1
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Li X, Huo X, Zhao C, Chen Z, Xu Z, Yu J, Sun X. A novel chromatin regulator signature predicts the prognosis, clinical features and immunotherapy of colon cancer. Epigenomics 2022; 14:1325-1341. [PMID: 36545887 DOI: 10.2217/epi-2022-0266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Aim: To elucidate the potential function and prognostic value of chromatin regulators (CRs) in colon cancer. Materials & methods: A comprehensive analysis of CR RNA expression data from public databases was conducted. Results: The authors successfully established and validated a 17 CR-based signature using public databases. Ten CRs of the signature were eventually verified at the protein level using the Human Protein Atlas database. Functional enrichment showed that CRs were significantly enriched in cancer-related pathways. This signature was remarkably relevant to immune cell infiltration, immune checkpoints, tumor immune dysfunction and exclusion (TIDE) score and drug sensitivity. Conclusion: The authors identified a novel, reliable prognostic signature for colon cancer. The study provided new insights into the function of CRs and has important clinical implications for immunotherapy for colon cancer.
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Affiliation(s)
- Xiaopeng Li
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Xiongwei Huo
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Chenye Zhao
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Zilu Chen
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Zhengshui Xu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, China
| | - Junhui Yu
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Xuejun Sun
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
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2
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Ghavami S, Zamani M, Ahmadi M, Erfani M, Dastghaib S, Darbandi M, Darbandi S, Vakili O, Siri M, Grabarek BO, Boroń D, Zarghooni M, Wiechec E, Mokarram P. Epigenetic regulation of autophagy in gastrointestinal cancers. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166512. [PMID: 35931405 DOI: 10.1016/j.bbadis.2022.166512] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/11/2022] [Accepted: 07/28/2022] [Indexed: 11/09/2022]
Abstract
The development of novel therapeutic approaches is necessary to manage gastrointestinal cancers (GICs). Considering the effective molecular mechanisms involved in tumor growth, the therapeutic response is pivotal in this process. Autophagy is a highly conserved catabolic process that acts as a double-edged sword in tumorigenesis and tumor inhibition in a context-dependent manner. Depending on the stage of malignancy and cellular origin of the tumor, autophagy might result in cancer cell survival or death during the GICs' progression. Moreover, autophagy can prevent the progression of GIC in the early stages but leads to chemoresistance in advanced stages. Therefore, targeting specific arms of autophagy could be a promising strategy in the prevention of chemoresistance and treatment of GIC. It has been revealed that autophagy is a cytoplasmic event that is subject to transcriptional and epigenetic regulation inside the nucleus. The effect of epigenetic regulation (including DNA methylation, histone modification, and expression of non-coding RNAs (ncRNAs) in cellular fate is still not completely understood. Recent findings have indicated that epigenetic alterations can modify several genes and modulators, eventually leading to inhibition or promotion of autophagy in different cancer stages, and mediating chemoresistance or chemosensitivity. The current review focuses on the links between autophagy and epigenetics in GICs and discusses: 1) How autophagy and epigenetics are linked in GICs, by considering different epigenetic mechanisms; 2) how epigenetics may be involved in the alteration of cancer-related phenotypes, including cell proliferation, invasion, and migration; and 3) how epidrugs modulate autophagy in GICs to overcome chemoresistance.
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Affiliation(s)
- Saeid Ghavami
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada; Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Research Institute of Hematology and Oncology, Cancer Care Manitoba, Winnipeg, MB R3E 0V9, Canada; Faculty of Medicine in Zabrze, University of Technology in Katowice, Academia of Silesia, 41-800 Zabrze, Poland.
| | - Mozhdeh Zamani
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mazaher Ahmadi
- Department of Analytical Chemistry, Faculty of Chemistry, Bu-Ali Sina University, Hamedan, Iran
| | - Mehran Erfani
- Department of Biochemistry, School of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Sanaz Dastghaib
- Endocrinology and Metabolism Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mahsa Darbandi
- Fetal Health Research Center, Hope Generation Foundation, Tehran, Iran; Gene Therapy and Regenerative Medicine Research Center, Hope Generation Foundation, Tehran, Iran
| | - Sara Darbandi
- Fetal Health Research Center, Hope Generation Foundation, Tehran, Iran; Gene Therapy and Regenerative Medicine Research Center, Hope Generation Foundation, Tehran, Iran
| | - Omid Vakili
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Morvarid Siri
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Beniamin Oskar Grabarek
- Department of Histology, Cytophysiology, and Embryology in Zabrze, Faculty of Medicine in Zabrze, University of Technology in Katowice, Academia of Silesia, 41-800 Zabrze, Poland; Department of Gynecology and Obstetrics in Zabrze, Faculty of Medicine in Zabrze, University of Technology in Katowice, Academia of Silesia, 41-800 Zabrze, Poland
| | - Dariusz Boroń
- Department of Histology, Cytophysiology, and Embryology in Zabrze, Faculty of Medicine in Zabrze, University of Technology in Katowice, Academia of Silesia, 41-800 Zabrze, Poland; Department of Gynecology and Obstetrics in Zabrze, Faculty of Medicine in Zabrze, University of Technology in Katowice, Academia of Silesia, 41-800 Zabrze, Poland
| | - Maryam Zarghooni
- Department of Laboratory Medicine and Pathobiology, University of Toronto Alumni, Toronto, Canada
| | - Emilia Wiechec
- Division of Cell Biology, Department of Biomedical and Clinical Sciences, Linköping University, 58185 Linköping, Sweden
| | - Pooneh Mokarram
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
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3
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Xu L, Shao F, Luo T, Li Q, Tan D, Tan Y. Pan-Cancer Analysis Identifies CHD5 as a Potential Biomarker for Glioma. Int J Mol Sci 2022; 23:ijms23158489. [PMID: 35955624 PMCID: PMC9369136 DOI: 10.3390/ijms23158489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/19/2022] [Accepted: 07/27/2022] [Indexed: 02/01/2023] Open
Abstract
The chromodomain helicase DNA binding domain 5 (CHD5) is required for neural development and plays an important role in the regulation of gene expression. Although CHD5 exerts a broad tumor suppressor effect in many tumor types, its specific functions regarding its expression levels, and impact on immune cell infiltration, proliferation and migration in glioma remain unclear. Here, we evaluated the role of CHD5 in tumor immunity in a pan-cancer multi-database using the R language. The Cancer Genome Atlas (TCGA), Genotype Tissue Expression (GTEx), and Cancer Cell Lines Encyclopedia (CCLE) datasets were utilized to determine the role of CHD5 in 33 types of cancers, including the expression level, prognosis, tumor progression, and immune microenvironment. Furthermore, we explored the effect of CHD5 on glioma proliferation and migration using the cell counting kit 8 (CCK-8) assay, transwell assays and western blot analysis. The findings from our pan-cancer analysis showed that CHD5 was differentially expressed in the tumor tissues as compared to the normal tissues. Survival analysis showed that CHD5 was generally associated with the prognosis of glioblastoma (GBM), low Grade Glioma (LGG) and neuroblastoma, where the low expression of CHD5 was associated with a worse prognosis in glioma patients. Then, we confirmed that the expression level of CHD5 was associated with tumor immune infiltration and tumor microenvironment, especially in glioma. Moreover, si-RNA mediated knockdown of CHD5 promoted the proliferation and migration of glioma cells in vitro. In conclusion, CHD5 was found to be differentially expressed in the pan-cancer analysis and might play an important role in antitumor immunity. CHD5 is expected to be a potential tumor prognostic marker, especially in glioma.
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Affiliation(s)
- Lei Xu
- Laboratory Animal Center, Chongqing Medical University, Chongqing 400016, China; (L.X.); (T.L.); (Q.L.); (D.T.)
| | - Fengling Shao
- The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China;
| | - Tengling Luo
- Laboratory Animal Center, Chongqing Medical University, Chongqing 400016, China; (L.X.); (T.L.); (Q.L.); (D.T.)
| | - Qijun Li
- Laboratory Animal Center, Chongqing Medical University, Chongqing 400016, China; (L.X.); (T.L.); (Q.L.); (D.T.)
| | - Dongmei Tan
- Laboratory Animal Center, Chongqing Medical University, Chongqing 400016, China; (L.X.); (T.L.); (Q.L.); (D.T.)
| | - Yi Tan
- Laboratory Animal Center, Chongqing Medical University, Chongqing 400016, China; (L.X.); (T.L.); (Q.L.); (D.T.)
- Correspondence:
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4
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Heidari Z, Asemi-Rad A, Moudi B, Mahmoudzadeh-Sagheb H. mRNA expression and epigenetic-based role of chromodomain helicase DNA-binding 5 in hepatocellular carcinoma. J Int Med Res 2022; 50:3000605221105344. [PMID: 35808817 PMCID: PMC9274423 DOI: 10.1177/03000605221105344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Objective Chromodomain helicase DNA-binding 5 (CHD5) acts as a tumor
suppressor gene in some cancers. CHD5 expression levels may affect an
individual’s susceptibility to hepatocellular carcinoma (HCC). This study
aimed to evaluate the methylation pattern of the CHD5
promoter region and the gene’s corresponding mRNA expression in HCC patients
compared with healthy individuals. Methods In this case–control study, CHD5 mRNA gene expression levels
and DNA methylation patterns were analyzed in 81 HCC patients and 90 healthy
individuals by quantitative reverse transcription polymerase chain reaction
and methylation-specific polymerase chain reaction, respectively. Results The CHD5 gene was hypermethylated in 61.8% of the HCC
patients and 54.4% of the controls, and this difference was statistically
significant. The CHD5 mRNA expression levels were
significantly lower in the HCC patient group. Conclusions Hypermethylation of the CHD5 promoter region may
significantly lower the expression of this gene, affecting the incidence and
severity of HCC. The methylation status of CHD5 can also be
further studied as a prognostic factor in HCC.
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Affiliation(s)
- Zahra Heidari
- Infectious Disease and Tropical Medicine Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran.,Department of Histology, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Azam Asemi-Rad
- Department of Anatomical Sciences, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran.,Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Bita Moudi
- Infectious Disease and Tropical Medicine Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran.,Department of Histology, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Hamidreza Mahmoudzadeh-Sagheb
- Infectious Disease and Tropical Medicine Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran.,Department of Histology, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
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5
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The Role of DNA Methylation and DNA Methyltransferases in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:317-348. [DOI: 10.1007/978-3-031-11454-0_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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6
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Abstract
Chromatin is highly dynamic, undergoing continuous global changes in its structure and type of histone and DNA modifications governed by processes such as transcription, repair, replication, and recombination. Members of the chromodomain helicase DNA-binding (CHD) family of enzymes are ATP-dependent chromatin remodelers that are intimately involved in the regulation of chromatin dynamics, altering nucleosomal structure and DNA accessibility. Genetic studies in yeast, fruit flies, zebrafish, and mice underscore essential roles of CHD enzymes in regulating cellular fate and identity, as well as proper embryonic development. With the advent of next-generation sequencing, evidence is emerging that these enzymes are subjected to frequent DNA copy number alterations or mutations and show aberrant expression in malignancies and other human diseases. As such, they might prove to be valuable biomarkers or targets for therapeutic intervention.
