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Chen X, Wang L, Yang M, Zhao W, Tu J, Liu B, Yuan X. RUNX transcription factors: biological functions and implications in cancer. Clin Exp Med 2024; 24:50. [PMID: 38430423 PMCID: PMC10908630 DOI: 10.1007/s10238-023-01281-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 11/10/2023] [Indexed: 03/03/2024]
Abstract
Runt-related transcription factors (RUNX) are a family of transcription factors that are essential for normal and malignant hematopoietic processes. Their most widely recognized role in malignancy is to promote the occurrence and development of acute myeloid leukemia. However, it is worth noting that during the last decade, studies of RUNX proteins in solid tumors have made considerable progress, suggesting that these proteins are directly involved in different stages of tumor development, including tumor initiation, progression, and invasion. RUNX proteins also play a role in tumor angiogenesis, the maintenance of tumor cell stemness, and resistance to antitumor drugs. These findings have led to the consideration of RUNX as a tumor biomarker. All RUNX proteins are involved in the occurrence and development of solid tumors, but the role of each RUNX protein in different tumors and the major signaling pathways involved are complicated by tumor heterogeneity and the interacting tumor microenvironment. Understanding how the dysregulation of RUNX in tumors affects normal biological processes is important to elucidate the molecular mechanisms by which RUNX affects malignant tumors.
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Affiliation(s)
- Xinyi Chen
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jie Fang Road 1095, Wuhan, Hubei Province, China
| | - Lu Wang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jie Fang Road 1095, Wuhan, Hubei Province, China
| | - Mu Yang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jie Fang Road 1095, Wuhan, Hubei Province, China
| | - Weiheng Zhao
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jie Fang Road 1095, Wuhan, Hubei Province, China
| | - Jingyao Tu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jie Fang Road 1095, Wuhan, Hubei Province, China.
| | - Bo Liu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jie Fang Road 1095, Wuhan, Hubei Province, China.
| | - Xianglin Yuan
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jie Fang Road 1095, Wuhan, Hubei Province, China.
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Ferreira WAS, Vitiello GAF, da Silva Medina T, de Oliveira EHC. Comprehensive analysis of epigenetics regulation, prognostic and the correlation with immune infiltrates of GPX7 in adult gliomas. Sci Rep 2022; 12:6442. [PMID: 35440701 PMCID: PMC9018725 DOI: 10.1038/s41598-022-10114-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 03/24/2022] [Indexed: 12/15/2022] Open
Abstract
Gliomas are the most commonly occurring malignant brain tumor characterized by an immunosuppressive microenvironment accompanied by profound epigenetic changes, thus influencing the prognosis. Glutathione peroxidase 7 (GPX7) is essential for regulating reactive oxygen species homeostasis under oxidative stress. However, little is known about the function of GPX7 in gliomas. In this study, we hypothesized that GPX7 methylation status could influence biological functions and local immune responses that ultimately impact prognosis in adult gliomas. We conducted an integrated bioinformatics analysis mining GPX7 DNA methylation status, transcriptional and survival data of glioma patients. We discovered that GPX7 was remarkably increased in glioma tissues and cell lines, and was associated with poor prognosis. This upregulation was significantly linked to clinicopathological and molecular features, besides being expressed in a cell cycle-dependent manner. Our results consistently demonstrated that upregulation of GPX7 is tightly modulated by epigenetic processes, which also impacted the overall survival of patients with low-grade gliomas (LGG). Based on the analysis of biological functions, we found that GPX7 might be involved in immune mechanisms involving both innate and adaptive immunity, type I interferon production and regulation of synaptic transmission in LGG, whereas in GBM, it is mainly related to metabolic regulation of mitochondrial dynamics. We also found that GPX7 strongly correlates with immune cell infiltration and diverse immune cell markers, suggesting its role in tumor-specific immune response and in regulating the migration of immune cell types to the tumor microenvironment. Combining these multiple data, we provided the first evidence regarding the epigenetic-mediated regulatory mechanisms underlying GPX7 activation in gliomas. Furthermore, our study brings key insights into the significant effect of GPX7 in modulating both immune molecules and in immune cell infiltration in the microenvironment of gliomas, which might impact the patient outcome, opening up future opportunities to regulate the local immune response.
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Affiliation(s)
- Wallax Augusto Silva Ferreira
- Laboratory of Cytogenomics and Environmental Mutagenesis, Environment Section (SAMAM), Evandro Chagas Institute (IEC), Ananindeua, Brazil.
| | | | - Tiago da Silva Medina
- Translational Immuno-Oncology Group, International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil.,National Institute of Science and Technology in Oncogenomics and Therapeutic Innovation, São Paulo, Brazil
| | - Edivaldo Herculano Correa de Oliveira
- Laboratory of Cytogenomics and Environmental Mutagenesis, Environment Section (SAMAM), Evandro Chagas Institute (IEC), Ananindeua, Brazil.,Institute of Exact and Natural Sciences, Faculty of Natural Sciences, Federal University of Pará (UFPA), Belém, Brazil
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3
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Silencing of Testin expression is a frequent event in spontaneous lymphomas from Trp53-mutant mice. Sci Rep 2020; 10:16255. [PMID: 33004921 PMCID: PMC7530732 DOI: 10.1038/s41598-020-73229-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 09/09/2020] [Indexed: 02/03/2023] Open
Abstract
The tumour suppressor gene, TES, is frequently methylated in many human tumours. Previously, we demonstrated that TES promoter methylation and transcriptional silencing was the most common molecular abnormality detected in childhood acute lymphoblastic leukaemia (ALL). Trp53-mutant mouse models predominantly develop B- and T-cell lymphomas, which are widely considered equivalent to childhood T and B ALL. In this study, we examined expression of Tes transcript and Testin protein in spontaneous tumours obtained from three Trp53-mutant mouse models. Using immunohistochemistry, we report that 47% of lymphomas lacked Testin protein compared to only 7% of non-lymphoid tumours. Further examination of the lymphomas from Trp53-null and Trp53-mΔpro homozygous mutant mice revealed that 63% and 69% respectively of the isolated lymphomas were Testin negative, which is similar to reported rates in childhood T-ALL. Surprisingly, lymphomas from Trp53-Δ122 mice were frequently Testin positive (> 60%), suggesting that the presence of the Trp53-Δ122 protein appeared to mitigate the requirement for Tes silencing in lymphomagenesis. Quantitative RT-PCR results confirmed that this lack of Testin protein was due to Tes transcriptional silencing, although bisulfite sequencing demonstrated that this was not due to promoter methylation. These results are consistent with the Testin protein having lymphoid tumour suppressor activity in both mice and humans.
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Abramczyk H, Brozek-Pluska B, Jarota A, Surmacki J, Imiela A, Kopec M. A look into the use of Raman spectroscopy for brain and breast cancer diagnostics: linear and non-linear optics in cancer research as a gateway to tumor cell identity. Expert Rev Mol Diagn 2020; 20:99-115. [PMID: 32013616 DOI: 10.1080/14737159.2020.1724092] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 01/28/2020] [Indexed: 12/14/2022]
Abstract
Introduction: Currently, intensely developing of linear and non-linear optical methods for cancer detection provides a valuable tool to improve sensitivity and specificity. One of the main reasons for insufficient progress in cancer diagnostics is related to the fact that most cancer types are not only heterogeneous in their genetic composition but also reside in varying microenvironments and interact with different cell types. Until now, no technology has been fully proven for effective detecting of invasive cancer, which infiltrating the extracellular matrix.Areas covered: This review investigates the current status of Raman spectroscopy and Raman imaging for brain and breast cancer diagnostics. Moreover, the review provides a comprehensive overview of the applicability of atomic force microscopy (AFM), linear and non-linear optics in cancer research as a gateway to tumor cell identity.Expert commentary: A combination of linear and non-linear optics, particularly Raman-driven methods, has many additional advantages to identify alterations in cancer cells that are crucial for their proliferation and that distinguish them from normal cells.
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Affiliation(s)
- Halina Abramczyk
- Laboratory of Laser Molecular Spectroscopy, Lodz University of Technology, Lodz, Poland
| | - Beata Brozek-Pluska
- Laboratory of Laser Molecular Spectroscopy, Lodz University of Technology, Lodz, Poland
| | - Arkadiusz Jarota
- Laboratory of Laser Molecular Spectroscopy, Lodz University of Technology, Lodz, Poland
| | - Jakub Surmacki
- Laboratory of Laser Molecular Spectroscopy, Lodz University of Technology, Lodz, Poland
| | - Anna Imiela
- Laboratory of Laser Molecular Spectroscopy, Lodz University of Technology, Lodz, Poland
| | - Monika Kopec
- Laboratory of Laser Molecular Spectroscopy, Lodz University of Technology, Lodz, Poland
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Abstract
Testin is a protein expressed in almost all normal human tissues. It locates in the cytoplasm along stress fibers being recruited to focal adhesions. Together with zyxin and vasodilator stimulated protein it forms complexes with various cytoskeleton proteins such as actin, talin and paxilin. They jointly play significant role in cell motility and adhesion. In addition, their involvement in the cell cycle has been demonstrated. Expression of testin protein level correlates positively with percentage of cells in G1 phase, while overexpression can induce apoptosis and decreased colony forming ability. Decreased testin expression associate with loss by cells epithelial morphology and gain migratory and invasive properties of mesenchymal cells. Latest reports indicate that TES is a tumor suppressor gene which can contribute to cancerogenesis but the mechanism of loss TES gene expression is still unknown. Some authors point out hypermethylation of the CpG island as a main factor, however loss of heterozygosity may also play an important role [4, 5]. The altered expression of testin was found in malignant neoplasm, i.a. ovarian, lung, head and neck squamous cell cancer, breast, endometrial, colorectal, prostate and gastric cancers [1-9]. Testin participate in the processes of tumor growth, angiogenesis, and metastasis [10]. Many researchers stated involvement of testin in tumor progression, what suggest its potential usage in immunotherapy [7, 11]. Understanding the molecular functions of testin may be crucial in development personalized treatment. In the present manuscript up-to-date review of literature can be found.
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Affiliation(s)
- Aneta Popiel
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, Wroclaw, Poland.
- Wroclaw Medical University, Wroclaw, Poland.
| | - Christopher Kobierzycki
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, Wroclaw, Poland
| | - Piotr Dzięgiel
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, Wroclaw, Poland
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Oncosuppressive Role of RUNX3 in Human Astrocytomas. JOURNAL OF ONCOLOGY 2019; 2019:1232434. [PMID: 31467531 PMCID: PMC6699290 DOI: 10.1155/2019/1232434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/30/2019] [Accepted: 06/10/2019] [Indexed: 01/29/2023]
Abstract
Background Gliomas are the most common and aggressive among primary malignant brain tumours with significant inter- and intratumour heterogeneity in histology, molecular profile, and patient outcome. However, molecular targets that could provide reliable diagnostic and prognostic information on this type of cancer are currently unknown. Recent studies show that certain phenotypes of gliomas such as malignancy, resistance to therapy, and relapses are associated with the epigenetic alterations of tumour-specific genes. Runt-related transcription factor 3 (RUNX3) is feasible tumour suppressor gene since its inactivation was shown to be related to carcinogenesis. Aim The aim of the study was to elucidate RUNX3 changes in different regulation levels of molecular biology starting from epigenetics to function in particular cases of astrocytic origin tumours of different grade evaluating significance of molecular changes of RUNX3 for patient clinical characteristics as well as evaluate RUNX3 reexpression effect to GBM cells. Methods The methylation status and protein expression levels of RUNX3 were measured by methylation-specific PCR and Western blot in 136 and 72 different malignancy grade glioma tissues, respectively. Lipotransfection and MTT were applied for proliferation assessment in U87-MG cells. Results We found that RUNX3 was highly methylated and downregulated in GBM. RUNX3 promoter methylation was detected in 69.4% of GBM (n=49) as compared to 0 to 17.2% in I-III grade astrocytomas (n=87). Weighty lower RUNX3 protein level was observed in GMB specimens compared to grade II-III astrocytomas. Correlation test revealed a weak but significant link among Runx3 methylation and protein level. Kaplan-Meier analysis showed that increased RUNX3 methylation and low protein level were both associated with shorter patient survival (p<0.05). Reexpression of RUNX3 in U87-MG cells significantly reduced glioma cell viability compared to control transfection. Conclusions The results demonstrate that RUNX3 gene methylation and protein expression downregulation are glioma malignancy dependent and contribute to tumour progression.
