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HOXA5: A crucial transcriptional factor in cancer and a potential therapeutic target. Biomed Pharmacother 2022; 155:113800. [DOI: 10.1016/j.biopha.2022.113800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/29/2022] [Accepted: 10/02/2022] [Indexed: 11/20/2022] Open
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Bücker L, Lehmann U. CDH1 (E-cadherin) Gene Methylation in Human Breast Cancer: Critical Appraisal of a Long and Twisted Story. Cancers (Basel) 2022; 14:cancers14184377. [PMID: 36139537 PMCID: PMC9497067 DOI: 10.3390/cancers14184377] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/05/2022] [Accepted: 09/05/2022] [Indexed: 11/27/2022] Open
Abstract
Simple Summary Genes can be inactivated by specific modifications of DNA bases, most often by adding a methyl group to the DNA base cytosine if it is followed by guanosine (CG methylation). This modification prevents gene expression and has been reported for many different genes in nearly all types of cancer. A prominent example is the gene CDH1, which encodes the cell-adhesion molecule E-cadherin. This is an important player in the spreading of tumor cells within the body (metastasis). Particularly in human breast cancer, many different research groups have studied the inactivation of the CDH1 gene via DNA methylation using various methods. Over the last 20 years, different, in part, even contradicting results have been published for the CDH1 gene in breast cancer. This review summarizes the most important publications and explains the bewildering heterogeneity of results through careful analysis of the methods which have been used. Abstract Epigenetic inactivation of a tumor suppressor gene by aberrant DNA methylation is a well-established defect in human tumor cells, complementing genetic inactivation by mutation (germline or somatic). In human breast cancer, aberrant gene methylation has diagnostic, prognostic, and predictive potential. A prominent example is the hypermethylation of the CDH1 gene, encoding the adhesion protein E-Cadherin (“epithelial cadherin”). In numerous publications, it is reported as frequently affected by gene methylation in human breast cancer. However, over more than two decades of research, contradictory results concerning CDH1 gene methylation in human breast cancer accumulated. Therefore, we review the available evidence for and against the role of DNA methylation of the CDH1 gene in human breast cancer and discuss in detail the methodological reasons for conflicting results, which are of general importance for the analysis of aberrant DNA methylation in human cancer specimens. Since the loss of E-cadherin protein expression is a hallmark of invasive lobular breast cancer (ILBC), special attention is paid to CDH1 gene methylation as a potential mechanism for loss of expression in this special subtype of human breast cancer. Proper understanding of the methodological basis is of utmost importance for the correct interpretation of results supposed to demonstrate the presence and clinical relevance of aberrant DNA methylation in cancer specimens.
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Affiliation(s)
| | - Ulrich Lehmann
- Correspondence: ; Tel.: +49-(0)511-532-4501; Fax: +49-(0)511-532-5799
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Qu M, Wan S, Wu H, Ren B, Chen Y, Liu L, Shen H. The Whole Blood DNA Methylation Patterns of Extrinsic Apoptotic Signaling Pathway Related Genes in Autoimmune Thyroiditis among Areas with Different Iodine Levels. Br J Nutr 2022; 129:1-35. [PMID: 35260211 DOI: 10.1017/s0007114522000721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Autoimmune thyroiditis (AIT) has a complex etiology and the susceptibility to it is determined by a combination of genetic and environmental factors, although these are not yet fully understood. The present research aimed to explore the DNA methylation patterns in whole blood of extrinsic apoptotic signaling pathway related genes in AIT among areas with different iodine levels. We selected the iodine-fortification areas (IFA), iodine-adequate areas (IAA) and water-based iodine-excess areas (IEA) from Shandong Province of China as survey sites. Totally 176 AIT cases and 176 controls were included. MethylTargetTM and QT-PCR technology were used to detect candidate genes' DNA methylation levels and mRNA expression levels, respectively. We found that DAPK1 DNA methylation levels in AIT cases (especially in female) were significantly higher than controls (t=2.7715, P=0.0059; t=2.4638, P=0.0143 in female). There were differences in DAPK1(t=2.5384, P=0.0121), TNFSF8(t=2.1667, P=0.0334) and TNFAIP8(t=2.5672, P=0.0121) genes methylation between cases and controls with different water iodine levels. The mRNA expression of DAPK1(t=4.329, P<0.001) and TNFAIP8(t=3.775, P<0.001) in the cases were increased. We identified the differences in the DNA methylation status of the extrinsic apoptotic signaling pathway related genes between AIT and controls and in different iodine levels areas. The results were verified at the mRNA level. The environmental iodine may affect DNA methylation to some extent.
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Affiliation(s)
- Mengying Qu
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang 150081, China
- Division of Health Risk Factor Monitoring and Control, Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504)
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University
| | - Siyuan Wan
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang 150081, China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504)
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University
- Department of Preventive Medicine, Qiqihar Medical University, Qiqihar, Heilongjiang 161006, China
| | - Huaiyong Wu
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang 150081, China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504)
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University
| | - Bingxuan Ren
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang 150081, China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504)
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University
| | - Yao Chen
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang 150081, China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504)
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University
| | - Lixiang Liu
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang 150081, China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504)
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University
| | - Hongmei Shen
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang 150081, China
- National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504)
- Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University
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Epigenetic Dysregulation of the Homeobox A5 ( HOXA5) Gene Associates with Subcutaneous Adipocyte Hypertrophy in Human Obesity. Cells 2022; 11:cells11040728. [PMID: 35203377 PMCID: PMC8870634 DOI: 10.3390/cells11040728] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 02/14/2022] [Indexed: 12/28/2022] Open
Abstract
Along with insulin resistance and increased risk of type 2 diabetes (T2D), lean first-degree relatives of T2D subjects (FDR) feature impaired adipogenesis in subcutaneous adipose tissue (SAT) and subcutaneous adipocyte hypertrophy well before diabetes onset. The molecular mechanisms linking these events have only partially been clarified. In the present report, we show that silencing of the transcription factor Homeobox A5 (HOXA5) in human preadipocytes impaired differentiation in mature adipose cells in vitro. The reduced adipogenesis was accompanied by inappropriate WNT-signaling activation. Importantly, in preadipocytes from FDR individuals, HOXA5 expression was attenuated, with hypermethylation of the HOXA5 promoter region found responsible for its downregulation, as revealed by luciferase assay. Both HOXA5 gene expression and DNA methylation were significantly correlated with SAT adipose cell hypertrophy in FDR, whose increased adipocyte size marks impaired adipogenesis. In preadipocytes from FDR, the low HOXA5 expression negatively correlated with enhanced transcription of the WNT signaling downstream genes NFATC1 and WNT2B. In silico evidence indicated that NFATC1 and WNT2B were directly controlled by HOXA5. The HOXA5 promoter region also was hypermethylated in peripheral blood leukocytes from these same FDR individuals, which was further revealed in peripheral blood leukocytes from an independent group of obese subjects. Thus, HOXA5 controlled adipogenesis in humans by suppressing WNT signaling. Altered DNA methylation of the HOXA5 promoter contributed to restricted adipogenesis in the SAT of lean subjects who were FDR of type 2 diabetics and in obese individuals.
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Feng Y, Zhang T, Wang Y, Xie M, Ji X, Luo X, Huang W, Xia L. Homeobox Genes in Cancers: From Carcinogenesis to Recent Therapeutic Intervention. Front Oncol 2021; 11:770428. [PMID: 34722321 PMCID: PMC8551923 DOI: 10.3389/fonc.2021.770428] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 09/28/2021] [Indexed: 12/11/2022] Open
Abstract
The homeobox (HOX) genes encoding an evolutionarily highly conserved family of homeodomain-containing transcriptional factors are essential for embryogenesis and tumorigenesis. HOX genes are involved in cell identity determination during early embryonic development and postnatal processes. The deregulation of HOX genes is closely associated with numerous human malignancies, highlighting the indispensable involvement in mortal cancer development. Since most HOX genes behave as oncogenes or tumor suppressors in human cancer, a better comprehension of their upstream regulators and downstream targets contributes to elucidating the function of HOX genes in cancer development. In addition, targeting HOX genes may imply therapeutic potential. Recently, novel therapies such as monoclonal antibodies targeting tyrosine receptor kinases, small molecular chemical inhibitors, and small interfering RNA strategies, are difficult to implement for targeting transcriptional factors on account of the dual function and pleiotropic nature of HOX genes-related molecular networks. This paper summarizes the current state of knowledge on the roles of HOX genes in human cancer and emphasizes the emerging importance of HOX genes as potential therapeutic targets to overcome the limitations of present cancer therapy.
