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Morotti A, Cetani F, Passoni G, Borsari S, Pardi E, Guarnieri V, Verdelli C, Tavanti GS, Valenti L, Bianco C, Ferrero S, Corbetta S, Vaira V. The Long Non-Coding BC200 Is a Novel Circulating Biomarker of Parathyroid Carcinoma. Front Endocrinol (Lausanne) 2022; 13:869006. [PMID: 35586620 PMCID: PMC9108332 DOI: 10.3389/fendo.2022.869006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/04/2022] [Indexed: 01/10/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are an important class of epigenetic regulators involved in both physiological processes and cancer development. Preliminary evidence suggested that lncRNAs could act as accurate prognostic and diagnostic biomarkers. Parathyroid cancer is a rare endocrine neoplasia, whose management represents a clinical challenge due to the lack of accurate molecular biomarkers. Our previous findings showed that human parathyroid tumors are characterized by a different lncRNAs signature, suggesting heterogeneity through the different histotypes. Particularly, we found that the lncRNA BC200/BCYRN1 could represent a candidate biomarker for parathyroid carcinomas (PCas). Here we aimed to extend our preliminary data evaluating whether BC200 could be an accurate non-invasive biomarker of PCas to support the clinical management of patients affected by parathyroid tumors at diagnosis, prognosis and follow-up. To provide a non-invasive point-of-care for parathyroid carcinoma diagnosis and follow-up, we analyzed BC200 expression in patients' serum through digital PCR. Our results show that BC200 counts are higher in serum from patients harboring PCa (n=4) compared to patients with parathyroid adenoma (PAd; n=27). Further, in PAd patients circulating BC200 levels are positively correlated with serum total calcium. Then, we found that BC200 is overexpressed in metastatic PCas (n=4) compared to non-metastatic ones (n=9). Finally, the lncRNA expression in PCa patients' serum drops are reduced after parathyroidectomy, suggesting its possible use in the post-operative setting for patients follow-up. Overall, these findings extend the knowledge on BC200 in parathyroid tumors, supporting its role as a useful biomarker for management of PCa.
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Affiliation(s)
- Annamaria Morotti
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
- Division of Pathology, Fondazione IRCCS Ca’ Granda-Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Giulia Passoni
- Division of Pathology, Fondazione IRCCS Ca’ Granda-Ospedale Maggiore Policlinico, Milan, Italy
| | - Simona Borsari
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Elena Pardi
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Vito Guarnieri
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, Foggia, Italy
| | - Chiara Verdelli
- Laboratory of Experimental Endocrinology, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
| | - Giulia Stefania Tavanti
- Endocrinology and Diabetology Service, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - Luca Valenti
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
- Precision Medicine – Department of Transfusion Medicine and Hematology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Cristiana Bianco
- Precision Medicine – Department of Transfusion Medicine and Hematology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefano Ferrero
- Division of Pathology, Fondazione IRCCS Ca’ Granda-Ospedale Maggiore Policlinico, Milan, Italy
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - Sabrina Corbetta
- Endocrinology and Diabetology Service, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
- *Correspondence: Valentina Vaira, ; Sabrina Corbetta,
| | - Valentina Vaira
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
- Division of Pathology, Fondazione IRCCS Ca’ Granda-Ospedale Maggiore Policlinico, Milan, Italy
- *Correspondence: Valentina Vaira, ; Sabrina Corbetta,
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The expression and clinical significance of the tRNA aspartic acid methyltransferase 1 protein in gastric cancer. Int J Clin Oncol 2021; 26:2229-2236. [PMID: 34689291 DOI: 10.1007/s10147-021-02019-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 07/27/2021] [Indexed: 11/27/2022]
Abstract
OBJECTIVES This study aimed to investigate the role of the tRNA aspartic acid methyltransferase 1 (TRDMT1) protein in the development and progression of gastric cancer (GC). METHODS The 90 GC tissues and 35 paracancerous tissues (gastric mucosa) were collected from patients (31 males and 59 females; average age 66), who were pathologically diagnosed as GC. The expression of TRDMT1 in three GC cell lines (MKN28, BGC823, and MGC803) and tissues from GC patients were detected by western blotting and immunological staining, respectively. The relationship between TRDMT1 expression and clinicopathological parameters in GC patients was explored. TRDMT1 was knocked down by RNAi lentivirus in GC cells. GC cell migration and invasion were analyzed using scratch and transwell assays. RESULTS TRDMT1 expression in the GC cell lines was higher than that in the normal gastric mucosal epithelial cell line (P < 0.05). Positive TRDMT1 protein expression in the GC tissue was higher than that in the adjacent tissue. The expression of TRDMT1 was positively associated with tumor size, histological grade, invasion depth, lymph node metastasis, and tumor node metastasis (TNM) stage (P < 0.05). High TRDMT1 expression predicted poor OS of GC patients. Tumor size, differentiation degree, invasion depth, lymph node metastasis, TNM stage, and TRDMT1 expression were independent predictors of the OS of GC patients. Knockdown of TRDMT1 inhibited the migration and invasion of MKN28 cells. CONCLUSION TRDMT1 was highly expressed in GC cell lines and tissues. TRDMT1 expression was independent predictor of the OS of GC patients. TRDMT1 knockdown reduced GC cell migration and invasion. All these results suggested that TRDMT1 has the potential to be used as a target for the diagnosis and treatment of GC.