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Wang DD, Chen YB, Zhao JJ, Zhang XF, Zhu GC, Weng DS, Pan K, Lv L, Pan QZ, Jiang SS, Wang LL, Xia JC. TES functions as a Mena-dependent tumor suppressor in gastric cancer carcinogenesis and metastasis. Cancer Commun (Lond) 2019; 39:3. [PMID: 30728082 PMCID: PMC6366075 DOI: 10.1186/s40880-019-0347-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 01/23/2019] [Indexed: 12/15/2022] Open
Abstract
Background In our previous study, we identified a candidate tumor suppressor gene, testin LIM domain protein (TES), in primary gastric cancer (GC). TES contains three LIM domains, which are specific interacting regions for the cell adhesion and cytoskeleton regulatory proteins. Mena is a known cytoskeleton regulator that regulates the assembly of actin filaments and modulates cell adhesion and motility by interacting with Lamellipodin (Lpd). Therefore, we hypothesized that TES plays a role as tumor suppressor in GC through interacting with Mena. This study aimed to investigate the tumor suppressive functions of TES in GC. Methods We explored the tumor suppressive effect of TES in GC by in vitro cell proliferation assay, colony formation assay, cell cycle analysis, Transwell assays, and in vivo tumorigenicity and metastasis assays. The interaction of TES and Mena was investigated through immunoprecipitation-based mass spectrometry. We also analyzed the expression of TES and Mena in 172 GC specimens using immunohistochemistry and investigated the clinicopathological and prognostic significance of TES and Mena in GC. Results TES suppressed GC cell proliferation and colony formation, induced cell cycle arrest, and inhibited tumorigenicity in vitro. Additionally, it inhibited GC cell migration and invasion in vitro and suppressed metastasis in vivo. TES interacted with Mena, and inhibited the interaction of Mena with Lpd. Transwell assays suggested that TES suppressed migration and invasion of GC cells in a Mena-dependent fashion. In GC patients with high Mena expression, the expression of TES was associated with tumor infiltration (P = 0.005), lymph node metastasis (P = 0.003), TNM stage (P = 0.003), and prognosis (P = 0.010). However, no significant association was observed in GC patients with low Mena expression. Conclusions We believe that TES functions as a Mena-dependent tumor suppressor. TES represents a valuable prognostic marker and potential target for GC treatment. Electronic supplementary material The online version of this article (10.1186/s40880-019-0347-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dan-Dan Wang
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, Guangdong, P.R. China.,Department of Biotherapy, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, Guangdong, P.R. China.,Shandong Medicinal Biotechnology Centre, Back and Neck Pain Hospital, Shandong Academy of Medical Sciences, Jinan, 250062, Shandong, P.R. China
| | - Yi-Bing Chen
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, Guangdong, P.R. China.,Department of Biotherapy, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, Guangdong, P.R. China.,Genetic and Prenatal Diagnosis Center, Department of Gynecology and Obstetrics, First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Jing-Jing Zhao
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, Guangdong, P.R. China.,Department of Biotherapy, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, Guangdong, P.R. China
| | - Xiao-Fei Zhang
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, Guangdong, P.R. China.,Department of Biotherapy, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, Guangdong, P.R. China
| | - Guang-Chao Zhu
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, Guangdong, P.R. China.,Department of Biotherapy, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, Guangdong, P.R. China
| | - De-Sheng Weng
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, Guangdong, P.R. China.,Department of Biotherapy, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, Guangdong, P.R. China
| | - Ke Pan
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, Guangdong, P.R. China.,Department of Biotherapy, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, Guangdong, P.R. China
| | - Lin Lv
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, Guangdong, P.R. China.,Department of Biotherapy, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, Guangdong, P.R. China
| | - Qiu-Zhong Pan
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, Guangdong, P.R. China.,Department of Biotherapy, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, Guangdong, P.R. China
| | - Shan-Shan Jiang
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, Guangdong, P.R. China.,Department of Biotherapy, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, Guangdong, P.R. China
| | - Lei-Lei Wang
- Key Laboratory for Applied Microbiology of Shandong Province, Ecology Institute of Shandong Academy of Sciences, Jinan, 250014, Shandong, P.R. China
| | - Jian-Chuan Xia
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, Guangdong, P.R. China. .,Department of Biotherapy, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, Guangdong, P.R. China.
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Deshmukh RS, Sharma S, Das S. Cyclin F-Dependent Degradation of RBPJ Inhibits IDH1 R132H-Mediated Tumorigenesis. Cancer Res 2018; 78:6386-6398. [PMID: 30254149 DOI: 10.1158/0008-5472.can-18-1772] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/22/2018] [Accepted: 09/18/2018] [Indexed: 11/16/2022]
Abstract
Cyclin F is a substrate recognition subunit of Skp1-Cul1-F-box protein (SCF) E3 ubiquitin ligase complex. Although there have been reports describing the role of cyclin F in the genotoxic stress response, its function under conditions of altered metabolic homeostasis remain unexplored. Here we report that cyclin F is induced upon metabolic stress in a FOXO1-dependent manner. Under metabolic stress conditions, cyclin F mediated polyubiquitylation of RBPJ at Lys315, leading to its proteasomal degradation. RBPJ regulated the expression of IDH1, which is often mutated to an oncogenic form IDH1R132H in cancers. Thus, metabolic stress-induced cyclin F attenuated the oncogenic functions of IDH1R132H in an RBPJ-dependent manner. Studies in mouse tumor models indicated that abrogation of cyclin F expression facilitates IDH1R132H-mediated tumorigenesis and metastasis. In addition, increased IDH1R132H levels correlated with reduced cyclin F levels in increasing grades of glioma. These findings highlight a novel aspect of cyclin F functions in inhibiting tumorigenesis and provide mechanistic insights into regulation of IDH1R132H Significance: These findings reveal mechanistic insights into the key role of the cyclin F-RBPJ axis in response to metabolic stress in cancer cells. Cancer Res; 78(22); 6386-98. ©2018 AACR.
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Affiliation(s)
- Ruhi S Deshmukh
- Molecular Oncology Laboratory, National Institute of Immunology, New Delhi, India
| | - Shalakha Sharma
- Molecular Oncology Laboratory, National Institute of Immunology, New Delhi, India
| | - Sanjeev Das
- Molecular Oncology Laboratory, National Institute of Immunology, New Delhi, India.
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Tuncel G, Kalkan R. Receptor tyrosine kinase-Ras-PI 3 kinase-Akt signaling network in glioblastoma multiforme. Med Oncol 2018; 35:122. [PMID: 30078108 DOI: 10.1007/s12032-018-1185-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 07/31/2018] [Indexed: 02/06/2023]
Abstract
Glioblastoma multiforme (GBM) is the most malignant form of the brain tumors and shows different genetic and epigenetic abnormalities. Gene amplification, genetic instability, disruption of apoptotic pathways, deregulated oncogene expression, invasive phenotypical changes, abnormal angiogenesis, and epigenetic changes have all been described in GBMs. These abnormalities indicate that a number of different signaling pathways are deregulated in GBM. Increasing number of studies provide a better understanding of the tumor biology, genetic, and epigenetic background of the GBM. Also, current research provides us useful approaches in designing novel therapies for GBM. In this review, we summarize the receptor tyrosine kinase-Ras-PI 3 kinase-Akt signaling network, focusing on the potential molecular targets for anti-signaling molecular therapies in this pathway.
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Affiliation(s)
- Gulten Tuncel
- Department of Medical Genetics, Faculty of Medicine, Near East University, Near East Boulevard, Nicosia, 99138, Cyprus
| | - Rasime Kalkan
- Department of Medical Genetics, Faculty of Medicine, Near East University, Near East Boulevard, Nicosia, 99138, Cyprus.
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Molina JR, Sun Y, Protopopova M, Gera S, Bandi M, Bristow C, McAfoos T, Morlacchi P, Ackroyd J, Agip ANA, Al-Atrash G, Asara J, Bardenhagen J, Carrillo CC, Carroll C, Chang E, Ciurea S, Cross JB, Czako B, Deem A, Daver N, de Groot JF, Dong JW, Feng N, Gao G, Gay J, Do MG, Greer J, Giuliani V, Han J, Han L, Henry VK, Hirst J, Huang S, Jiang Y, Kang Z, Khor T, Konoplev S, Lin YH, Liu G, Lodi A, Lofton T, Ma H, Mahendra M, Matre P, Mullinax R, Peoples M, Petrocchi A, Rodriguez-Canale J, Serreli R, Shi T, Smith M, Tabe Y, Theroff J, Tiziani S, Xu Q, Zhang Q, Muller F, DePinho RA, Toniatti C, Draetta GF, Heffernan TP, Konopleva M, Jones P, Di Francesco ME, Marszalek JR. An inhibitor of oxidative phosphorylation exploits cancer vulnerability. Nat Med 2018; 24:1036-1046. [PMID: 29892070 DOI: 10.1038/s41591-018-0052-4] [Citation(s) in RCA: 566] [Impact Index Per Article: 94.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/27/2018] [Indexed: 12/19/2022]
Abstract
Metabolic reprograming is an emerging hallmark of tumor biology and an actively pursued opportunity in discovery of oncology drugs. Extensive efforts have focused on therapeutic targeting of glycolysis, whereas drugging mitochondrial oxidative phosphorylation (OXPHOS) has remained largely unexplored, partly owing to an incomplete understanding of tumor contexts in which OXPHOS is essential. Here, we report the discovery of IACS-010759, a clinical-grade small-molecule inhibitor of complex I of the mitochondrial electron transport chain. Treatment with IACS-010759 robustly inhibited proliferation and induced apoptosis in models of brain cancer and acute myeloid leukemia (AML) reliant on OXPHOS, likely owing to a combination of energy depletion and reduced aspartate production that leads to impaired nucleotide biosynthesis. In models of brain cancer and AML, tumor growth was potently inhibited in vivo following IACS-010759 treatment at well-tolerated doses. IACS-010759 is currently being evaluated in phase 1 clinical trials in relapsed/refractory AML and solid tumors.
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Affiliation(s)
- Jennifer R Molina
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuting Sun
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marina Protopopova
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sonal Gera
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Madhavi Bandi
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher Bristow
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Timothy McAfoos
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pietro Morlacchi
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Agilent Technologies Inc., Lexington, MA, USA
| | - Jeffrey Ackroyd
- Department of Cancer Imaging Systems, University of Texas MD Cancer Center, Houston, TX, USA
| | - Ahmed-Noor A Agip
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge, UK
| | - Gheath Al-Atrash
- Department of Stem Cell Transplantation and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John Asara
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jennifer Bardenhagen
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Caroline C Carrillo
- Department of Neuro-Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher Carroll
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Edward Chang
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stefan Ciurea
- Department of Stem Cell Transplantation and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason B Cross
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Barbara Czako
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Angela Deem
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Naval Daver
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John Frederick de Groot
- Department of Neuro-Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jian-Wen Dong
- Department of Neuro-Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ningping Feng
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Guang Gao
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason Gay
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mary Geck Do
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer Greer
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Virginia Giuliani
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jing Han
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lina Han
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Verlene K Henry
- Department of Neuro-Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Judy Hirst
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge, UK
| | - Sha Huang
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yongying Jiang
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhijun Kang
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tin Khor
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sergej Konoplev
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yu-Hsi Lin
- Department of Cancer Imaging Systems, University of Texas MD Cancer Center, Houston, TX, USA
| | - Gang Liu
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alessia Lodi
- Department of Nutritional Sciences, University of Texas at Austin, Austin, TX, USA
| | - Timothy Lofton
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Helen Ma
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mikhila Mahendra
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Polina Matre
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert Mullinax
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Peoples
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alessia Petrocchi
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jaime Rodriguez-Canale
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Riccardo Serreli
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge, UK
| | - Thomas Shi
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Melinda Smith
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yoko Tabe
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Next Generation Hematology Laboratory Medicine, Department of Laboratory Medicine, Juntendo University School of Medicine, Tokyo, Japan
| | - Jay Theroff
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stefano Tiziani
- Department of Nutritional Sciences, University of Texas at Austin, Austin, TX, USA
| | - Quanyun Xu
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Qi Zhang
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Florian Muller
- Department of Cancer Imaging Systems, University of Texas MD Cancer Center, Houston, TX, USA
| | - Ronald A DePinho
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carlo Toniatti
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Giulio F Draetta
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Timothy P Heffernan
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marina Konopleva
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Philip Jones
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - M Emilia Di Francesco
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joseph R Marszalek
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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11
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RUNX3 inhibits glioma survival and invasion via suppression of the β-catenin/TCF-4 signaling pathway. J Neurooncol 2018; 140:15-26. [PMID: 29916101 DOI: 10.1007/s11060-018-2927-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/09/2018] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Runt-related transcription factor 3 (RUNX3) exerts a tumor suppressor gene associated with gastric and other cancers, including glioma. However, how its anti-tumor mechanism in functions glioma is unclear. METHODS We assayed expression of RUNX3 with a tissue microarray (TMA), frozen cancer tissues and malignant glioma cell lines using immunohistochemistry, qRT-PCR and Western bolt analysis. Cell proliferation, invasion, cell cycle distribution and apoptosis were also examined to confirm the effect of RUNX3 medicated malignant phenotype. TOP/FOP experiment was used to detect the β-catenin/Tcf-4 transcription activity by RUNX3. RESULTS Enforced RUNX3 expression inhibited proliferation and invasion, induced cell cycle arrest and promoted apoptosis in vitro and in vivo, Bim siRNA partically reversed the effect of RUNX3-induced apoptosis in LN229 and U87 cells, suggesting a dependent role of Bim-caspase pathway. Moreover, Mechanism investigations revealed that restoration of RUNX3 suppressed β-catenin/Tcf-4 transcription activity. CONCLUSIONS RUNX3 plays a pivotal role in glioma initiation and progression as a tumor suppressor via attenuation of Wnt signaling, highlighting it as a potential therapeutic target for glioma.
