes were detected in only two samples, and the G105G polymorphism (rs11554137:C>T) was identified in ten patients. Additionally, we observed two mutations out of the usual hotspots at IDH1 and IDH2 genes. We observed a smaller frequency of mutations in IDHs genes than previously described, but since the prior studies were composed of adult or mixed (adults and children) samples, we believe that our results represent a relevant contribution to the growing knowledge in low grade childhood astrocytomas.
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Affiliation(s)
- Gabriela Rampazzo Cruz
- Department of Pediatrics, Pediatrics Oncology Institute-GRAACC (Grupo de Apoio ao Adolescente e à Criança com Câncer), UNIFESP (Federal University of São Paulo), Rua Botucatu, no 743, Floor 8 - Genetics Laboratory, Vila Clementino, São Paulo, SP, 04023-062, Brazil,
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Valente FOF, Dias da Silva MR, Camacho CP, Kunii IS, Bastos AU, da Fonseca CCN, Simião HPC, Tamanaha R, Maciel RMB, Cerutti JM. Comprehensive analysis of RET gene should be performed in patients with multiple endocrine neoplasia type 2 (MEN 2) syndrome and no apparent genotype-phenotype correlation: an appraisal of p.Y791F and p.C634Y RET mutations in five unrelated Brazilian families. J Endocrinol Invest 2013; 36:975-81. [PMID: 23723040 DOI: 10.3275/8997] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
BACKGROUND We previously identified a four-generation family with medullary thyroid cancer (MTC) and a germline p.Y791F RET mutation whose cancer lacked a strong genotype-phenotype correlation. The entire gene coding region of the RET gene should be sequenced when genotype-phenotype discrepancies are observed in patients with multiple endocrine neoplasia type 2 (MEN 2), even if a RET hotspot mutation has been identified. METHODS A new genetic test was performed in the index case of this family with the p.Y791F RET germline mutation. The entire coding region of the RET gene was investigated by direct sequencing of PCR products. Once a mutation was identified, the target exon was sequenced in all at-risk relatives. RESULTS An additional p.C634Y germline mutation in the RET gene was identified in the reported family. The double mutation occurred in cis and segregated with the phenotype. Through the Brazilian Genetic Screening Program developed at our institution, we additionally report the combination of these two mutations (p.C634Y/p.Y791F) in the RET gene in four other unrelated families. The overall penetrance of MTC and pheochromocytoma in patients with the p.C634Y/p.Y791F mutations was 79% and 13%, respectively. CONCLUSION Our data emphasises that a comprehensive analysis of the RET gene may reveal multiple germline mutations in MEN 2 patients who exhibit an atypical clinical course of the disease.
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Affiliation(s)
- F O F Valente
- Laboratory of Molecular and Translational Endocrinology, Division of Endocrinology, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
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