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Hegde M, Joshi MB. Comprehensive analysis of regulation of DNA methyltransferase isoforms in human breast tumors. J Cancer Res Clin Oncol 2021; 147:937-971. [PMID: 33604794 PMCID: PMC7954751 DOI: 10.1007/s00432-021-03519-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/10/2021] [Indexed: 12/14/2022]
Abstract
Significant reprogramming of epigenome is widely described during pathogenesis of breast cancer. Transformation of normal cell to hyperplastic cell and to neoplastic phenotype is associated with aberrant DNA (de)methylation, which, through promoter and enhancer methylation changes, activates oncogenes and silence tumor suppressor genes in variety of tumors including breast. DNA methylation, one of the major epigenetic mechanisms is catalyzed by evolutionarily conserved isoforms namely, DNMT1, DNMT3A and DNMT3B in humans. Over the years, studies have demonstrated intricate and complex regulation of DNMT isoforms at transcriptional, translational and post-translational levels. The recent findings of allosteric regulation of DNMT isoforms and regulation by other interacting chromatin modifying proteins emphasizes functional integrity and their contribution for the development of breast cancer and progression. DNMT isoforms are regulated by several intrinsic and extrinsic parameters. In the present review, we have extensively performed bioinformatics analysis of expression of DNMT isoforms along with their transcriptional and post-transcriptional regulators such as transcription factors, interacting proteins, hormones, cytokines and dietary elements along with their significance during pathogenesis of breast tumors. Our review manuscript provides a comprehensive understanding of key factors regulating DNMT isoforms in breast tumor pathology and documents unsolved issues.
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Affiliation(s)
- Mangala Hegde
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Planetarium Complex, Manipal, 576104, India
| | - Manjunath B Joshi
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Planetarium Complex, Manipal, 576104, India.
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Li C, Lyu Y, Liu C, Yin S. The Role of PBK as a Potential Prognostic and Diagnostic Biomarker in Ovarian Cancer. Cancer Biother Radiopharm 2021; 37:569-579. [PMID: 33794097 DOI: 10.1089/cbr.2020.4249] [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: 11/12/2022] Open
Abstract
Aim: As one of the three malignant genital tumors, mortality in women with ovarian cancer is consistently high worldwide. It is of great importance to find prognostic markers for diagnosis and treatment of ovarian cancer. In this study, the authors utilized the bioinformatics analysis to identify the potential key genes to reveal the potential mechanism for ovarian cancer. Methods: The authors used the gene expression profile (GSE14407) to perform differentially expressed gene (DEG) analysis and the weighted gene co-expression network analysis. They selected the key module and performed the gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis for the genes in the hub module. Then they screened the key genes in the hub module, and further validated their expression level. Results: A total of 3124 DEGs were detected after differential gene expression analysis; of these, 433 were upregulated genes and 2691 were downregulated genes. The authors selected the brown module that is significantly associated with the BRCA gene expression. Then they selected 30 hub genes from the protein-protein interaction network. And the authors identify the PDZ binding kinase (PBK) as the prognosis-associated hub gene whose expression was significantly high in the ovarian cancer tissue. Conclusions: The bioinformatics analysis for the DEGs could be important to understand the pathogenesis for ovarian cancer. In this study, PBK is identified as a potential marker that might improve the understanding of the molecular mechanism and the diagnosis level for ovarian cancer.
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Affiliation(s)
- Chuang Li
- Department of Obstetrics & Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China
| | - Yuan Lyu
- Department of Obstetrics & Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Shenyang, China
| | - Caixia Liu
- Department of Obstetrics & Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Shenyang, China
| | - Shaowei Yin
- Department of Obstetrics & Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Shenyang, China
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Wu F, Lin X, Shan SK, Li F, Xu F, Zhong JY, Guo B, Zheng MH, Wang Y, Mo ZH, Yuan LQ. The Suppression of miR-199a-3p by Promoter Methylation Contributes to Papillary Thyroid Carcinoma Aggressiveness by Targeting RAP2a and DNMT3a. Front Cell Dev Biol 2020; 8:594528. [PMID: 33365310 PMCID: PMC7750465 DOI: 10.3389/fcell.2020.594528] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/21/2020] [Indexed: 12/24/2022] Open
Abstract
Background It was previously demonstrated that miR-199a-3p plays an important role in tumor progression; especially, its down-regulation in papillary thyroid cancer (PTC) is associated with cancer cell invasion and proliferation. In the present report, we investigated the mechanism involved in the down-regulation of miR-199a-3p in PTC and how miR-199a-3p regulates PTC invasion both in vivo and in vitro. Methods qRT-PCR and Western blot assays were used to determine the expression of the investigated genes. Bisulfite sequencing PCR was used to investigate miR-199a-3p methylation. The functions of miR-199a-3p were investigated by a series of in vitro and in vivo experiments. Results Our results showed hypermethylation of the miR-199a-3p promoter, which resulted in decreased miR-199a-3p expression both in PTC cell lines and PTC tissues. DNA-methyltransferase 3a (DNMT3a), a target gene of miR-199a-3p, was increased both in PTC cell lines and PTC tissues, while 5-aza-2′-deoxycytidine (methyltransferase-specific inhibitor) or knock-down using DNMT3a Small-Interfering RNA could restore the expression of miR-199a-3p, and the over-expression of miR-199a-3p could decrease the expression of DNMT3a; this suggests that miR-199a-3p/DNMT3a constructs a regulatory circuit in regulating miR-199a-3p/DNMT3a expression. Moreover, gain- and loss-of-function studies revealed that miR-199a-3p is involved in cancer cell migration, invasion, and growth. Meanwhile, we found that RAP2a was also a direct target of miR-199a-3p, which might mediate the tumor-growth-inhibiting effect of miR-199a-3p. To further confirm the tumor-suppressive properties of miR-199a-3p, stable overexpression of miR-199a-3p in a PTC cell line (BCPAP cells) was xenografted to athymic BALB/c nude mice, resulting in delayed tumor growth in vivo. In clinical PTC samples, the expression of RAP2a and DNMT3a was increased significantly, and the expression of RAP2a was inversely correlated with that of miR-199a-3p. Conclusion Our studies demonstrate that an epigenetic change in the promoter region of miR-199a contributes to the aggressive behavior of PTC via the miR-199a-3p/DNMT3a regulatory circuit and directly targets RAP2a.