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12
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Shen S, Yu H, Liu X, Liu Y, Zheng J, Wang P, Gong W, Chen J, Zhao L, Xue Y. PIWIL1/piRNA-DQ593109 Regulates the Permeability of the Blood-Tumor Barrier via the MEG3/miR-330-5p/RUNX3 Axis. MOLECULAR THERAPY-NUCLEIC ACIDS 2017; 10:412-425. [PMID: 29499952 PMCID: PMC5862138 DOI: 10.1016/j.omtn.2017.12.020] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 12/27/2017] [Accepted: 12/27/2017] [Indexed: 02/06/2023]
Abstract
The blood-tumor barrier (BTB) restricts the efficient delivery of anti-glioma drugs to cranial glioma tissues. Increased BTB permeability may allow greater delivery of the therapeutic agents. Increasing evidence has revealed that PIWI proteins and PIWI-interacting RNAs (piRNAs) play an important role in tumor progression. However, whether PIWI proteins and piRNAs regulate BTB permeability remains unclear. In the present study, we demonstrated that the PIWIL1/piRNA-DQ593109 (piR-DQ593109) complex was the predominant regulator of BTB permeability. Briefly, PIWIL1 was upregulated in glioma endothelial cells (GECs). Furthermore, piR-DQ593109 was also overexpressed in GECs, as revealed via a piRNA microarray. Downregulation of PIWIL1 or piR-DQ593109 increased the permeability of the BTB. Moreover, PIWIL1 and piR-DQ593109, which formed a piRNA-induced silencing complex, degraded the long non-coding RNA maternally expressed 3 (MEG3) in a sequenced-dependent manner. Furthermore, restoring MEG3 released post-transcriptional inhibition of Runt related transcription factor 3 (RUNX3) by sponging miR-330-5p. In addition, RUNX3 bounded to the promoter regions and reduced the promoter activities of ZO-1, occludin, and claudin-5, which significantly impaired the expression levels of ZO-1, occludin, and claudin-5. In conclusion, downregulating PIWIL1 and piR-DQ593109 increased BTB permeability through the MEG3/miR-330-5p/RUNX3 axis. These data may provide insight into glioma treatment.
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Affiliation(s)
- Shuyuan Shen
- Department of Neurobiology, College of Basic Medicine, China Medical University, Shenyang 110122, People's Republic of China; Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang 110122, People's Republic of China; Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, People's Republic of China
| | - Hai Yu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, People's Republic of China; Liaoning Research Center for Clinical Medicine in Nervous System Disease, Shenyang 110004, People's Republic of China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, People's Republic of China
| | - Xiaobai Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, People's Republic of China; Liaoning Research Center for Clinical Medicine in Nervous System Disease, Shenyang 110004, People's Republic of China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, People's Republic of China
| | - Yunhui Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, People's Republic of China; Liaoning Research Center for Clinical Medicine in Nervous System Disease, Shenyang 110004, People's Republic of China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, People's Republic of China
| | - Jian Zheng
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, People's Republic of China; Liaoning Research Center for Clinical Medicine in Nervous System Disease, Shenyang 110004, People's Republic of China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, People's Republic of China
| | - Ping Wang
- Department of Neurobiology, College of Basic Medicine, China Medical University, Shenyang 110122, People's Republic of China; Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang 110122, People's Republic of China; Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, People's Republic of China
| | - Wei Gong
- Department of Neurobiology, College of Basic Medicine, China Medical University, Shenyang 110122, People's Republic of China; Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang 110122, People's Republic of China; Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, People's Republic of China
| | - Jiajia Chen
- Department of Neurobiology, College of Basic Medicine, China Medical University, Shenyang 110122, People's Republic of China; Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang 110122, People's Republic of China; Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, People's Republic of China
| | - Lini Zhao
- Department of Neurobiology, College of Basic Medicine, China Medical University, Shenyang 110122, People's Republic of China; Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang 110122, People's Republic of China; Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, People's Republic of China
| | - Yixue Xue
- Department of Neurobiology, College of Basic Medicine, China Medical University, Shenyang 110122, People's Republic of China; Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang 110122, People's Republic of China; Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, People's Republic of China.
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13
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Bo L, Wei B, Wang Z, Kong D, Gao Z, Miao Z. Identification of key genes in glioma CpG island methylator phenotype via network analysis of gene expression data. Mol Med Rep 2017; 16:9503-9511. [PMID: 29152649 PMCID: PMC5780009 DOI: 10.3892/mmr.2017.7834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 08/16/2017] [Indexed: 12/13/2022] Open
Abstract
Gene expression data were analysed using bioinformatic tools to demonstrate molecular mechanisms underlying the glioma CpG island methylator phenotype (CIMP). A gene expression data set (accession no. GSE30336) was downloaded from Gene Expression Omnibus, including 36 CIMP+ and 16 CIMP- glioma samples. Differential analysis was performed for CIMP+ vs. CIMP‑ samples using the limma package in R. Functional enrichment analysis was subsequently conducted for differentially expressed genes (DEGs) using Database for Annotation, Visualization and Integration Discovery. Protein‑protein interaction (PPI) networks were constructed for upregulated and downregulated genes with information from STRING. MicroRNAs (miRNAs) targeting DEGs were also predicted using WebGestalt. A total of 439 DEGs were identified, including 214 upregulated and 198 downregulated genes. The upregulated genes were involved in extracellular matrix organisation, defence and immune response, collagen fibril organisation and regulation of cell motion and the downregulated genes in cell adhesion, sensory organ development, regulation of system process, neuron differentiation and membrane organisation. A PPI network containing 134 nodes and 314 edges was constructed from the upregulated genes, whereas a PPI network consisting of 85 nodes and 80 edges was obtained from the downregulated genes. miRNAs regulating upregulated and downregulated genes were predicted, including miRNA‑124a and miRNA‑34a. Numerous key genes associated with glioma CIMP were identified in the present study. These findings may advance the understanding of glioma and facilitate the development of appropriate therapies.
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Affiliation(s)
- Lijuan Bo
- Department of Infections, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Bo Wei
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Zhanfeng Wang
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Daliang Kong
- Department of Orthopaedics, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Zheng Gao
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Zhuang Miao
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
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14
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Sun J, Jia Z, Li B, Zhang A, Wang G, Pu P, Chen Z, Wang Z, Yang W. MiR-19 regulates the proliferation and invasion of glioma by RUNX3 via β-catenin/Tcf-4 signaling. Oncotarget 2017; 8:110785-110796. [PMID: 29340016 PMCID: PMC5762284 DOI: 10.18632/oncotarget.22720] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 10/28/2017] [Indexed: 12/20/2022] Open
Abstract
Accumulating data demonstrates that the network dysregulation of microRNA-medicated target genes is involved in glioma. We have previously found miR-19a/b overexpression in glioma cell lines and specimens with various tumour grades. However, there was no report on the function and regulatory mechanism of miR-19a/b in glioma. In this study, based on our previous research data, we first determine the inverse relationship between miR-19 (miR-19a and miR-19b) and RUNX3 which is also identified the reduced expression in tumour tissues by real-time PCR and IHC. Luciferase reporter assay and western blot analysis revealed that RUNX3 was a direct target of miR-19. Down-regulation of miR-19 dramatically inhibited proliferation, invasion and induced the cell cycle G1 arrest and apoptosis, at least partly via the up-regulation of RUNX3. Furthermore, Mechanistic investigation indicated that knockdown of miR-19 repressed the β-catenin/TCF4 transcription activity. In conclusion, our study validates a pathogenetic role of miR-19 in glioma and establishes a potentially regulatory and signaling involving miR-19 /RUNX3/β-catenin, also suggesting miR-19 may be a candidate therapeutic target in glioma.
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Affiliation(s)
- Jikui Sun
- Department of Neurosurgery, Affiliated Hospital of Taishan Medical University, Life Science Research Center of Taishan Medical University, Taian, 271000, P.R. China
| | - Zhifan Jia
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin Neurological Institute, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin, 300052, P.R. China
| | - Banban Li
- Department of Hematopathology, Affiliated Taishan Hospital of Taishan Medical University, Taian, 271000, P.R. China
| | - Anling Zhang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin Neurological Institute, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin, 300052, P.R. China
| | - Guangxiu Wang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin Neurological Institute, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin, 300052, P.R. China
| | - Peiyu Pu
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin Neurological Institute, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin, 300052, P.R. China
| | - Zhijuan Chen
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin Neurological Institute, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin, 300052, P.R. China
| | - Zengguang Wang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin Neurological Institute, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin, 300052, P.R. China
| | - Weidong Yang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin Neurological Institute, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin, 300052, P.R. China
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15
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Ning T, Cui H, Sun F, Zou J. Systemic analysis of genome-wide expression profiles identified potential therapeutic targets of demethylation drugs for glioblastoma. Gene 2017; 627:387-392. [PMID: 28669930 DOI: 10.1016/j.gene.2017.06.052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 06/26/2017] [Accepted: 06/28/2017] [Indexed: 12/31/2022]
Abstract
Glioblastoma represents one of the most aggressive malignant brain tumors with high morbidity and motility. Demethylation drugs have been developed for its treatment with little efficacy has been observed. The purpose of this study was to screen therapeutic targets of demethylation drugs or bioactive molecules for glioblastoma through systemic bioinformatics analysis. We firstly downloaded genome-wide expression profiles from the Gene Expression Omnibus (GEO) and conducted the primary analysis through R software, mainly including preprocessing of raw microarray data, transformation between probe ID and gene symbol and identification of differential expression genes (DEGs). Secondly, functional enrichment analysis was conducted via the Database for Annotation, Visualization and Integrated Discovery (DAVID) to explore biological processes involved in the development of glioblastoma. Thirdly, we constructed protein-protein interaction (PPI) network of interested genes and conducted cross analysis for multi datasets to obtain potential therapeutic targets for glioblastoma. Finally, we further confirmed the therapeutic targets through real-time RT-PCR. As a result, biological processes that related to cancer development, amino metabolism, immune response and etc. were found to be significantly enriched in genes that differential expression in glioblastoma and regulated by 5'aza-dC. Besides, network and cross analysis identified ACAT2, UFC1 and CYB5R1 as novel therapeutic targets of demethylation drugs which also confirmed by real time RT-PCR. In conclusions, our study identified several biological processes and genes that involved in the development of glioblastoma and regulated by 5'aza-dC, which would be helpful for the treatment of glioblastoma.
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Affiliation(s)
- Tongbo Ning
- Department of Neurosurgery, Weihai Central Hospital, Shandong, China
| | - Hao Cui
- Department of Neurosurgery, Weihai Central Hospital, Shandong, China
| | - Feng Sun
- Department of Neurosurgery, Weihai Central Hospital, Shandong, China
| | - Jidian Zou
- Department of Neurosurgery, Weihai Central Hospital, Shandong, China.
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16
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Yang G, Fu Y, Zhang L, Lu X, Li Q. miR106b regulates retinoblastoma Y79 cells through Runx3. Oncol Rep 2017; 38:3039-3043. [PMID: 28901461 DOI: 10.3892/or.2017.5931] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 07/21/2017] [Indexed: 11/06/2022] Open
Abstract
MicroRNAs are increasingly recognized as important regulators of cancer. The aim of the present study was to investigate the role of miR-106b in the regulation of Y79 retinoblastoma. Y79 cells were transfected with antisense oligonucleotides (ASO) against miR-106b (ASO-miR-106b) or ASO-control. After transfection, the levels of miR-106b were monitored with real-time PCR (RT-PCR). The effects of ASO-miR-106b transfection on cell viability was evaluated by Cell Counting Kit-8 (CCK-8) analysis at 24, 48 and 72 h after transfection. Subsequently, the cells were stained with Annexin V-FITC and propidium iodide (PI) and subjected to flow cytometry to assess cell apoptosis. Transwell assay was used to analyze cell migration. Changes in Runt-related transcription factor 3 (Runx3) mRNA and proteins levels were also evaluated. miR-106b was downregulated by ASO-miR-106b at 48 and 72 h after transfection, accompanied by a decrease in cell viability and proliferation, as well as an increase in cell apoptosis. Transwell analysis indicated that cells treated with ASO-miR-106b exhibited significantly lower cell migratory abilities. The mRNA and protein level of Runx3 were upregulated after transfection. These results demonstrated that suppression of miR-106b inhibited Y79 cell proliferation and migration. The upregulation of Runx3 after miR-106b suppression ascertained that Runx3 is a tumor-suppressor in retinoblastoma and is a target of miR-106b.
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Affiliation(s)
- Ge Yang
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Yang Fu
- Department of General Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Luxi Zhang
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Xiaoyan Lu
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Qiuming Li
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
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17
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Wang JW, Stifani S. Roles of Runx Genes in Nervous System Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 962:103-116. [PMID: 28299654 DOI: 10.1007/978-981-10-3233-2_8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Runt-related (Runx) transcription factors play essential roles during development and adult tissue homeostasis and are responsible for several human diseases. They regulate a variety of biological mechanisms in numerous cell lineages. Recent years have seen significant progress in our understanding of the functions performed by Runx proteins in the developing and postnatal mammalian nervous system. In both central and peripheral nervous systems, Runx1 and Runx3 display remarkably specific expression in mostly non-overlapping groups of postmitotic neurons. In the central nervous system, Runx1 is involved in the development of selected motor neurons controlling neural circuits mediating vital functions such as chewing, swallowing, breathing, and locomotion. In the peripheral nervous system, Runx1 and Runx3 play essential roles during the development of sensory neurons involved in circuits mediating pain, itch, thermal sensation and sense of relative position. Runx1 and Runx3 orchestrate complex gene expression programs controlling neuronal subtype specification and axonal connectivity. Runx1 is also important in the olfactory system, where it regulates the progenitor-to-neuron transition in undifferentiated neural progenitor cells in the olfactory epithelium as well as the proliferation and developmental maturation of specific glial cells termed olfactory ensheathing cells. Moreover, upregulated Runx expression is associated with brain injury and disease. Increasing knowledge of the functions of Runx proteins in the developing and postnatal nervous system is therefore expected to improve our understanding of nervous system development, homeostasis and disease.