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Affiliation(s)
- Andrej Alendar
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
| | - Anton Berns
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
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7
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Pei S, Chen Z, Tan H, Fan L, Zhang B, Zhao C. SLC16A1-AS1 enhances radiosensitivity and represses cell proliferation and invasion by regulating the miR-301b-3p/CHD5 axis in hepatocellular carcinoma. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:42778-42790. [PMID: 32748357 DOI: 10.1007/s11356-020-09998-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/02/2020] [Indexed: 06/11/2023]
Abstract
Hepatocellular carcinoma (HCC), a common type of human malignancies, leads to increasing incidence and fairly high mortality. An increasing number of studies have verified that long noncoding RNAs (lncRNAs) played key roles in the development of multiple human cancers. As a biomarker, SLC16A1-AS1 has been reported in non-small cell lung cancer (NSCLC) and oral squamous cell carcinoma (OSCC). Thus, we decided to investigate whether SLC16A1-AS1 exerts its biological function in HCC. In this study, we discovered that SLC16A1-AS1 was obviously downregulated in HCC tissues and cells. Overexpression of SLC16A1-AS1 inhibited HCC cell proliferation, invasion, and epithelial-mesenchymal transition (EMT) process as well as promoted cell apoptosis. Moreover, SLC16A1-AS1 was confirmed to enhance the radiosensitivity of HCC cells. Molecular mechanism exploration suggested that SLC16A1-AS1 served as a sponge for miR-301b-3p and CHD5 was the downstream target gene of miR-301b-3p in HCC cells. Rescue assays implied that CHD5 knockdown could recover the effects of SLC16A1-AS1 overexpression on HCC cellular processes. In brief, our study clarified that SLC16A1-AS1 acted as a tumor suppressor in HCC by targeting the miR-301b-3p/CHD5 axis, which may be a promising diagnostic biomarker and provide promising treatment for HCC patients.
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Affiliation(s)
- Shenglin Pei
- Department of Anesthesiology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
| | - Zuyi Chen
- Department of Intervention, Affiliated Tumor Hospital of Guangxi Medical University, No. 71 Hedi Road, Qingxiu District, Nanning, 530021, Guangxi, China
| | - Huajun Tan
- Department of Intervention, Affiliated Tumor Hospital of Guangxi Medical University, No. 71 Hedi Road, Qingxiu District, Nanning, 530021, Guangxi, China
| | - Liwei Fan
- Department of Intervention, Affiliated Tumor Hospital of Guangxi Medical University, No. 71 Hedi Road, Qingxiu District, Nanning, 530021, Guangxi, China
| | - Baina Zhang
- Department of Intervention, Affiliated Tumor Hospital of Guangxi Medical University, No. 71 Hedi Road, Qingxiu District, Nanning, 530021, Guangxi, China
| | - Chang Zhao
- Department of Intervention, Affiliated Tumor Hospital of Guangxi Medical University, No. 71 Hedi Road, Qingxiu District, Nanning, 530021, Guangxi, China.
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8
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Chromodomain Helicase DNA-Binding Protein 5 Inhibits Renal Cell Carcinoma Tumorigenesis by Activation of the p53 and RB Pathways. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5425612. [PMID: 33062682 PMCID: PMC7542531 DOI: 10.1155/2020/5425612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 06/15/2020] [Accepted: 08/05/2020] [Indexed: 12/24/2022]
Abstract
Chromodomain helicase DNA-binding protein 5 (CHD5) plays a crucial tumor suppressor role in multiple types of tumors. For this study, we investigated its clinical significance and the molecular mechanism(s) underlying tumorigenesis in renal cell carcinoma (RCC). Initially, CHD5 expression was assessed in primary tumor tissue and in tissue array. Correlations among CHD5 expression and clinicopathological characteristics were analyzed. Next, lentivirus-mediated CHD5 overexpression in the ACHN and 769-P cells was used to assess effects on proliferation, migration, invasion ability, and the regulation of the p14ARF/p53 and p16INK4a/RB signaling pathways. Finally, a xenograft mouse model was used to verify its impact on tumor growth in vivo. Results demonstrated that CHD5 was downregulated in tumor tissues and that low CHD5 expression was correlated with advanced TNM stage, high Fuhrman grade, lymph node metastasis, and poor survival. Overexpression of CHD5 inhibited proliferation, migration, and invasion in vitro; prompted cell cycle G1 phase arrest; induced apoptosis; and suppressed tumor growth in vivo. Furthermore, we confirmed that CHD5 activates the p53 and RB pathways to inhibit tumorigenesis in RCC. In summary, CHD5 is involved in the initiation and progression of RCC and may serve as a diagnostic biomarker and a potential therapeutic target for RCC.
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9
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Hashimoto T, Kurokawa Y, Wada N, Takahashi T, Miyazaki Y, Tanaka K, Makino T, Yamasaki M, Nakajima K, Mori M, Doki Y. Clinical significance of chromatin remodeling factor CHD5 expression in gastric cancer. Oncol Lett 2020; 19:1066-1073. [PMID: 31897220 PMCID: PMC6924149 DOI: 10.3892/ol.2019.11138] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/08/2019] [Indexed: 12/19/2022] Open
Abstract
Chromodomain helicase DNA-binding 5 (CHD5), which is a member of the CHD family, has been identified as a tumor suppressor gene in a variety of malignancies. The aim of the current study was to clarify the clinical significance of CHD5 expression in gastric cancer. CHD5 expression was evaluated using immunohistochemistry (IHC) in 154 specimens resected from patients with gastric cancer from January 2011 to December 2013, and assessed its relationships with clinicopathological characteristics and survival. In vitro cell proliferation, invasion, and migration assays and western blotting analysis were performed to clarify the role of CHD5 in human gastric cancer cell lines. Of a total of 154 patients, 57 (37.0%) exhibited low CHD5 expression, which was significantly associated with positive lymphatic invasion (P=0.032), advanced pT status (P=0.011), and advanced pStage (P=0.014). Overall survival (OS) in patients with low CHD5 expression was significantly worse compared with patients with high CHD5 expression (hazard ratio, 1.96; 95% confidence interval, 1.09-3.45; log-rank P=0.023). Cox multivariate analysis for OS revealed that CHD5 expression was an independent prognostic factor with age and pN status. In vitro, the upregulation of CHD5 in gastric cancer cells with low CHD5 expression significantly decreased cell proliferation, migration and invasion. CHD5 was associated with the regulation of multiple cancer-related targets, including p53 and enhancer of zeste homolog 2 (EZH2) in western blotting analysis. In conclusion, since CHD5 regulated multiple cancer-related targets, its expression may be a useful prognostic biomarker in patients with gastric cancer.
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Affiliation(s)
- Tadayoshi Hashimoto
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Yukinori Kurokawa
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Noriko Wada
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Tsuyoshi Takahashi
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Yasuhiro Miyazaki
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Koji Tanaka
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Tomoki Makino
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Makoto Yamasaki
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Kiyokazu Nakajima
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Masaki Mori
- Department of Surgery and Science, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
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10
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Koroknai V, Szász I, Hernandez-Vargas H, Fernandez-Jimenez N, Cuenin C, Herceg Z, Vízkeleti L, Ádány R, Ecsedi S, Balázs M. DNA hypermethylation is associated with invasive phenotype of malignant melanoma. Exp Dermatol 2020; 29:39-50. [PMID: 31602702 DOI: 10.1111/exd.14047] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 08/29/2019] [Accepted: 10/06/2019] [Indexed: 01/01/2023]
Abstract
Tumor cell invasion is one of the key processes during cancer progression, leading to life-threatening metastatic lesions in melanoma. As methylation of cancer-related genes plays a fundamental role during tumorigenesis and may lead to cellular plasticity which promotes invasion, our aim was to identify novel epigenetic markers on selected invasive melanoma cells. Using Illumina BeadChip assays and Affymetrix Human Gene 1.0 microarrays, we explored the DNA methylation landscape of selected invasive melanoma cells and examined the impact of DNA methylation on gene expression patterns. Our data revealed predominantly hypermethylated genes in the invasive cells affecting the neural crest differentiation pathway and regulation of the actin cytoskeleton. Integrative analysis of the methylation and gene expression profiles resulted in a cohort of hypermethylated genes (IL12RB2, LYPD6B, CHL1, SLC9A3, BAALC, FAM213A, SORCS1, GPR158, FBN1 and ADORA2B) with decreased expression. On the other hand, hypermethylation in the gene body of the EGFR and RBP4 genes was positively correlated with overexpression of the genes. We identified several methylation changes that can have role during melanoma progression, including hypermethylation of the promoter regions of the ARHGAP22 and NAV2 genes that are commonly altered in locally invasive primary melanomas as well as during metastasis. Interestingly, the down-regulation of the methylcytosine dioxygenase TET2 gene, which regulates DNA methylation, was associated with hypermethylated promoter region of the gene. This can probably lead to the observed global hypermethylation pattern of invasive cells and might be one of the key changes during the development of malignant melanoma cells.
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Affiliation(s)
- Viktória Koroknai
- Public Health Research Institute, University of Debrecen, Debrecen, Hungary
- MTA-DE Public Health Research Group, Public Health Research Institute, University of Debrecen, Debrecen, Hungary
| | - István Szász
- Public Health Research Institute, University of Debrecen, Debrecen, Hungary
- MTA-DE Public Health Research Group, Public Health Research Institute, University of Debrecen, Debrecen, Hungary
| | | | | | - Cyrille Cuenin
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Laura Vízkeleti
- Public Health Research Institute, University of Debrecen, Debrecen, Hungary
- MTA-DE Public Health Research Group, Public Health Research Institute, University of Debrecen, Debrecen, Hungary
| | - Róza Ádány
- Public Health Research Institute, University of Debrecen, Debrecen, Hungary
- MTA-DE Public Health Research Group, Public Health Research Institute, University of Debrecen, Debrecen, Hungary
| | - Szilvia Ecsedi
- Public Health Research Institute, University of Debrecen, Debrecen, Hungary
- MTA-DE Public Health Research Group, Public Health Research Institute, University of Debrecen, Debrecen, Hungary
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Margit Balázs
- Public Health Research Institute, University of Debrecen, Debrecen, Hungary
- MTA-DE Public Health Research Group, Public Health Research Institute, University of Debrecen, Debrecen, Hungary
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11
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Hasan N, Ahuja N. The Emerging Roles of ATP-Dependent Chromatin Remodeling Complexes in Pancreatic Cancer. Cancers (Basel) 2019; 11:E1859. [PMID: 31769422 PMCID: PMC6966483 DOI: 10.3390/cancers11121859] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 02/08/2023] Open
Abstract
Pancreatic cancer is an aggressive cancer with low survival rates. Genetic and epigenetic dysregulation has been associated with the initiation and progression of pancreatic tumors. Multiple studies have pointed to the involvement of aberrant chromatin modifications in driving tumor behavior. ATP-dependent chromatin remodeling complexes regulate chromatin structure and have critical roles in stem cell maintenance, development, and cancer. Frequent mutations and chromosomal aberrations in the genes associated with subunits of the ATP-dependent chromatin remodeling complexes have been detected in different cancer types. In this review, we summarize the current literature on the genomic alterations and mechanistic studies of the ATP-dependent chromatin remodeling complexes in pancreatic cancer. Our review is focused on the four main subfamilies: SWItch/sucrose non-fermentable (SWI/SNF), imitation SWI (ISWI), chromodomain-helicase DNA-binding protein (CHD), and INOsitol-requiring mutant 80 (INO80). Finally, we discuss potential novel treatment options that use small molecules to target these complexes.