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Affiliation(s)
- Yangyang Feng
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tongyue Zhang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yijun Wang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Meng Xie
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyu Ji
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiangyuan Luo
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenjie Huang
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Limin Xia
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Maćkowska N, Drobna-Śledzińska M, Witt M, Dawidowska M. DNA Methylation in T-Cell Acute Lymphoblastic Leukemia: In Search for Clinical and Biological Meaning. Int J Mol Sci 2021; 22:ijms22031388. [PMID: 33573325 PMCID: PMC7866817 DOI: 10.3390/ijms22031388] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/22/2021] [Accepted: 01/23/2021] [Indexed: 12/21/2022] Open
Abstract
Distinct DNA methylation signatures, related to different prognosis, have been observed across many cancers, including T-cell acute lymphoblastic leukemia (T-ALL), an aggressive hematological neoplasm. By global methylation analysis, two major phenotypes might be observed in T-ALL: hypermethylation related to better outcome and hypomethylation, which is a candidate marker of poor prognosis. Moreover, DNA methylation holds more than a clinical meaning. It reflects the replicative history of leukemic cells and most likely different mechanisms underlying leukemia development in these T-ALL subtypes. The elucidation of the mechanisms and aberrations specific to (epi-)genomic subtypes might pave the way towards predictive diagnostics and precision medicine in T-ALL. We present the current state of knowledge on the role of DNA methylation in T-ALL. We describe the involvement of DNA methylation in normal hematopoiesis and T-cell development, focusing on epigenetic aberrations contributing to this leukemia. We further review the research investigating distinct methylation phenotypes in T-ALL, related to different outcomes, pointing to the most recent research aimed to unravel the biological mechanisms behind differential methylation. We highlight how technological advancements facilitated broadening the perspective of the investigation into DNA methylation and how this has changed our understanding of the roles of this epigenetic modification in T-ALL.
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Yang Y, Zhong F, Huang X, Zhang N, Du J, Long Z, Zheng B, Lin W, Liu W, Ma W. High expression of HOXA5 is associated with poor prognosis in acute myeloid leukemia. Curr Probl Cancer 2020; 45:100673. [PMID: 33223227 DOI: 10.1016/j.currproblcancer.2020.100673] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 11/19/2022]
Abstract
BACKGROUND HOXA5 is considered as an oncogene in many tumors. This study in- vestigated the HOXA5 expression in Chinese acute myeloid leukemia (AML) patients and evaluated the predictive significance of HOXA5 with a single-center retrospective study. METHODS We investigated the expression pattern and prognostic value of HOXA5 in patients with AML through by using a series of databases and various datasets, including the ONCOMINE, TCGA, and STRING datasets. The bone marrow samples of 53 newly diagnosed AML patients (non-M3 subtype) and 19 benign individuals were collected in our center. HOXA5 mRNA expression levels were detected by real-time qPCR, HOXA5 protein expression levels were detected by Western Blot. Clinical data was obtained from inpatient medical records. RESULTS Two microarrays in Oncomine showed that the expression level of HOXA5 was significantly upregulated in AML. Our data revealed that AML patients had higher HOXA5 mRNA and protein expression levels than the controls (P < 0.001). The blast percentage in bone marrow of HOXA5 high-expression group was higher that of HOXA5 low-expression group (P < 0.05). Higher expression level of HOXA5 revealed a worse OS in AML (P < 0.05). CONCLUSION Our findings suggested that HOXA5 might have the potential ability to act as a diagnostic biomarker and potential therapeutic target for AML.
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Affiliation(s)
- You Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China; Department of Pediatrics, Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China
| | - Fangfang Zhong
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China; Department of Pediatrics, Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China
| | - Xiaoming Huang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Na Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Jingjing Du
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Ze Long
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Bowen Zheng
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Wanjun Lin
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Wenjun Liu
- Department of Pediatrics, Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China.
| | - Wenzhe Ma
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China.
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Lin R, Li C, Liu Z, Wu R, Lu J. Genome-wide DNA methylation profiling identifies epigenetic signatures of gastric cardiac intestinal metaplasia. J Transl Med 2020; 18:292. [PMID: 32736574 PMCID: PMC7393819 DOI: 10.1186/s12967-020-02453-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 07/21/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Measuring the DNA methylome may offer the opportunity to identify novel disease biomarkers and insights into disease mechanisms. Although aberrant DNA methylation has been investigated in many human cancers and precancerous lesions, the DNA methylation landscape of gastric cardiac intestinal metaplasia (IM) remains unknown. Therefore, we aimed to investigate the genome-wide DNA methylation landscape and to search for potential epigenetic biomarkers of gastric cardiac IM. METHODS Histopathologic profiling was performed on a total of 118 gastric cardiac biopsies from cancer-free individuals. Genome-wide DNA methylation analysis was performed on 11 gastric cardiac mucosal biopsies (IM = 7; normal = 4) using Illumina 850K microarrays. Transcriptional relevance of any candidate epigenetic biomarker was validated by qRT-PCR. RESULTS The detection rate of gastric cardiac IM was 23% (27/118) in cancer-free individuals. Genome-wide DNA methylation profiling showed a global decrease in methylation in IM compared with normal tissues (median methylation = 0.64 and 0.70 for gastric cardiac IM and normal tissues, respectively). Differential methylation analysis between gastric cardiac IM and normal tissues identified 38,237 differentially methylated probes (DMPs) with a majority of sites showing hypermethylation in IM compared with normal tissues (56.3% vs. 43.7%). Subsequent analysis revealed a significant enrichment of hypermethylated DMPs in promoter and CpG islands (p < 0.001 for both, Pearson χ2 test). For DMPs located in promoter CpG islands showing extreme hypermethylation, the candidate gene with the largest number of DMPs (n = 7) was mapped to HOXA5. Accordingly, mRNA expression of HOXA5 was significantly reduced in IM compared to normal tissue. CONCLUSIONS Our results suggest the implication of alterations in DNA methylation in gastric cardiac IM and highlight that HOXA5 hypermethylation may be a promising epigenetic biomarker, emphasizing the role of aberrant HOXA5 expression in the pathogenesis of gastric cardiac IM.
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Affiliation(s)
- Runhua Lin
- Department of Pathology, Shantou University Medical College, Shantou, 515041, China.
| | - Chenxi Li
- Department of Pathology, Shantou University Medical College, Shantou, 515041, China
| | - Zhaohui Liu
- The Second People's Hospital of Shenzhen/The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Ruinuan Wu
- The Second People's Hospital of Shenzhen/The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Jianghong Lu
- Department of Pathology, Shantou University Medical College, Shantou, 515041, China
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Yu T, Chen D, Zhang L, Wan D. microRNA-26a-5p Promotes Proliferation and Migration of Osteosarcoma Cells by Targeting HOXA5 in vitro and in vivo. Onco Targets Ther 2019; 12:11555-11565. [PMID: 32021239 PMCID: PMC6941950 DOI: 10.2147/ott.s232100] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/05/2019] [Indexed: 12/25/2022] Open
Abstract
Background Osteosarcoma is the most common primary malignant tumor of bone. However, the underlying pathogenic mechanisms are still unclear. miR-26a was an endogenous non-coding small RNAs that have been showed to play a critical role in regulating varieties of biological and pathological processes. In this study, we will investigate the function of miR-26a-5p in osteosarcoma cells. Methods In this study, we explored the role of miR-26a-5p in osteosarcoma cell lines using qPCR, detected the proliferation, cell cycle and cell migration by CCK-8, PI and transwell. Results We found that compared with noncancerous cells, miR-26a-5p was highly expressed in osteosarcoma cell lines, especially in U2OS cells. Overexpression of miR-26a-5p promotes cell proliferation, cell cycle, and cell migration, but inhibits cell apoptosis. But down-regulation of miR-26a-5p in U2OS cells exhibits opposite effects. We also confirmed that miR-26a-5p directly targets HOXA5 in U2OS cells. Overexpression of HOXA5 reversed the effect of miR-26a-5p on cell proliferation, migration, and apoptosis. Besides, we showed in that knock-down of miR-26a-5p or overexpression of HOXA5 increased cell sensitivity to chemotherapeutic drug paclitaxel. Conclusion These findings indicate that highly expressed miR-26a-5p in osteosarcoma cells, and promotes proliferation and migration, but inhibits apoptosis of osteosarcoma cells by targeting HOXA5 which suggest that miR-26a-5p could serve as a novel therapeutic target for osteosarcoma.
