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Liu R, Wang Y, Bu J, Li Q, Chen F, Zhu M, Chi H, Yu G, Zhu T, Zhu X, Zhao G. Construction and Validation of Novel Ferroptosis-related Risk Score Signature and Prognostic Prediction Nomogram for Patients with Colorectal Cancer. Int J Med Sci 2024; 21:1103-1116. [PMID: 38774759 PMCID: PMC11103399 DOI: 10.7150/ijms.91446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 03/25/2024] [Indexed: 05/24/2024] Open
Abstract
Background: Colorectal cancer (CRC) has a high morbidity and mortality. Ferroptosis is a phenomenon in which metabolism and cell death are closely related. The role of ferroptosis-related genes in the progression of CRC is still not clear. Therefore, we screened and validated the ferroptosis-related genes which could determine the prevalence, risk and prognosis of patients with CRC. Methods: We firstly screened differentially expressed ferroptosis-related genes by The Cancer Genome Atlas (TCGA) database. Then, these genes were used to construct a risk-score model using the least absolute shrinkage and selection operator (LASSO) regression algorithm. The function and prognosis of the ferroptosis-related genes were confirmed using multi-omics analysis. The gene expression results were validated using publicly available databases and qPCR. We also used publicly available data and ferroptosis-related genes to construct a prognostic prediction nomogram. Results: A total of 24 differential expressed genes associated with ferroptosis were screened in this study. A three-gene risk score model was then established based on these 24 genes and GPX3, CDKN2A and SLC7A11 were selected. The significant prognostic value of this novel three-gene signature was also assessed. Furthermore, we conducted RT-qPCR analysis on cell lines and tissues, and validated the high expression of CDKN2A, GPX3 and low expression of SLC7A11 in CRC cells. The observed mRNA expression of GPX3, CDKN2A and SLC7A11 was consistent with the predicted outcomes. Besides, eight variables including selected ferroptosis related genes were included to establish the prognostic prediction nomogram for patients with CRC. The calibration plots showed favorable consistency between the prediction of the nomogram and actual observations. Also, the time-dependent AUC (>0.7) indicated satisfactory discriminative ability of the nomogram. Conclusions: The present study constructed and validated a novel ferroptosis-related three-gene risk score signature and a prognostic prediction nomogram for patients with CRC. Also, we screened and validated the ferroptosis-related genes GPX3, CDKN2A, and SLC7A11 which could serve as novel biomarkers for patients with CRC.
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Affiliation(s)
- Ruibin Liu
- Department of General Surgery, Cancer Hospital of Dalian University of Technology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning 110042, China
- Liaoning University of Traditional Chinese Medicine, Shenyang, Liaoning 110847, China
| | - Yue Wang
- Department of General Surgery, Cancer Hospital of Dalian University of Technology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning 110042, China
| | - Jiawen Bu
- Department of Colorectal Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Qingqing Li
- Department of Endoscopy, Cancer Hospital of Dalian University of Technology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning 110042, China
| | - Fang Chen
- Department of Gynecology, People's Hospital of Liaoning Province, Shenyang, Liaoning 110016, China
| | - Mengying Zhu
- Department of General Surgery, Cancer Hospital of Dalian University of Technology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning 110042, China
| | - Huanyu Chi
- Department of General Surgery, Cancer Hospital of Dalian University of Technology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning 110042, China
| | - Guilin Yu
- Department of General Surgery, Cancer Hospital of Dalian University of Technology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning 110042, China
| | - Tong Zhu
- Department of Breast Surgery, Panjin Central Hospital, Panjin, Liaoning 124010, China
| | - Xudong Zhu
- Department of General Surgery, Cancer Hospital of Dalian University of Technology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning 110042, China
- Liaoning Provincial Key Laboratory of Precision Medicine for Malignant Tumors, Shenyang, Liaoning 110042, China
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, United States of America
| | - Guohua Zhao
- Department of General Surgery, Cancer Hospital of Dalian University of Technology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning 110042, China
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2
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Kozakiewicz P, Grzybowska-Szatkowska L, Ciesielka M, Całka P, Osuchowski J, Szmygin P, Jarosz B, Ostrowska-Leśko M, Dudka J, Tkaczyk-Wlizło A, Ślaska B. Mitochondrial DNA Changes in Respiratory Complex I Genes in Brain Gliomas. Biomedicines 2023; 11:biomedicines11041183. [PMID: 37189801 DOI: 10.3390/biomedicines11041183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 05/17/2023] Open
Abstract
Mitochondria are organelles necessary for oxidative phosphorylation. The interest in the role of mitochondria in the process of carcinogenesis results from the fact that a respiratory deficit is found in dividing cells, especially in cells with accelerated proliferation. The study included tumor and blood material from 30 patients diagnosed with glioma grade II, III and IV according to WHO (World Health Organization). DNA was isolated from the collected material and next-generation sequencing was performed on the MiSeqFGx apparatus (Illumina). The study searched for a possible relationship between the occurrence of specific mitochondrial DNA polymorphisms in the respiratory complex I genes and brain gliomas of grade II, III and IV. The impact of missense changes on the biochemical properties, structure and functioning of the encoded protein, as well as their potential harmfulness, were assessed in silico along with their belonging to a given mitochondrial subgroup. The A3505G, C3992T, A4024G, T4216C, G5046A, G7444A, T11253C, G12406A and G13604C polymorphisms were assessed as deleterious changes in silico, indicating their association with carcinogenesis.