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Affiliation(s)
| | - Nita Ahuja
- Department of Surgery, Yale University School of Medicine, New Haven, CT 06520, USA;
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12
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Hu YH, Ma S, Zhang XN, Zhang ZY, Zhu HF, Ji YH, Li J, Qian XL, Wang YX. Hypermethylation Of ADHFE1 Promotes The Proliferation Of Colorectal Cancer Cell Via Modulating Cell Cycle Progression. Onco Targets Ther 2019; 12:8105-8115. [PMID: 31632063 PMCID: PMC6782030 DOI: 10.2147/ott.s223423] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 09/18/2019] [Indexed: 12/24/2022] Open
Abstract
Background Colorectal cancer (CRC) is one of the most common malignancies worldwide. Studies have demonstrated that epigenetic modifications play essential roles in the development of CRC. ADHFE1 is a differentially expressed gene that has been reported to be hypermethylated in CRC. However, the role and mechanism of ADHFE1 in the proliferation of CRC remain unclear. Materials and methods ADHFE1 expression was analyzed in CRC tissues by IHC and qRT-PCR, and the relationship between ADHFE1 expression and the clinicopathological parameters was analyzed. Cell proliferation were assessed by the in vitro and in vivo experimental models. GSEA assay was performed to explore the mechanism of ADHFE1 in the proliferation of CRC. Flow cytometry and Western blot were used to detect the activation of the cell cycle signaling. Bisulfite genomic sequence (BSP) assay was used to test the methylation degree of ADHFE1 gene promoter in CRC tissues. Results Here, we verified that ADHFE1 was down-regulated and hypermethylated in CRC tissues. The down-regulation of ADHFE1 was correlated with poor differentiation and advanced TNM stage of CRC patients. And ADHFE1 expression restored when the CRC cell line SW620 was treated with the demethylating agent 5-Aza-CdR. Overexpression of ADHFE1 inhibited the proliferation of CRC, while ADHFE1 knockdown promoted the proliferation of CRC cells in vitro and in vivo. Moreover, ADHFE1 overexpression could induce a significant G1-S cell cycle arrest in CRC cells and vice versa. Conclusion Hypermethylation of ADHFE1 might promote cell proliferation by modulating cell cycle progression in CRC, potentially providing a new therapeutic target for CRC patients.
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Affiliation(s)
- Yu-Han Hu
- Department of Pathology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453000, People's Republic of China
| | - Shuai Ma
- Department of Pathology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453000, People's Republic of China
| | - Xiang-Nan Zhang
- Department of Pathology, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan 453000, People's Republic of China
| | - Zhe-Ying Zhang
- Department of Pathology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453000, People's Republic of China
| | - Hui-Fang Zhu
- Department of Pathology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453000, People's Republic of China.,Department of Pathology, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan 453000, People's Republic of China
| | - Ying-Hua Ji
- Department of Oncology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan 453000, People's Republic of China
| | - Jian Li
- Department of Surgery, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan 453000, People's Republic of China
| | - Xin-Lai Qian
- Department of Pathology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453000, People's Republic of China.,Department of Pathology, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan 453000, People's Republic of China
| | - Yong-Xia Wang
- Department of Pathology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453000, People's Republic of China.,Department of Pathology, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan 453000, People's Republic of China
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13
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Xicola RM, Manojlovic Z, Augustus GJ, Kupfer SS, Emmadi R, Alagiozian-Angelova V, Triche T, Salhia B, Carpten J, Llor X, Ellis NA. Lack of APC somatic mutation is associated with early-onset colorectal cancer in African Americans. Carcinogenesis 2019; 39:1331-1341. [PMID: 30239619 DOI: 10.1093/carcin/bgy122] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 09/11/2018] [Indexed: 02/06/2023] Open
Abstract
African Americans (AAs) have higher incidence and mortality rates of colorectal cancer (CRC) compared with other US populations. They present with more right-sided, microsatellite stable disease and are diagnosed at earlier ages compared with non-Hispanic Whites (NHWs). To gain insight into these trends, we conducted exome sequencing (n = 45), copy number (n = 33) and methylation analysis (n = 11) of microsatellite stable AA CRCs. Results were compared with data from The Cancer Genome Atlas (TCGA). Two of the 45 tumors contained POLE mutations. In the remaining 43 tumors, only 27 (63%) contained loss-of-function mutations in APC compared with 80% of TCGA NHW CRCs. APC-mutation-negative CRCs were associated with an earlier onset of CRC (P = 0.01). They were also associated with lower overall mutation burden, fewer copy number variants and a DNA methylation signature that was distinct from the CpG island methylator phenotype characterized in microsatellite unstable disease. Three of the APC-mutation-negative CRCs had loss-of-function mutations in BCL9L. Mutations in driver genes identified by TCGA exome analysis were less frequent in AA CRC cases than TCGA NHWs. Genes that regulate the WNT signaling pathway, including SOX9, GATA6, TET1, GLIS1 and FAT1, were differentially hypermethylated in APC-mutation-negative CRCs, suggesting a novel mechanism for cancer development in these tumors. In summary, we have identified a subtype of CRC that is associated with younger age of diagnosis, lack of APC mutation, microsatellite and chromosome stability, lower mutation burden and distinctive methylation changes.
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Affiliation(s)
- Rosa M Xicola
- Department of Internal Medicine and Yale Cancer Center, Yale University, New Haven, CT, USA
| | - Zarko Manojlovic
- Translational Genomics Research Institute, Division of Integrated Cancer Genomics, Phoenix, AZ, USA.,Department of Translational Genomics, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Gaius J Augustus
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, USA
| | - Sonia S Kupfer
- University of Chicago Medicine, Section of Gastroenterology, Hepatology and Nutrition, Chicago, IL, USA
| | - Rajyasree Emmadi
- Department of Pathology, University of Illinois at Chicago, Chicago, IL, USA
| | | | - Tim Triche
- Department of Translational Genomics, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA.,Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Bodour Salhia
- Department of Translational Genomics, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - John Carpten
- Translational Genomics Research Institute, Division of Integrated Cancer Genomics, Phoenix, AZ, USA.,Department of Translational Genomics, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Xavier Llor
- Department of Internal Medicine and Yale Cancer Center, Yale University, New Haven, CT, USA
| | - Nathan A Ellis
- Department of Cellular and Molecular Medicine and University of Arizona Cancer Center, University of Arizona., Tucson, AZ, USA
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14
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Zhu L, Wang R, Zhang L, Zuo C, Zhang R, Zhao S. rs187960998 polymorphism in miR-211 prevents development of human colon cancer by deregulation of 3'UTR in CHD5. Onco Targets Ther 2019; 12:405-412. [PMID: 30655677 PMCID: PMC6322703 DOI: 10.2147/ott.s180935] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Background Previous research indicated that overexpression of miRNA-211 could promote colorectal cancer cell growth by targeting tumor suppressive gene Chromodomain-helicase-DNA-binding protein 5 (CHD5) in human colon cancer (CC). Moreover, the function of the single-nucleotide polymorphism (SNP) located in the mature region of miR-211 has not been investigated. In this study, we found that SNP of rs187960998 in miR-211 was involved in the occurrence of CC by acting as a tumor suppressor by mal-regulation of its target gene CHD5. Materials and methods The genotype of total 685 CC patients was detected by real-time PCR, the proliferation of CC cell lines with different genotypes of miR-211 was determined by Cell Counting Kit-8, cell invasion evaluated by transwell and the activity of the CHD5 promoter in CC cell lines transfected with different miR-211 was determined by luciferase assay. The expression of CHD5 in CC patients was determined by the immunohistochemistry, and the relapse-free survival rate was analyzed by Kaplan–Meier analysis. Results C/T SNP of miR-211 could inhibit CC cell proliferation and invasion by upregulation of CHD5. And SNP in rs187960998 of miR-211 was associated with tumor size, metastasis and tumor differentiation in CC patients. Patients with CC genotype have significantly low CHD5 expression than the T-carrier, while no significant expression difference in miR-211 expression among different genotype subsets. Patients with CC genotype have significantly shorter postsurgery survival rate compared to the T-carrier. Conclusion rs187960998 in miR-211 was highly associated with a decreased risk of CC in the Chinese population by deregulating a tumor suppressive gene CHD5.
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Affiliation(s)
- Limei Zhu
- Department of Clinical Laboratory, The First People's Hospital of Lianyungang, Lianyungang, Jiangsu, China,
| | - Ran Wang
- Department of Clinical Laboratory, The First People's Hospital of Lianyungang, Lianyungang, Jiangsu, China,
| | - Li Zhang
- Department of Clinical Laboratory, The First People's Hospital of Lianyungang, Lianyungang, Jiangsu, China,
| | - Chunlei Zuo
- Department of Clinical Laboratory, The First People's Hospital of Lianyungang, Lianyungang, Jiangsu, China,
| | - Rui Zhang
- Department of Clinical Laboratory, The First People's Hospital of Lianyungang, Lianyungang, Jiangsu, China,
| | - Shaolin Zhao
- Department of Clinical Laboratory, The First People's Hospital of Lianyungang, Lianyungang, Jiangsu, China,
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15
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Ashktorab H, Rahi H, Nouraie M, Shokrani B, Lee E, Haydari T, Laiyemo AO, Siegel P, Brim H. GPNMB methylation: a new marker of potentially carcinogenic colon lesions. BMC Cancer 2018; 18:1068. [PMID: 30400781 PMCID: PMC6219212 DOI: 10.1186/s12885-018-4903-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 10/04/2018] [Indexed: 01/09/2023] Open
Abstract
Background Epigenetic plays an important role in colorectal neoplasia process. There is a need to determine sound biomarkers of colorectal cancer (CRC) progression with clinical and therapeutic implications. Therefore, we aimed to examine the role and methylation status of Glyco Protein Non-Metastatic GPNM B (GPNMB) gene in normal, adenoma and CRC in African American (AA) patients. Methods The methylation status of 13 CpG sites (chr7: 23287345–23,287,426) in GPNMB gene’s promoter, was analyzed by pyrosequencing in human CRC cell lines (HCT116, SW480, and HT29) and microdissected African American paraffin embedded samples (20 normal, 21 non-advanced adenoma (NA), 48 advanced adenoma (AD), and 20 cancer tissues. GPNMB expression was analyzed by immunohistochemistry (IHC) on tissue microarrays (TMA). Correlations between GPNMB methylation and expression with clinicopathological features were analyzed. GPNMB functional analysis was performed in triplicates using cell proliferation, migration and invasion assays in HCT116 colon cell line after stable transfection with a GPNMB-cDNA expression vector. Results GPNMB methylation was lower in normal mucosa compared to CRC samples (1/20 [5%] vs. 18/20 [90%]; P < 0.001). AD also had a significantly higher GPNMB methylation frequency than normal colon samples (42/48 [88%] vs 1/20 [5%]; P < 0.001). GPNMB was more frequently methylated in AD than in matched normal mucosa from three patients (3/3 [100%] vs 1/3 [33.3%]; P < 0.001). The frequency of GPNMB methylation in NA differed significantly from that in the normal mucosa (16/21 [76%] vs 1/20 [5%]; P = 0.008). There was statistically significant correlation of higher methylation at advanced stages and lower methylation at stage 1 CRCs (P < 0.05). In agreement with these findings, GPNMB protein expression decreased in CRC tissues compared with AD and NA colon mucosa (p < 0.05). GPNMB overexpression in HCT116 colon cancer cell line decreased cell proliferation [(24 h, P = 0.02), (48 h, P < 0.001, 72 h, P = 0.007)], invasion (p < 0.05) and migration (p > 0.05) compared to the mock-transfected cells. Conclusion Our data indicate a high methylation profile leading to a lower GPNMB expression in adenoma and CRC samples. The functional analysis established GPNMB as a potential tumor suppressor gene. As such, GPNMB might be useful as a biomarker of adenomas with high carcinogenic potential.