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Affiliation(s)
- Feng Wu
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, China.,Department of Metabolism and Endocrinology, National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiao Lin
- Department of Radiology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Su-Kang Shan
- Department of Metabolism and Endocrinology, National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Fuxingzi Li
- Department of Metabolism and Endocrinology, National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Feng Xu
- Department of Metabolism and Endocrinology, National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jia-Yu Zhong
- Department of Metabolism and Endocrinology, National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Bei Guo
- Department of Metabolism and Endocrinology, National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Ming-Hui Zheng
- Department of Metabolism and Endocrinology, National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yi Wang
- Department of Metabolism and Endocrinology, National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Zhao-Hui Mo
- Department of Endocrinology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Ling-Qing Yuan
- Department of Metabolism and Endocrinology, National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital, Central South University, Changsha, China
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Kataoka I, Funata S, Nagahama K, Isogaya K, Takeuchi H, Abe N, Shibahara J. DNMT3A overexpression is associated with aggressive behavior and enteroblastic differentiation of gastric adenocarcinoma. Ann Diagn Pathol 2020; 44:151456. [PMID: 31862523 DOI: 10.1016/j.anndiagpath.2019.151456] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/05/2019] [Indexed: 01/26/2023]
Abstract
Gastric adenocarcinoma (GA) with enteroblastic differentiation is a subset of gastric cancer with poor prognosis. RNA-Seq data of The Cancer Genome Atlas of GA (TCGA-STAD) revealed a positive correlation between SALL4, a representative enteroblastic marker, and DNMT3A expression. Here, we conducted immunohistochemical analysis of GA to clarify the clinicopathological significance of DNMT3A expression and its correlation with enteroblastic differentiation. Of the 346 cases of solitary GA analyzed, 120 (34.7%) showed unequivocal DNMT3A nuclear expression. DNMT3A expression was associated with Lauren's intestinal type, papillary and tubular architectures, high frequency of lymphatic and vascular invasion, and lymph node metastasis (each, P < 0.01). Log-rank test revealed that DNMT3A-positive cases recurred more frequently with a predilection for liver metastasis (P < 0.01) and showed poorer overall and recurrence-free survival (each, P < 0.05). With respect to surrogate markers of molecular subtypes, DNMT3A-positive cases more frequently showed p53 overexpression (P < 0.001). Consistent with the results of TCGA data analysis, DNMT3A-positive cases exhibited enteroblastic morphology (18.3% vs. 0.9%, P < 0.001) and expressed enteroblastic markers, SALL4 (32.5% vs. 3.1%, P < 0.001) and glypican-3 (22.5% vs. 4.4%, P < 0.001) more frequently than did DNMT3A-negative cases. Additionally, GAs showing enteroblastic differentiation, morphologically or immunohistochemically, expressed DNMT3A with significantly higher frequency and intensity than did conventional GAs (P < 0.001). Our findings suggest DNMT3A as a potential therapeutic target for this conventional therapy-refractory cancer subtype.
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Affiliation(s)
- Isao Kataoka
- Department of Pathology, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka, Tokyo 181-8611, Japan; Department of Gastrointestinal and General Surgery, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka, Tokyo 181-8611, Japan
| | - Sayaka Funata
- Department of Pathology, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka, Tokyo 181-8611, Japan
| | - Kiyotaka Nagahama
- Department of Pathology, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka, Tokyo 181-8611, Japan
| | - Kazunobu Isogaya
- Department of Pathology, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka, Tokyo 181-8611, Japan
| | - Hirohisa Takeuchi
- Department of Gastrointestinal and General Surgery, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka, Tokyo 181-8611, Japan
| | - Nobutsugu Abe
- Department of Gastrointestinal and General Surgery, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka, Tokyo 181-8611, Japan
| | - Junji Shibahara
- Department of Pathology, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka, Tokyo 181-8611, Japan.
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Wang J, Zhao H, Dong H, Zhu L, Wang S, Wang P, Ren Q, Zhu H, Chen J, Lin Z, Cheng Y, Qian B, Zhang Y, Jia R, Wu W, Lu J, Tan J. LAT, HOXD3 and NFE2L3 identified as novel DNA methylation-driven genes and prognostic markers in human clear cell renal cell carcinoma by integrative bioinformatics approaches. J Cancer 2019; 10:6726-6737. [PMID: 31777602 PMCID: PMC6856894 DOI: 10.7150/jca.35641] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 08/26/2019] [Indexed: 12/30/2022] Open
Abstract
Background: Abnormal DNA methylation of is one of the important mechanisms leading to tumor pathogenesis. The purpose of this study was to explore differentially methylated genes that may drive the development of renal clear cell carcinoma through a comprehensive analysis of the TCGA database. Materials and methods: Methylation data and RNA-seq data for clear cell renal cell carcinoma were downloaded from The Cancer Genome Atlas (TCGA). Differentially methylated genes and the differential genes associated with survival were then screened by MethylMix R package and univariate Cox proportional-hazards model, respectively. Their common genes were then intersected and obtained for further analysis. Correlation of gene expression and methylation levels, gene set enrichment analysis (GSEA) enrichments, survival curve, and ROC curve plotting for DNA methylation-driven genes were finally performed. The methylation alterations of the three genes were validated via two GEO datasets (GSE70303 and GSE113501), and the genes expression level was verified through two GEO datasets (GSE6344 and GSE53757). Results: Three novel DNA methylation-driven genes LAT, HOXD3 and NFE2L3 were identified in clear cell renal cell carcinoma. Expression analysis further revealed that hypomethylation levels of LAT and NFE2L3 showed higher gene expression levels, while HOXD3 exhibited opposite methylation-expression pattern. The CpG sites of LAT (cg16462073), HOXD3 (cg24000528) and NFE2L3 (cg16882373) that may affect respective gene expressions were also identified. For the survival analysis, we found that hypomethylation and over-expression of LAT and NFE2L3 were correlated with poor survival, while hypermethylation and low-expression HOXD3 was correlated with poor survival of clear cell renal cell carcinoma patients. In addition, GSEA KEGG analysis and biological processes of these genes were also enriched for functional analysis. Kaplan-Meier survival and ROC analyses of these genes showed an average risk score of 0.9140593, AUC = 0.692, which suggested a good clinical application value. Finally, the opposite methylation-expression pattern of these three genes were verified in GEO datasets. Conclusions: In this study, we successfully exhibited the potential DNA methylation-driven genes LAT, HOXD3, and NFE2L3 involved in clear cell renal cell carcinoma. Moreover, gene functions and prognostic risk models were also elucidated, which facilitated the expansion of the current study on the role of methylation in the pathology process of clear cell renal cell carcinoma.