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Affiliation(s)
- Paulina Kozakiewicz
- Department of Radiotherapy, Oncology Centre of Lublin St. Jana z Dukli Jaczewskiego 7, 20-090 Lublin, Poland
| | | | - Marzanna Ciesielka
- Chair and Department of Forensic Medicine, Medical University in Lublin, Jaczewskiego 8b, 20-090 Lublin, Poland
| | - Paulina Całka
- Chair and Department of Forensic Medicine, Medical University in Lublin, Jaczewskiego 8b, 20-090 Lublin, Poland
| | - Jacek Osuchowski
- Chair and Department of Neurosurgery and Pediatric Neurosurgery, Medical University in Lublin, Jaczewskiego 8, 20-090 Lublin, Poland
| | - Paweł Szmygin
- Chair and Department of Neurosurgery and Pediatric Neurosurgery, Medical University in Lublin, Jaczewskiego 8, 20-090 Lublin, Poland
| | - Bożena Jarosz
- Chair and Department of Neurosurgery and Pediatric Neurosurgery, Medical University in Lublin, Jaczewskiego 8, 20-090 Lublin, Poland
| | - Marta Ostrowska-Leśko
- Chair and Department of Toxicology, Medical University in Lublin, Jaczewskiego 8b, 20-090 Lublin, Poland
| | - Jarosław Dudka
- Chair and Department of Toxicology, Medical University in Lublin, Jaczewskiego 8b, 20-090 Lublin, Poland
| | - Angelika Tkaczyk-Wlizło
- Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
| | - Brygida Ślaska
- Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
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3
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Chang LC, Chiang SK, Chen SE, Hung MC. Targeting 2-oxoglutarate dehydrogenase for cancer treatment. Am J Cancer Res 2022; 12:1436-1455. [PMID: 35530286 PMCID: PMC9077069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/02/2022] [Indexed: 06/14/2023] Open
Abstract
Tricarboxylic acid (TCA) cycle, also called Krebs cycle or citric acid cycle, is an amphoteric pathway, contributing to catabolic degradation and anaplerotic reactions to supply precursors for macromolecule biosynthesis. Oxoglutarate dehydrogenase complex (OGDHc, also called α-ketoglutarate dehydrogenase) a highly regulated enzyme in TCA cycle, converts α-ketoglutarate (αKG) to succinyl-Coenzyme A in accompany with NADH generation for ATP generation through oxidative phosphorylation. The step collaborates with glutaminolysis at an intersectional point to govern αKG levels for energy production, nucleotide and amino acid syntheses, and the resources for macromolecule synthesis in cancer cells with rapid proliferation. Despite being a flavoenzyme susceptible to electron leakage contributing to mitochondrial reactive oxygen species (ROS) production, OGDHc is highly sensitive to peroxides such as HNE (4-hydroxy-2-nonenal) and moreover, its activity mediates the activation of several antioxidant pathways. The characteristics endow OGDHc as a critical redox sensor in mitochondria. Accumulating evidences suggest that dysregulation of OGDHc impairs cellular redox homeostasis and disturbs substrate fluxes, leading to a buildup of oncometabolites along the pathogenesis and development of cancers. In this review, we describe molecular interactions, regulation of OGDHc expression and activity and its relationships with diseases, specifically focusing on cancers. In the end, we discuss the potential of OGDHs as a therapeutic target for cancer treatment.