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Affiliation(s)
- Tianhua Yu
- Department of Orthopedics, Orthopedic Institute of Harbin, The Fifth Hospital in Harbin, Harbin, People's Republic of China
| | - Dexin Chen
- School of Materials Engineering, Shanghai University of Engineering Science, Shanghai, People's Republic of China
| | - Lei Zhang
- Department of Orthopedics, The First Affiliated Hospital of Shandong First Medical University, Shandong, People's Republic of China
| | - Daqian Wan
- Department of Orthopedics, Orthopedic Institute of Harbin, The Fifth Hospital in Harbin, Harbin, People's Republic of China.,Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration, Ministry of Education of the People's Republic of China, Shanghai, People's Republic of China.,Department of Orthopedics, Tongji Hospital Affiliated to Tongji University School of Medicine, Shanghai, People's Republic of China
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Wang SL, Huang Y, Su R, Yu YY. Silencing long non-coding RNA HOTAIR exerts anti-oncogenic effect on human acute myeloid leukemia via demethylation of HOXA5 by inhibiting Dnmt3b. Cancer Cell Int 2019; 19:114. [PMID: 31168296 PMCID: PMC6489230 DOI: 10.1186/s12935-019-0808-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 03/28/2019] [Indexed: 11/10/2022] Open
Abstract
Background As an aggressive hematological malignancy, acute myeloid leukemia (AML) remains a dismal disease with poor prognosis. Long non-coding RNAs (lncRNAs) have been widely reported to be involved in tumorigenesis of AML. Here, we define an important role of lncRNA HOTAIR in AML in relation to HOXA5 methylation. Methods Firstly, the expression of HOTAIR was examined in AML samples and cells collected. Next, gain- or loss-of function experiments were conducted in AML cells to explore the effect of HOTAIR on AML. Then, relationship among HOXA5 promoter methylation, HOTAIR and Dnmt3b was measured. Expression of HOXA5 and cell proliferation/apoptosis-related genes was also detected. A last, in vivo assay was performed to assess the tumor formation in nude mice in order to explore the roles of HOTAIR and HOXA5 in cell apoptosis and proliferation. Results LncRNA HOTAIR was found to be upregulated in AML cells and tissues. With silencing of HOTAIR and overexpression of HOXA5, AML cell proliferation was decreased while the apoptosis was induced. Furthermore, HOTAIR was observed to recruit Dnmt3b and to increase HOXA5 promoter methylation. Moreover, silencing HOTAIR and upregulating HOXA5 were found to induce apoptosis and reduce proliferation of AML cells in vivo. Conclusion Our findings highlight the anti-tumor ability of HOTAIR silencing in AML, suggesting that silencing HOTAIR was able to inhibit AML progression through HOXA5 promoter demethylation by decreasing Dnmt3b. Electronic supplementary material The online version of this article (10.1186/s12935-019-0808-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Si-Li Wang
- 1Department of Hematology, The First Affiliated Hospital of Xiamen University, No. 55, Zhenhai Road, Xiamen, 361003 Fujian People's Republic of China.,2Department of Clinical Medicines, Fujian Medical University, No. 1, Xuefu North Road, Fuzhou, 350108 Fujian People's Republic of China
| | - Yun Huang
- 1Department of Hematology, The First Affiliated Hospital of Xiamen University, No. 55, Zhenhai Road, Xiamen, 361003 Fujian People's Republic of China
| | - Rui Su
- 1Department of Hematology, The First Affiliated Hospital of Xiamen University, No. 55, Zhenhai Road, Xiamen, 361003 Fujian People's Republic of China
| | - Yong-Yang Yu
- 3Department of General Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, 361003 People's Republic of China
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Wu Y, Zhou T, Tang Q, Xiao J. HOXA5 inhibits tumor growth of gastric cancer under the regulation of microRNA-196a. Gene 2018; 681:62-68. [PMID: 30267809 DOI: 10.1016/j.gene.2018.09.051] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 09/19/2018] [Accepted: 09/25/2018] [Indexed: 12/28/2022]
Abstract
Homeobox A5 (HOXA5) is a member of the HOX protein family which were implicated in serval critical process and was cancer-specific dysregulated in human cancers. However, its expression and function in human gastric cancer (GC) was still largely unknown. In this study, we confirmed for the first time that HOXA5 mRNA and protein was down-regulated in GC tissues and cell lines. Clinical data showed that low HOXA5 was significantly associated poor prognostic features, including large tumor size and advanced TNM stage. For 5-year survival, HOXA5 served as a potential prognostic marker of GC patients. Notably, HOXA5 inhibited cell viability, colony formation, proliferation, cell cycle progression and promoted apoptosis in vitro and in vivo. Furthermore, we demonstrated that HOXA5 expression was regulated by miR-196a. In GC tissues, miR-196a has an inverse correlation with HOXA5 expression. Conclusively, our results demonstrated that HOXA5 functions as a tumor suppressor in regulating tumor growth of GC under regulation of miR-196a, supporting its potential utility as a therapeutic target for GC.
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Affiliation(s)
- Yingxin Wu
- Department of Gastrointestinal surgery, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan 610500, China
| | - Tong Zhou
- Department of Gastrointestinal surgery, The Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637000, China
| | - Qian Tang
- Department of Emergency, The Third People's Hospital of Chengdu, Chengdu, Sichuan 610000, China
| | - Jiangwei Xiao
- Department of Gastrointestinal surgery, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan 610500, China.
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12
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Huang YH, Su J, Lei Y, Brunetti L, Gundry MC, Zhang X, Jeong M, Li W, Goodell MA. DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A. Genome Biol 2017; 18:176. [PMID: 28923089 PMCID: PMC5604343 DOI: 10.1186/s13059-017-1306-z] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 08/23/2017] [Indexed: 12/15/2022] Open
Abstract
Background DNA methylation has widespread effects on gene expression during development. However, our ability to assign specific function to regions of DNA methylation is limited by the poor correlation between global patterns of DNA methylation and gene expression. Results Here, we utilize nuclease-deactivated Cas9 protein fused to repetitive peptide epitopes (SunTag) recruiting multiple copies of antibody-fused de novo DNA methyltransferase 3A (DNMT3A) (dCas9-SunTag-DNMT3A) to amplify the local DNMT3A concentration to methylate genomic sites of interest. We demonstrate that dCas9-SunTag-DNMT3A dramatically increases CpG methylation at the HOXA5 locus in human embryonic kidney (HEK293T) cells. Furthermore, using a single guide RNA, dCas9-SunTag-DNMT3A is able to methylate a 4.5-kb genomic region and repress HOXA5 gene expression. Reduced representation bisulfite sequencing and RNA-seq show that dCas9-SunTag-DNMT3A methylates regions of interest with minimal impact on the global DNA methylome and transcriptome. Conclusions This effective and precise tool enables site-specific manipulation of DNA methylation and may be used to address the relationship between DNA methylation and gene expression. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1306-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yung-Hsin Huang
- Department of Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jianzhong Su
- Division of Biostatistics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yong Lei
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lorenzo Brunetti
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Michael C Gundry
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xiaotian Zhang
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Mira Jeong
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Wei Li
- Division of Biostatistics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Margaret A Goodell
- Department of Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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13
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High resolution methylation analysis of the HoxA5 regulatory region in different somatic tissues of laboratory mouse during development. Gene Expr Patterns 2017; 23-24:59-69. [DOI: 10.1016/j.gep.2017.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/02/2017] [Accepted: 03/26/2017] [Indexed: 11/18/2022]
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14
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Jeannotte L, Gotti F, Landry-Truchon K. Hoxa5: A Key Player in Development and Disease. J Dev Biol 2016; 4:E13. [PMID: 29615582 PMCID: PMC5831783 DOI: 10.3390/jdb4020013] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/08/2016] [Accepted: 03/16/2016] [Indexed: 12/28/2022] Open
Abstract
A critical position in the developmental hierarchy is occupied by the Hox genes, which encode transcription factors. Hox genes are crucial in specifying regional identity along the embryonic axes and in regulating morphogenesis. In mouse, targeted mutations of Hox genes cause skeletal transformations and organ defects that can impair viability. Here, we present the current knowledge about the Hoxa5 gene, a paradigm for the function and the regulation of Hox genes. The phenotypic survey of Hoxa5-/- mice has unveiled its critical role in the regional specification of the skeleton and in organogenesis. Most Hoxa5-/- mice die at birth from respiratory distress due to tracheal and lung dysmorphogenesis and impaired diaphragm innervation. The severity of the phenotype establishes that Hoxa5 plays a predominant role in lung organogenesis versus other Hox genes. Hoxa5 also governs digestive tract morphogenesis, thyroid and mammary glands development, and ovary homeostasis. Deregulated Hoxa5 expression is reported in cancers, indicating Hoxa5 involvement in tumor predisposition and progression. The dynamic Hoxa5 expression profile is under the transcriptional control of multiple cis-acting sequences and trans-acting regulators. It is also modulated by epigenetic mechanisms, implicating chromatin modifications and microRNAs. Finally, lncRNAs originating from alternative splicing and distal promoters encompass the Hoxa5 locus.