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Affiliation(s)
- Jie Wang
- Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Dongfang Hospital (900 Hospital of the Joint Logistics Team), Xiamen University, Fuzhou, 350025, Fujian, P.R. China
| | - Hu Zhao
- Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Dongfang Hospital (900 Hospital of the Joint Logistics Team), Xiamen University, Fuzhou, 350025, Fujian, P.R. China
| | - Huiyue Dong
- Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Dongfang Hospital (900 Hospital of the Joint Logistics Team), Xiamen University, Fuzhou, 350025, Fujian, P.R. China
| | - Ling Zhu
- Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Dongfang Hospital (900 Hospital of the Joint Logistics Team), Xiamen University, Fuzhou, 350025, Fujian, P.R. China
| | - Shuiliang Wang
- Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Dongfang Hospital (900 Hospital of the Joint Logistics Team), Xiamen University, Fuzhou, 350025, Fujian, P.R. China
| | - Ping Wang
- Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Dongfang Hospital (900 Hospital of the Joint Logistics Team), Xiamen University, Fuzhou, 350025, Fujian, P.R. China
| | - Qun Ren
- Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Dongfang Hospital (900 Hospital of the Joint Logistics Team), Xiamen University, Fuzhou, 350025, Fujian, P.R. China
| | - Hehuan Zhu
- Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Dongfang Hospital (900 Hospital of the Joint Logistics Team), Xiamen University, Fuzhou, 350025, Fujian, P.R. China
| | - Junqiu Chen
- Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Dongfang Hospital (900 Hospital of the Joint Logistics Team), Xiamen University, Fuzhou, 350025, Fujian, P.R. China
| | - Zhijie Lin
- Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Fuzhou General Clinical College, Fujian Medical University, Fuzhou, 350025, Fujian, P.R. China
| | - Yuanhang Cheng
- Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Dongfang Hospital (900 Hospital of the Joint Logistics Team), Xiamen University, Fuzhou, 350025, Fujian, P.R. China
| | - Benjiang Qian
- Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Dongfang Hospital (900 Hospital of the Joint Logistics Team), Xiamen University, Fuzhou, 350025, Fujian, P.R. China
| | - Yi Zhang
- Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Dongfang Hospital (900 Hospital of the Joint Logistics Team), Xiamen University, Fuzhou, 350025, Fujian, P.R. China
| | - Ruxue Jia
- Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Dongfang Hospital (900 Hospital of the Joint Logistics Team), Xiamen University, Fuzhou, 350025, Fujian, P.R. China
| | - Weizheng Wu
- Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Dongfang Hospital (900 Hospital of the Joint Logistics Team), Xiamen University, Fuzhou, 350025, Fujian, P.R. China.,Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Fuzhou General Clinical College, Fujian Medical University, Fuzhou, 350025, Fujian, P.R. China
| | - Jun Lu
- Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Dongfang Hospital (900 Hospital of the Joint Logistics Team), Xiamen University, Fuzhou, 350025, Fujian, P.R. China.,Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Fuzhou General Clinical College, Fujian Medical University, Fuzhou, 350025, Fujian, P.R. China
| | - Jianming Tan
- Fujian Provincial Key Laboratory of Transplant Biology, Department of Urology, Dongfang Hospital (900 Hospital of the Joint Logistics Team), Xiamen University, Fuzhou, 350025, Fujian, P.R. China.,Fujian Hongyi Health Institute, Fuzhou, 350025, Fujian, P.R. China
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Liu D, Wong CC, Fu L, Chen H, Zhao L, Li C, Zhou Y, Zhang Y, Xu W, Yang Y, Wu B, Cheng G, Lai PBS, Wong N, Sung JJY, Yu J. Squalene epoxidase drives NAFLD-induced hepatocellular carcinoma and is a pharmaceutical target. Sci Transl Med 2019; 10:10/437/eaap9840. [PMID: 29669855 DOI: 10.1126/scitranslmed.aap9840] [Citation(s) in RCA: 174] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 03/14/2018] [Indexed: 12/14/2022]
Abstract
Nonalcoholic fatty liver disease (NAFLD)-induced hepatocellular carcinoma (HCC) is an emerging malignancy in the developed world; however, mechanisms that contribute to its formation are largely unknown, and targeted therapy is currently not available. Our RNA sequencing analysis of NAFLD-HCC samples revealed squalene epoxidase (SQLE) as the top outlier metabolic gene overexpressed in NAFLD-HCC patients. Hepatocyte-specific Sqle transgenic expression in mice accelerated the development of high-fat, high-cholesterol diet-induced HCC. SQLE exerts its oncogenic effect via its metabolites, cholesteryl ester and nicotinamide adenine dinucleotide phosphate (NADP+). Increased SQLE expression promotes the biosynthesis of cholesteryl ester, which induces NAFLD-HCC cell growth. SQLE increased the NADP+/NADPH (reduced form of NADP+) ratio, which triggered a cascade of events involving oxidative stress-induced DNA methyltransferase 3A (DNMT3A) expression, DNMT3A-mediated epigenetic silencing of PTEN, and activation of AKT-mTOR (mammalian target of rapamycin). In human NAFLD-HCC and HCC, SQLE is overexpressed and its expression is associated with poor patient outcomes. Terbinafine, a U.S. Food and Drug Administration-approved antifungal drug targeting SQLE, markedly inhibited SQLE-induced NAFLD-HCC cell growth in NAFLD-HCC and HCC cells and attenuated tumor development in xenograft models and in Sqle transgenic mice. Suppression of tumor growth by terbinafine is associated with decreased cholesteryl ester concentrations, restoration of PTEN expression, and inhibition of AKT-mTOR, consistent with blockade of SQLE function. Collectively, we established SQLE as an oncogene in NAFLD-HCC and propose that repurposing SQLE inhibitors may be a promising approach for the prevention and treatment of NAFLD-HCC.