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Affiliation(s)
- Ling-Chu Chang
- Center for Molecular Medicine, China Medical University Hospital, China Medical UniversityTaichung 404, Taiwan
| | - Shih-Kai Chiang
- Department of Animal Science, National Chung Hsing UniversityTaichung 40227, Taiwan
| | - Shuen-Ei Chen
- Department of Animal Science, National Chung Hsing UniversityTaichung 40227, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing UniversityTaichung 40227, Taiwan
- Innovation and Development Center of Sustainable Agriculture (IDCSA), National Chung Hsing UniversityTaiwan
- Research Center for Sustainable Energy and Nanotechnology, National Chung Hsing UniversityTaichung 40227, Taiwan
| | - Mien-Chie Hung
- Center for Molecular Medicine, China Medical University Hospital, China Medical UniversityTaichung 404, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical UniversityTaichung 404, Taiwan
- Deparment of Biotechnology, Asia UniversityTaichung 413, Taiwan
- Research Center for Cancer Biology, China Medical UniversityTaichung 404, Taiwan
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4
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Xu S, Wang Z, Ye J, Mei S, Zhang J. Identification of Iron Metabolism-Related Genes as Prognostic Indicators for Lower-Grade Glioma. Front Oncol 2021; 11:729103. [PMID: 34568059 PMCID: PMC8458946 DOI: 10.3389/fonc.2021.729103] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/23/2021] [Indexed: 12/13/2022] Open
Abstract
Lower-grade glioma (LGG) is characterized by genetic and transcriptional heterogeneity, and a dismal prognosis. Iron metabolism is considered central for glioma tumorigenesis, tumor progression and tumor microenvironment, although key iron metabolism-related genes are unclear. Here we developed and validated an iron metabolism-related gene signature LGG prognosis. RNA-sequence and clinicopathological data from The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA) were downloaded. Prognostic iron metabolism-related genes were screened and used to construct a risk-score model via differential gene expression analysis, univariate Cox analysis, and the Least Absolute Shrinkage and Selection Operator (LASSO)-regression algorithm. All LGG patients were stratified into high- and low-risk groups, based on the risk score. The prognostic significance of the risk-score model in the TCGA and CGGA cohorts was evaluated with Kaplan-Meier (KM) survival and receiver operating characteristic (ROC) curve analysis. Risk- score distributions in subgroups were stratified by age, gender, the World Health Organization (WHO) grade, isocitrate dehydrogenase 1 (IDH1) mutation status, the O6-methylguanine-DNA methyl-transferase (MGMT) promoter-methylation status, and the 1p/19q co-deletion status. Furthermore, a nomogram model with a risk score was developed, and its predictive performance was validated with the TCGA and CGGA cohorts. Additionally, the gene set enrichment analysis (GSEA) identified signaling pathways and pathological processes enriched in the high-risk group. Finally, immune infiltration and immune checkpoint analysis were utilized to investigate the tumor microenvironment characteristics related to the risk score. We identified a prognostic 15-gene iron metabolism-related signature and constructed a risk-score model. High risk scores were associated with an age of > 40, wild-type IDH1, a WHO grade of III, an unmethylated MGMT promoter, and 1p/19q non-codeletion. ROC analysis indicated that the risk-score model accurately predicted 1-, 3-, and 5-year overall survival rates of LGG patients in the both TCGA and CGGA cohorts. KM analysis showed that the high-risk group had a much lower overall survival than the low-risk group (P < 0.0001). The nomogram model showed a strong ability to predict the overall survival of LGG patients in the TCGA and CGGA cohorts. GSEA analysis indicated that inflammatory responses, tumor-associated pathways, and pathological processes were enriched in high-risk group. Moreover, a high risk score correlated with the infiltration immune cells (dendritic cells, macrophages, CD4+ T cells, and B cells) and expression of immune checkpoint (PD1, PDL1, TIM3, and CD48). Our prognostic model was based on iron metabolism-related genes in LGG, can potentially aid in LGG prognosis, and provides potential targets against gliomas.