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Affiliation(s)
- Jae Woong Wang
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, QC, H3A2B4, Canada
| | - Stefano Stifani
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, QC, H3A2B4, Canada.
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18
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Wang M, Wang Q, Peng WJ, Hu JF, Wang ZY, Liu H, Huang LN. Testin is a tumor suppressor in non-small cell lung cancer. Oncol Rep 2016; 37:1027-1035. [PMID: 28000866 DOI: 10.3892/or.2016.5316] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 07/14/2016] [Indexed: 11/05/2022] Open
Abstract
The Testin gene was previously identified in the fragile chromosomal region FRA7G at 7q31.2. It has been implicated in several types of cancers including prostate, ovarian, breast and gastric cancer. In the present study, we investigated the function of the candidate tumor-suppressor Testin gene in non-small cell lung cancer (NSCLC). In NSCLC cell lines, we observed lower expression of Testin compared to that noted in normal human bronchial epithelial cells. MTT assays, flow cytometry, clonogenic assay and invasion assay showed that the overexpression of the Testin gene inhibited cancer cell proliferation, invasion and colony formation. In tumor xenograft models, Testin markedly inhibited lung cancer cell xenograft formation and growth in athymic nude mice. Taken together, these data suggest that Testin plays an important role in the development and progression of NSCLC. Testin may be an effective novel target in NSCLC prevention and treatment.
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Affiliation(s)
- Ming Wang
- Department of Respiratory and Critical Care Medicine, Anhui Provincial Key Laboratory of Clinical Basic Research on Respiratory Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Qian Wang
- Department of Respiration, The People's Hospital of Lingbi, Suzhou, Anhui 234000, P.R. China
| | - Wen-Jia Peng
- Department of Epidemiology and Health Statistics, Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Jun-Feng Hu
- Department of Respiratory and Critical Care Medicine, Anhui Provincial Key Laboratory of Clinical Basic Research on Respiratory Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Zu-Yi Wang
- Department of Cardiothoracic Surgery of the First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Hao Liu
- Department of Pharmacy, Engineering Technology Research Center of Biochemical Pharmaceuticals, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Li-Nian Huang
- Department of Respiratory and Critical Care Medicine, Anhui Provincial Key Laboratory of Clinical Basic Research on Respiratory Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
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Ferreira WAS, Pinheiro DDR, Costa Junior CAD, Rodrigues-Antunes S, Araújo MD, Leão Barros MB, Teixeira ACDS, Faro TAS, Burbano RR, Oliveira EHCD, Harada ML, Borges BDN. An update on the epigenetics of glioblastomas. Epigenomics 2016; 8:1289-305. [PMID: 27585647 DOI: 10.2217/epi-2016-0040] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Glioblastomas, also known as glioblastoma multiforme (GBM), are the most aggressive and malignant type of primary brain tumor in adults, exhibiting notable variability at the histopathological, genetic and epigenetic levels. Recently, epigenetic alterations have emerged as a common hallmark of many tumors, including GBM. Considering that a deeper understanding of the epigenetic modifications that occur in GBM may increase the knowledge regarding the tumorigenesis, progression and recurrence of this disease, in this review we discuss the recent major advances in GBM epigenetics research involving histone modification, glioblastoma stem cells, DNA methylation, noncoding RNAs expression, including their main alterations and the use of epigenetic therapy as a valid option for GBM treatment.
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Affiliation(s)
- Wallax Augusto Silva Ferreira
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Danilo do Rosário Pinheiro
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Carlos Antonio da Costa Junior
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Symara Rodrigues-Antunes
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Mariana Diniz Araújo
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Mariceli Baia Leão Barros
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Adriana Corrêa de Souza Teixeira
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Thamirys Aline Silva Faro
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | | | | | - Maria Lúcia Harada
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Bárbara do Nascimento Borges
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
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Steponaitis G, Kazlauskas A, Skiriute D, Valiulyte I, Skauminas K, Tamasauskas A, Vaitkiene P. Testin ( TES) as a candidate tumour suppressor and prognostic marker in human astrocytoma. Oncol Lett 2016; 12:3305-3311. [PMID: 27899997 PMCID: PMC5103931 DOI: 10.3892/ol.2016.5077] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 07/22/2016] [Indexed: 01/01/2023] Open
Abstract
Astrocytomas are one of the most common brain tumours; however, the current methods used to characterize these tumours are inadequate. The establishment of molecular markers may identify variables required to improve tumour characterization and subtyping, and may aid to specify targets for improved treatment with essential prognostic value for patient survival. One such candidate is testin (TES), which was reported to have prognostic value for glioblastoma patients. However, the role of TES protein in gliomagenesis is currently unknown. In the present study, the methylation status of the TES promoter was investigated in post-operative astrocytoma tumours of different malignancy grade, and its association with the survival of astrocytoma patients was evaluated. In addition, the expression of TES protein was investigated in the same set of astrocytoma tumours tissue, and the association of protein expression with glioma patients survival was evaluated. The methylation status of TES was assessed by methylation-specific polymerase chain reaction in 138 different grade astrocytoma samples. Western blot analysis was used to characterize the expression pattern of TES in 86 different grade astrocytoma specimens: 13 of pathological grade I, 31 of pathological grade II, 17 of pathological grade III and 25 of pathological grade IV (glioblastoma). Statistical analyses were conducted to investigate the association between tumour molecular pattern, patient clinical variables and overall survival. The methylation analysis of the TES promoter exhibited a distinct profile between astrocytomas of different malignancy grade (P<0.001). Furthermore, gene promoter methylation was significantly associated with patients' age, survival and pathological grade (P<0.001). The protein expression level of TES was significantly lower in glioblastoma (grade IV astrocytoma) than in lower grade (II–III) astrocytoma tissue (P=0.028 and P=0.04, respectively). Additionally, short overall survival of patients was markedly associated with low TES protein expression (P=0.007). However, no association between TES methylation and TES protein expression was noticed. The present study demonstrated that decreased expression of TES may be important in tumour progression and prognosis in human astrocytomas. TES may be a useful marker for predicting the clinical outcome of astrocytoma patients.
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Affiliation(s)
- Giedrius Steponaitis
- Laboratory of Neuro-Oncology and Genetics, Neuroscience Institute, Lithuanian University of Health Sciences, LT-50009 Kaunas, Lithuania
| | - Arunas Kazlauskas
- Laboratory of Neuro-Oncology and Genetics, Neuroscience Institute, Lithuanian University of Health Sciences, LT-50009 Kaunas, Lithuania
| | - Daina Skiriute
- Laboratory of Neuro-Oncology and Genetics, Neuroscience Institute, Lithuanian University of Health Sciences, LT-50009 Kaunas, Lithuania
| | - Indre Valiulyte
- Laboratory of Neuro-Oncology and Genetics, Neuroscience Institute, Lithuanian University of Health Sciences, LT-50009 Kaunas, Lithuania
| | - Kestutis Skauminas
- Laboratory of Neuro-Oncology and Genetics, Neuroscience Institute, Lithuanian University of Health Sciences, LT-50009 Kaunas, Lithuania
| | - Arimantas Tamasauskas
- Laboratory of Neuro-Oncology and Genetics, Neuroscience Institute, Lithuanian University of Health Sciences, LT-50009 Kaunas, Lithuania
| | - Paulina Vaitkiene
- Laboratory of Neuro-Oncology and Genetics, Neuroscience Institute, Lithuanian University of Health Sciences, LT-50009 Kaunas, Lithuania
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Abstract
Adult diffuse gliomas account for the majority of primary malignant brain tumours, and are in most cases lethal. Current therapies are often only marginally effective, and improved options will almost certainly benefit from further insight into the various processes contributing to gliomagenesis and pathology. While molecular characterization of these tumours classifies them on the basis of genetic alterations and chromosomal abnormalities, DNA methylation patterns are increasingly understood to play a role in glioma pathogenesis. Indeed, a subset of gliomas associated with improved survival is characterized by the glioma CpG island methylator phenotype (G-CIMP), which can be induced by the expression of mutant isocitrate dehydrogenase (IDH1/2). Aberrant methylation of particular genes or regulatory elements, within the context of G-CIMP-positive and/or negative tumours, has also been shown to be associated with differential survival. In this review, we provide an overview of the current knowledge regarding the role of DNA methylation in adult diffuse gliomas. In particular, we discuss IDH mutations and G-CIMP, MGMT promoter methylation, DNA methylation-mediated microRNA regulation and aberrant methylation of specific genes or groups of genes.
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Weeks RJ, Ludgate JL, LeMée G, Morison IM. TESTIN Induces Rapid Death and Suppresses Proliferation in Childhood B Acute Lymphoblastic Leukaemia Cells. PLoS One 2016; 11:e0151341. [PMID: 26985820 PMCID: PMC4795691 DOI: 10.1371/journal.pone.0151341] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 02/07/2016] [Indexed: 12/22/2022] Open
Abstract
Background Childhood acute lymphoblastic leukaemia (ALL) is the most common malignancy in children. Despite high cure rates, side effects and late consequences of the intensive treatments are common. Unquestionably, the identification of new therapeutic targets will lead to safer, more effective treatments. We identified TES promoter methylation and transcriptional silencing as a very common molecular abnormality in childhood ALL, irrespective of molecular subtype. The aims of the present study were to demonstrate that TES promoter methylation is aberrant, to determine the effects of TES re-expression in ALL, and to determine if those effects are mediated via TP53 activity. Methods Normal fetal and adult tissue DNA was isolated and TES promoter methylation determined by Sequenom MassARRAY. Quantitative RT-PCR and immunoblot were used to confirm re-expression of TES in ALL cell lines after 5’-aza-2’-deoxycytidine (decitabine) exposure or transfection with TES expression plasmids. The effects of TES re-expression on ALL cells were investigated using standard cell proliferation, cell death and cell cycle assays. Results In this study, we confirm that the TES promoter is unmethylated in normal adult and fetal tissues. We report that decitabine treatment of ALL cell lines results in demethylation of the TES promoter and attendant expression of TES mRNA. Re-expression of TESTIN protein in ALL cells using expression plasmid transfection results in rapid cell death or cell cycle arrest independent of TP53 activity. Conclusions These results suggest that TES is aberrantly methylated in ALL and that re-expression of TESTIN has anti-leukaemia effects which point to novel therapeutic opportunities for childhood ALL.
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Affiliation(s)
- Robert J. Weeks
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
- * E-mail:
| | - Jackie L. Ludgate
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Gwenn LeMée
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Ian M. Morison
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
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Li X, Zheng J, Diao H, Liu Y. RUNX3 is down-regulated in glioma by Myc-regulated miR-4295. J Cell Mol Med 2016; 20:518-25. [PMID: 26756701 PMCID: PMC4759466 DOI: 10.1111/jcmm.12736] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/16/2015] [Indexed: 12/25/2022] Open
Abstract
MicroRNAs are increasingly reported as tumour suppressors that regulate gene expression after transcription. Our results demonstrated that miR-4295 is overexpression in glioma tissues and its level is significantly correlated with clinical stage. We also found that miR-4295 inhibited the cell G0/G1 arrest and apoptosis leading to promoted cell proliferation and activity. The murine modelling study revealed that female nude mice injected with U87/anti-miR-4295 exhibit subcutaneous tumours in the right groin. Compared with anti-NC, the tumour volume was significantly decreased in anti-miR-4295 treatment group. Furthermore, we confirmed miR-4295 mediates the expression of RUNX3 by targeting its 3'untranslation region. In addition, N-myc protein also could bind to the promoter of pri-miR-4295 and inhibit the expression of RUNX3 in glioma cells. These results validate a pathogenetic role of a miR-4295 in gliomas and establish a potentially regulatory and signalling pathway involving N-myc/miR-4295/RUNX3 in gliomas.