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Affiliation(s)
- Hassan Ashktorab
- Department of Medicine, Department of Pathology and Cancer Center, Howard University College of Medicine, 2041 Georgia Avenue, N.W, Washington, D.C, 20060, USA.
| | - Hamed Rahi
- Department of Medicine, Department of Pathology and Cancer Center, Howard University College of Medicine, 2041 Georgia Avenue, N.W, Washington, D.C, 20060, USA
| | - Mehdi Nouraie
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Babak Shokrani
- Department of Medicine, Department of Pathology and Cancer Center, Howard University College of Medicine, 2041 Georgia Avenue, N.W, Washington, D.C, 20060, USA
| | - Edward Lee
- Department of Medicine, Department of Pathology and Cancer Center, Howard University College of Medicine, 2041 Georgia Avenue, N.W, Washington, D.C, 20060, USA
| | - Tahmineh Haydari
- Department of Medicine, Department of Pathology and Cancer Center, Howard University College of Medicine, 2041 Georgia Avenue, N.W, Washington, D.C, 20060, USA
| | - Adeyinka O Laiyemo
- Department of Medicine, Department of Pathology and Cancer Center, Howard University College of Medicine, 2041 Georgia Avenue, N.W, Washington, D.C, 20060, USA
| | - Peter Siegel
- Goodman Cancer Research Centre, Department of Medicine, McGill University, Montréal, Québec, Canada
| | - Hassan Brim
- Department of Medicine, Department of Pathology and Cancer Center, Howard University College of Medicine, 2041 Georgia Avenue, N.W, Washington, D.C, 20060, USA
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16
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Xiao Q, Chen L, Luo H, Li H, Kong Q, Jiao F, Pang S, Zhang M, Lan F, Fan W, Luo H, Tao T, Zhu X. A rare CHD5 haplotype and its interactions with environmental factors predicting hepatocellular carcinoma risk. BMC Cancer 2018; 18:658. [PMID: 29907144 PMCID: PMC6003142 DOI: 10.1186/s12885-018-4551-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 05/24/2018] [Indexed: 01/10/2023] Open
Abstract
Background CHD5 is a conventional tumour-suppressing gene in many tumours. The aim of this study was to determine whether CHD5 variants contribute to the risk of hepatocellular carcinoma (HCC). Methods Gene variants were identified using next-generation sequencing targeted on referenced mutations followed by TaqMan genotyping in two case-control studies. Results We discovered a rare variant (haplotype AG) in CHD5 (rs12564469-rs9434711) that was markedly associated with the risk of HCC in a Chinese population. A logistical regression model and permutation test confirmed the association. Indeed, the association quality increased in a gene dose-dependent manner as the number of samples increased. In the stratified analysis, this haplotype risk effect was statistically significant in a subgroup of alcohol drinkers. The false-positive report probability and multifactor dimensionality reduction further supported the finding. Conclusions Our results suggest that the rare CHD5 gene haplotype and alcohol intake contribute to the risk of HCC. Our findings can be valuable to researchers of cancer precision medicine looking to improve diagnosis and treatment of HCC. Electronic supplementary material The online version of this article (10.1186/s12885-018-4551-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qin Xiao
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Department of Blood Transfusion, Peking University Shenzhen Hospital, Shenzhen, China
| | - Lianzhou Chen
- Digestive System Tumor Tissue Bank, Center of Surgery Laboratory, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Haiqing Luo
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,The Affiliated Hospital Cancer Center, Guangdong Medical University, Zhanjiang, China
| | - Hongmei Li
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Department of Pathology, Guangdong Medical University, Dongguan, China
| | - Qingming Kong
- Immunity and Biochemical Research Lab, Zhejiang Academy of Medical Sciences, Hangzhou, China
| | - Fei Jiao
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai, China
| | - Shifeng Pang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China
| | - Ming Zhang
- Department of Gastroenterology, Zibo Central Hospital, Zibo, China
| | - Feifei Lan
- Forensic Identification Institute, Guangdong Women and Children Hospital, Guangzhou, China
| | - Wenguo Fan
- Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Hui Luo
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.
| | - Tao Tao
- Department of Gastroenterology, Zibo Central Hospital, Zibo, China.
| | - Xiao Zhu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.
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17
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Zhou Y, Qiu YE, Qin SL, Luo Y, Cui R, Qin J, Chen JJ, Yu MH, Zhong M, Shi XY. Expression of CHD5 may serve as an independent biomarker of prognosis in colorectal cancer via immunohistochemical staining. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:2792-2798. [PMID: 31938397 PMCID: PMC6958296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 03/24/2018] [Indexed: 06/10/2023]
Abstract
Chromodomain helicase DNA binding protein 5 (CHD5) acts as a tumor suppressor in various types of cancer and belongs to CHD protein family. However, no prognostic role for CHD5 has yet been indicated in colorectal cancer. Therefore, the aim of this study was to investigate a possible association between CHD5 expression and colorectal cancer prognosis. Furthermore, immunochemistry was used to investigate CHD5 expression in 310 CRC tissue specimens. Expression of CHD5 significantly positively correlated with the lymphatic metastasis (P=0.007). The prognostic value of CHD5 in relation to overall survival was analyzed by Kaplan-Meier analysis and Cox proportional hazard models. The mean and medium follow-up times after surgery were 5.5 and 6.6 years, respectively. A total of 150 patients died during the 13 years of follow-up in the survey period. We also demonstrated that overall survival was poor in CRC patients with low expression of CHD5 (P=0.003). Accordingly, multivariate analysis identified low CHD5 expression as an independent risk factor (P=0.014), especially in elderly patients or those with late stage cancers. We suggest that CHD5 could serve as an independent prognostic biomarker for colorectal patients. This finding also should be verified by other research groups.
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Affiliation(s)
- Yong Zhou
- Department of Gastrointestinal Surgery, Jiading Hospital of Traditional Chinese Medicine222 Bole Road, Shanghai 201800, PR China
| | - Yi-Er Qiu
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghai, PR China
| | - Shao-Lan Qin
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghai, PR China
| | - Yang Luo
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghai, PR China
| | - Ran Cui
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghai, PR China
| | - Jun Qin
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghai, PR China
| | - Jian-Jun Chen
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghai, PR China
| | - Min-Hao Yu
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghai, PR China
| | - Ming Zhong
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghai, PR China
| | - Xing-Yao Shi
- Department of Gastrointestinal Surgery, Jiading Hospital of Traditional Chinese Medicine222 Bole Road, Shanghai 201800, PR China
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18
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Hu YH, Chen Q, Lu YX, Zhang JM, Lin C, Zhang F, Zhang WJ, Li XM, Zhang W, Li XN. Hypermethylation of NDN promotes cell proliferation by activating the Wnt signaling pathway in colorectal cancer. Oncotarget 2018; 8:46191-46203. [PMID: 28521288 PMCID: PMC5542259 DOI: 10.18632/oncotarget.17580] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 04/07/2017] [Indexed: 12/18/2022] Open
Abstract
The progression of CRC is a multistep process involving several genetic changes or epigenetic modifications. NDN is a member of the MAGE family, encoding a protein that generally suppresses cell proliferation and acting as a transcriptional repressor. Immunohistochemical staining revealed that the expression of NDN was significantly down-regulated in CRC tissues compared with normal tissues and the down-regulation of NDN in CRC could reflect the hypermethylation of the NDN promoter. Treatment of the CRC cell line SW480 with the demethylating agent 5-Aza-CdR restored the NDN expression level. The down-regulation of NDN was closely related to poor differentiation, advanced TNM stage and poor prognosis of CRC. The inhibition of NDN promoted CRC cell proliferation by enriching cells in the S phase. Furthermore, we observed that NDN binds to the GN box in the promoter of LRP6 to attenuate LRP6 transcription and inhibit the Wnt signaling pathway in CRC. In conclusion, our study revealed that the hypermethylation of NDN promotes cell proliferation by activating the Wnt signaling pathway through directly increasing the transcription of LRP6 in CRC. These findings might provide a new theoretical basis for the pathogenesis of CRC and facilitate the development of new therapeutic strategies against CRC.
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Affiliation(s)
- Yu-Han Hu
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Qing Chen
- Department of Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yan-Xia Lu
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jian-Ming Zhang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Department of Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Chun Lin
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Fan Zhang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Wen-Juan Zhang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xiao-Min Li
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Wei Zhang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xue-Nong Li
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
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19
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Guerra-Calderas L, González-Barrios R, Patiño CC, Alcaraz N, Salgado-Albarrán M, de León DC, Hernández CC, Sánchez-Pérez Y, Maldonado-Martínez HA, De la Rosa-Velazquez IA, Vargas-Romero F, Herrera LA, García-Carrancá A, Soto-Reyes E. CTCF-KDM4A complex correlates with histone modifications that negatively regulate CHD5 gene expression in cancer cell lines. Oncotarget 2018; 9:17028-17042. [PMID: 29682202 PMCID: PMC5908303 DOI: 10.18632/oncotarget.24798] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 02/26/2018] [Indexed: 11/25/2022] Open
Abstract
Histone demethylase KDM4A is involved in H3K9me3 and H3K36me3 demethylation, which are epigenetic modifications associated with gene silencing and RNA Polymerase II elongation, respectively. KDM4A is abnormally expressed in cancer, affecting the expression of multiple targets, such as the CHD5 gene. This enzyme localizes at the first intron of CHD5, and the dissociation of KDM4A increases gene expression. In vitro assays showed that KDM4A-mediated demethylation is enhanced in the presence of CTCF, suggesting that CTCF could increase its enzymatic activity in vivo, however the specific mechanism by which CTCF and KDM4A might be involved in the CHD5 gene repression is poorly understood. Here, we show that CTCF and KDM4A form a protein complex, which is recruited into the first intron of CHD5. This is related to a decrease in H3K36me3/2 histone marks and is associated with its transcriptional downregulation. Depletion of CTCF or KDM4A by siRNA, triggered the reactivation of CHD5 expression, suggesting that both proteins are involved in the negative regulation of this gene. Furthermore, the knockout of KDM4A restored the CHD5 expression and H3K36me3 and H3K36me2 histone marks. Such mechanism acts independently of CHD5 promoter DNA methylation. Our findings support a novel mechanism of epigenetic repression at the gene body that does not involve promoter silencing.
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Affiliation(s)
- Lissania Guerra-Calderas
- Cancer Biomedical Research Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Rodrigo González-Barrios
- Cancer Biomedical Research Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Carlos César Patiño
- Cancer Biomedical Research Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Nicolás Alcaraz
- The Bioinformatics Centre, Section for RNA and Computational Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Marisol Salgado-Albarrán
- Cancer Biomedical Research Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - David Cantú de León
- Clinical Research, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Clementina Castro Hernández
- Cancer Biomedical Research Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico.,Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Yesennia Sánchez-Pérez
- Cancer Biomedical Research Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | | | - Inti A De la Rosa-Velazquez
- Genomics Lab, Universidad Nacional Autónoma de México, Red de Apoyo a la Investigación-CIC and Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán", Mexico City, Mexico
| | - Fernanda Vargas-Romero
- Instituto de Fisiologia Celular-Neurociencias, Universidad Nacional Autonoma de Mexico (UNAM), Mexico City, Mexico
| | - Luis A Herrera
- Cancer Biomedical Research Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico.,Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Alejandro García-Carrancá
- Cancer Biomedical Research Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico.,Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Ernesto Soto-Reyes
- Cancer Biomedical Research Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
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20
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Xu G, Zhu H, Zhang M, Xu J. Histone deacetylase 3 is associated with gastric cancer cell growth via the miR-454-mediated targeting of CHD5. Int J Mol Med 2018; 41:155-163. [PMID: 29115379 PMCID: PMC5746286 DOI: 10.3892/ijmm.2017.3225] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/07/2017] [Indexed: 12/20/2022] Open
Abstract
Gastric cancer (GC) is the third leading cause of cancer-related mortality in China and worlwide; hence, the identification of GC-related genes is necessary for the development of effective treatment strategies. In this study, histone deacetylase 3 (HDAC3) was identified as the most significantly upregulated cancer-related gene in GC tissues by microarray. In accordance with this, HDAC3 expression was found to be upregulated in GC cell lines/tissues. Further experiments indicated that the knockdown of HDAC3 decreased GC cell viability, reduced the colony formation number and decreased tumor weight. To explore the underlying mechanisms, the overexpression of HDAC3 was induced by transfection with an overexpression plasmid, followed by miRNA microarray, and we identified miR-454 as the most markedly upregulated miRNA. Accordingly, miR-454 expression was upregulated in GC cell lines/tissues and a high level of miR-454 indicated a high HDAC3 expression in GC tissues, and miR-454 knockdown reduced cell viability. In addition, a high level of miR-454 was significantly associated with an advanced clinical stage, lymph node metastases and a poor prognosis of patients with GC. Furthermore, CHD5 was identified as a direct target of miR-454. CHD5 was downregulated in GC tissues/cell lines and the expresssion of CHD5 inversely correlated with the level of miR-454 in GC tissues. Taken together, these observations indicate that HDAC3 is associated with GC cell growth via the miR-454-mediated targeting of CHD5.