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Affiliation(s)
- Shenbin Xu
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
- Department of Gastroenterology Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Zefeng Wang
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Juan Ye
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Shuhao Mei
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jianmin Zhang
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Brain Research Institute, Zhejiang University, Hangzhou, China
- Collaborative Innovation Center for Brain Science, Zhejiang University, Hangzhou, China
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5
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Panina SB, Pei J, Kirienko NV. Mitochondrial metabolism as a target for acute myeloid leukemia treatment. Cancer Metab 2021; 9:17. [PMID: 33883040 PMCID: PMC8058979 DOI: 10.1186/s40170-021-00253-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/30/2021] [Indexed: 02/06/2023] Open
Abstract
Acute myeloid leukemias (AML) are a group of aggressive hematologic malignancies resulting from acquired genetic mutations in hematopoietic stem cells that affect patients of all ages. Despite decades of research, standard chemotherapy still remains ineffective for some AML subtypes and is often inappropriate for older patients or those with comorbidities. Recently, a number of studies have identified unique mitochondrial alterations that lead to metabolic vulnerabilities in AML cells that may present viable treatment targets. These include mtDNA, dependency on oxidative phosphorylation, mitochondrial metabolism, and pro-survival signaling, as well as reactive oxygen species generation and mitochondrial dynamics. Moreover, some mitochondria-targeting chemotherapeutics and their combinations with other compounds have been FDA-approved for AML treatment. Here, we review recent studies that illuminate the effects of drugs and synergistic drug combinations that target diverse biomolecules and metabolic pathways related to mitochondria and their promise in experimental studies, clinical trials, and existing chemotherapeutic regimens.
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Affiliation(s)
| | - Jingqi Pei
- Department of BioSciences, Rice University, Houston, TX, USA
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6
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Braun Y, Filipski K, Bernatz S, Baumgarten P, Roller B, Zinke J, Zeiner PS, Ilina E, Senft C, Ronellenfitsch MW, Plate KH, Bähr O, Hattingen E, Steinbach JP, Mittelbronn M, Harter PN. Linking epigenetic signature and metabolic phenotype in IDH mutant and IDH wildtype diffuse glioma. Neuropathol Appl Neurobiol 2020; 47:379-393. [PMID: 33080075 DOI: 10.1111/nan.12669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/23/2020] [Accepted: 10/14/2020] [Indexed: 01/17/2023]
Abstract
AIMS Changes in metabolism are known to contribute to tumour phenotypes. If and how metabolic alterations in brain tumours contribute to patient outcome is still poorly understood. Epigenetics impact metabolism and mitochondrial function. The aim of this study is a characterisation of metabolic features in molecular subgroups of isocitrate dehydrogenase mutant (IDHmut) and isocitrate dehydrogenase wildtype (IDHwt) gliomas. METHODS We employed DNA methylation pattern analyses with a special focus on metabolic genes, large-scale metabolism panel immunohistochemistry (IHC), qPCR-based determination of mitochondrial DNA copy number and immune cell content using IHC and deconvolution of DNA methylation data. We analysed molecularly characterised gliomas (n = 57) for in depth DNA methylation, a cohort of primary and recurrent gliomas (n = 22) for mitochondrial copy number and validated these results in a large glioma cohort (n = 293). Finally, we investigated the potential of metabolic markers in Bevacizumab (Bev)-treated gliomas (n = 29). RESULTS DNA methylation patterns of metabolic genes successfully distinguished the molecular subtypes of IDHmut and IDHwt gliomas. Promoter methylation of lactate dehydrogenase A negatively correlated with protein expression and was associated with IDHmut gliomas. Mitochondrial DNA copy number was increased in IDHmut tumours and did not change in recurrent tumours. Hierarchical clustering based on metabolism panel IHC revealed distinct subclasses of IDHmut and IDHwt gliomas with an impact on patient outcome. Further quantification of these markers allowed for the prediction of survival under anti-angiogenic therapy. CONCLUSION A mitochondrial signature was associated with increased survival in all analyses, which could indicate tumour subgroups with specific metabolic vulnerabilities.