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Affiliation(s)
- Xinxing Li
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jihui Zheng
- Department of Radiology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Hongyu Diao
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yunhui Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
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Dong R, Pu H, Wang Y, Yu J, Lian K, Mao C. TESTIN was commonly hypermethylated and involved in the epithelial-mesenchymal transition of endometrial cancer. APMIS 2015; 123:394-400. [PMID: 25720371 DOI: 10.1111/apm.12361] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 12/01/2014] [Indexed: 12/18/2022]
Affiliation(s)
- Ruofan Dong
- Department of Reproductive Center; First Affiliated Hospital of Soochow University; Suzhou Jiangsu Province China
- Department of Obstetrics and Gynecology; The Affiliated Hospital of Jiangnan University and the Fourth People's Hospital of Wuxi; Wuxi Jiangsu Province China
| | - Hong Pu
- Department of Obstetrics and Gynecology; The Affiliated Hospital of Jiangnan University and the Fourth People's Hospital of Wuxi; Wuxi Jiangsu Province China
| | - Yuan Wang
- Department of Obstetrics and Gynecology; The Affiliated Hospital of Jiangnan University and the Fourth People's Hospital of Wuxi; Wuxi Jiangsu Province China
| | - Jinjin Yu
- Department of Obstetrics and Gynecology; The Affiliated Hospital of Jiangnan University and the Fourth People's Hospital of Wuxi; Wuxi Jiangsu Province China
| | - Kuixian Lian
- Department of Obstetrics and Gynecology; Affiliated Hospital of Binzhou Medical College; Binzhou Shandong Province China
| | - Caiping Mao
- Department of Reproductive Center; First Affiliated Hospital of Soochow University; Suzhou Jiangsu Province China
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25
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Majchrzak-Celińska A, Paluszczak J, Szalata M, Barciszewska AM, Nowak S, Kleszcz R, Sherba A, Baer-Dubowska W. The methylation of a panel of genes differentiates low-grade from high-grade gliomas. Tumour Biol 2015; 36:3831-41. [PMID: 25563195 DOI: 10.1007/s13277-014-3025-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 12/26/2014] [Indexed: 12/29/2022] Open
Abstract
Epigenetic changes play an important role in the pathogenesis of gliomas and have the potential to become clinically useful biomarkers. The aim of this study was the evaluation of the profile of promoter methylation of 13 genes selected based on their anticipated diagnostic and/or prognostic value. Methylation-specific PCR (MSP) was used to assess the methylation status of MGMT, ERCC1, hMLH1, ATM, CDKN2B (p15INK4B), p14ARF, CDKN2A (p16INK4A), RASSF1A, RUNX3, GATA6, NDRG2, PTEN, and RARβ in a subset of 95 gliomas of different grades. Additionally, the methylation status of MGMT and NDRG2 was analyzed using pyrosequencing (PSQ). The results revealed that the methylation index of individual glioma patients correlates with World Health Organization (WHO) tumor grade and patient's age. RASSF1A, RUNX3, GATA6, and MGMT were most frequently methylated, whereas the INK4B-ARF-INK4A locus, PTEN, RARβ, and ATM were methylated to a lesser extent. ERCC1, hMLH1, and NDRG2 were unmethylated. RUNX3 methylation correlated with WHO tumor grade and patient's age. PSQ confirmed significantly higher methylation levels of MGMT and NDRG2 as compared with normal, non-cancerous brain tissue. To conclude, DNA methylation of a whole panel of selected genes can serve as a tool for glioma aggressiveness prediction.
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Affiliation(s)
- Aleksandra Majchrzak-Celińska
- Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, ul. Święcickiego 4, 60-781, Poznań, Poland
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Bai Y, Zhang QG, Wang XH. Downregulation of TES by hypermethylation in glioblastoma reduces cell apoptosis and predicts poor clinical outcome. Eur J Med Res 2014; 19:66. [PMID: 25498217 PMCID: PMC4279594 DOI: 10.1186/s40001-014-0066-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Accepted: 11/17/2014] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Gliomas are the most common human brain tumors. Glioblastoma, also known as glioblastoma multiform (GBM), is the most aggressive, malignant, and lethal glioma. The investigation of prognostic and diagnostic molecular biomarkers in glioma patients to provide direction on clinical practice is urgent. Recent studies demonstrated that abnormal DNA methylation states play a key role in the pathogenesis of this kind of tumor. In this study, we want to identify a novel biomarker related to glioma initiation and find the role of the glioma-related gene. METHODS We performed a methylation-specific microarray on the promoter region to identify methylation gene(s) that may affect outcome of GBM patients. Normal and GBM tissues were collected from Tiantan Hospital. Genomic DNA was extracted from these tissues and analyzed with a DNA promoter methylation microarray. Testis derived transcript (TES) protein expression was analyzed by immunohistochemistry in paraffin-embedded patient tissues. Western blotting was used to detect TES protein expression in the GBM cell line U251 with or without 5-aza-dC treatment. Cell apoptosis was evaluated by flow cytometry analysis using Annexin V/PI staining. RESULTS We found that the TES promoter was hypermethylated in GBM compared to normal brain tissues under DNA promoter methylation microarray analysis. The GBM patients with TES hypermethylation had a short overall survival (P <0.05, log-rank test). Among GBM samples, reduced TES protein level was detected in 33 (89.2%) of 37 tumor tissues by immunohistochemical staining. Down regulation of TES was also correlated with worse patient outcome (P <0.05, log-rank test). Treatment on the GBM cell line U251 with 5-aza-dC can greatly increase TES expression, confirming the hypermethylation of TES promoter in GBM. Up-regulation of TES prompts U251 apoptosis significantly. This study demonstrated that both TES promoter hypermethylation and down-regulated protein expression significantly correlated with worse patient outcome. Treatment on the GBM cell line (U251) with 5-aza-dC can highly release TES expression resulting in significant apoptosis in these cells. CONCLUSIONS Our findings suggest that the TES gene is a novel tumor suppressor gene and might represent a valuable prognostic marker for glioblastoma, indicating a potential target for future GBM therapy.
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Affiliation(s)
- Yu Bai
- Department of Blood transfusion, The Central Hospital of China Aerospace Corporation, Beijing, 100049, China.
| | - Quan-Geng Zhang
- Department of Immunology, Capital Medical University, Beijing, 100069, China.
| | - Xin-Hua Wang
- Department of Blood transfusion, The Central Hospital of China Aerospace Corporation, Beijing, 100049, China.
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Saraiva-Esperón U, Ruibal A, Herranz M. The contrasting epigenetic role of RUNX3 when compared with that of MGMT and TIMP3 in glioblastoma multiforme clinical outcomes. J Neurol Sci 2014; 347:325-31. [DOI: 10.1016/j.jns.2014.10.043] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 10/25/2014] [Accepted: 10/29/2014] [Indexed: 02/02/2023]
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28
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Jeitany M, Pineda JR, Liu Q, Porreca RM, Hoffschir F, Desmaze C, Silvestre DC, Mailliet P, Junier MP, Londoño-Vallejo A, Ségal-Bendirdjian E, Chneiweiss H, Boussin FD. A preclinical mouse model of glioma with an alternative mechanism of telomere maintenance (ALT). Int J Cancer 2014; 136:1546-58. [PMID: 25175359 PMCID: PMC4303977 DOI: 10.1002/ijc.29171] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 07/04/2014] [Accepted: 07/25/2014] [Indexed: 12/12/2022]
Abstract
Glioblastoma multiforme is the most aggressive primary tumor of the central nervous system. Glioma stem cells (GSCs), a small population of tumor cells with stem-like properties, are supposedly responsible for glioblastoma multiforme relapse after current therapies. In approximately thirty percent of glioblastoma multiforme tumors, telomeres are not maintained by telomerase but through an alternative mechanism, termed alternative lengthening of telomere (ALT), suggesting potential interest in developing specific therapeutic strategies. However, no preclinical model of ALT glioma was available until the isolation of TG20 cells from a human ALT glioma. Herein, we show that TG20 cells exhibit a high level of telomeric recombination but a stable karyotype, indicating that their telomeres retain their protective function against chromosomal instability. TG20 cells possess all of the characteristic features of GSCs: the expression of neural stem cell markers, the generation of intracerebral tumors in NOD-SCID-IL2Rγ (NSG) mice as well as in nude mice, and the ability to sustain serial intracerebral transplantations without expressing telomerase, demonstrating the stability of the ALT phenotype in vivo. Furthermore, we also demonstrate that 360B, a G-quadruplex ligand of the pyridine derivative series that impairs telomere replication and mitotic progression in cancer cells, prevents the development of TG20 tumors. Together, our results show that intracerebral grafts of TG20 cells in immunodeficient mice constitute an efficient preclinical model of ALT glioblastoma multiforme and that G-quadruplex ligands are a potential therapy for this specific type of tumor.
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Affiliation(s)
- Maya Jeitany
- Laboratoire de Radiopathologie, CEA, Institut de Radiobiologie Cellulaire et Moléculaire, 18 route du Panorama, 92265, Fontenay-aux-Roses, France; INSERM UMR967, 18 route du Panorama, 92265, Fontenay-aux-Roses, France; Université Paris VII, UMR967, 18 route du Panorama, 92265, Fontenay-aux-Roses, France; Université Paris XI, UMR967, 18 route du Panorama, 92265, Fontenay-aux-Roses, France
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Yoo S, Bieda MC. Differences among brain tumor stem cell types and fetal neural stem cells in focal regions of histone modifications and DNA methylation, broad regions of modifications, and bivalent promoters. BMC Genomics 2014; 15:724. [PMID: 25163646 PMCID: PMC4155105 DOI: 10.1186/1471-2164-15-724] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 08/04/2014] [Indexed: 12/15/2022] Open
Abstract
Background Aberrational epigenetic marks are believed to play a major role in establishing the abnormal features of cancer cells. Rational use and development of drugs aimed at epigenetic processes requires an understanding of the range, extent, and roles of epigenetic reprogramming in cancer cells. Using ChIP-chip and MeDIP-chip approaches, we localized well-established and prevalent epigenetic marks (H3K27me3, H3K4me3, H3K9me3, DNA methylation) on a genome scale in several lines of putative glioma stem cells (brain tumor stem cells, BTSCs) and, for comparison, normal human fetal neural stem cells (fNSCs). Results We determined a substantial “core” set of promoters possessing each mark in every surveyed BTSC cell type, which largely overlapped the corresponding fNSC sets. However, there was substantial diversity among cell types in mark localization. We observed large differences among cell types in total number of H3K9me3+ positive promoters and peaks and in broad modifications (defined as >50 kb peak length) for H3K27me3 and, to a lesser extent, H3K9me3. We verified that a change in a broad modification affected gene expression of CACNG7. We detected large numbers of bivalent promoters, but most bivalent promoters did not display direct overlap of contrasting epigenetic marks, but rather occupied nearby regions of the proximal promoter. There were significant differences in the sets of promoters bearing bivalent marks in the different cell types and few consistent differences between fNSCs and BTSCs. Conclusions Overall, our “core set” data establishes sets of potential therapeutic targets, but the diversity in sets of sites and broad modifications among cell types underscores the need to carefully consider BTSC subtype variation in epigenetic therapy. Our results point toward substantial differences among cell types in the activity of the production/maintenance systems for H3K9me3 and for broad regions of modification (H3K27me3 or H3K9me3). Finally, the unexpected diversity in bivalent promoter sets among these multipotent cells indicates that bivalent promoters may play complex roles in the overall biology of these cells. These results provide key information for forming the basis for future rational drug therapy aimed at epigenetic processes in these cells. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-724) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Mark C Bieda
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada.
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Yongbin Y, Jinghua L, Zhanxue Z, Aimin Z, Youchao J, Yanhong S, Manjing J. TES was epigenetically silenced and suppressed the epithelial–mesenchymal transition in breast cancer. Tumour Biol 2014; 35:11381-9. [DOI: 10.1007/s13277-014-2472-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 08/07/2014] [Indexed: 11/28/2022] Open
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Gu Z, Ding G, Liang K, Zhang H, Guo G, Zhang L, Cui J. TESTIN suppresses tumor growth and invasion via manipulating cell cycle progression in endometrial carcinoma. Med Sci Monit 2014; 20:980-7. [PMID: 24929083 PMCID: PMC4067424 DOI: 10.12659/msm.890544] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The TESTIN gene was demonstrated to be a tumor suppressor in prostate and breast cancer through inhibiting tumor growth and invasion. Herein, we aimed to investigate the detailed functions of TESTIN in the highly sexual hormone (estrogen)-dependent malignancy, endometrial carcinoma. MATERIAL AND METHODS TESTIN mRNA and protein expression were measured by qRT-PCR, Western blot and immunohistochemistry. Upregulation of TESTIN was achieved by transfecting the pcDNA3.1-TESTIN plasmids into AN3CA cells. Knockdown of TESTIN was achieved by transfecting the shRNA-TESTIN into Ishikawa cells. MTT assay, colony formation assay, and Transwell assay were used to investigate the effects of TESTIN on cellular proliferation and invasion. The apoptotic status and cell cycle were analyzed using flow cytometry. MMP2 secretion was determined by ELISA assay. The xenograft assay was used to investigate the functions of TESTIN in nude mice. RESULTS Compared to the non-malignant adjacent endometrium, 54% of tumor samples presented downregulation of TESTIN (P<0.001). Loss of TESTIN protein was correlated with advanced tumor stage (P=0.047), high grade (P=0.034), and lymphatic vascular space invasion (P=0.036). In vitro, overexpression of TESTIN suppressed cell proliferation, induced dramatic G1 arrest, and inhibited tumor invasion through blocking the secretion of MMP2. Loss of TESTIN accelerated cellular proliferation, promoted cell cycle progression, and enhanced tumor invasion by increasing the secretion of MMP2. Consistently, TESTIN could significantly delay the growth of xenografts in nude mice. CONCLUSIONS TESTIN was commonly downregulated in human endometrial carcinoma and was associated with poor prognostic markers. Moreover, TESTIN significantly inhibited tumor growth and invasion via arresting cell cycle in in vitro and in vivo experiments. Therefore, we propose that TESTIN might be a prognostic marker and therapeutic target for endometrial carcinoma.