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Affiliation(s)
- Dabin Liu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, 999077, Hong Kong
| | - Chi Chun Wong
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, 999077, Hong Kong
| | - Li Fu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, 999077, Hong Kong.,Guangdong Key Laboratory for Genome Stability and Human Disease Prevention, Department of Pharmacology and Cancer Research Centre, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Huarong Chen
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, 999077, Hong Kong
| | - Liuyang Zhao
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, 999077, Hong Kong
| | - Chuangen Li
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, 999077, Hong Kong
| | - Yunfei Zhou
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, 999077, Hong Kong
| | - Yanquan Zhang
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, 999077, Hong Kong
| | - Weiqi Xu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, 999077, Hong Kong
| | - Yidong Yang
- Department of Gastroenterology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Bin Wu
- Department of Gastroenterology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Gong Cheng
- Department of Surgery, The Chinese University of Hong Kong, 999077, Hong Kong
| | - Paul Bo-San Lai
- Department of Surgery, The Chinese University of Hong Kong, 999077, Hong Kong
| | - Nathalie Wong
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, 999077, Hong Kong
| | - Joseph J Y Sung
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, 999077, Hong Kong
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, 999077, Hong Kong.
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9
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Fattahi S, Golpour M, Amjadi-Moheb F, Sharifi-Pasandi M, Khodadadi P, Pilehchian-Langroudi M, Ashrafi GH, Akhavan-Niaki H. DNA methyltransferases and gastric cancer: insight into targeted therapy. Epigenomics 2018; 10:1477-1497. [PMID: 30325215 DOI: 10.2217/epi-2018-0096] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Gastric cancer is a major health problem worldwide occupying most frequent causes of cancer-related mortality. In addition to genetic modifications, epigenetic alterations catalyzed by DNA methyltransferases (DNMTs) are a well-characterized epigenetic hallmark in gastric cancer. The reversible nature of epigenetic alterations and central role of DNA methylation in diverse biological processes provides an opportunity for using DNMT inhibitors to enhance the efficacy of chemotherapeutics. In this review, we discussed key factors or mechanisms such as SNPs, infections and genetic modifications that trigger DNMTs level modification in gastric cancer, and their potential roles in cancer progression. Finally, we focused on how inhibitors of the DNMTs can most effectively be used for the treatment of gastric cancer with multidrug resistance.
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Affiliation(s)
- Sadegh Fattahi
- Cellular & Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, 4717647745, Babol, Iran.,North Research Center, Pasteur Institute, Amol, 4615885399, Iran
| | - Monireh Golpour
- Molecular & Cell Biology Research Center, Student Research Committee, Faculty of Medicine, Mazandaran University of Medical Science, Sari, 4817844718, Iran
| | - Fatemeh Amjadi-Moheb
- Department of Genetics, Faculty of Medicine, Babol University of Medical Sciences, 4717647745, Babol, Iran
| | - Marzieh Sharifi-Pasandi
- Molecular & Cell Biology Research Center, Student Research Committee, Faculty of Medicine, Mazandaran University of Medical Science, Sari, 4817844718, Iran
| | - Parastesh Khodadadi
- Department of Genetics, Faculty of Medicine, Babol University of Medical Sciences, 4717647745, Babol, Iran
| | | | - Gholam Hossein Ashrafi
- School of Life Science, Pharmacy & Chemistry, SEC Faculty, Cancer Theme, Kingston University London, Kingston upon Thames, London KT1 2EE, UK
| | - Haleh Akhavan-Niaki
- Department of Genetics, Faculty of Medicine, Babol University of Medical Sciences, 4717647745, Babol, Iran
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10
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Jang K, Kim M, Gilbert CA, Simpkins F, Ince TA, Slingerland JM. VEGFA activates an epigenetic pathway upregulating ovarian cancer-initiating cells. EMBO Mol Med 2017; 9:304-318. [PMID: 28179359 PMCID: PMC5331266 DOI: 10.15252/emmm.201606840] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The angiogenic factor, VEGFA, is a therapeutic target in ovarian cancer (OVCA). VEGFA can also stimulate stem‐like cells in certain cancers, but mechanisms thereof are poorly understood. Here, we show that VEGFA mediates stem cell actions in primary human OVCA culture and OVCA lines via VEGFR2‐dependent Src activation to upregulate Bmi1, tumor spheres, and ALDH1 activity. The VEGFA‐mediated increase in spheres was abrogated by Src inhibition or SRC knockdown. VEGFA stimulated sphere formation only in the ALDH1+ subpopulation and increased OVCA‐initiating cells and tumor formation in vivo through Bmi1. In contrast to its action in hemopoietic malignancies, DNA methyl transferase 3A (DNMT3A) appears to play a pro‐oncogenic role in ovarian cancer. VEGFA‐driven Src increased DNMT3A leading to miR‐128‐2 methylation and upregulation of Bmi1 to increase stem‐like cells. SRC knockdown was rescued by antagomir to miR‐128. DNMT3A knockdown prevented VEGFA‐driven miR‐128‐2 loss, and the increase in Bmi1 and tumor spheres. Analysis of over 1,300 primary human OVCAs revealed an aggressive subset in which high VEGFA is associated with miR‐128‐2 loss. Thus, VEGFA stimulates OVCA stem‐like cells through Src‐DNMT3A‐driven miR‐128‐2 methylation and Bmi1 upregulation.