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Affiliation(s)
- Lucie Jeannotte
- Centre de recherche sur le cancer de l'Université Laval; CRCHU de Québec, L'Hôtel-Dieu de Québec, QC G1R 3S3, Canada.
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, QC G1V 0A6, Canada.
| | - Florian Gotti
- Centre de recherche sur le cancer de l'Université Laval; CRCHU de Québec, L'Hôtel-Dieu de Québec, QC G1R 3S3, Canada.
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, QC G1V 0A6, Canada.
| | - Kim Landry-Truchon
- Centre de recherche sur le cancer de l'Université Laval; CRCHU de Québec, L'Hôtel-Dieu de Québec, QC G1R 3S3, Canada.
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, QC G1V 0A6, Canada.
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15
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Dunn J, Simmons R, Thabet S, Jo H. The role of epigenetics in the endothelial cell shear stress response and atherosclerosis. Int J Biochem Cell Biol 2015; 67:167-76. [PMID: 25979369 DOI: 10.1016/j.biocel.2015.05.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Revised: 04/30/2015] [Accepted: 05/02/2015] [Indexed: 12/15/2022]
Abstract
Currently in the field of vascular biology, the role of epigenetics in endothelial cell biology and vascular disease has attracted more in-depth study. Using both in vitro and in vivo models of blood flow, investigators have recently begun to reveal the underlying epigenetic regulation of endothelial gene expression. Recently, our group, along with two other independent groups, have demonstrated that blood flow controls endothelial gene expression by DNA methyltransferases (DNMT1 and 3A). Disturbed flow (d-flow), characterized by low and oscillating shear stress (OS), is pro-atherogenic and induces expression of DNMT1 both in vivo and in vitro. D-flow regulates genome-wide DNA methylation patterns in a DNMT-dependent manner. The DNMT inhibitor 5-Aza-2'deoxycytidine (5Aza) or DNMT1 siRNA reduces OS-induced endothelial inflammation. Moreover, 5Aza inhibits the development of atherosclerosis in ApoE(-/-) mice. Through a systems biological analysis of genome-wide DNA methylation patterns and gene expression data, we found 11 mechanosensitive genes which were suppressed by d-flow in vivo, experienced hypermethylation in their promoter region in response to d-flow, and were rescued by 5Aza treatment. Interestingly, among these mechanosensitive genes, the two transcription factors HoxA5 and Klf3 contain cAMP-response-elements (CRE), which may indicate that methylation of CRE sites could serve as a mechanosensitive master switch in gene expression. These findings provide new insight into the mechanism by which flow controls epigenetic DNA methylation patterns, which in turn alters endothelial gene expression, regulates vascular biology, and induces atherosclerosis. These novel findings have broad implications for understanding the biochemical mechanisms of atherogenesis and provide a basis for identifying potential therapeutic targets for atherosclerosis. This article is part of a Directed Issue entitled: Epigenetics dynamics in development and disease.
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Affiliation(s)
- Jessilyn Dunn
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, USA
| | - Rachel Simmons
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, USA
| | - Salim Thabet
- Division of Cardiology, Georgia Institute of Technology and Emory University, USA
| | - Hanjoong Jo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, USA; Division of Cardiology, Georgia Institute of Technology and Emory University, USA.
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16
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Musialik E, Bujko M, Kober P, Grygorowicz MA, Libura M, Przestrzelska M, Juszczyński P, Borg K, Florek I, Jakóbczyk M, Siedlecki JA. Promoter DNA methylation and expression levels of HOXA4, HOXA5 and MEIS1 in acute myeloid leukemia. Mol Med Rep 2015; 11:3948-54. [PMID: 25585874 DOI: 10.3892/mmr.2015.3196] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 11/03/2014] [Indexed: 11/06/2022] Open
Abstract
HOXA genes encode transcription factors, which are crucial for embryogenesis and tissue differentiation and are involved in the early stages of hematopoiesis. Aberrations in HOXA genes and their cofactor MEIS1 are found in human neoplasms, including acute myeloid leukemia (AML). The present study investigated the role of HOXA4, HOXA5 and MEIS1 promoter DNA methylation and mRNA expression in AML. Samples from 78 AML patients and 12 normal bone marrow (BM) samples were included. The levels of promoter DNA methylation were determined using quantitative methylation‑specific polymerase chain reaction (PCR; qMSP) and the relative expression levels were measured using reverse transcription quantitative PCR in Ficoll‑separated BM mononuclear cells and in fluorescent activated cell sorting‑sorted populations of normal hematopoietic progenitors. In total, 38.1 and 28.9% of the patients exhibited high methylation levels of HOXA4 and HOXA5, respectively, compared with the control samples, and MEIS1 methylation was almost absent. An inverse correlation between HOXA4 methylation and expression was identified in a group of patients with a normal karyotype (NK AML). An association between the genes was observed and correlation between the DNA methylation and expression levels of the HOXA gene promoter with the expression of MEIS1 was observed. Patients with favorable chromosomal aberrations revealed a low level of HOXA4 methylation and decreased expression levels of HOXA5 and MEIS1 compared with the NK AML and the adverse cytogenetic risk patients. The NK AML patients with NPM1 mutations exhibited elevated HOXA4 methylation and expression levels of HOXA5 and MEIS1 compared with the NPM1 wild‑type patients. Comparison of the undifferentiated BM‑derived hematopoietic CD34+CD38low, CD34+CD38+ and CD15+ cells revealed a gradual decrease in the expression levels of these three genes and an increase in HOXA4 promoter methylation. This differentiation‑associated variability was not observed in AML, which was classified according to the French‑American‑British system.
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Affiliation(s)
- Ewa Musialik
- Department of Molecular and Translational Oncology, Maria Sklodowska‑Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02‑781, Poland
| | - Mateusz Bujko
- Department of Molecular and Translational Oncology, Maria Sklodowska‑Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02‑781, Poland
| | - Paulina Kober
- Department of Molecular and Translational Oncology, Maria Sklodowska‑Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02‑781, Poland
| | - Monika Anna Grygorowicz
- Department of Immunology, Maria Sklodowska‑Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02‑781, Poland
| | - Marta Libura
- Department of Hematology, Oncology and Internal Diseases, The Medical University of Warsaw, Warsaw 02‑097, Poland
| | - Marta Przestrzelska
- Department of Hematology, Oncology and Internal Diseases, The Medical University of Warsaw, Warsaw 02‑097, Poland
| | - Przemysław Juszczyński
- Department of Diagnostic Hematology, Institute of Hematology and Transfusion Medicine, Warsaw 02‑109, Poland
| | - Katarzyna Borg
- Department of Diagnostic Hematology, Institute of Hematology and Transfusion Medicine, Warsaw 02‑109, Poland
| | - Izabela Florek
- Department of Hematology, Jagiellonian University, Cracow 31‑501, Poland
| | | | - Janusz Aleksander Siedlecki
- Department of Molecular and Translational Oncology, Maria Sklodowska‑Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02‑781, Poland
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17
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Yang J, Chen L, Kong X, Huang T, Cai YD. Analysis of tumor suppressor genes based on gene ontology and the KEGG pathway. PLoS One 2014; 9:e107202. [PMID: 25207935 PMCID: PMC4160198 DOI: 10.1371/journal.pone.0107202] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Accepted: 08/07/2014] [Indexed: 12/31/2022] Open
Abstract
Cancer is a serious disease that causes many deaths every year. We urgently need to design effective treatments to cure this disease. Tumor suppressor genes (TSGs) are a type of gene that can protect cells from becoming cancerous. In view of this, correct identification of TSGs is an alternative method for identifying effective cancer therapies. In this study, we performed gene ontology (GO) and pathway enrichment analysis of the TSGs and non-TSGs. Some popular feature selection methods, including minimum redundancy maximum relevance (mRMR) and incremental feature selection (IFS), were employed to analyze the enrichment features. Accordingly, some GO terms and KEGG pathways, such as biological adhesion, cell cycle control, genomic stability maintenance and cell death regulation, were extracted, which are important factors for identifying TSGs. We hope these findings can help in building effective prediction methods for identifying TSGs and thereby, promoting the discovery of effective cancer treatments.