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Affiliation(s)
| | | | - Minghui Zhang
- Department of Oncology, People's Hospital of Pudong, Shanghai 201299, P.R. China
| | - Jinhua Xu
- Department of Oncology, People's Hospital of Pudong, Shanghai 201299, P.R. China
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21
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Augustus GJ, Ellis NA. Colorectal Cancer Disparity in African Americans: Risk Factors and Carcinogenic Mechanisms. THE AMERICAN JOURNAL OF PATHOLOGY 2017; 188:291-303. [PMID: 29128568 DOI: 10.1016/j.ajpath.2017.07.023] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/01/2017] [Accepted: 07/20/2017] [Indexed: 12/13/2022]
Abstract
African Americans have the highest incidence and mortality rates of colorectal cancer (CRC) of any ethnic group in the United States. Although some of these disparities can be explained by differences in access to care, cancer screening, and other socioeconomic factors, disparities remain after adjustment for these factors. Consequently, an examination of recent advances in the understanding of ethnicity-specific factors, including genetic and environmental factors relating to risk of CRC, the biology of CRC progression, and the changes in screening and mortality, is important for evaluating our progress toward eliminating the disparities. An overarching limitation in this field is the number and sample size of studies performed to characterize the etiological bases of CRC incidence and mortality in African Americans. Despite this limitation, significant differences in etiology are manifest in many studies. These differences need validation, and their impacts on disparities need more detailed investigation. Perhaps most heartening, improvements in CRC screening can be attributed to the smallest difference in CRC incidence between African Americans and whites since the late 1980s. Cancer mortality, however, remains a persistent difference.
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Affiliation(s)
- Gaius J Augustus
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, Arizona.
| | - Nathan A Ellis
- University of Arizona Cancer Center, University of Arizona, Tucson, Arizona; Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona.
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22
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A systems medicine approach for finding target proteins affecting treatment outcomes in patients with non-Hodgkin lymphoma. PLoS One 2017; 12:e0183969. [PMID: 28892521 PMCID: PMC5593188 DOI: 10.1371/journal.pone.0183969] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 08/15/2017] [Indexed: 02/07/2023] Open
Abstract
Autoantibody profiling with a systems medicine approach can help identify critical dysregulated signaling pathways (SPs) in cancers. In this way, immunoglobulins G (IgG) purified from the serum samples of 92 healthy controls, 10 pre-treated (PR) non-Hodgkin lymphoma (NHL) patients, and 20 NHL patients who underwent chemotherapy (PS) were screened with a phage-displayed random peptide library. Protein-protein interaction networks of the PR and PS groups were analyzed and visualized by Gephi. The results indicated AXIN2, SENP2, TOP2A, FZD6, NLK, HDAC2, HDAC1, and EHMT2, in addition to CAMK2A, PLCG1, PLCG2, GRM5, GRIN2B, GRIN2D, CACNA2D3, and SPTAN1 as hubs in 11 and 7 modules of PR and PS networks, respectively. PR- and PS-specific hubs were evaluated in the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Reactome databases. The PR-specific hubs were involved in Wnt SP, signaling by Notch1 in cancer, telomere maintenance, and transcriptional misregulation. In contrast, glutamate receptor SP, Fc receptor-related pathways, growth factors-related SPs, and Wnt SP were statistically significant enriched pathways, based on the pathway analysis of PS hubs. The results revealed that the most PR-specific proteins were associated with events involved in tumor development, while chemotherapy in the PS group was associated with side effects of drugs and/or cancer recurrence. As the findings demonstrated, PR- and PS-specific proteins in this study can be promising therapeutic targets in future studies.
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Abstract
The malignant transformation of normal cells is driven by both genetic and epigenetic changes. With the advent of next-generation sequencing and large-scale multinational consortium studies, it has become possible to profile the genomes and epigenomes of thousands of primary tumors from nearly every cancer type. From these genome-wide studies, it became clear that the dynamic regulation of DNA methylation is a critical epigenetic mechanism of cancer initiation, maintenance, and progression. Proper control of DNA methylation is not only crucial for regulating gene transcription, but its broader consequences include maintaining the integrity of the genome and modulating immune response. Here, we describe the aberrant DNA methylation changes that take place in cancer and how they contribute to the disease phenotype. Further, we highlight potential clinical implications of these changes in the context of prognostic and diagnostic biomarkers, as well as therapeutic targets.
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Baykara O, Tansarikaya M, Bulut P, Demirkaya A, Buyru N. CHD5 is a potential tumor suppressor in non small cell lung cancer (NSCLC). Gene 2017; 618:65-68. [PMID: 28400267 DOI: 10.1016/j.gene.2017.04.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/17/2017] [Accepted: 04/07/2017] [Indexed: 01/17/2023]
Abstract
Lung cancer is one of the deadliest types of cancers and genetic and epigenetic alterations play major roles in its development. Chromodomain (CHD) protein family acts in chromatin organization, regulation of transcription and also genomic stability and cancer prevention. Although CHD5, a member of this family was shown to contribute to major cellular events and functions as a tumor suppressor gene in various types of cancer, it is not clear whether CHD5 plays a role in lung carcinogenesis. The aim of this study was to investigate the possible role of CHD5 in progression of non-small cell lung cancer (NSCLC). Expression levels of CHD5 gene in 59 tumor and corresponding non-cancerous lung tissue samples were analyzed by qRT-PCR and the methylation status of the promoter region was investigated by methylation specific PCR (MS-PCR). The Akt phosphorylation levels were investigated by Western Blot (WB). CHD5 was down-regulated in 17 (39.5%) and up-regulated in 24 (55.8%) of tumor specimens. Even though the promoter of CHD5 was hypermethylated in 8 patients, it was not found associated with CHD5 gene expression (p=0.08). Akt phosphorylation was increased in 14 (53.8%) and decreased in 12 (46.2%) of the samples but no significant association was found between p-Akt phosphorylation and CHD5 expression (p=0.67). We suggest that CHD5 may act as a tumor suppressor gene in NSCLC.
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Affiliation(s)
- Onur Baykara
- Istanbul University Cerrahpasa Medical Faculty, Dept. of Medical Biology and Genetics, Istanbul 34098, Turkey
| | - Merve Tansarikaya
- Istanbul University Cerrahpasa Medical Faculty, Dept. of Medical Biology and Genetics, Istanbul 34098, Turkey
| | - Pelin Bulut
- Istanbul University Cerrahpasa Medical Faculty, Dept. of Medical Biology and Genetics, Istanbul 34098, Turkey
| | - Ahmet Demirkaya
- Istanbul University Cerrahpasa Medical Faculty, Dept. of Thoracic Surgery, Istanbul 34098, Turkey
| | - Nur Buyru
- Istanbul University Cerrahpasa Medical Faculty, Dept. of Medical Biology and Genetics, Istanbul 34098, Turkey.
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25
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Mills AA. The Chromodomain Helicase DNA-Binding Chromatin Remodelers: Family Traits that Protect from and Promote Cancer. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026450. [PMID: 28096241 DOI: 10.1101/cshperspect.a026450] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A plethora of mutations in chromatin regulators in diverse human cancers is emerging, attesting to the pivotal role of chromatin dynamics in tumorigenesis. A recurrent theme is inactivation of the chromodomain helicase DNA-binding (CHD) family of proteins-ATP-dependent chromatin remodelers that govern the cellular machinery's access to DNA, thereby controlling fundamental processes, including transcription, proliferation, and DNA damage repair. This review highlights what is currently known about how genetic and epigenetic perturbation of CHD proteins and the pathways that they regulate set the stage for cancer, providing new insight for designing more effective anti-cancer therapies.
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Affiliation(s)
- Alea A Mills
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724
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26
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Ali H, Bitar MS, Al Madhoun A, Marafie M, Al-Mulla F. Functionally-focused algorithmic analysis of high resolution microarray-CGH genomic landscapes demonstrates comparable genomic copy number aberrations in MSI and MSS sporadic colorectal cancer. PLoS One 2017; 12:e0171690. [PMID: 28231327 PMCID: PMC5322957 DOI: 10.1371/journal.pone.0171690] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 01/23/2017] [Indexed: 12/25/2022] Open
Abstract
Array-based comparative genomic hybridization (aCGH) emerged as a powerful technology for studying copy number variations at higher resolution in many cancers including colorectal cancer. However, the lack of standardized systematic protocols including bioinformatic algorithms to obtain and analyze genomic data resulted in significant variation in the reported copy number aberration (CNA) data. Here, we present genomic aCGH data obtained using highly stringent and functionally relevant statistical algorithms from 116 well-defined microsatellites instable (MSI) and microsatellite stable (MSS) colorectal cancers. We utilized aCGH to characterize genomic CNAs in 116 well-defined sets of colorectal cancer (CRC) cases. We further applied the significance testing for aberrant copy number (STAC) and Genomic Identification of Significant Targets in Cancer (GISTIC) algorithms to identify functionally relevant (nonrandom) chromosomal aberrations in the analyzed colorectal cancer samples. Our results produced high resolution genomic landscapes of both, MSI and MSS sporadic CRC. We found that CNAs in MSI and MSS CRCs are heterogeneous in nature but may be divided into 3 distinct genomic patterns. Moreover, we show that although CNAs in MSI and MSS CRCs differ with respect to their size, number and chromosomal distribution, the functional copy number aberrations obtained from MSI and MSS CRCs were in fact comparable but not identical. These unifying CNAs were verified by MLPA tumor-loss gene panel, which spans 15 different chromosomal locations and contains 50 probes for at least 20 tumor suppressor genes. Consistently, deletion/amplification in these frequently cancer altered genes were identical in MSS and MSI CRCs. Our results suggest that MSI and MSS copy number aberrations driving CRC may be functionally comparable.
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Affiliation(s)
- Hamad Ali
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Kuwait University, Jabriya, Kuwait
- Research Division, Immunology Unit, Dasman Diabetes Institute (DDI), Dasman, Kuwait
- * E-mail: (HA); (FA)
| | - Milad S. Bitar
- Research Division, Immunology Unit, Dasman Diabetes Institute (DDI), Dasman, Kuwait
- Department of Pharmacology & Toxicology, Faculty of Medicine, Kuwait University, Jabriya, Kuwait
| | - Ashraf Al Madhoun
- Research Division, Immunology Unit, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | | | - Fahd Al-Mulla
- Molecular Pathology Unit, Department of Pathology, Faculty of Medicine, Kuwait University, Jabriya, Kuwait
- Research Division, Genomics Unit, Dasman Diabetes Institute (DDI), Dasman, Kuwait
- * E-mail: (HA); (FA)
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miR-454 functions as an oncogene by inhibiting CHD5 in hepatocellular carcinoma. Oncotarget 2016; 6:39225-34. [PMID: 26287602 PMCID: PMC4770768 DOI: 10.18632/oncotarget.4407] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/17/2015] [Indexed: 01/04/2023] Open
Abstract
Previous studies showed that miR-454 acted as an oncogene or tumor suppressor in cancer. However, its function in HCC remains unknown. In this study, we found that miR-454 expression was upregulated in HCC cell lines and tissues. Knockdown of miR-454 inhibited HCC cell proliferation and invasion and epithelial mesenchymal transition (EMT), whereas overexpression of miR-454 promoted HCC cell proliferation and invasion and EMT. Furthermore, we identified the CHD5 as a direct target of miR-454. CHD5 was downregulated in HCC tissues and cell lines and the expression level of CHD5 was inversely correlated with the expression of miR-454 in HCC tissues. In addition, knockdown of miR-454 inhibited the growth of HepG2-engrafted tumors in vivo. Taken together, these results indicated that miR-454 functioned as an oncogene in HCC.