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Affiliation(s)
- Zhenpeng Gu
- Department of Obstetrics and Gynecology, Affiliated Hospital of Binzhou Medical College, Binzhou, China (mainland)
| | - Guofeng Ding
- Department of Infectious Diseases, Affiliated Hospital of Binzhou Medical College, Binzhou, China (mainland)
| | - Kuixiang Liang
- Department of Obstetrics and Gynecology, Affiliated Hospital of Binzhou Medical College, Binzhou, China (mainland)
| | - Hongtao Zhang
- Department of Obstetrics and Gynecology, Affiliated Hospital of Binzhou Medical College, Binzhou, China (mainland)
| | - Guanghong Guo
- Department of Obstetrics and Gynecology, Affiliated Hospital of Binzhou Medical College, Binzhou, China (mainland)
| | - Lili Zhang
- Department of Obstetrics and Gynecology, Affiliated Hospital of Binzhou Medical College, Binzhou, China (mainland)
| | - Jinxiu Cui
- Department of Obstetrics and Gynecology, Affiliated Hospital of Binzhou Medical College, Binzhou, China (mainland)
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Wang Z, Curry E, Montana G. Network-guided regression for detecting associations between DNA methylation and gene expression. ACTA ACUST UNITED AC 2014; 30:2693-701. [PMID: 24919878 DOI: 10.1093/bioinformatics/btu361] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION High-throughput profiling in biological research has resulted in the availability of a wealth of data cataloguing the genetic, epigenetic and transcriptional states of cells. These data could yield discoveries that may lead to breakthroughs in the diagnosis and treatment of human disease, but require statistical methods designed to find the most relevant patterns from millions of potential interactions. Aberrant DNA methylation is often a feature of cancer, and has been proposed as a therapeutic target. However, the relationship between DNA methylation and gene expression remains poorly understood. RESULTS We propose Network-sparse Reduced-Rank Regression (NsRRR), a multivariate regression framework capable of using prior biological knowledge expressed as gene interaction networks to guide the search for associations between gene expression and DNA methylation signatures. We use simulations to show the advantage of our proposed model in terms of variable selection accuracy over alternative models that do not use prior network information. We discuss an application of NsRRR to The Cancer Genome Atlas datasets on primary ovarian tumours. AVAILABILITY AND IMPLEMENTATION R code implementing the NsRRR model is available at http://www2.imperial.ac.uk/∼gmontana CONTACT giovanni.montana@kcl.ac.uk SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zi Wang
- Department of Mathematics, Imperial College London, London SW7 2AZ, Division of Cancer, Imperial College London, Hammersmith Hospital, London W12 0NN and Department of Biomedical Engineering, King's College London, St Thomas' Hospital, London SE1 7EH, UK
| | - Edward Curry
- Department of Mathematics, Imperial College London, London SW7 2AZ, Division of Cancer, Imperial College London, Hammersmith Hospital, London W12 0NN and Department of Biomedical Engineering, King's College London, St Thomas' Hospital, London SE1 7EH, UK
| | - Giovanni Montana
- Department of Mathematics, Imperial College London, London SW7 2AZ, Division of Cancer, Imperial College London, Hammersmith Hospital, London W12 0NN and Department of Biomedical Engineering, King's College London, St Thomas' Hospital, London SE1 7EH, UK Department of Mathematics, Imperial College London, London SW7 2AZ, Division of Cancer, Imperial College London, Hammersmith Hospital, London W12 0NN and Department of Biomedical Engineering, King's College London, St Thomas' Hospital, London SE1 7EH, UK
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Martínez R, Carmona FJ, Vizoso M, Rohde V, Kirsch M, Schackert G, Ropero S, Paulus W, Barrantes A, Gomez A, Esteller M. DNA methylation alterations in grade II- and anaplastic pleomorphic xanthoastrocytoma. BMC Cancer 2014; 14:213. [PMID: 24650279 PMCID: PMC4000050 DOI: 10.1186/1471-2407-14-213] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 03/13/2014] [Indexed: 12/31/2022] Open
Abstract
Background Pleomorphic xanthoastrocytoma (PXA) is a rare WHO grade II tumor accounting for less than 1% of all astrocytomas. Malignant transformation into PXA with anaplastic features, is unusual and correlates with poorer outcome of the patients. Methods Using a DNA methylation custom array, we have quantified the DNA methylation level on the promoter sequence of 807 cancer-related genes of WHO grade II (n = 11) and III PXA (n = 2) and compared to normal brain tissue (n = 10) and glioblastoma (n = 87) samples. DNA methylation levels were further confirmed on independent samples by pyrosequencing of the promoter sequences. Results Increasing DNA promoter hypermethylation events were observed in anaplastic PXA as compared with grade II samples. We further validated differential hypermethylation of CD81, HCK, HOXA5, ASCL2 and TES on anaplastic PXA and grade II tumors. Moreover, these epigenetic alterations overlap those described in glioblastoma patients, suggesting common mechanisms of tumorigenesis. Conclusions Even taking into consideration the small size of our patient populations, our data strongly suggest that epigenome-wide profiling of PXA is a valuable tool to identify methylated genes, which may play a role in the malignant progression of PXA. These methylation alterations may provide useful biomarkers for decision-making in those patients with low-grade PXA displaying a high risk of malignant transformation.
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Affiliation(s)
- Ramón Martínez
- Department of Neurosurgery, University of Goettingen, Robert Koch, Str, 40, 37075 Goettingen, Germany.
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Karakoula K, Jacques TS, Phipps KP, Harkness W, Thompson D, Harding BN, Darling JL, Warr TJ. Epigenetic genome-wide analysis identifies BEX1 as a candidate tumour suppressor gene in paediatric intracranial ependymoma. Cancer Lett 2013; 346:34-44. [PMID: 24333734 DOI: 10.1016/j.canlet.2013.12.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 12/02/2013] [Accepted: 12/04/2013] [Indexed: 12/13/2022]
Abstract
Promoter hypermethylation and transcriptional silencing is a common epigenetic mechanism of gene inactivation in cancer. To identify targets of epigenetic silencing in paediatric intracranial ependymoma, we used a pharmacological unmasking approach through treatment of 3 ependymoma short-term cell cultures with the demethylating agent 5-Aza-2'-deoxycytidine followed by global expression microarray analysis. We identified 55 candidate epigenetically silenced genes, which are involved in the regulation of apoptosis, Wnt signalling, p53 and cell differentiation. The methylation status of 26 of these genes was further determined by combined bisulfite restriction analysis (COBRA) and genomic sequencing in a cohort of 40 ependymoma samples. The most frequently methylated genes were BEX1 (27/40 cases), BAI2 (20/40), CCND2 (18/40), and CDKN2A (14/40). A high correlation between promoter hypermethylation and decreased gene expression levels was established by real-time quantitative PCR, suggesting the involvement of these genes in ependymoma tumourigenesis. Furthermore, ectopic expression of brain-expressed X-linked 1 (BEX1) in paediatric ependymoma short-term cell cultures significantly suppressed cell proliferation and colony formation. These data suggest that promoter hypermethylation contributes to silencing of target genes in paediatric intracranial ependymoma. Epigenetic inactivation of BEX1 supports its role as a candidate tumour suppressor gene in intracranial ependymoma, and a potential target for novel therapies for ependymoma in children.
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Affiliation(s)
- Katherine Karakoula
- Brain Tumour Research Centre, School of Applied Sciences, University of Wolverhampton, Wolverhampton WV1 1LY, UK.
| | - Thomas S Jacques
- Neural Development Unit, Birth Defects Research Centre, UCL Institute of Child Health, University College London, London WC1E 6BT, UK; Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Kim P Phipps
- Department of Neurosurgery, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - William Harkness
- Department of Neurosurgery, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Dominic Thompson
- Department of Neurosurgery, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Brian N Harding
- Division of Neuropathology, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104-4399, USA
| | - John L Darling
- Brain Tumour Research Centre, School of Applied Sciences, University of Wolverhampton, Wolverhampton WV1 1LY, UK
| | - Tracy J Warr
- Brain Tumour Research Centre, School of Applied Sciences, University of Wolverhampton, Wolverhampton WV1 1LY, UK
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Fouse SD, Nakamura JL, James CD, Chang S, Costello JF. Response of primary glioblastoma cells to therapy is patient specific and independent of cancer stem cell phenotype. Neuro Oncol 2013; 16:361-71. [PMID: 24311636 DOI: 10.1093/neuonc/not223] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Glioblastoma multiforme (GBM) contains a population of cells that exhibit stem cell phenotypes. These cancer stem cells (CSCs) may be a source of therapeutic resistance, although support for this important concept is limited. METHODS We determined whether early-passage GBM CSCs respond differently than patient-matched, genotypically similar non-CSCs to clinically relevant single or serial doses of temozolomide (TMZ), radiation therapy (XRT), or alternating TMZ treatment and XRT, which is the standard of care for GBM patients. RESULTS Despite the phenotypic differences, including the presence of stem cell markers and formation of intracranial tumors, the CSCs and matched non-CSCs were equally resistant to TMZ in a majority of patients, using 2 independent assays. TMZ response was consistent with methylated O(6)-DNA methylguanine-methyltransferase (MGMT) and MGMT protein levels in both culture types. In contrast, CSCs were unexpectedly more responsive to XRT compared with matched non-CSCs from 2 patients despite having relatively equal resistance to TMZ. However, for the majority of culture pairs from individual patients, responses in CSCs were indistinguishable from non-CSC cultures. CONCLUSIONS In our patient-matched primary cultures, response to TMZ was tightly linked to the individual tumor's MGMT status and independent of their phenotypic differences. TMZ and XRT together revealed no additive benefit compared with monotherapy for either culture type, in contrast to the notion that the CSC population is more resistant to XRT. If the tumor cell response in vitro mirrors therapeutic response in larger patient cohorts, these rapid assays in primary cultures could allow -empirical selection of efficacious therapeutic agents on a patient-specific basis.
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Affiliation(s)
- Shaun D Fouse
- Department of Neurological Surgery, Brain Tumor Research Center, University of California, San Francisco, San Francisco, California (S.D.F., C.D.J., S.C., J.F.C); Department of Radiation Oncology, University of California, San Francisco, California (J.L.N.)
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Jamshidi N, Diehn M, Bredel M, Kuo MD. Illuminating radiogenomic characteristics of glioblastoma multiforme through integration of MR imaging, messenger RNA expression, and DNA copy number variation. Radiology 2013; 270:1-2. [PMID: 24056404 DOI: 10.1148/radiol.13130078] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
PURPOSE To perform a multilevel radiogenomics study to elucidate the glioblastoma multiforme (GBM) magnetic resonance (MR) imaging radiogenomic signatures resulting from changes in messenger RNA (mRNA) expression and DNA copy number variation (CNV). MATERIALS AND METHODS Radiogenomic analysis was performed at MR imaging in 23 patients with GBM in this retrospective institutional review board-approved HIPAA-compliant study. Six MR imaging features-contrast enhancement, necrosis, contrast-to-necrosis ratio, infiltrative versus edematous T2 abnormality, mass effect, and subventricular zone (SVZ) involvement-were independently evaluated and correlated with matched genomic profiles (global mRNA expression and DNA copy number profiles) in a significant manner that also accounted for multiple hypothesis testing by using gene set enrichment analysis (GSEA), resampling statistics, and analysis of variance to gain further insight into the radiogenomic signatures in patients with GBM. RESULTS GSEA was used to identify various oncogenic pathways with MR imaging features. Correlations between 34 gene loci were identified that showed concordant variations in gene dose and mRNA expression, resulting in an MR imaging, mRNA, and CNV radiogenomic association map for GBM. A few of the identified gene-to-trait associations include association of the contrast-to-necrosis ratio with KLK3 and RUNX3; association of SVZ involvement with Ras oncogene family members, such as RAP2A, and the metabolic enzyme TYMS; and association of vasogenic edema with the oncogene FOXP1 and PIK3IP1, which is a member of the PI3K signaling network. CONCLUSION Construction of an MR imaging, mRNA, and CNV radiogenomic association map has led to identification of MR traits that are associated with some known high-grade glioma biomarkers and association with genomic biomarkers that have been identified for other malignancies but not GBM. Thus, the traits and genes identified on this map highlight new candidate radiogenomic biomarkers for further evaluation in future studies.
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Affiliation(s)
- Neema Jamshidi
- From the Department of Radiological Sciences, UCLA School of Medicine, Box 951721, CHS 17-135, Los Angeles, CA 90095-1721 (N.J., M.D.K.); Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Palo Alto, Calif (M.D.); and Department of Radiation Oncology, University of Alabama at Birmingham School of Medicine, Birmingham, Ala (M.B.)