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Affiliation(s)
- Jing Yang
- The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine (SJTUSM) and Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, People’s Republic of China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, People’s Republic of China
| | - Xiangyin Kong
- The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine (SJTUSM) and Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, People’s Republic of China
| | - Tao Huang
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Yu-Dong Cai
- Institute of Systems Biology, Shanghai University, Shanghai, People’s Republic of China
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18
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β-Arrestin1 promotes the progression of chronic myeloid leukaemia by regulating BCR/ABL H4 acetylation. Br J Cancer 2014; 111:568-76. [PMID: 24937675 PMCID: PMC4119990 DOI: 10.1038/bjc.2014.335] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 03/31/2014] [Accepted: 05/15/2014] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND β-Arrestins are scaffold proteins that interact with various cellular signals. Although β-arrestin2 mediates the initiation and progression of myeloid leukaemia, the critical role of β-arrestin1 in the chronic myeloid leukaemia (CML) is still unknown. The aim of this study is to investigate the essential function of β-arrestin1 in CML. METHODS The expressions of β-arrestin1 and BCR/ABL in CML patients, animal models and K562 cells were measured by RT-PCR, immunofluorescence and western blotting. The effect of β-arrestin1 on CML animal models and K562 cells by colony formation, MTT and survival analysis were assessed. BCR/ABL H4 acetylation was analysed through the use of Chromatin-immunoprecipitation (ChIP) -on-chip and confirmed by ChIP respectively. Co-immunoprecipitation and confocal were examined for the binding of β-arrestin1 with enhancer of zeste homologue 2 (EZH2). RESULTS The higher expression of β-arrestin1 is positively correlated with clinical phases of CML patients. Depletion of β-arrestin1 decelerates progression of K562 and primary cells, and increases survival of CML mice. Importantly, silenced β-arrestin1 results in the decrease of BCR/ABL H4 acetylation level in K562 cells. Further data illustrate that nuclear β-arrestin1 binds to EZH2 to mediate BCR/ABL acetylation and thus regulates cell progression in K562 cells and the survival of CML mice. CONCLUSIONS Our findings reveal a novel function of β-arrestin1 binding to EZH2 to promote CML progression by regulating BCR/ABL H4 acetylation.
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19
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Gautrey HE, van Otterdijk SD, Cordell HJ, Mathers JC, Strathdee G. DNA methylation abnormalities at gene promoters are extensive and variable in the elderly and phenocopy cancer cells. FASEB J 2014; 28:3261-72. [PMID: 24858281 DOI: 10.1096/fj.13-246173] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Abnormal patterns of DNA methylation are one of the hallmarks of cancer cells. The process of aging has also been associated with similar, albeit less dramatic, changes in methylation patterns, leading to the hypothesis that age-related changes in DNA methylation may partially underlie the increased risk of cancer in the elderly. Here we studied 377 participants aged 85 yr from the Newcastle 85+ Study to investigate the extent of, and interindividual variation in, age-related changes in DNA methylation at specific CpG islands. Using highly quantitative pyrosequencing analysis, we found extensive and highly variable methylation of promoter-associated CpG islands with levels ranging from 4% to 35%, even at known tumor suppressor genes such as TWIST2. Furthermore, the interindividual differences in methylation seen across this elderly population phenocopies multiple features of the altered methylation patterns seen in cancer cells. Both aging- and cancer-related methylation can occur at similar sets of genes, both result in the formation of densely methylated, and likely transcriptionally repressed, alleles, and both exhibit coordinate methylation across multiple loci. In addition, high methylation levels were associated with subsequent diagnosis of leukemia or lymphoma during a 3-yr follow-up period (P=0.00008). These data suggest that the accumulation of age-related changes in promoter-associated CpG islands may contribute to the increased cancer risk seen during aging.-Gautrey, H. E., van Otterdijk, S. D., Cordell, H. J., Newcastle 85+ study core team, Mathers, J. C., Strathdee, G. DNA methylation abnormalities at gene promoters are extensive and variable in the elderly and phenocopy cancer cells.
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Affiliation(s)
| | | | | | | | - John C Mathers
- Human Nutrition Research Centre, Institute for Ageing and Health, Campus for Ageing and Vitality, Newcastle University, Newcastle Upon Tyne, UK; and
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20
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Loh M, Liem N, Vaithilingam A, Lim PL, Sapari NS, Elahi E, Mok ZY, Cheng CL, Yan B, Pang B, Salto-Tellez M, Yong WP, Iacopetta B, Soong R. DNA methylation subgroups and the CpG island methylator phenotype in gastric cancer: a comprehensive profiling approach. BMC Gastroenterol 2014; 14:55. [PMID: 24674026 PMCID: PMC3986689 DOI: 10.1186/1471-230x-14-55] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 03/25/2014] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Methylation-induced silencing of promoter CpG islands in tumor suppressor genes plays an important role in human carcinogenesis. In colorectal cancer, the CpG island methylator phenotype (CIMP) is defined as widespread and elevated levels of DNA methylation and CIMP+ tumors have distinctive clinicopathological and molecular features. In contrast, the existence of a comparable CIMP subtype in gastric cancer (GC) has not been clearly established. To further investigate this issue, in the present study we performed comprehensive DNA methylation profiling of a well-characterised series of primary GC. METHODS The methylation status of 1,421 autosomal CpG sites located within 768 cancer-related genes was investigated using the Illumina GoldenGate Methylation Panel I assay on DNA extracted from 60 gastric tumors and matched tumor-adjacent gastric tissue pairs. Methylation data was analysed using a recursively partitioned mixture model and investigated for associations with clinicopathological and molecular features including age, Helicobacter pylori status, tumor site, patient survival, microsatellite instability and BRAF and KRAS mutations. RESULTS A total of 147 genes were differentially methylated between tumor and matched tumor-adjacent gastric tissue, with HOXA5 and hedgehog signalling being the top-ranked gene and signalling pathway, respectively. Unsupervised clustering of methylation data revealed the existence of 6 subgroups under two main clusters, referred to as L (low methylation; 28% of cases) and H (high methylation; 72%). Female patients were over-represented in the H tumor group compared to L group (36% vs 6%; P = 0.024), however no other significant differences in clinicopathological or molecular features were apparent. CpG sites that were hypermethylated in group H were more frequently located in CpG islands and marked for polycomb occupancy. CONCLUSIONS High-throughput methylation analysis implicates genes involved in embryonic development and hedgehog signaling in gastric tumorigenesis. GC is comprised of two major methylation subtypes, with the highly methylated group showing some features consistent with a CpG island methylator phenotype.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Richie Soong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
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Petrini M, Felicetti F, Bottero L, Errico MC, Morsilli O, Boe A, De Feo A, Carè A. HOXB1 restored expression promotes apoptosis and differentiation in the HL60 leukemic cell line. Cancer Cell Int 2013; 13:101. [PMID: 24148231 PMCID: PMC3874656 DOI: 10.1186/1475-2867-13-101] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 10/19/2013] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Homeobox (HOX) genes deregulation has been largely implicated in the development of human leukemia. Among the HOXB cluster, HOXB1 was silent in a number of analyzed acute myeloid leukemia (AML) primary cells and cell lines, whereas it was expressed in normal terminally differentiated peripheral blood cells. METHODS We evaluated the biological effects and the transcriptome changes determined by the retroviral transduction of HOXB1 in the human promyelocytic cell line HL60. RESULTS Our results suggest that the enforced expression of HOXB1 reduces cell growth proliferation, inducing apoptosis and cell differentiation along the monocytic and granulocytic lineages. Accordingly, gene expression analysis showed the HOXB1-dependent down-regulation of some tumor promoting genes, paralleled by the up-regulation of apoptosis- and differentiation-related genes, thus supporting a tumor suppressor role for HOXB1 in AML. Finally, we indicated HOXB1 promoter hypermethylation as a mechanism responsible for HOXB1 silencing. CONCLUSIONS We propose HOXB1 as an additional member of the HOX family with tumour suppressor properties suggesting a HOXB1/ATRA combination as a possible future therapeutic strategy in AML.