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Affiliation(s)
- Yannick Braun
- Neurological Institute (Edinger Institute), University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Katharina Filipski
- Neurological Institute (Edinger Institute), University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany.,German Cancer Consortium (DKTK) partner site Frankfurt/Mainz, Frankfurt, Germany.,German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Simon Bernatz
- Neurological Institute (Edinger Institute), University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Peter Baumgarten
- Neurological Institute (Edinger Institute), University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany.,Department of Neurosurgery, University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Bastian Roller
- Neurological Institute (Edinger Institute), University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Jenny Zinke
- Neurological Institute (Edinger Institute), University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Pia S Zeiner
- Neurological Institute (Edinger Institute), University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany.,Dr. Senckenberg Institute for Neurooncology, University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Elena Ilina
- Neurological Institute (Edinger Institute), University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Christian Senft
- Department of Neurosurgery, University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Michael W Ronellenfitsch
- German Cancer Consortium (DKTK) partner site Frankfurt/Mainz, Frankfurt, Germany.,German Cancer Research Centre (DKFZ), Heidelberg, Germany.,Dr. Senckenberg Institute for Neurooncology, University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany.,Frankfurt Cancer Institute (FCI), Frankfurt, Germany
| | - Karl H Plate
- Neurological Institute (Edinger Institute), University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany.,German Cancer Consortium (DKTK) partner site Frankfurt/Mainz, Frankfurt, Germany.,German Cancer Research Centre (DKFZ), Heidelberg, Germany.,Frankfurt Cancer Institute (FCI), Frankfurt, Germany
| | - Oliver Bähr
- Dr. Senckenberg Institute for Neurooncology, University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Elke Hattingen
- Frankfurt Cancer Institute (FCI), Frankfurt, Germany.,Department of Neuroradiology, University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Joachim P Steinbach
- German Cancer Consortium (DKTK) partner site Frankfurt/Mainz, Frankfurt, Germany.,German Cancer Research Centre (DKFZ), Heidelberg, Germany.,Dr. Senckenberg Institute for Neurooncology, University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany.,Frankfurt Cancer Institute (FCI), Frankfurt, Germany
| | - Michel Mittelbronn
- Neurological Institute (Edinger Institute), University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany.,Luxembourg Centre of Neuropathology (LCNP), Luxembourg.,Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg.,National Centre of Pathology (NCP), Laboratoire national de santé (LNS), Luxembourg.,Department of Oncology (DONC), Luxembourg Institute of Health (LIH), Luxembourg
| | - Patrick N Harter
- Neurological Institute (Edinger Institute), University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany.,German Cancer Consortium (DKTK) partner site Frankfurt/Mainz, Frankfurt, Germany.,German Cancer Research Centre (DKFZ), Heidelberg, Germany.,Frankfurt Cancer Institute (FCI), Frankfurt, Germany
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7
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Liu L, Lu JY, Li F, Xing X, Li T, Yang X, Shen X. IDH1 fine-tunes cap-dependent translation initiation. J Mol Cell Biol 2020; 11:816-828. [PMID: 31408165 PMCID: PMC6884706 DOI: 10.1093/jmcb/mjz082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 06/02/2019] [Accepted: 06/18/2019] [Indexed: 12/15/2022] Open
Abstract
The metabolic enzyme isocitrate dehydrogenase 1 (IDH1) catalyzes the oxidative decarboxylation of isocitrate to α-ketoglutarate (α-KG). Its mutation often leads to aberrant gene expression in cancer. IDH1 was reported to bind thousands of RNA transcripts in a sequence-dependent manner; yet, the functional significance of this RNA-binding activity remains elusive. Here, we report that IDH1 promotes mRNA translation via direct associations with polysome mRNA and translation machinery. Comprehensive proteomic analysis in embryonic stem cells (ESCs) revealed striking enrichment of ribosomal proteins and translation regulators in IDH1-bound protein interactomes. We performed ribosomal profiling and analyzed mRNA transcripts that are associated with actively translating polysomes. Interestingly, knockout of IDH1 in ESCs led to significant downregulation of polysome-bound mRNA in IDH1 targets and subtle upregulation of ribosome densities at the start codon, indicating inefficient translation initiation upon loss of IDH1. Tethering IDH1 to a luciferase mRNA via the MS2-MBP system promotes luciferase translation, independently of the catalytic activity of IDH1. Intriguingly, IDH1 fails to enhance luciferase translation driven by an internal ribosome entry site. Together, these results reveal an unforeseen role of IDH1 in fine-tuning cap-dependent translation via the initiation step.