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Maleszewska M, Kaminska B. Is glioblastoma an epigenetic malignancy? Cancers (Basel) 2013; 5:1120-39. [PMID: 24202337 PMCID: PMC3795382 DOI: 10.3390/cancers5031120] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 08/13/2013] [Accepted: 08/19/2013] [Indexed: 01/01/2023] Open
Abstract
Epigenetic modifications control gene expression by regulating the access of nuclear proteins to their target DNA and have been implicated in both normal cell differentiation and oncogenic transformation. Epigenetic abnormalities can occur both as a cause and as a consequence of cancer. Oncogenic transformation can deeply alter the epigenetic information enclosed in the pattern of DNA methylation or histone modifications. In addition, in some cancers epigenetic dysfunctions can drive oncogenic transformation. Growing evidence emphasizes the interplay between metabolic disturbances, epigenomic changes and cancer, i.e., mutations in the metabolic enzymes SDH, FH, and IDH may contribute to cancer development. Epigenetic-based mechanisms are reversible and the possibility of “resetting” the abnormal cancer epigenome by applying pharmacological or genetic strategies is an attractive, novel approach. Gliomas are incurable with all current therapeutic approaches and new strategies are urgently needed. Increasing evidence suggests the role of epigenetic events in development and/or progression of gliomas. In this review, we summarize current data on the occurrence and significance of mutations in the epigenetic and metabolic enzymes in pathobiology of gliomas. We discuss emerging therapies targeting specific epigenetic modifications or chromatin modifying enzymes either alone or in combination with other treatment regimens.
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Affiliation(s)
- Marta Maleszewska
- Laboratory of Molecular Neurobiology, Neurobiology Center, The Nencki Institute of Experimental Biology, 3 Pasteur Str., Warsaw 02-093, Poland.
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Avci CB, Dodurga Y, Susluer SY, Sıgva ZOD, Yucebas M, Caglar HO, Akalin T, Dalbasti T, Oktar N, Gunduz C. Promoter hypermethylation-mediated down-regulation of RUNX3 gene in human brain tumors. Ir J Med Sci 2013; 183:259-64. [PMID: 23934435 DOI: 10.1007/s11845-013-1001-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Accepted: 08/02/2013] [Indexed: 01/12/2023]
Abstract
BACKGROUND The Runx family proteins, including RUNX3, are tissue-restricted transcription factors and play role in neuronal development and tumorigenesis. RUNX3 has an important role in glioblastoma (GBM) tumorigenesis because of its promoter hypermethylation. AIM We aimed to evaluate the methylation-mediated expression regulation of RUNX3 gene in brain tumors. PATIENTS AND METHODS Cases of meningiomas WHO grade III (3), anaplastic astrocytomas (3), diffuse astrocytoma (3), and GBM (12) were recruited into this study. Real-time quantitative PCR was performed for analyses of DNA promoter methylation and analyses of methylation-mediated expression status of RUNX3 gene was performed by real-time quantitative RT-PCR. RESULTS There was no significant difference between methylated and unmethylated quantitative ratio of RUNX3 gene promoter region and also no significant difference in relative ratio of RUNX3 gene expression in brain tumor groups. Methylated and unmethylated ratio in anaplastic astrocytoma, diffuse astrocytoma, GBM, meningioma (WHO grade III) and in all groups were; 1.44, 1.09, 1.51, 1.52 and 1.43, respectively. One allele was found methylated necessarily. No methylation was detected in one case of GBM group and one case of anaplastic astrocytoma group. There was no unmethylated promoter in one of the GBM cases. There were significant differences between relative ratio of RUNX3 gene expression and methylated/unmethylated ratio rates for all cases (p = 0.001) and GBM groups (p = 0.041). CONCLUSION This study overemphasized the RUNX3 gene importance in brain tumors, due to the existence of at least one methylated allele.
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Affiliation(s)
- C B Avci
- Department of Medical Biology, Ege University Medical Faculty, Bornova, 35100, Izmir, Turkey,
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Carén H, Pollard SM, Beck S. The good, the bad and the ugly: epigenetic mechanisms in glioblastoma. Mol Aspects Med 2013; 34:849-62. [PMID: 22771539 PMCID: PMC3714597 DOI: 10.1016/j.mam.2012.06.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 06/27/2012] [Indexed: 12/31/2022]
Abstract
Cell type-specific patterns of gene expression reflect epigenetic changes imposed through a particular developmental lineage as well as those triggered by environmental cues within adult tissues. There is great interest in elucidating the molecular basis and functional importance of epigenetic mechanisms in both normal physiology and disease - particularly in cancer, where abnormal '-omic' states are often observed. In this article we review recent progress in studies of epigenetic mechanisms in the most common primary adult brain cancer, glioblastoma multiforme. Three distinct areas are discussed. First, the evidence in support of ongoing 'normal' epigenetic processes associated with differentiation - as predicted by 'cancer stem cell' models of the disease. Second, identification of site-specific and global epigenetic abnormalities. Third, genetic disruptions directly within the core epigenetic machinery, exemplified by the recently identified mutations within isocitrate dehydrogenase genes IDH1/2 and variant histone genes H3.3/H3F3A. These constitute the 'good, the bad and the ugly' of epigenetic mechanisms in cancer.
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Affiliation(s)
- Helena Carén
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, United Kingdom
| | - Steven M. Pollard
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, United Kingdom
| | - Stephan Beck
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, United Kingdom
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Yang Y, Niu CS, Cheng CD. Pin1-Nanog expression in human glioma is correlated with advanced tumor progression. Oncol Rep 2013; 30:560-6. [PMID: 23708493 PMCID: PMC3776722 DOI: 10.3892/or.2013.2481] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 04/24/2013] [Indexed: 11/20/2022] Open
Abstract
The stemness gene Nanog has been shown to play an important role in tumor development, including glioma. Nanog is phosphorylated at multiple Ser/Thr-Pro motifs, which promotes the interaction between Nanog and the prolyl isomerase Pin1, leading to Nanog stabilization by suppressing its ubiquitination. The present study investigated the expression and relationship of Pin1 and Nanog in human gliomas. Significantly higher mRNA and protein expression levels of Pin1 and Nanog were demonstrated in 120 glioma specimens of different pathological grades by RT-PCR, immunohistochemistry staining and western blot analysis. The relative levels of Pin1 expression, as well as Nanog expression, were significantly positively correlated with pathological grade. Moreover, a positive correlation of Pin1 and Nanog expression in human gliomas was noted. Co-localization of Pin1 and Nanog was observed in the perinuclear space in the cytoplasm of glioma cells detected by immunofluorescence staining. Significantly positive correlation between Pin1 and Nanog in gliomas indicated that Pin1 and Nanog may be related to tumorigenesis and development of glioma cells.
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Affiliation(s)
- Yang Yang
- Department of Neurosurgery, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, Anhui 230001, PR China
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Skiriutė D, Vaitkienė P, Ašmonienė V, Steponaitis G, Deltuva VP, Tamašauskas A. Promoter methylation of AREG, HOXA11, hMLH1, NDRG2, NPTX2 and Tes genes in glioblastoma. J Neurooncol 2013; 113:441-9. [PMID: 23624749 DOI: 10.1007/s11060-013-1133-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 04/21/2013] [Indexed: 12/29/2022]
Abstract
Epigenetic alterations alone or in combination with genetic mechanisms play a key role in brain tumorigenesis. Glioblastoma is one of the most common, lethal and poor clinical outcome primary brain tumors with extraordinarily miscellaneous epigenetic alterations profile. The aim of this study was to investigate new potential prognostic epigenetic markers such as AREG, HOXA11, hMLH1, NDRG2, NTPX2 and Tes genes promoter methylation, frequency and value for patients outcome. We examined the promoter methylation status using methylation-specific polymerase chain reaction in 100 glioblastoma tissue samples. The value for clinical outcome was calculated using Kaplan-Meier estimation with log-rank test. DNA promoter methylation was frequent event appearing more than 45 % for gene. AREG and HOXA11 methylation status was significantly associated with patient age. HOXA11 showed the tendency to be associated with patient outcome in glioblastomas. AREG gene promoter methylation showed significant correlation with poor patient outcome. AREG methylation remained significantly associated with patient survival in a Cox multivariate model including MGMT promoter methylation status. This study of new epigenetic targets has shown considerably high level of analyzed genes promoter methylation variability in glioblastoma tissue. AREG gene might be valuable marker for glioblastoma patient survival prognosis, however further analysis is needed to clarify the independence and appropriateness of the marker.
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Affiliation(s)
- Daina Skiriutė
- Laboratory of Neurooncology and Genetics, Neuroscience Institute, Lithuanian University of Health Sciences, Eiveniu str 4, 50161 Kaunas, Lithuania.
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Chimge NO, Frenkel B. The RUNX family in breast cancer: relationships with estrogen signaling. Oncogene 2013; 32:2121-30. [PMID: 23045283 PMCID: PMC5770236 DOI: 10.1038/onc.2012.328] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 06/20/2012] [Accepted: 06/20/2012] [Indexed: 12/22/2022]
Abstract
The three RUNX family members are lineage specific master regulators, which also have important, context-dependent roles in carcinogenesis as either tumor suppressors or oncogenes. Here we review evidence for such roles in breast cancer (BCa). RUNX1, the predominant RUNX family member in breast epithelial cells, has a tumor suppressor role reflected by many somatic mutations found in primary tumor biopsies. The classical tumor suppressor gene RUNX3 does not consist of such a mutation hot spot, but it too seems to inhibit BCa; it is often inactivated in human BCa tumors and its haploinsufficiency in mice leads to spontaneous BCa development. The tumor suppressor activities of RUNX1 and RUNX3 are mediated in part by antagonism of estrogen signaling, a feature recently attributed to RUNX2 as well. Paradoxically, however RUNX2, a master osteoblast regulator, has been implicated in various aspects of metastasis in general and bone metastasis in particular. Reciprocating the anti-estrogenic tumor suppressor activity of RUNX proteins, inhibition of RUNX2 by estrogens may help explain their context-dependent anti-metastatic roles. Such roles are reserved to non-osseous metastasis, because ERα is associated with increased, not decreased skeletal dissemination of BCa cells. Finally, based on diverse expression patterns in BCa subtypes, the successful use of future RUNX-based therapies will most likely require careful patient selection.
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Affiliation(s)
- N-O Chimge
- Department of Biochemistry and Molecular Biology, Institute for Genetic Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - B Frenkel
- Departments of Orthopaedic Surgery and Biochemistry and Molecular Biology, Institute for Genetic Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
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Sahm F, Lass U, Herold-Mende C, von Deimling A, Hartmann C, Mueller W. Analysis of CIC-associated CpG island methylation in oligoastrocytoma. Neuropathol Appl Neurobiol 2013; 39:831-6. [PMID: 23521081 DOI: 10.1111/nan.12045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 03/15/2013] [Indexed: 11/29/2022]
Abstract
AIMS Combined deletion of the whole chromosomal arms 1p and 19q is a frequent event in oligodendroglial tumours. Recent identification of recurrent mutations in CIC on 19q and FUBP1 on 1p and their mutational patterns suggest a loss of function of the respective proteins. Surprisingly, oligoastrocytomas harbouring identical genetic characteristics regarding 1p/19q codeletion and frequent IDH1/2 mutations have been shown to carry CIC mutations in a significantly lower number of cases. The present study investigates whether epigenetic modification may result in silencing of CIC. METHODS As IDH1/2 mutation-mediated DNA hypermethylation is a prominent feature of these tumours, we analysed a set of CIC wild-type oligoastrocytomas and other diffuse gliomas with regard to 1p/19q status for presence of CIC-associated CpG island methylation by methylation-specific PCR. RESULTS Both methylation-specific PCR and subsequent bisulphite-sequencing of selected cases revealed an unmethylated status in all samples. CONCLUSION Despite the hypermethylator phenotype in IDH1/2 mutant tumours and recent detection of gene silencing particularly on retained alleles in oligodendroglial tumours, hypermethylation of CIC-associated CpG islands does not provide an alternative mechanism of functional CIC protein abrogation.
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Affiliation(s)
- F Sahm
- Department of Neuropathology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Neuropathology G380, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Stricker SH, Feber A, Engström PG, Carén H, Kurian KM, Takashima Y, Watts C, Way M, Dirks P, Bertone P, Smith A, Beck S, Pollard SM. Widespread resetting of DNA methylation in glioblastoma-initiating cells suppresses malignant cellular behavior in a lineage-dependent manner. Genes Dev 2013; 27:654-69. [PMID: 23512659 PMCID: PMC3613612 DOI: 10.1101/gad.212662.112] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 02/20/2013] [Indexed: 02/06/2023]
Abstract
Epigenetic changes are frequently observed in cancer. However, their role in establishing or sustaining the malignant state has been difficult to determine due to the lack of experimental tools that enable resetting of epigenetic abnormalities. To address this, we applied induced pluripotent stem cell (iPSC) reprogramming techniques to invoke widespread epigenetic resetting of glioblastoma (GBM)-derived neural stem (GNS) cells. GBM iPSCs (GiPSCs) were subsequently redifferentiated to the neural lineage to assess the impact of cancer-specific epigenetic abnormalities on tumorigenicity. GiPSCs and their differentiating derivatives display widespread resetting of common GBM-associated changes, such as DNA hypermethylation of promoter regions of the cell motility regulator TES (testis-derived transcript), the tumor suppressor cyclin-dependent kinase inhibitor 1C (CDKN1C; p57KIP2), and many polycomb-repressive complex 2 (PRC2) target genes (e.g., SFRP2). Surprisingly, despite such global epigenetic reconfiguration, GiPSC-derived neural progenitors remained highly malignant upon xenotransplantation. Only when GiPSCs were directed to nonneural cell types did we observe sustained expression of reactivated tumor suppressors and reduced infiltrative behavior. These data suggest that imposing an epigenome associated with an alternative developmental lineage can suppress malignant behavior. However, in the context of the neural lineage, widespread resetting of GBM-associated epigenetic abnormalities is not sufficient to override the cancer genome.