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Affiliation(s)
- Kibeom Jang
- Braman Family Breast Cancer Institute at Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA.,Department of Biochemistry & Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Minsoon Kim
- Braman Family Breast Cancer Institute at Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA.,Department of Biochemistry & Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Candace A Gilbert
- Braman Family Breast Cancer Institute at Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Fiona Simpkins
- Braman Family Breast Cancer Institute at Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA.,Department of Obstetrics & Gynecology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Tan A Ince
- Braman Family Breast Cancer Institute at Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA.,Department of Pathology, University of Miami Miller School of Medicine, Miami, FL, USA.,Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Joyce M Slingerland
- Braman Family Breast Cancer Institute at Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA .,Department of Biochemistry & Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, USA.,Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
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11
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The rs1550117 A>G variant in DNMT3A gene promoter significantly increases non-small cell lung cancer susceptibility in a Han Chinese population. Oncotarget 2017; 8:23470-23478. [PMID: 28423585 PMCID: PMC5410319 DOI: 10.18632/oncotarget.15625] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 02/14/2017] [Indexed: 12/31/2022] Open
Abstract
In this study, we conducted a case-control study to explore the association between rs1550117 A>G variant of DNMT3A gene promoter and non-small cell lung cancer (NSCLC) susceptibility in a Han Chinese population. The genotyping of rs1550117 A>G variant was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and confirmed by sequencing. Allele G of rs1550117 was associated with an increased risk of NSCLC. Moreover, individuals carrying the GG genotypes had a higher risk to develop NSCLC than the AA and GA genotype carriers. Further stratified analysis showed that rs1550117 A>G was significantly related to age (> 60 years), male, smoking and drinking. In vivo detection of DNMT3A mRNA levels in NSCLC tissues and in vitro luciferase assays consistently showed that the allele G significantly decreased DNMT3A transcription. Additional functional analysis revealed that the increased binding affinity of transcription repressor SP1, which was associated with allele G of rs1550117, led to the significant decreased expression of DNMT3A. Collectively, our results propose a suppression role of DNMT3A in NSCLC development and emphasize the dual roles of DNMT3A in tumorigenesis.
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12
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3,6-Dihydroxyflavone regulates microRNA-34a through DNA methylation. BMC Cancer 2017; 17:619. [PMID: 28870206 PMCID: PMC5584326 DOI: 10.1186/s12885-017-3638-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 08/29/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Breast cancer is the common cancer in China. In previous study, we determined that 3,6-dihydroxyflavone (3,6-DHF) increases miR-34a significantly in breast carcinogenesis, but the mechanism remains unclear. METHODS We used qRT-PCR to analyze miR-34a and ten-eleven translocation (TET)1, TET2, TET3 levels in breast cancer cells. With a cellular breast carcinogenesis model and an experimental model of carcinogenesis in rats, TET1 levels were evaluated by western blot analysis and immunofluorescence. TET1 and 5hmC (5-hydroxymethylcytosine) levels were evaluated by immunofluorescence in nude mouse xenografts of MDA-MB-231 cells. Chromatin immunoprecipitation(ChIP) assayed for TET1 on the TET1 promoter, and dot blot analysis of DNA 5hmC was performed in MDA-MB-231 cells. We evaluated the mechanism of 3,6-DHF on the expression of tumor suppressor miR-34a by transfecting them with DNA methyltransferase (DNMT)1 plasmid and TET1 siRNA in breast cancer cells. Methylation-specific PCR detected methylation of the miR-34a promoter. RESULTS First, we found that 3,6-DHF promotes the expression of TET1 during carcinogen-induced breast carcinogenesis in MCF10A cells and in rats. 3,6-DHF also increased TET1 and 5hmC levels in MDA-MB-231 cells. Further study indicated that TET1 siRNA and pcDNA3/Myc-DNMT1 inhibited the 3,6-DHF reactivation effect on expression of miR-34a in breast cancer cells. Methylation-specific PCR assays indicated that TET1 siRNA and pcDNA3/Myc-DNMT1 inhibit the effect of 3,6-DHF on the demethylation of the miR-34a promoter. CONCLUSIONS Our study showed that 3,6-DHF effectively increases TET1 expression by inhibiting DNMT1 and DNA hypermethylation, and consequently up-regulates miR-34a in breast carcinogenesis.
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13
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Fu RJ, He W, Wang XB, Li L, Zhao HB, Liu XY, Pang Z, Chen GQ, Huang L, Zhao KW. DNMT1-maintained hypermethylation of Krüppel-like factor 5 involves in the progression of clear cell renal cell carcinoma. Cell Death Dis 2017; 8:e2952. [PMID: 28749461 PMCID: PMC5550868 DOI: 10.1038/cddis.2017.323] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 05/27/2017] [Accepted: 06/08/2017] [Indexed: 12/13/2022]
Abstract
Clear cell renal cell carcinoma (ccRCC) is the major subtype of renal cell carcinoma (RCC) that is resistant to conventional radiation and chemotherapy. It is a challenge to explore effective therapeutic targets and drugs for this kind of cancer. Transcription factor Krüppel-like factor 5 (KLF5) exerts diverse functions in various tumor types. By analyzing cohorts of the Cancer Genome Atlas (TCGA) data sets, we find that KLF5 expression is suppressed in ccRCC patients and higher level of KLF5 expression is associated with better prognostic outcome. Our further investigations demonstrate that KLF5 genomic loci are hypermethylated at proximal exon 4 and suppression of DNA methyltransferase 1 (DNMT1) expression by ShRNAs or a methylation inhibitor 5-Aza-CdR can recover KLF5 expression. Meanwhile, there is a negative correlation between expressions of KLF5 and DNMT1 in ccRCC tissues. Ectopic KLF5 expression inhibits ccRCC cell proliferation and migration/invasion in vitro and decreases xenograft growth and metastasis in vivo. Moreover, 5-Aza-CdR, a chemotherapy drug as DNMTs' inhibitor that can induce KLF5 expression, suppresses ccRCC cell growth, while knockdown of KLF5 abolishes 5-Aza-CdR-induced growth inhibition. Collectively, our data demonstrate that KLF5 inhibits ccRCC growth as a tumor suppressor and highlight the potential of 5-Aza-CdR to release KLF5 expression as a therapeutic modality for the treatment of ccRCC.