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Affiliation(s)
- Marina Petrini
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore Sanità, Rome 00161, Italy
| | - Federica Felicetti
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore Sanità, Rome 00161, Italy
| | - Lisabianca Bottero
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore Sanità, Rome 00161, Italy
| | - Maria Cristina Errico
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore Sanità, Rome 00161, Italy
| | - Ornella Morsilli
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore Sanità, Rome 00161, Italy
| | - Alessandra Boe
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore Sanità, Rome 00161, Italy
| | - Alessandra De Feo
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore Sanità, Rome 00161, Italy
| | - Alessandra Carè
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore Sanità, Rome 00161, Italy
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22
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Kanduri M, Sander B, Ntoufa S, Papakonstantinou N, Sutton LA, Stamatopoulos K, Kanduri C, Rosenquist R. A key role for EZH2 in epigenetic silencing of HOX genes in mantle cell lymphoma. Epigenetics 2013; 8:1280-8. [PMID: 24107828 DOI: 10.4161/epi.26546] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The chromatin modifier EZH2 is overexpressed and associated with inferior outcome in mantle cell lymphoma (MCL). Recently, we demonstrated preferential DNA methylation of HOX genes in MCL compared with chronic lymphocytic leukemia (CLL), despite these genes not being expressed in either entity. Since EZH2 has been shown to regulate HOX gene expression, to gain further insight into its possible role in differential silencing of HOX genes in MCL vs. CLL, we performed detailed epigenetic characterization using representative cell lines and primary samples. We observed significant overexpression of EZH2 in MCL vs. CLL. Chromatin immune precipitation (ChIP) assays revealed that EZH2 catalyzed repressive H3 lysine 27 trimethylation (H3K27me3), which was sufficient to silence HOX genes in CLL, whereas in MCL H3K27me3 is accompanied by DNA methylation for a more stable repression. More importantly, hypermethylation of the HOX genes in MCL resulted from EZH2 overexpression and subsequent recruitment of the DNA methylation machinery onto HOX gene promoters. The importance of EZH2 upregulation in this process was further underscored by siRNA transfection and EZH2 inhibitor experiments. Altogether, these observations implicate EZH2 in the long-term silencing of HOX genes in MCL, and allude to its potential as a therapeutic target with clinical impact.
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Affiliation(s)
- Meena Kanduri
- Department of Clinical Chemistry and Transfusion Medicine; Institute of Biomedicine; Gothenburg University; Gothenburg, Sweden
| | - Birgitta Sander
- Department of Laboratory Medicine; Division of Pathology; Karolinska Institutet and Karolinska University Hospital; Huddinge, Sweden
| | - Stavroula Ntoufa
- Hematology Department and HCT Unit G. Papanicolaou Hospital; Thessaloniki, Greece; Institute of Applied Biosciences; CERTH; Thessaloniki, Greece
| | - Nikos Papakonstantinou
- Hematology Department and HCT Unit G. Papanicolaou Hospital; Thessaloniki, Greece; Institute of Applied Biosciences; CERTH; Thessaloniki, Greece
| | - Lesley-Ann Sutton
- Department of Immunology, Genetics and Pathology; Uppsala University; Uppsala, Sweden
| | - Kostas Stamatopoulos
- Hematology Department and HCT Unit G. Papanicolaou Hospital; Thessaloniki, Greece; Institute of Applied Biosciences; CERTH; Thessaloniki, Greece
| | - Chandrasekhar Kanduri
- Department of Medical and Clinical Genetics; Department of Biomedicine; The Sahlgrenska Academy; Gothenburg University; Gothenburg, Sweden
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology; Uppsala University; Uppsala, Sweden
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Cillo C, Schiavo G, Cantile M, Bihl MP, Sorrentino P, Carafa V, D' Armiento M, Roncalli M, Sansano S, Vecchione R, Tornillo L, Mori L, De Libero G, Zucman-Rossi J, Terracciano L. The HOX gene network in hepatocellular carcinoma. Int J Cancer 2011; 129:2577-87. [PMID: 21626505 DOI: 10.1002/ijc.25941] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2010] [Accepted: 12/20/2010] [Indexed: 12/22/2022]
Abstract
Liver organogenesis and cancerogenesis share common mechanisms. HOX genes control normal development, primary cellular processes and are characterized by a unique genomic network organization. Less is known about the involvement of HOX genes with liver cancerogenesis. The comparison of the HOX gene network expression between nontumorous livers and hepatocellular carcinomas (HCCs) highlights significant differences in the locus A HOX genes, located on chromosome 7, with a consistent overexpression of HOXA13 mRNA thus validating this gene deregulation as a feature of HCC. HOXA13 is a determinant of gut primordia and posterior body structures. Transcriptome analysis of HCC/nontumorous liver mRNAs, selected on the basis of HOXA13 overexpression, recognizes a set of deregulated genes. The matching of these genes with previously reported HCC transcriptome analysis identifies cell-cycle and nuclear pore-related HCC phenotype displaying poor prognosis. HOXA13 and HOXA7 homeoproteins share a consensus sequence that physically links eIF4E nuclear bodies acting on the export of specific mRNAs (c-myc, FGF-2, vascular endothelial growth factor (VEGF), ornithine decarboxylase (ODC) and cyclin D1). We report the protein-protein interaction between HOXA13 and eIF4E in liver cancer cells and the deregulation of eIF4E mRNA and protein in cell cycle/nuclear pore HCC group phenotype and in T4 stage HCCs, respectively. Thus, transcriptional and post-transcriptional HOXA13 deregulation is involved in HCC possibly through the mRNA nuclear export of eIF4E-dependent transcripts.
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Affiliation(s)
- Clemente Cillo
- Department of Clinical and Experimental Medicine, Federico II University Medical School, Naples, Italy.
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Abstract
BACKGROUND The HLXB9 gene encodes a homeodomain containing transcription factor which has been implicated in the development of both solid and hematological malignancies. In leukemia it is one of the two fused genes, along with ETV6, in a recurrent translocation frequently observed in infant AML. PROCEDURE Here we investigate the role of epigenetic inactivation of the HLXB9 gene in leukemia. Quantitative DNA methylation analysis was performed using the COBRA assay, and qRT-PCR was used to assess the effects of methylation on expression in hematological cell lines and primary ALL samples. RESULTS Hypermethylation of the HLXB9 gene was found to be a frequent event in childhood ALL, occurring in 33% of cases. However, it was rarely or never observed in other types of leukemia, including AML, CML, and CLL, with the exception of adult ALL, in which 39% of cases were hypermethylated. Furthermore, hypermethylation of HLXB9 results in loss of expression in hematological cell lines and primary ALL samples. CONCLUSION These results suggest that HLXB9 may have a dual role in childhood leukemia, as an oncogene in infant AML but as a tumor suppressor in childhood ALL.
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Affiliation(s)
- Stuart Ferguson
- Crucible Laboratory, Institute for Ageing and Health, Newcastle University, Newcastle upon Tyne, UK
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Zhang Y, Liu H, Lv J, Xiao X, Zhu J, Liu X, Su J, Li X, Wu Q, Wang F, Cui Y. QDMR: a quantitative method for identification of differentially methylated regions by entropy. Nucleic Acids Res 2011; 39:e58. [PMID: 21306990 PMCID: PMC3089487 DOI: 10.1093/nar/gkr053] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
DNA methylation plays critical roles in transcriptional regulation and chromatin remodeling. Differentially methylated regions (DMRs) have important implications for development, aging and diseases. Therefore, genome-wide mapping of DMRs across various temporal and spatial methylomes is important in revealing the impact of epigenetic modifications on heritable phenotypic variation. We present a quantitative approach, quantitative differentially methylated regions (QDMRs), to quantify methylation difference and identify DMRs from genome-wide methylation profiles by adapting Shannon entropy. QDMR was applied to synthetic methylation patterns and methylation profiles detected by methylated DNA immunoprecipitation microarray (MeDIP-chip) in human tissues/cells. This approach can give a reasonable quantitative measure of methylation difference across multiple samples. Then DMR threshold was determined from methylation probability model. Using this threshold, QDMR identified 10 651 tissue DMRs which are related to the genes enriched for cell differentiation, including 4740 DMRs not identified by the method developed by Rakyan et al. QDMR can also measure the sample specificity of each DMR. Finally, the application to methylation profiles detected by reduced representation bisulphite sequencing (RRBS) in mouse showed the platform-free and species-free nature of QDMR. This approach provides an effective tool for the high-throughput identification of potential functional regions involved in epigenetic regulation.
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Affiliation(s)
- Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
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26
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Berdasco M, Esteller M. Aberrant epigenetic landscape in cancer: how cellular identity goes awry. Dev Cell 2010; 19:698-711. [PMID: 21074720 DOI: 10.1016/j.devcel.2010.10.005] [Citation(s) in RCA: 411] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Appropriate patterns of DNA methylation and histone modifications are required to assure cell identity, and their deregulation can contribute to human diseases, such as cancer. Our aim here is to provide an overview of how epigenetic factors, including genomic DNA methylation, histone modifications, and microRNA regulation, contribute to normal development, paying special attention to their role in regulating tissue-specific genes. In addition, we summarize how these epigenetic patterns go awry during human cancer development. The possibility of "resetting" the abnormal cancer epigenome by applying pharmacological or genetic strategies is also discussed.