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Affiliation(s)
- Lichao Liu
- Tsinghua-Peking Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - J Yuyang Lu
- Tsinghua-Peking Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fajin Li
- MOE Key Laboratory of Bioinformatics, Center for Synthetic & Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xudong Xing
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Tong Li
- Tsinghua-Peking Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xuerui Yang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic & Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaohua Shen
- Tsinghua-Peking Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China
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8
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Urbanovska I, Megova MH, Dwight Z, Kalita O, Uvirova M, Simova J, Tuckova L, Buzrla P, Palecek T, Hajduch M, Dvorackova J, Drabek J. IDH Mutation Analysis in Glioma Patients by CADMA Compared with SNaPshot Assay and two Immunohistochemical Methods. Pathol Oncol Res 2018; 25:971-978. [PMID: 29556922 PMCID: PMC6614140 DOI: 10.1007/s12253-018-0413-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 03/08/2018] [Indexed: 02/02/2023]
Abstract
Mutations in IDH1/2 genes are a marker of good prognosis for glioma patients, associated with low grade gliomas and secondary glioblastomas. Immunohistochemistry and Sanger sequencing are current standards for IDH1/2 genotyping while many other methods exist. The aim of this study was to validate Competitive amplification of differentially melting amplicons (CADMA) PCR for IDH genotyping by comparison with SNaPshot assay and two immunohistochemical methods. In our study, 87 glioma patients (46 from Olomouc and 41 from Ostrava) were analyzed. IDH1/2 mutations in native bioptical samples were analyzed at DNA level by CADMA and SNaPshot while IDH1 mutations in FFPE samples were analyzed at protein level by two IHC methods. CADMA PCR sensitivity for IDH1 was 96.4% and specificity 100% for 86 concluded samples. SNaPshot assay sensitivity was 92.9% and specificity of 100% for 85 concluded samples. IHC in the laboratory no. 2 reached sensitivity 85.7% and specificity 100% for 86 concluded samples. IHC in the laboratory no. 4 reached sensitivity of 96.4% and specificity of 79.7% in 74 concluded samples. Only one IDH2 mutation was found by SNaPshot while CADMA yielded false negative result. In conclusion, CADMA is a valid method for IDH1 p.(R132H) testing with higher sensitivity than SNaPshot assay. Also, molecular genetic methods of IDH1 testing from native samples were more robust than IHC from FFPE.
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Affiliation(s)
- Irena Urbanovska
- CGB Laboratory Inc., Ostrava, Czech Republic.,Department of Biomedical Sciences, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - Magdalena Houdova Megova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Hnevotinska 5, 779 00, Olomouc, Czech Republic
| | - Zachary Dwight
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Ondrej Kalita
- Department of Neurosurgery, University Hospital Olomouc, Olomouc, Czech Republic
| | | | | | - Lucie Tuckova
- Department of Clinical and Molecular Pathology, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Olomouc, Czech Republic
| | - Petr Buzrla
- Institute of Pathology, Faculty of Medicine and University Hospital, University of Ostrava, Syllabova 19, 703 00, Ostrava - Zábřeh, Czech Republic
| | - Tomas Palecek
- Neurosurgery Clinic, University Hospital Ostrava, Ostrava, Czech Republic
| | - Marian Hajduch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Hnevotinska 5, 779 00, Olomouc, Czech Republic
| | - Jana Dvorackova
- Department of Biomedical Sciences, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic. .,Institute of Pathology, Faculty of Medicine and University Hospital, University of Ostrava, Syllabova 19, 703 00, Ostrava - Zábřeh, Czech Republic.
| | - Jiri Drabek
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Hnevotinska 5, 779 00, Olomouc, Czech Republic.
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9
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Ciccarone F, Vegliante R, Di Leo L, Ciriolo MR. The TCA cycle as a bridge between oncometabolism and DNA transactions in cancer. Semin Cancer Biol 2017. [PMID: 28645607 DOI: 10.1016/j.semcancer.2017.06.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cancer cells exploit metabolic rearrangements for sustaining their high proliferation rate and energy demand. The TCA cycle is a central metabolic hub necessary for ATP production and for providing precursors used in many biosynthetic pathways. Thus, dysregulation of the TCA cycle flux is frequently observed in cancer. The identification of mutations in several enzymes of the TCA cycle in human tumours demonstrated a direct connection between this metabolic pathway and cancer occurrence. Moreover, changes in the expression/activity of these enzymes were also shown to promote metabolic adaptation of cancer cells. In this review, the main genetic and non-genetic alterations of TCA cycle in cancer will be described. Particular attention will be given to extrametabolic roles of TCA cycle enzymes and metabolites underlying the regulation of nuclear and mitochondrial DNA transactions.
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Affiliation(s)
- Fabio Ciccarone
- Department of Biology, University of Rome 'Tor Vergata', via della Ricerca Scientifica, 00133, Rome, Italy
| | - Rolando Vegliante
- Department of Biology, University of Rome 'Tor Vergata', via della Ricerca Scientifica, 00133, Rome, Italy
| | - Luca Di Leo
- Department of Biology, University of Rome 'Tor Vergata', via della Ricerca Scientifica, 00133, Rome, Italy
| | - Maria Rosa Ciriolo
- Department of Biology, University of Rome 'Tor Vergata', via della Ricerca Scientifica, 00133, Rome, Italy; IRCCS San Raffaele 'La Pisana', Via di Val Cannuta, 00166, Rome, Italy.
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