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Affiliation(s)
- Rong-Jie Fu
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences (SIBS), University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS) &Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, China
| | - Wei He
- Department of Pathology, Ren-Ji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao-Bo Wang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, China
| | - Lei Li
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, China
| | - Huan-Bin Zhao
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, China
| | - Xiao-Ye Liu
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences (SIBS), University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS) &Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, China
| | - Zhi Pang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, China
| | - Guo-Qiang Chen
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences (SIBS), University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS) &Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, China.,Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, China
| | - Lei Huang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, China
| | - Ke-Wen Zhao
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, China
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14
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Noël A, Xiao R, Perveen Z, Zaman H, Le Donne V, Penn A. Sex-specific lung functional changes in adult mice exposed only to second-hand smoke in utero. Respir Res 2017. [PMID: 28651580 PMCID: PMC5485620 DOI: 10.1186/s12931-017-0591-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Background An increasing number of epidemiological and experimental studies have associated exposure to second-hand smoke (SHS) during pregnancy with adverse outcomes in newborns. As we have previously shown in mice, in utero exposure to SHS at critical stages of fetal development, results in altered lung responses and increased disease susceptibility upon re-exposure to irritants (SHS or ovalbumin) in adulthood. In this study, we asked whether the in utero SHS exposure alone is sufficient to alter lung structure and function in adult mice. Methods Pregnant BALB/c mice were exposed from days 6 to 19 of pregnancy to 10 mg/m3 of SHS or HEPA-filtered air. Male and female offspring (n = 13–15/group) were sacrificed at 15 weeks of age. We measured lung function with non-invasive and invasive methods, performed lung morphometric analysis on trichrome-stained lung tissue samples, and assessed lung gene expression via RNA sequencing and protein assays. Results In utero SHS exposure significantly increased mean linear intercept and decreased the surface area per unit volume of the lungs in both males and females, indicating perturbation in alveolar developmental processes. Tidal volume, minute volume and inspiratory capacity were significantly decreased compared with the controls only in male mice exposed in utero to SHS, suggesting that males are more sensitive than females to an SHS insult during lung development. This also suggests that in our model, lung structure changes may be necessary but are not sufficient to impair lung function. SERPINA1A, the mouse ortholog of human α1-antitrypsin, deficiency of which is a known genetic risk factor for emphysema, was down-regulated at the protein level in the in utero SHS-exposed mice. Additionally, DNMT3A protein expression was dysregulated, indicating that DNA methylation occurred in the lungs. Conclusions Our results indicate that in utero SHS exposure alone alters both lung function and structure well into adulthood (15 weeks) in male mice. Furthermore, lung function alterations in this model are sex-specific, with males being more susceptible to in utero SHS effects. Overall, our data suggest that in utero SHS exposure alone can predispose to adult lung diseases.
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Affiliation(s)
- Alexandra Noël
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Skip Bertman Drive, Baton Rouge, 70803, LA, USA
| | - Rui Xiao
- Department of Anesthesiology, Columbia University Medical Center, 622 West 168th Street, New York, 10032, NY, USA
| | - Zakia Perveen
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Skip Bertman Drive, Baton Rouge, 70803, LA, USA
| | - Hasan Zaman
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Skip Bertman Drive, Baton Rouge, 70803, LA, USA
| | - Viviana Le Donne
- Translational Medicine and Comparative Pathobiology, R&D Platform Technology and Science, GlaxoSmithKline, Park Road, Ware, SG12 ODP, UK
| | - Arthur Penn
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Skip Bertman Drive, Baton Rouge, 70803, LA, USA.
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15
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Lopomo A, Ricciardi R, Maestri M, De Rosa A, Melfi F, Lucchi M, Mussi A, Coppedè F, Migliore L. Gene-Specific Methylation Analysis in Thymomas of Patients with Myasthenia Gravis. Int J Mol Sci 2016; 17:E2121. [PMID: 27999265 PMCID: PMC5187921 DOI: 10.3390/ijms17122121] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 12/06/2016] [Accepted: 12/12/2016] [Indexed: 12/21/2022] Open
Abstract
Thymomas are uncommon neoplasms that arise from epithelial cells of the thymus and are often associated with myasthenia gravis (MG), an autoimmune disease characterized by autoantibodies directed to different targets at the neuromuscular junction. Little is known, however, concerning epigenetic changes occurring in thymomas from MG individuals. To further address this issue, we analyzed DNA methylation levels of genes involved in one-carbon metabolism (MTHFR) and DNA methylation (DNMT1, DNMT3A, and DNMT3B) in blood, tumor tissue, and healthy thymic epithelial cells from MG patients that underwent a surgical resection of a thymic neoplasm. For the analyses we applied the methylation-sensitive high-resolution melting technique. Both MTHFR and DNMT3A promoters showed significantly higher methylation in tumor tissue with respect to blood, and MTHFR also showed significantly higher methylation levels in tumor tissue respect to healthy adjacent thymic epithelial cells. Both DNMT1 and DNMT3B promoter regions were mostly hypomethylated in all the investigated tissues. The present study suggests that MTHFR methylation is increased in thymomas obtained from MG patients; furthermore, some degrees of methylation of the DNMT3A gene were observed in thymic tissue with respect to blood.
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Affiliation(s)
- Angela Lopomo
- Department of Translational Research and New Technologies in Medicine and Surgery, Division of Medical Genetics, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy.
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy.
| | - Roberta Ricciardi
- Department of Clinical and Experimental Medicine, Neurology Unit, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy.
- Division of Thoracic Surgery, Cardiothoracic and Vascular Surgery Department, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy.
| | - Michelangelo Maestri
- Department of Clinical and Experimental Medicine, Neurology Unit, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy.
| | - Anna De Rosa
- Department of Clinical and Experimental Medicine, Neurology Unit, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy.
| | - Franca Melfi
- Division of Thoracic Surgery, Cardiothoracic and Vascular Surgery Department, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy.
| | - Marco Lucchi
- Division of Thoracic Surgery, Cardiothoracic and Vascular Surgery Department, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy.
| | - Alfredo Mussi
- Division of Thoracic Surgery, Cardiothoracic and Vascular Surgery Department, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy.
| | - Fabio Coppedè
- Department of Translational Research and New Technologies in Medicine and Surgery, Division of Medical Genetics, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy.
| | - Lucia Migliore
- Department of Translational Research and New Technologies in Medicine and Surgery, Division of Medical Genetics, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy.