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28
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Sun X, Xiao D, Xu T, Yuan Y. miRNA-24-3p promotes cell proliferation and regulates chemosensitivity in head and neck squamous cell carcinoma by targeting CHD5. Future Oncol 2016; 12:2701-2712. [PMID: 27513190 DOI: 10.2217/fon-2016-0179] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Aim: To investigate the role of miR-24-3p in tumorigenesis and chemosensitivity in head and neck squamous cell carcinoma (HNSCC). Methods: Growth rate and colony formation assays were performed after transfection with miR-24-3p mimic and inhibitor in cultured SCC-15 cells, followed by a CellTiter-Glo® assay. Western blot and luciferase assays were performed to investigate the direct target of miR-24-3p. Xenograft mouse model was used to evaluate combinatorial effects of miR-24-3p inhibitor and 5-fluorouracil. Results & conclusion: Inhibition of miR-24-3p reduced cell proliferation, colony formation efficiency and reversed chemoresistance in HNSCC cells. CHD5 is the direct target of miR-24-3p which is required for the regulatory role of miR-24-3p in chemoresistance. miR-24-3p may represent a new therapeutic target for the improvement of clinical outcome in HNSCC.
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Affiliation(s)
- Xiaofeng Sun
- Department of Stomatology, The Second People’s Hospital of Wuxi, 68 Zhong Shan Road, Wuxi 214002, Jiangsu, PR China
| | - Dajiang Xiao
- Department of Otolaryngology, The Second People’s Hospital of Wuxi, 68 Zhong Shan Road, Wuxi 214002, Jiangsu, PR China
| | - Ting Xu
- Department of Otolaryngology, The Second People’s Hospital of Wuxi, 68 Zhong Shan Road, Wuxi 214002, Jiangsu, PR China
| | - Yuan Yuan
- Department of Otolaryngology, The Second People’s Hospital of Wuxi, 68 Zhong Shan Road, Wuxi 214002, Jiangsu, PR China
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Abstract
Genome-wide studies are increasingly becoming a must, especially for complex diseases such as cancer where multiple genes and diverse molecular mechanisms are known to be involved in genes' function alteration. In this review, we report our latest genomic and epigenomic findings in African-American colorectal cancer patients. This population suffers a higher burden of the disease and most investigators in this field are looking for the underlying genetic and epigenetic targets that might be responsible for this disparity. We here report genome-wide copy number variations, single nucleotide mutations and DNA methylation findings that might be specific to this population.
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Affiliation(s)
- Hassan Brim
- Pathology Department, Howard University College of Medicine, Gastroenterology Division and Cancer Center, Washington DC, USA
| | - Hassan Ashktorab
- Howard University College of Medicine, Department of Medicine and Cancer Center, 2041 Georgia Avenue, Washington, DC, 20060, USA
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Ma Z, Song J, Liu S, Han L, Chen Y, Wang Y, Yu C, Hou L. Decreased expression of the CHD5 gene and its clinicopathological significance in breast cancer: Correlation with aberrant DNA methylation. Oncol Lett 2016; 12:4021-4026. [PMID: 27895765 DOI: 10.3892/ol.2016.5147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Accepted: 08/09/2016] [Indexed: 12/23/2022] Open
Abstract
Chromodomain helicase DNA binding protein 5 (CHD5) has been identified as a tumor suppressor in mouse models. Downregulation of CHD5 gene expression is frequently observed in breast cancer cells and tissues. This may be explained by deletions or other mutations; however, alternative mechanisms require investigation. Therefore, the present study evaluated whether CHD5 aberrant methylation has a role in primary breast tumors. A total of 389 patients with primary breast cancer (including 252 paraffin-embedded specimens and 137 fresh-frozen samples) were enrolled in the present study. In the current study, reverse transcription-polymerase chain reaction (RT-PCR) and nested-methylation-specific PCR were used to analyze the mRNA expression and promoter methylation of CHD5 genes in a large cohort of breast cancer patients, and to investigate their associations with the clinicopathological features of tumors. CHD5 expression was significantly suppressed in breast cancer tissues compared with normal breast tissues when analyzed by RT-PCR. Furthermore, DNA methylation of CHD5 was more prevalent in breast tumors than in normal tissues. CHD5 mRNA levels correlated with the degree of CHD5 methylation in breast cancer tissues. Clinicopathological correlation analysis revealed that CHD5 promoter methylation was associated with estrogen receptor and progesterone receptor status. Thus, downregulation of CHD5, mediated by abnormal methylation, may contribute to the development and progression of breast cancer.
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Affiliation(s)
- Zhongliang Ma
- Department of Breast Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, P.R. China
| | - Jinlian Song
- Department of Laboratory Medicine, The Affiliated Qingdao Women and Children's Hospital of Qingdao, Qingdao, Shandong 266034, P.R. China
| | - Simin Liu
- Department of PET Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, P.R. China
| | - Linlin Han
- Department of Pediatrics, Jinan Children's Hospital, Jinan, Shandong 250022, P.R. China
| | - Yangping Chen
- Department of Laboratory Medicine, The Affiliated Qingdao Women and Children's Hospital of Qingdao, Qingdao, Shandong 266034, P.R. China
| | - Yaqiu Wang
- Department of Laboratory Medicine, The Affiliated Qingdao Women and Children's Hospital of Qingdao, Qingdao, Shandong 266034, P.R. China
| | - Chundong Yu
- Department of Laboratory Medicine, The Affiliated Qingdao Women and Children's Hospital of Qingdao, Qingdao, Shandong 266034, P.R. China
| | - Lin Hou
- Department of Biochemistry, Medical College, Qingdao University, Qingdao, Shandong 266021, P.R. China
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31
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Liu WB, Han F, Jiang X, Chen HQ, Zhao H, Liu Y, Li YH, Huang C, Cao J, Liu JY. TMEM196 acts as a novel functional tumour suppressor inactivated by DNA methylation and is a potential prognostic biomarker in lung cancer. Oncotarget 2016; 6:21225-39. [PMID: 26056045 PMCID: PMC4673261 DOI: 10.18632/oncotarget.4237] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 05/12/2015] [Indexed: 12/31/2022] Open
Abstract
Epigenetic silencing of tumour suppressors contributes to the development and progression of lung cancer. We recently found that TMEM196 was hypermethylated in lung cancer. This study aimed to clarify its epigenetic regulation, possible roles and clinical significance. TMEM196 methylation correlated with loss of protein expression in chemical-induced rat lung pathologic lesions and human lung cancer tissues and cell lines. 5-aza-2′-deoxycytidine restored TMEM196 expression. Moreover, TMEM196 hypermethylation was detected in 61.2% of primary lung tumours and found to be associated with poor differentiation and pathological stage of lung cancer. Functional studies showed that ectopic re-expression of TMEM196 in lung cancer cells inhibited cell proliferation, clonogenicity, cell motility and tumour formation. However, TMEM196 knockdown increased cell proliferation and inhibited apoptosis and cell-cycle arrest. These effects were associated with upregulation of p21 and Bax, and downregulation of cyclin D1, c-myc, CD44 and β-catenin. Kaplan–Meier survival curves showed that TMEM196 downregulation was significantly associated with shortened survival in lung cancer patients. Multivariate analysis showed that patients with TMEM196 expression had a better overall survival. Our results revealed for the first time that TMEM196 acts as a novel functional tumour suppressor inactivated by DNA methylation and is an independent prognostic factor of lung cancer.
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Affiliation(s)
- Wen-bin Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, P. R. China
| | - Fei Han
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, P. R. China
| | - Xiao Jiang
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, P. R. China
| | - Hong-qiang Chen
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, P. R. China
| | - Huan Zhao
- Department of Internal Neurology, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Yong Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, P. R. China
| | - Yong-hong Li
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, P. R. China
| | - Chuanshu Huang
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, New York, USA
| | - Jia Cao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, P. R. China
| | - Jin-yi Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, P. R. China
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32
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Song L, Jiang W, Liu W, Ji J, Shi T, Zhang J, Xia C. Protein tyrosine phosphatases receptor type D is a potential tumour suppressor gene inactivated by deoxyribonucleic acid methylation in paediatric acute myeloid leukaemia. Acta Paediatr 2016; 105:e132-41. [PMID: 26607758 DOI: 10.1111/apa.13284] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 09/27/2015] [Accepted: 11/20/2015] [Indexed: 01/09/2023]
Abstract
AIM Protein tyrosine phosphatases receptor type D (PTPRD) is a tumour suppressor gene, and its epigenetic silencing is frequently found in glioblastoma. As aberrant deoxyribonucleic acid (DNA) methylation patterning has been shown to play a role in leukaemogenesis, we studied the promoter methylation, expression profiles and molecular functions of PTPRD in paediatric patients with acute myeloid leukaemia (AML). METHODS Bone marrow specimens were obtained from 32 Chinese patients with a mean age of 7.2 years (range 1.1-16.5). PTPRD and methylation status were evaluated by real-time polymerase chain reaction (PCR) and methylation-specific PCR. Western blot and flow cytometry techniques were also used. RESULTS PTPRD expression was decreased by promoter region methylation in six AML cells and methylated in 21 (65.6%) of the 32 samples. In addition, PTPRD expression could be induced by the DNA demethylating agent 5-aza-2'-deoxycytidine. Furthermore, functional studies showed that overexpression of PTPRD in AML cells inhibited cell proliferation and clonogenicity as well as inducing apoptosis. However, PTPRD knockdown increased cell proliferation. These effects were associated with downregulation of cyclin D1, c-myc and upregulation of Bax. CONCLUSION The results of this study demonstrated that PTPRD was a potential tumour suppressor gene inactivated by DNA methylation in paediatric AML.
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Affiliation(s)
- Lei Song
- Department of Paediatrics The Second Affiliated Hospital of Nantong University Nantong Jiangsu China
| | - Wen Jiang
- Department of Gastroenterology Nantong Third People's Hospital Nantong Jiangsu China
| | - Wei Liu
- Department of Surgery The Second Affiliated Hospital of Nantong University Nantong Jiangsu China
| | - Ju‐Hua Ji
- Department of Gastroenterology Nantong Third People's Hospital Nantong Jiangsu China
| | - Tai‐Feng Shi
- Department of Gastroenterology Nantong Third People's Hospital Nantong Jiangsu China
| | - Jie Zhang
- School of Medicine Nantong University Nantong Jiangsu China
| | - Chun‐Qiu Xia
- Department of Surgery The Second Affiliated Hospital of Nantong University Nantong Jiangsu China
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Xie CR, Li Z, Sun HG, Wang FQ, Sun Y, Zhao WX, Zhang S, Zhao WX, Wang XM, Yin ZY. Mutual regulation between CHD5 and EZH2 in hepatocellular carcinoma. Oncotarget 2015; 6:40940-52. [PMID: 26517514 PMCID: PMC4747380 DOI: 10.18632/oncotarget.5724] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 09/20/2015] [Indexed: 11/25/2022] Open
Abstract
Chromodomain helicase DNA binding protein 5 (CHD5) acts as a tumor suppressor in many cancers. In the present study, we demonstrated that reduced levels of CHD5 in hepatocellular carcinoma (HCC) tissues were significantly associated with metastasis and poor prognosis. Gain-of-function assays revealed that CHD5 suppressed motility and invasion of HCC cells. Subsequent investigations showed that CHD5 was epigenetically silenced by polycomb repressive complex 2 (PRC2)-mediated the trimethylation of histone H3 at lysine 27 (H3K27me3) in HCC cells. Furthermore, overexpression of CHD5 repressed enhancer of zeste homolog 2 (EZH2) and activated PRC2 target genes, such as p16 and p21. Chromatin immunoprecipitation and luciferase reporter assays also showed that CHD5 and EZH2 bind to each other's promoters and inhibit transcription. These findings uncovered, for the first time, a mutual suppression regulation between CHD5 and EZH2, which may provide new insights into their potential therapeutic significance for HCC.