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Affiliation(s)
- María Berdasco
- Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, 08907 Barcelona, Catalonia, Spain
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27
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Kim SY, Hwang SH, Song EJ, Shin HJ, Jung JS, Lee EY. Level of HOXA5 Hypermethylation in Acute Myeloid Leukemia is Associated with Short-term Outcome. Ann Lab Med 2010; 30:469-73. [DOI: 10.3343/kjlm.2010.30.5.469] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Shine Young Kim
- Departments of Laboratory Medicine, Pusan National University School of Medicine, Busan, Korea
| | - Sang-Hyun Hwang
- Departments of Laboratory Medicine, Pusan National University School of Medicine, Busan, Korea
- Medical Research Institute, Pusan National University School of Medicine, Busan, Korea
| | - Eun Joo Song
- Departments of Laboratory Medicine, Pusan National University School of Medicine, Busan, Korea
| | - Ho Jin Shin
- Departments of Internal Medicine, Pusan National University School of Medicine, Busan, Korea
| | - Joo Seop Jung
- Departments of Internal Medicine, Pusan National University School of Medicine, Busan, Korea
| | - Eun Yup Lee
- Departments of Laboratory Medicine, Pusan National University School of Medicine, Busan, Korea
- Medical Research Institute, Pusan National University School of Medicine, Busan, Korea
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28
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Gao S, Nielsen BS, Krogdahl A, Sørensen JA, Tagesen J, Dabelsteen S, Dabelsteen E, Andreasen PA. Epigenetic alterations of the SERPINE1 gene in oral squamous cell carcinomas and normal oral mucosa. Genes Chromosomes Cancer 2010; 49:526-38. [PMID: 20222049 DOI: 10.1002/gcc.20762] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
A high level of plasminogen activator inhibitor-1 (PAI-1 or SERPINE1) in tumor extracts is a marker of a poor prognosis in human cancers, including oral carcinomas. However, the mechanisms responsible for the upregulation of PAI-1 in cancers remain unclear. Investigating specific PAI-1 expressing cells in oral carcinomas by immunohistochemistry, we found that PAI-1 was expressed in 18 of the 20 patients, mainly by cancer cells. Two showed PAI-1 positive stromal cells surrounding the tumor areas and five showed PAI-1 positive cells in tumor-adjacent normal epithelium. By real-time RT-PCR analysis, 17 of 20 patients with oral carcinoma were found to have between 2.5- and 50-fold increased tumor PAI-1 mRNA level, as compared with the matched tumor-adjacent normal tissues. The PAI-1 mRNA level in connective tissues from 15 healthy volunteers was similar to the level in tumor-adjacent normal tissues, but the level in epithelium was 5- to 10-fold lower. Analyzing DNA methylation of 25 CpG sites within 960 bp around the transcription initiation site of the SERPINE1 gene by bisulfite sequencing, we did the surprising observation that both tumors and tumor-adjacent normal tissue had a significant level of methylation, whereas there was very little methylation in tissue from healthy volunteers, suggesting that tumor-adjacent normal tissue already contains transformation-associated epigenetic changes. However, there was no general inverse correlation between PAI-1 mRNA levels and SERPINE1 gene methylation in all tissues, showing that CpG methylation is not the main determinant of the PAI-1 expression level in oral tissue.
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Affiliation(s)
- Shan Gao
- Department of Molecular Biology, Danish-Chinese Centre for Proteases and Cancer, University of Aarhus, 8000 Aarhus C, Denmark.
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Abstract
Abstract
HOX homeobox genes are important regulators of normal and malignant hematopoiesis. Abdominal-type HOXA genes like HOXA9 are highly leukemogenic. However, little is known about transformation by anterior HOXA genes. Here we performed a comprehensive assessment of the oncogenic potential of every HOXA gene in primary hematopoietic cells. With exception of HOXA2 and HOXA5, all HOXA genes caused a block or delay of hematopoietic differentiation and cooperated with Meis1. No evidence for the alleged tumor-suppressor function of HOXA5 could be found. Whereas all active HOXA genes immortalized mixed granulocytic/monocytic populations, HOXA13 preferentially specified monocytoid development. The anterior HOXA genes HOXA1, HOXA4, and HOXA6 transformed cells, generating permanent cell lines, although they did so less potently than HOXA9. Upon transplantation these lines induced myeloproliferation and acute myeloid leukemia in recipient animals. Kinetic studies with inducible HOX derivatives demonstrated that anterior HOXA genes autonomously contributed to cellular transformation. This function was not mediated by endogenous Hoxa9, which was persistently expressed in cells transformed by anterior HOX genes. In summary our results demonstrate a hitherto unexpected role of anterior HOXA genes in hematopoietic malignancy.
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30
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Tao Y, Xi S, Briones V, Muegge K. Lsh mediated RNA polymerase II stalling at HoxC6 and HoxC8 involves DNA methylation. PLoS One 2010; 5:e9163. [PMID: 20161795 PMCID: PMC2820093 DOI: 10.1371/journal.pone.0009163] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 01/22/2010] [Indexed: 11/18/2022] Open
Abstract
DNA cytosine methylation is an important epigenetic mechanism that is involved in transcriptional silencing of developmental genes. Several molecular pathways have been described that interfere with Pol II initiation, but at individual genes the molecular mechanism of repression remains uncertain. Here, we study the molecular mechanism of transcriptional regulation at Hox genes in dependence of the epigenetic regulator Lsh that controls CpG methylation at selected Hox genes. Wild type cells show a nucleosomal deprived region around the transcriptional start site at methylated Hox genes and mediate gene silencing via Pol II stalling. Hypomethylation in Lsh-/- cells is associated with efficient transcriptional elongation and splicing, in part mediated by the chromodomain protein Chd1. Dynamic modulation of DNA methylation in Lsh-/- and wild type cells demonstrates that catalytically active DNA methyltransferase activity is required for Pol II stalling. Taken together, the data suggests that DNA methylation can be compatible with Pol II binding at selected genes and Pol II stalling can act as alternate mechanism to explain transcriptional silencing associated with DNA methylation.
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Affiliation(s)
- Yongguang Tao
- Laboratory of Cancer Prevention, SAIC-Frederick, National Cancer Institute, Frederick, Maryland, United States of America
| | - Sichuan Xi
- Laboratory of Cancer Prevention, SAIC-Frederick, National Cancer Institute, Frederick, Maryland, United States of America
| | - Victorino Briones
- Laboratory of Cancer Prevention, SAIC-Frederick, National Cancer Institute, Frederick, Maryland, United States of America
| | - Kathrin Muegge
- Laboratory of Cancer Prevention, SAIC-Frederick, National Cancer Institute, Frederick, Maryland, United States of America
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31
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Kim DS, Kim MJ, Lee JY, Lee SM, Choi JY, Yoon GS, Na YK, Hong HS, Kim SG, Choi JE, Lee SY, Park JY. Epigenetic inactivation of Homeobox A5 gene in nonsmall cell lung cancer and its relationship with clinicopathological features. Mol Carcinog 2009; 48:1109-15. [PMID: 19554572 DOI: 10.1002/mc.20561] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Promoter methylation is an important mechanism in gene silencing and is a key epigenetic event in cancer development. Homeobox A5 (HOXA5) is a master regulator of the morphogenesis and cell differentiation to be implicated as a tumor suppressor gene in breast cancer, but its role in lung cancer is still unknown. In this study, we have investigated the methylation status of the promoter region of the HOXA5 gene in nonsmall cell lung cancers (NSCLCs) using nested and standard methylation-specific PCR (MSP) and correlated the methylation status with clinicopathological features. With standard MSP analysis, HOXA5 methylation were found in 113 (81.3%) of 139 NSCLCs and 72 (51.8%) in their corresponding nonmalignant lung tissues. RT-PCR and immunohistochemical analysis showed that HOXA5 methylation correlates with gene expression. Moreover, in the patients with stage I disease, HOXA5 methylation was more frequent in smokers than in never-smokes (P = 0.01). There was no influence of HOXA5 methylation on survival in all NSCLCs or at stages II-IV. However, in the patients with stage I disease, HOXA5 methylation was associated with a borderline significantly worse survival (P = 0.09). These findings suggest that downregulation of the HOXA5 gene by aberrant promoter methylation occurs in the vast majority of NSCLCs and that it may play a role in the pathogenesis of NSCLC. Additional studies with larger sample sizes are required to evaluate the prognostic value of HOXA5 methylation in patients with stage I NSCLC.