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Affiliation(s)
- Stefan H. Stricker
- Department of Cancer Biology, UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
- Samantha Dickson Brain Cancer Unit
| | - Andrew Feber
- Department of Cancer Biology, UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | - Pär G. Engström
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, United Kingdom
| | - Helena Carén
- Department of Cancer Biology, UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | - Kathreena M. Kurian
- Department of Neuropathology, Frenchay Hospital, Bristol BS16 1LE, United Kingdom
| | - Yasuhiro Takashima
- Wellcome Trust-Medical Research Council Stem Cell Institute
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, United Kingdom
| | - Colin Watts
- Department of Clinical Neurosciences, Cambridge Centre for Brain Repair, University of Cambridge, Cambridge CB2 0PY, United Kingdom
- Division of Neurosurgery, Department of Clinical Neurosciences, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - Michael Way
- Lincoln's Inn Fields Laboratories, Cancer Research UK London Research Institute, London WC2A 3LY, United Kingdom
| | - Peter Dirks
- Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, University of Toronto, Toronto, Ontario M5G 1X8, Canada
| | - Paul Bertone
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, United Kingdom
- Wellcome Trust-Medical Research Council Stem Cell Institute
- Genome Biology Unit
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Austin Smith
- Wellcome Trust-Medical Research Council Stem Cell Institute
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, United Kingdom
| | - Stephan Beck
- Department of Cancer Biology, UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | - Steven M. Pollard
- Department of Cancer Biology, UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
- Samantha Dickson Brain Cancer Unit
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Yuryev A, Kotelnikova E, Daraselia N. Ariadne's ChemEffect and Pathway Studio knowledge base. Expert Opin Drug Discov 2013; 4:1307-18. [PMID: 23480468 DOI: 10.1517/17460440903413488] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
IMPORTANCE OF THE FIELD Drug discovery and development is a very complex and costly process. Understanding the detailed molecular mechanisms of a disease and drug actions can make it more efficient not only for new target discovery but also for lead prioritization, drug repositioning and development of biomarkers for drug efficacy and safety. Access to formalized knowledge about functions of proteins and small molecules is crucial for rationalization of the drug development process, and scientific publications are the main source of this knowledge. Protein knowledge networks capturing protein functions, protein-protein relations and organization of proteins in complex cellular sub-systems are making their way into modern drug discovery. Chemical networks representing multiple aspects of chemical functional information integrated into a protein systems biology network is even more advanced and promising paradigm. AREAS COVERED IN THIS REVIEW This review describes utilization of literature-derived protein and chemical functional knowledge bases in drug development. WHAT THE READER WILL GAIN Readers will gain an understanding of how integrated protein and chemical knowledge networks can be used for understanding and building the models of cellular events, disease mechanisms, and drug actions, finding biomarkers of drug efficacy and safety, as well as interpretation of high-throughput gene expression, proteomic and metabolomic experiments. TAKE HOME MESSAGE Integrated literature-derived protein and chemical knowledge bases can rationalize many aspects of drug development process including drug repositioning and biomarker design.
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Affiliation(s)
- Anton Yuryev
- Ariadne Genomics, Inc. 9430 Key West Ave, Rockville MD, 20850, USA +1 240 453 6296 ; +1 240 453 9026 ;
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Nagarajan RP, Fouse SD, Bell RJA, Costello JF. Methods for cancer epigenome analysis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 754:313-38. [PMID: 22956508 DOI: 10.1007/978-1-4419-9967-2_15] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Accurate detection of epimutations in tumor cells is crucial for -understanding the molecular pathogenesis of cancer. Alterations in DNA methylation in cancer are functionally important and clinically relevant, but even this well-studied area is continually re-evaluated in light of unanticipated results, such as the strong association between aberrant DNA methylation in adult tumors and polycomb group profiles in embryonic stem cells, cancer-associated genetic mutations in epigenetic regulators such as DNMT3A and TET family genes, and the discovery of altered 5-hydroxymethylcytosine, a product of TET proteins acting on 5-methylcytosine, in human tumors with TET mutations. The abundance and distribution of covalent histone modifications in primary cancer tissues relative to normal cells is an important but largely uncharted area, although there is good evidence for a mechanistic role of cancer-specific alterations in histone modifications in tumor etiology, drug response, and tumor progression. Meanwhile, the discovery of new epigenetic marks continues, and there are many useful methods for epigenome analysis applicable to primary tumor samples, in addition to cancer cell lines. For DNA methylation and hydroxymethylation, next-generation sequencing allows increasingly inexpensive and quantitative whole-genome profiling. Similarly, the refinement and maturation of chromatin immunoprecipitation with next-generation sequencing (ChIP-seq) has made possible genome-wide mapping of histone modifications, open chromatin, and transcription factor binding sites. Computational tools have been developed apace with these epigenome methods to better enable accurate interpretation of the profiling data.
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Acute hypersensitivity of pluripotent testicular cancer-derived embryonal carcinoma to low-dose 5-aza deoxycytidine is associated with global DNA Damage-associated p53 activation, anti-pluripotency and DNA demethylation. PLoS One 2012; 7:e53003. [PMID: 23300844 PMCID: PMC3531428 DOI: 10.1371/journal.pone.0053003] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Accepted: 11/26/2012] [Indexed: 12/28/2022] Open
Abstract
Human embryonal carcinoma (EC) cells are the stem cells of nonseminoma testicular germ cells tumors (TGCTs) and share remarkable similarities to human embryonic stem (ES) cells. In prior work we found that EC cells are hypersensitive to low nanomolar doses of 5-aza deoxycytidine (5-aza) and that this hypersensitivity partially depended on unusually high levels of the DNA methyltransferase, DNMT3B. We show here that low-dose 5-aza treatment results in DNA damage and induction of p53 in NT2/D1 cells. In addition, low-dose 5-aza results in global and gene specific promoter DNA hypomethylation. Low-dose 5-aza induces a p53 transcriptional signature distinct from that induced with cisplatin in NT2/D1 cells and also uniquely downregulates genes associated with pluripotency including NANOG, SOX2, GDF3 and Myc target genes. Changes in the p53 and pluripotency signatures with 5-aza were to a large extent dependent on high levels of DNMT3B. In contrast to the majority of p53 target genes upregulated by 5-aza that did not show DNA hypomethylation, several other genes induced with 5-aza had corresponding decreases in promoter methylation. These genes include RIN1, SOX15, GPER, and TLR4 and are novel candidate tumors suppressors in TGCTs. Our studies suggest that the hypersensitivity of NT2/D1 cells to low-dose 5-aza is multifactorial and involves the combined activation of p53 targets, repression of pluripotency genes, and activation of genes repressed by DNA methylation. Low-dose 5-aza therapy may be a general strategy to treat those tumors that are sustained by cells with embryonic stem-like properties.GEO NUMBER FOR THE MICROARRAY DATA: GSE42647.
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Zhu J, Li X, Kong X, Moran MS, Su P, Haffty BG, Yang Q. Testin is a tumor suppressor and prognostic marker in breast cancer. Cancer Sci 2012; 103:2092-101. [PMID: 22957844 DOI: 10.1111/cas.12020] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 08/23/2012] [Accepted: 09/01/2012] [Indexed: 12/11/2022] Open
Abstract
The testin (TES) gene was previously identified in the fragile chromosomal region FRA7G at 7q31.2. In the present study, we aimed to investigate the candidate tumor suppressor function of TES and explore its correlations to clinicopathologic features and prognosis in breast cancer. In clinical samples, we showed that the expression of TES decreased gradually from normal through ductal hyperplasia without atypia, atypical ductal hyperplasia, and ductal carcinoma in situ, to invasive ductal carcinoma. To explore the possible tumor suppressing function of TES, the expression of TES in breast cancer cells was manipulated by ectopic expression or by RNAi. We revealed that ectopic TES expression significantly inhibited cell proliferation, invasive ability, and angiogenesis, whereas knockdown of TES by RNAi enhanced cell proliferation, invasive ability, and angiogenesis. In an animal model, TES markedly inhibited breast cancer cell xenograft formation in athymic nude mice and reduced breast cancer cell metastasis to lung. Moreover, we revealed that TES inhibited the invasion and angiogenesis of breast cancer partially through miR-29b-mediated MMP-2 inhibition. Using the tissue microarray of breast cancer from Yale University, we found that lower TES expression was an independent prognostic factor for shorter overall survival and disease-free survival with univariate and multivariate analyses. Taken together, these data suggest that TES, as a valuable marker of breast cancer prognosis, plays an important role in the development and progression of breast cancer. TES may be an effective novel target in breast cancer prevention and treatment.
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Affiliation(s)
- Jiang Zhu
- Department of Breast Surgery, Qilu Hospital, Shandong University, Jinan, China
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Engström PG, Tommei D, Stricker SH, Ender C, Pollard SM, Bertone P. Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival. Genome Med 2012; 4:76. [PMID: 23046790 PMCID: PMC3556652 DOI: 10.1186/gm377] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 09/20/2012] [Accepted: 10/09/2012] [Indexed: 02/07/2023] Open
Abstract
Background Glioblastoma multiforme, the most common type of primary brain tumor in adults, is driven by cells with neural stem (NS) cell characteristics. Using derivation methods developed for NS cells, it is possible to expand tumorigenic stem cells continuously in vitro. Although these glioblastoma-derived neural stem (GNS) cells are highly similar to normal NS cells, they harbor mutations typical of gliomas and initiate authentic tumors following orthotopic xenotransplantation. Here, we analyzed GNS and NS cell transcriptomes to identify gene expression alterations underlying the disease phenotype. Methods Sensitive measurements of gene expression were obtained by high-throughput sequencing of transcript tags (Tag-seq) on adherent GNS cell lines from three glioblastoma cases and two normal NS cell lines. Validation by quantitative real-time PCR was performed on 82 differentially expressed genes across a panel of 16 GNS and 6 NS cell lines. The molecular basis and prognostic relevance of expression differences were investigated by genetic characterization of GNS cells and comparison with public data for 867 glioma biopsies. Results Transcriptome analysis revealed major differences correlated with glioma histological grade, and identified misregulated genes of known significance in glioblastoma as well as novel candidates, including genes associated with other malignancies or glioma-related pathways. This analysis further detected several long non-coding RNAs with expression profiles similar to neighboring genes implicated in cancer. Quantitative PCR validation showed excellent agreement with Tag-seq data (median Pearson r = 0.91) and discerned a gene set robustly distinguishing GNS from NS cells across the 22 lines. These expression alterations include oncogene and tumor suppressor changes not detected by microarray profiling of tumor tissue samples, and facilitated the identification of a GNS expression signature strongly associated with patient survival (P = 1e-6, Cox model). Conclusions These results support the utility of GNS cell cultures as a model system for studying the molecular processes driving glioblastoma and the use of NS cells as reference controls. The association between a GNS expression signature and survival is consistent with the hypothesis that a cancer stem cell component drives tumor growth. We anticipate that analysis of normal and malignant stem cells will be an important complement to large-scale profiling of primary tumors.
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Affiliation(s)
- Pär G Engström
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Diva Tommei
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Stefan H Stricker
- Samantha Dickson Brain Cancer Unit and Department of Cancer Biology, UCL Cancer Institute, University College London, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Christine Ender
- Samantha Dickson Brain Cancer Unit and Department of Cancer Biology, UCL Cancer Institute, University College London, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Steven M Pollard
- Samantha Dickson Brain Cancer Unit and Department of Cancer Biology, UCL Cancer Institute, University College London, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Paul Bertone
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK ; Genome Biology and Developmental Biology Units, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany ; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
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Muller FL, Colla S, Aquilanti E, Manzo VE, Genovese G, Lee J, Eisenson D, Narurkar R, Deng P, Nezi L, Lee MA, Hu B, Hu J, Sahin E, Ong D, Fletcher-Sananikone E, Ho D, Kwong L, Brennan C, Wang YA, Chin L, DePinho RA. Passenger deletions generate therapeutic vulnerabilities in cancer. Nature 2012; 488:337-42. [PMID: 22895339 PMCID: PMC3712624 DOI: 10.1038/nature11331] [Citation(s) in RCA: 253] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 06/15/2012] [Indexed: 01/17/2023]
Abstract
Inactivation of tumour-suppressor genes by homozygous deletion is a prototypic event in the cancer genome, yet such deletions often encompass neighbouring genes. We propose that homozygous deletions in such passenger genes can expose cancer-specific therapeutic vulnerabilities when the collaterally deleted gene is a member of a functionally redundant family of genes carrying out an essential function. The glycolytic gene enolase 1 (ENO1) in the 1p36 locus is deleted in glioblastoma (GBM), which is tolerated by the expression of ENO2. Here we show that short-hairpin-RNA-mediated silencing of ENO2 selectively inhibits growth, survival and the tumorigenic potential of ENO1-deleted GBM cells, and that the enolase inhibitor phosphonoacetohydroxamate is selectively toxic to ENO1-deleted GBM cells relative to ENO1-intact GBM cells or normal astrocytes. The principle of collateral vulnerability should be applicable to other passenger-deleted genes encoding functionally redundant essential activities and provide an effective treatment strategy for cancers containing such genomic events.
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Affiliation(s)
- Florian L Muller
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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