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Affiliation(s)
- Cheng-Rong Xie
- Department of Hepatobiliary Surgery, Zhongshan Hospital, Xiamen University, Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Fujian, P.R. China
| | - Zhao Li
- Department of Hepatobiliary Surgery, Zhongshan Hospital, Xiamen University, Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Fujian, P.R. China
| | - Hong-Guang Sun
- Department of Hepatobiliary Surgery, Zhongshan Hospital, Xiamen University, Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Fujian, P.R. China
| | - Fu-Qiang Wang
- Department of Hepatobiliary Surgery, Zhongshan Hospital, Xiamen University, Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Fujian, P.R. China
| | - Yu Sun
- Department of Hepatobiliary Surgery, Zhongshan Hospital, Xiamen University, Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Fujian, P.R. China
| | - Wen-Xiu Zhao
- Department of Hepatobiliary Surgery, Zhongshan Hospital, Xiamen University, Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Fujian, P.R. China
| | - Sheng Zhang
- Department of Hepatobiliary Surgery, Zhongshan Hospital, Xiamen University, Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Fujian, P.R. China
| | - Wen-Xing Zhao
- Department of Hepatobiliary Surgery, Zhongshan Hospital, Xiamen University, Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Fujian, P.R. China
| | - Xiao-Min Wang
- Department of Hepatobiliary Surgery, Zhongshan Hospital, Xiamen University, Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Fujian, P.R. China
| | - Zhen-Yu Yin
- Department of Hepatobiliary Surgery, Zhongshan Hospital, Xiamen University, Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Fujian, P.R. China
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Higashi M, Kolla V, Iyer R, Naraparaju K, Zhuang T, Kolla S, Brodeur GM. Retinoic acid-induced CHD5 upregulation and neuronal differentiation of neuroblastoma. Mol Cancer 2015; 14:150. [PMID: 26245651 PMCID: PMC4527355 DOI: 10.1186/s12943-015-0425-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 07/30/2015] [Indexed: 01/09/2023] Open
Abstract
Background Chromodomain-helicase DNA binding protein 5 (CHD5) is an important tumor suppressor gene deleted from 1p36.31 in neuroblastomas (NBs). High CHD5 expression is associated with a favorable prognosis, but deletion or low expression is frequent in high-risk tumors. We explored the role of CHD5 expression in the neuronal differentiation of NB cell lines. Methods NB cell lines SH-SY5Y (SY5Y), NGP, SK-N-DZ, IMR5, LAN5, SK-N-FI, NB69 and SH-EP were treated with 1–10 μM 13-cis-retinoic acid (13cRA) for 3–12 days. qRT-PCR and Western blot analyses were performed to measure mRNA and protein expression levels, respectively. Morphological differences were examined by both phase contrast and immunofluorescence studies. Results Treatment of SY5Y cells with 13cRA caused upregulation of CHD5 expression in a time- and dose-dependent manner (1, 5, or 10 μM for 7 or 12 days) and also induced neuronal differentiation. Furthermore, both NGP and SK-N-DZ cells showed CHD5 upregulation and neuronal differentiation after 13cRA treatment. In contrast, 13cRA treatment of IMR5, LAN5, or SK-N-FI induced neither CHD5 expression nor neuronal differentiation. NB69 cells showed two different morphologies (neuronal and substrate adherent) after 12 days treatment with 10 μM of 13cRA. CHD5 expression was high in the neuronal cells, but low/absent in the flat, substrate adherent cells. Finally, NGF treatment caused upregulation of CHD5 expression and neuronal differentiation in SY5Y cells transfected to express TrkA (SY5Y-TrkA) but not in TrkA-null parental SY5Y cells, and both changes were blocked by a pan-TRK inhibitor. Conclusions Treatment with 13cRA induces neuronal differentiation only in NB cells that upregulate CHD5. In addition, NGF induced CHD5 upregulation and neuronal differentiation only in TrkA expressing cells. Together, these results suggest that CHD5 is downstream of TrkA, and CHD5 expression may be crucial for neuronal differentiation induced by either 13cRA or TrkA/NGF signaling. Electronic supplementary material The online version of this article (doi:10.1186/s12943-015-0425-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mayumi Higashi
- Division of Oncology, Children's Hospital of Philadelphia, and the Department of Pediatrics, University of Pennsylvania School of Medicine, CTRB Rm. 3018, 3501 Civic Center Blvd, Philadelphia, PA, 19104 - 4302, USA. .,Department of Pediatric Surgery, Kyoto Prefectural University of Medicine, Kyoto, 602 - 8566, Japan.
| | - Venkatadri Kolla
- Division of Oncology, Children's Hospital of Philadelphia, and the Department of Pediatrics, University of Pennsylvania School of Medicine, CTRB Rm. 3018, 3501 Civic Center Blvd, Philadelphia, PA, 19104 - 4302, USA.
| | - Radhika Iyer
- Division of Oncology, Children's Hospital of Philadelphia, and the Department of Pediatrics, University of Pennsylvania School of Medicine, CTRB Rm. 3018, 3501 Civic Center Blvd, Philadelphia, PA, 19104 - 4302, USA.
| | - Koumudi Naraparaju
- Division of Oncology, Children's Hospital of Philadelphia, and the Department of Pediatrics, University of Pennsylvania School of Medicine, CTRB Rm. 3018, 3501 Civic Center Blvd, Philadelphia, PA, 19104 - 4302, USA.
| | - Tiangang Zhuang
- Division of Oncology, Children's Hospital of Philadelphia, and the Department of Pediatrics, University of Pennsylvania School of Medicine, CTRB Rm. 3018, 3501 Civic Center Blvd, Philadelphia, PA, 19104 - 4302, USA.
| | - Sriharsha Kolla
- Division of Oncology, Children's Hospital of Philadelphia, and the Department of Pediatrics, University of Pennsylvania School of Medicine, CTRB Rm. 3018, 3501 Civic Center Blvd, Philadelphia, PA, 19104 - 4302, USA.
| | - Garrett M Brodeur
- Division of Oncology, Children's Hospital of Philadelphia, and the Department of Pediatrics, University of Pennsylvania School of Medicine, CTRB Rm. 3018, 3501 Civic Center Blvd, Philadelphia, PA, 19104 - 4302, USA.
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Li W, Mills AA. Architects of the genome: CHD dysfunction in cancer, developmental disorders and neurological syndromes. Epigenomics 2015; 6:381-95. [PMID: 25333848 DOI: 10.2217/epi.14.31] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Chromatin is vital to normal cells, and its deregulation contributes to a spectrum of human ailments. An emerging concept is that aberrant chromatin regulation culminates in gene expression programs that set the stage for the seemingly diverse pathologies of cancer, developmental disorders and neurological syndromes. However, the mechanisms responsible for such common etiology have been elusive. Recent evidence has implicated lesions affecting chromatin-remodeling proteins in cancer, developmental disorders and neurological syndromes, suggesting a common source for these different pathologies. Here, we focus on the chromodomain helicase DNA binding chromatin-remodeling family and the recent evidence for its deregulation in diverse pathological conditions, providing a new perspective on the underlying mechanisms and their implications for these prevalent human diseases.
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Affiliation(s)
- Wangzhi Li
- Cold Spring Harbor Laboratory Cold Spring Harbor, NY 11724, USA
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Bishop B, Ho KK, Tyler K, Smith A, Bonilla S, Leung YF, Ogas J. The chromatin remodeler chd5 is necessary for proper head development during embryogenesis of Danio rerio. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1040-50. [PMID: 26092436 DOI: 10.1016/j.bbagrm.2015.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 06/05/2015] [Accepted: 06/12/2015] [Indexed: 12/12/2022]
Abstract
The chromatin remodeler CHD5 plays a critical role in tumor suppression and neurogenesis in mammals. CHD5 contributes to gene expression during neurogenesis, but there is still much to learn regarding how this class of remodelers contributes to differentiation and development. CHD5 remodelers are vertebrate-specific, raising the prospect that CHD5 plays one or more conserved roles in this phylum. Expression of chd5 in adult fish closely mirrors expression of CHD5 in adult mammals. Knockdown of Chd5 during embryogenesis suggests new roles for CHD5 remodelers based on resulting defects in craniofacial development including reduced head and eye size as well as reduced cartilage formation in the head. In addition, knockdown of Chd5 results in altered expression of neural markers in the developing brain and eye as well as a profound defect in differentiation of dopaminergic amacrine cells. Recombinant zebrafish Chd5 protein exhibits nucleosome remodeling activity in vitro, suggesting that it is the loss of this activity that contributes to the observed phenotypes. Our studies indicate that zebrafish is an appropriate model for functional characterization of CHD5 remodelers in vertebrates and highlight the potential of this model for generating novel insights into the role of this vital class of remodelers.
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Affiliation(s)
- Brett Bishop
- Department of Biochemistry and Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, United States
| | - Kwok Ki Ho
- Department of Biochemistry and Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, United States
| | - Kim Tyler
- Department of Biochemistry and Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, United States
| | - Amanda Smith
- Department of Biochemistry and Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, United States
| | - Sylvia Bonilla
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, United States
| | - Yuk Fai Leung
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, United States
| | - Joe Ogas
- Department of Biochemistry and Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, United States.
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McCarty G, Loeb DM. Hypoxia-sensitive epigenetic regulation of an antisense-oriented lncRNA controls WT1 expression in myeloid leukemia cells. PLoS One 2015; 10:e0119837. [PMID: 25794157 PMCID: PMC4368825 DOI: 10.1371/journal.pone.0119837] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 01/19/2015] [Indexed: 01/09/2023] Open
Abstract
WT1 is a transcription factor expressed in hematopoietic stem cells and in most cases of myeloid leukemia. We investigated the roles of hypoxia and epigenetics in the regulation of WT1 expression in myeloid leukemia cells. WT1 expression correlates with hypomethylation of the CpG island in Intron 1, and pharmacologic demethylation of this CpG island induces WT1 mRNA expression. Hypoxia causes decreases in DNMT expression and activity and increased expression and activity of TET2 and TET3, resulting in demethylation of this CpG island and expression of WT1 mRNA. Demethylation of the CpG island, either from pharmacologic treatment or induction of hypoxia, results in transcription of an antisense-oriented lncRNA, and inhibiting lncRNA expression with shRNA blocks WT1 mRNA expression. These results reveal a novel model of hypoxia-mediated epigenetic gene regulation. In addition, this is the first report that TET2 and TET3, increasingly recognized as important epigenetic regulators of gene expression in stem cells and in cancer cells, can be regulated by hypoxia, providing a solid mechanistic link between hypoxia and epigenetic regulation of gene expression with important implications for the role of hypoxia in stem cell function.