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Affiliation(s)
- Dong-Sun Kim
- Department of Anatomy, Kyungpook National University, Daegu 702-422, Republic of Korea
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32
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Bahrani-Mostafavi Z, Tickle TL, Zhang J, Bennett KE, Vachris JC, Spencer MD, Mostafavi MT, Tait DL. Correlation analysis of HOX, ErbB and IGFBP family gene expression in ovarian cancer. Cancer Invest 2009; 26:990-8. [PMID: 19093257 DOI: 10.1080/07357900802074349] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Utilizing microarray gene expression data in cancer research possesses the ability to identify deregulated cellular pathways involved in malignant development. This study investigated the relationships of three gene families, HOX, ErbB and IGFBP, with regard to the development of ovarian cancer. These families were of interest because of similar chromosomal locations and their deregulated expression in ovarian cancer. Higher level statistics were used to differentially analyze microarray data in 65 ovarian samples to assess correlation and relationships among the gene families of interest. Fifteen genes in the three families were found to be significantly deregulated. Thirty-eight significant correlations were found within and between the genes of interest. Our data indicates that the significantly modeled relationships between HOX, ErbB and IGFBP gene pairs could provide insight into the underlying biological mechanisms in ovarian cancer.
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Affiliation(s)
- Zahra Bahrani-Mostafavi
- Cannon Research Center, Molecular Biology Core Facility, Carolinas Medical Center, Charlotte, NC 28203, USA.
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Genome-wide determination of DNA methylation by Hpa II tiny fragment enrichment by ligation-mediated PCR (HELP) for the study of acute leukemias. Methods Mol Biol 2009; 538:395-407. [PMID: 19277580 DOI: 10.1007/978-1-59745-418-6_20] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Aberrant distribution of cytosine methylation in cancer has been linked to deregulation of gene expression and genomic instability. DNA methylation changes in cancer include both hyper and hypomethylation, and the precise localization of these changes is directly related to the impact they have on gene regulation. To determine both the localization and extent of DNA methylation status under different conditions, we have developed the HpaII tiny fragment enrichment by ligation-mediated PCR (HELP) assay, a microarray-based technique that allows the simultaneous interrogation of the methylation status of hundreds of thousands of CpG dinucleotides. The HELP assay allows methylation levels throughout the genome to be accurately determined so that the epigenetic state of leukemia cells can be identified, compared, and contrasted.
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Grubach L, Juhl-Christensen C, Rethmeier A, Olesen LH, Aggerholm A, Hokland P, Østergaard M. Gene expression profiling of Polycomb, Hox and Meis genes in patients with acute myeloid leukaemia. Eur J Haematol 2008; 81:112-22. [DOI: 10.1111/j.1600-0609.2008.01083.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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35
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Prepubertal physical activity up-regulates estrogen receptor beta, BRCA1 and p53 mRNA expression in the rat mammary gland. Breast Cancer Res Treat 2008; 115:213-20. [PMID: 18516675 DOI: 10.1007/s10549-008-0062-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2008] [Accepted: 05/13/2008] [Indexed: 02/06/2023]
Abstract
Findings in BRCA1 mutation carriers suggest that physical activity, particularly during childhood, may be linked to a reduced risk of developing breast cancer. We investigated whether physical activity at puberty alters the expression of BRCA1 and two other tumor suppressor genes--p53 and estrogen receptor (ER)-beta--in rats. In addition, the effects on ER-alpha expression, mammary proliferation and functional epithelial differentiation were investigated as markers of altered mammary cancer risk in rats exposed to regular physical activity at puberty. Female Sprague Dawley rat pups were randomized to voluntary exercise, sham-exercise control and non-manipulated control groups. Treadmill training (20-25 m/min, 15% grade, 30 min/day, 5 days/week) started on postnatal day 14 and continued through day 32. Third thoracic mammary glands (n = 5 per group and age) were obtained at days 32, 48 and 100 and assessed for changes in morphology through wholemounts, and at 100 days cell proliferation by using Ki67 staining, protein levels of ER-alpha and ER-beta by immunohistochemistry, and mRNA expression levels of BRCA1, p53, ER-alpha and ER-beta by real-time PCR. Mammary glands of rats exposed to exercise during puberty contained fewer terminal end buds (TEBs) and a higher number of differentiated alveolar buds and lobules than the sham controls. However, cell proliferation was not significantly altered among the groups. ER-alpha protein levels were significantly reduced, while ER-beta levels were increased in the mammary ducts and lobular epithelial structures of 100-day old rays which were voluntarily exercised at puberty, compared to sham controls. ER-beta, BRCA1 and p53 mRNA levels were significantly higher in the mammary glands of 100-day-old exercised versus sham control rats. Pubertal physical activity reduced mammary epithelial targets for neoplastic transformation through epithelial differentiation and it also up-regulated tumor suppressor genes BRCA1, p53 and ER-beta, and reduced ER-alpha/ER-beta ratio in the mammary gland. It remains to be determined whether the up-regulation of BRCA1, and perhaps p53, explains the protective effect of childhood physical activity against breast cancer in women who carry a germline mutation in one of the BRCA1 alleles.
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Strathdee G, Holyoake TL, Sim A, Parker A, Oscier DG, Melo JV, Meyer S, Eden T, Dickinson AM, Mountford JC, Jorgensen HG, Soutar R, Brown R. Inactivation of HOXA genes by hypermethylation in myeloid and lymphoid malignancy is frequent and associated with poor prognosis. Clin Cancer Res 2007; 13:5048-55. [PMID: 17785556 DOI: 10.1158/1078-0432.ccr-07-0919] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE The HOX genes comprise a large family of homeodomain-containing transcription factors, present in four separate clusters, which are key regulators of embryonic development, hematopoietic differentiation, and leukemogenesis. We aimed to study the role of DNA methylation as an inducer of HOX gene silencing in leukemia. EXPERIMENTAL DESIGN Three hundred and seventy-eight samples of myeloid and lymphoid leukemia were quantitatively analyzed (by COBRA analysis and pyrosequencing of bisulfite-modified DNA) for methylation of eight HOXA and HOXB cluster genes. The biological significance of the methylation identified was studied by expression analysis and through re-expression of HOXA5 in a chronic myeloid leukemia (CML) blast crisis cell line model. RESULTS Here, we identify frequent hypermethylation and gene inactivation of HOXA and HOXB cluster genes in leukemia. In particular, hypermethylation of HOXA4 and HOXA5 was frequently observed (26-79%) in all types of leukemias studied. HOXA6 hypermethylation was predominantly restricted to lymphoid malignancies, whereas hypermethylation of other HOXA and HOXB genes was only observed in childhood leukemia. HOX gene methylation exhibited clear correlations with important clinical variables, most notably in CML, in which hypermethylation of both HOXA5 (P = 0.00002) and HOXA4 (P = 0.006) was strongly correlated with progression to blast crisis. Furthermore, re-expression of HOXA5 in CML blast crisis cells resulted in the induction of markers of granulocytic differentiation. CONCLUSION We propose that in addition to the oncogenic role of some HOX family members, other HOX genes are frequent targets for gene inactivation and normally play suppressor roles in leukemia development.
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Affiliation(s)
- Gordon Strathdee
- Centre for Oncology and Applied Pharmacology, Cancer Research UK.
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37
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Fandy TE, Carraway H, Gore SD. DNA Demethylating Agents and Histone Deacetylase Inhibitors in Hematologic Malignancies. Cancer J 2007; 13:40-8. [PMID: 17464245 DOI: 10.1097/ppo.0b013e31803c7359] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The pivotal role of aberrant promoter methylation in gene silencing and cancer development has fueled the interest in DNA methyltransferase inhibitors as novel anticancer drugs. Modulation of gene expression through targeting of epigenetic marks is one of the emerging and promising strategies that has demonstrated successful clinical outcome in hematologic malignancies. Epigenetic modifiers, including DNA methyltransferase inhibitors and histone deacetylase inhibitors, have demonstrated significant clinical activity; several are or are likely to soon be approved by the U.S. Food and Drug Administration. However, the exact mechanism of the clinical response achieved is not fully understood. This review focuses on the pharmacology of the known DNA methyltransferase and histone deacetylase inhibitors and their potential as promising anticancer drugs.
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Affiliation(s)
- Tamer E Fandy
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA
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