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MESH Headings
- Base Sequence
- Cell Line, Tumor
- CpG Islands
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- DNA Methylation
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Dioxygenases/genetics
- Dioxygenases/metabolism
- Epigenesis, Genetic
- Gene Expression Regulation, Leukemic
- Genetic Loci
- Humans
- Hypoxia/genetics
- Hypoxia-Inducible Factor 1, alpha Subunit/genetics
- Hypoxia-Inducible Factor 1, alpha Subunit/metabolism
- Introns
- Leukemia, Myeloid/genetics
- Leukemia, Myeloid/metabolism
- Molecular Sequence Data
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- RNA, Antisense/genetics
- RNA, Long Noncoding/chemistry
- RNA, Long Noncoding/genetics
- WT1 Proteins/chemistry
- WT1 Proteins/genetics
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Affiliation(s)
- Gregory McCarty
- Department of Oncology, Division of Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, United States of America
| | - David M. Loeb
- Department of Oncology, Division of Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, United States of America
- * E-mail:
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Ashktorab H, Daremipouran M, Devaney J, Varma S, Rahi H, Lee E, Shokrani B, Schwartz R, Nickerson ML, Brim H. Identification of novel mutations by exome sequencing in African American colorectal cancer patients. Cancer 2014; 121:34-42. [PMID: 25250560 DOI: 10.1002/cncr.28922] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 04/29/2014] [Accepted: 05/16/2014] [Indexed: 12/14/2022]
Abstract
BACKGROUND The purpose of this study was to identify genome-wide single nucleotide variants and mutations in African American patients with colorectal cancer (CRC). There is a need of such studies in African Americans, because they display a higher incidence of aggressive CRC tumors. METHODS We performed whole exome sequencing (WES) on DNA from 12 normal/tumor pairs of African American CRC patient tissues. Data analysis was performed using the software package GATK (Genome Analysis Tool Kit). Normative population databases (eg, 1000 Genomes SNP database, dbSNP, and HapMap) were used for comparison. Variants were annotated using analysis of variance and were validated via Sanger sequencing. RESULTS We identified somatic mutations in genes that are known targets in CRC such as APC, BRAF, KRAS, and PIK3CA. We detected novel alterations in the Wnt pathway gene, APC, within its exon 15, of which mutations are highly associated with CRC. CONCLUSIONS This WES study in African American patients with CRC provides insight into the identification of novel somatic mutations in APC. Our data suggest an association between specific mutations in the Wnt signaling pathway and an increased risk of CRC. The analysis of the pathogenicity of these novel variants may shed light on the aggressive nature of CRC in African Americans.
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Affiliation(s)
- Hassan Ashktorab
- Department of Medicine and Cancer Center, Howard University College of Medicine, Washington, DC
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39
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Mah WC, Thurnherr T, Chow PKH, Chung AYF, Ooi LLPJ, Toh HC, Teh BT, Saunthararajah Y, Lee CGL. Methylation profiles reveal distinct subgroup of hepatocellular carcinoma patients with poor prognosis. PLoS One 2014; 9:e104158. [PMID: 25093504 PMCID: PMC4122406 DOI: 10.1371/journal.pone.0104158] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/05/2014] [Indexed: 12/12/2022] Open
Abstract
Hepatocellular Carcinoma (HCC) is one of the leading causes of cancer-associated mortality worldwide. However, the role of epigenetic changes such as aberrant DNA methylation in hepatocarcinogenesis remains largely unclear. In this study, we examined the methylation profiles of 59 HCC patients. Using consensus hierarchical clustering with feature selection, we identified three tumor subgroups based on their methylation profiles and correlated these subgroups with clinicopathological parameters. Interestingly, one tumor subgroup is different from the other 2 subgroups and the methylation profile of this subgroup is the most distinctly different from the non-tumorous liver tissues. Significantly, this subgroup of patients was found to be associated with poor overall as well as disease-free survival. To further understand the pathways modulated by the deregulation of methylation in HCC patients, we integrated data from both the methylation as well as the gene expression profiles of these 59 HCC patients. In these patients, while 4416 CpG sites were differentially methylated between the tumors compared to the adjacent non-tumorous tissues, only 536 of these CpG sites were associated with differences in the expression of their associated genes. Pathway analysis revealed that forty-four percent of the most significant upstream regulators of these 536 genes were involved in inflammation-related NFκB pathway. These data suggest that inflammation via the NFκB pathway play an important role in modulating gene expression of HCC patients through methylation. Overall, our analysis provides an understanding on aberrant methylation profile in HCC patients.
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Affiliation(s)
- Way-Champ Mah
- Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore
| | - Thomas Thurnherr
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore
- Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Pierce K. H. Chow
- Duke-NUS Graduate Medical School, Singapore, Singapore
- Department of Surgery, Singapore General Hospital, Singapore, Singapore
| | | | - London L. P. J. Ooi
- Department of Surgery, Singapore General Hospital, Singapore, Singapore
- Department of Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Han Chong Toh
- Department of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Bin Tean Teh
- Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Graduate Medical School, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yogen Saunthararajah
- Department of Hematologic Oncology and Blood Disorders, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Caroline G. L. Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore
- Duke-NUS Graduate Medical School, Singapore, Singapore
- * E-mail:
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40
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Zhao Y, Yang H, Storey KB, Chen M. Differential gene expression in the respiratory tree of the sea cucumber Apostichopus japonicus during aestivation. Mar Genomics 2014; 18 Pt B:173-83. [PMID: 25038515 DOI: 10.1016/j.margen.2014.07.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 06/30/2014] [Accepted: 07/03/2014] [Indexed: 10/25/2022]
Abstract
Sea cucumbers, Apostichopus japonicus, experience seasonally high water temperatures during the summer months and enter aestivation to survive. Aestivation is characterized by strong metabolic rate depression which is supported by a series of strategies including reorganizing metabolic processes, suppressing cell functions, enhancing cytoprotective mechanisms, and altered gene expression. The respiratory tree tissue of the sea cucumber is an excellent material for studying aestivation, undergoing obvious atrophy during aestivation. The present study analyzed the global gene expression profile of respiratory tree tissue of A. japonicus during aestivation by constructing and screening three libraries representing key stages of aestivation: non-aestivation (NA), deep-aestivation (DA), and arousal from aestivation (AA) using RNA-seq. A total of 1240, 1184 and 303 differentially expressed genes (DEGs) were identified following the criteria of |log2 ratio|≥1 and FDR≤0.001 in comparisons of DA vs. NA, AA vs. NA and DA vs. AA. A set of respiratory tree specific DEGs was identified the first time and, in addition, common DEGs that were responsive to aestivation in both respiratory tree and intestine were identified. Functional analysis of DEGs was further performed by GO enrichment analysis and respiratory tree specific GO terms were screened out and provide interesting hints for further studies of the molecular regulation of aestivation in A. japonicus.
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Affiliation(s)
- Ye Zhao
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Hongsheng Yang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China.
| | - Kenneth B Storey
- Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Muyan Chen
- Fisheries College, Ocean University of China, Qingdao 266003, PR China.
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Ashktorab H, Daremipouran M, Goel A, Varma S, Leavitt R, Sun X, Brim H. DNA methylome profiling identifies novel methylated genes in African American patients with colorectal neoplasia. Epigenetics 2014; 9:503-12. [PMID: 24441198 DOI: 10.4161/epi.27644] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The identification of genes that are differentially methylated in colorectal cancer (CRC) has potential value for both diagnostic and therapeutic interventions specifically in high-risk populations such as African Americans (AAs). However, DNA methylation patterns in CRC, especially in AAs, have not been systematically explored and remain poorly understood. Here, we performed DNA methylome profiling to identify the methylation status of CpG islands within candidate genes involved in critical pathways important in the initiation and development of CRC. We used reduced representation bisulfite sequencing (RRBS) in colorectal cancer and adenoma tissues that were compared with DNA methylome from a healthy AA subject's colon tissue and peripheral blood DNA. The identified methylation markers were validated in fresh frozen CRC tissues and corresponding normal tissues from AA patients diagnosed with CRC at Howard University Hospital. We identified and validated the methylation status of 355 CpG sites located within 16 gene promoter regions associated with CpG islands. Fifty CpG sites located within CpG islands-in genes ATXN7L1 (2), BMP3 (7), EID3 (15), GAS7 (1), GPR75 (24), and TNFAIP2 (1)-were significantly hypermethylated in tumor vs. normal tissues (P<0.05). The methylation status of BMP3, EID3, GAS7, and GPR75 was confirmed in an independent, validation cohort. Ingenuity pathway analysis mapped three of these markers (GAS7, BMP3 and GPR) in the insulin and TGF-β1 network-the two key pathways in CRC. In addition to hypermethylated genes, our analysis also revealed that LINE-1 repeat elements were progressively hypomethylated in the normal-adenoma-cancer sequence. We conclude that DNA methylome profiling based on RRBS is an effective method for screening aberrantly methylated genes in CRC. While previous studies focused on the limited identification of hypermethylated genes, ours is the first study to systematically and comprehensively identify novel hypermethylated genes, as well as hypomethylated LINE-1 sequences, which may serve as potential biomarkers for CRC in African Americans. Our discovered biomarkers were intimately linked to the insulin/TGF-B1 pathway, further strengthening the association of diabetic disorders with colon oncogenic transformation.
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Affiliation(s)
- Hassan Ashktorab
- Department of Medicine and Cancer Center; Department of Pathology; Howard University College of Medicine; Washington DC, USA
| | - M Daremipouran
- Department of Medicine and Cancer Center; Department of Pathology; Howard University College of Medicine; Washington DC, USA
| | - Ajay Goel
- Department of Medicine and Cancer Center; Department of Pathology; Howard University College of Medicine; Washington DC, USA; Baylor Research Institute and Charles A Sammons Cancer Center; Baylor University Medical Center, Dallas, TX USA
| | - Sudhir Varma
- Department of Medicine and Cancer Center; Department of Pathology; Howard University College of Medicine; Washington DC, USA; Hithru; Laurel, MD USA
| | - R Leavitt
- Department of Medicine and Cancer Center; Department of Pathology; Howard University College of Medicine; Washington DC, USA; Zymo Research Corp.; Irvine, CA USA
| | | | - Hassan Brim
- Department of Medicine and Cancer Center; Department of Pathology; Howard University College of Medicine; Washington DC, USA
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42
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Kolla V, Zhuang T, Higashi M, Naraparaju K, Brodeur GM. Role of CHD5 in human cancers: 10 years later. Cancer Res 2014; 74:652-8. [PMID: 24419087 DOI: 10.1158/0008-5472.can-13-3056] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
CHD5 was first identified because of its location on 1p36 in a region of frequent deletion in neuroblastomas. CHD5 (chromodomain-helicase-DNA-binding-5) is the fifth member of a family of chromatin remodeling proteins, and it probably functions by forming a nucleosome remodeling and deacetylation (NuRD) complex that regulates transcription of particular genes. CHD5 is preferentially expressed in the nervous system and testis. On the basis of its position, pattern of expression, and function in neuroblastoma cells and xenografts, CHD5 was identified as a tumor suppressor gene (TSG). Evidence soon emerged that CHD5 also functioned as a TSG in gliomas and a variety of other tumor types, including breast, colon, lung, ovary, and prostate cancers. Although one copy of CHD5 is deleted frequently, inactivating mutations of the remaining allele are rare. However, DNA methylation of the CHD5 promoter is found frequently, and this epigenetic mechanism leads to biallelic inactivation. Furthermore, low CHD5 expression is strongly associated with unfavorable clinical and biologic features as well as outcome in neuroblastomas and many other tumor types. Thus, based on its likely involvement as a TSG in neuroblastomas, gliomas, and many common adult tumors, CHD5 may play an important developmental role in many other tissues besides the nervous system and testis.
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Affiliation(s)
- Venkatadri Kolla
- Authors' Affiliations: Division of Oncology, Department of Pediatrics, The Children's Hospital of Philadelphia; and The University of Pennsylvania, Philadelphia, Pennsylvania
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