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16
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Megiorni F, Camero S, Ceccarelli S, McDowell HP, Mannarino O, Marampon F, Pizer B, Shukla R, Pizzuti A, Marchese C, Clerico A, Dominici C. DNMT3B in vitro knocking-down is able to reverse embryonal rhabdomyosarcoma cell phenotype through inhibition of proliferation and induction of myogenic differentiation. Oncotarget 2016; 7:79342-79356. [PMID: 27764816 PMCID: PMC5346718 DOI: 10.18632/oncotarget.12688] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 09/29/2016] [Indexed: 01/08/2023] Open
Abstract
Aberrant DNA methylation has been frequently observed in many human cancers, including rhabdomyosarcoma (RMS), the most common soft tissue sarcoma in children. To date, the expression and function of the de novo DNA methyltransferase (DNMT) 3B in RMS have not yet been investigated. Our study show for the first time a significant up-regulation of DNMT3B levels in 14 RMS tumour samples and 4 RMS cell lines in comparison to normal skeletal muscle. Transfection of RD and TE671 cells, two in vitro models of embryonal RMS (ERMS), with a synthetic DNMT3B siRNA decreased cell proliferation by arresting cell cycle at G1 phase, as demonstrated by the reduced expression of Cyclin B1, Cyclin D1 and Cyclin E2, and by the concomitant up-regulation of the checkpoint regulators p21 and p27. DNMT3B depletion also impaired RB phosphorylation status and decreased migratory capacity and clonogenic potential. Interestingly, DNMT3B knock-down was able to commit ERMS cells towards myogenic terminal differentiation, as confirmed by the acquisition of a myogenic-like phenotype and by the increased expression of the myogenic markers MYOD1, Myogenin and MyHC. Finally, inhibition of MEK/ERK signalling by U0126 resulted in a reduction of DNMT3B protein, giving evidence that DNMT3B is a down-stream molecule of this oncogenic pathway.Taken together, our data indicate that altered expression of DNMT3B plays a key role in ERMS development since its silencing is able to reverse cell cancer phenotype by rescuing myogenic program. Epigenetic therapy, by targeting the DNA methylation machinery, may represent a novel therapeutic strategy against RMS.
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Affiliation(s)
- Francesca Megiorni
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
| | - Simona Camero
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
| | - Simona Ceccarelli
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Heather P. McDowell
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
- Department of Oncology, Alder Hey Children's NHS Foundation Trust, Liverpool, United Kingdom
| | - Olga Mannarino
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
| | - Francesco Marampon
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Barry Pizer
- Department of Oncology, Alder Hey Children's NHS Foundation Trust, Liverpool, United Kingdom
| | - Rajeev Shukla
- Department of Perinatal and Paediatric Pathology, Alder Hey Children's NHS Foundation Trust, Liverpool, United Kingdom
| | - Antonio Pizzuti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Cinzia Marchese
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Anna Clerico
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
| | - Carlo Dominici
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
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17
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Integrative functional genomic analysis identifies epigenetically regulated fibromodulin as an essential gene for glioma cell migration. Oncogene 2016; 36:71-83. [DOI: 10.1038/onc.2016.176] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/15/2016] [Accepted: 04/03/2016] [Indexed: 01/07/2023]
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18
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The cancer-promoting gene fatty acid-binding protein 5 (FABP5) is epigenetically regulated during human prostate carcinogenesis. Biochem J 2016; 473:449-61. [DOI: 10.1042/bj20150926] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/27/2015] [Indexed: 12/12/2022]
Abstract
The DNA methylation status of CpG islands in the FABP5 promoter is critical for its expression. Epigenetic regulation of FABP5 gene expression plays an important role during human prostate carcinogenesis, along with up-regulation of c-Myc and Sp1.
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19
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Fan H, Zhao Z, Cheng Y, Cui H, Qiao F, Wang L, Hu J, Wu H, Song W. Genome-wide profiling of DNA methylation reveals preferred sequences of DNMTs in hepatocellular carcinoma cells. Tumour Biol 2016; 37:877-85. [PMID: 26254611 DOI: 10.1007/s13277-015-3202-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 02/03/2015] [Indexed: 02/03/2023] Open
Abstract
Aberrant DNA methylation of CpG site is among the earliest and most frequent alterations in developmental process and diseases including cancer. To elucidate the functional preferred site of DNMTs, we analyzed the feature of distinct methylated sequences and established the defined relationship between DNMTs and preference genomic DNA sequences. Small interfering RNA (siRNA) construct of DNTM1, DNMT3A, and DNMT3B was transfected into the human hepatocellular carcinoma cell line SMMC-7721, respectively. Distinguishing methylated fragments pool was enriched by SHH method in cells which is knocked down DNMT1, DNMT3A, DNMT3B, separately. The defined binding transcription factors (TFs) containing of 5'CpG islands were obtained with bioinformatics software and website. In SMMC-7721 hepatocellular carcinoma (HCC) cell line, DNMT1, DNMT3A, and DNMT3B were specific suppressed by their corresponding siRNA construct, separately. A 46, 42, 67 distinctive methylated fragments from three different DNMTs were evaluated according to genomic DNA database. Those separated fragments were distributed among genomic DNA regions of all chromosome complements, including coding genes, repeat sequences, and genes with unknown function. The majority of coding genes contain CpG islands in their promoter region. Cluster analysis demonstrated all of preference sequences identified by three DNMTs shares their own conserved sequences. In depleting of different DNMTs cells, 80 % of 103 upregulation genes induced by DNMT1 knock-down contain CpG sites; 76 % of 25 upregulation genes induced by DNMT3A knock-down contain CpG sites; 63 % of 126 upregulation genes induced by DNMT3B knock-down contain CpG sites. Our findings suggested that distinctive DNMTs targeted DNA methylation site to their preference sequences, and this targeting might be associated with diverse roles of DNMTs in tumorigenesis. Meanwhile, the analysis of preference sequences provides an alternative way to find out the individual function of DNMTs.
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Affiliation(s)
- Hong Fan
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, 87 Ding JiaQiao Road, Nanjing, 210009, China.
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China.
| | - Zhujiang Zhao
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, 87 Ding JiaQiao Road, Nanjing, 210009, China
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China
| | - Yuchao Cheng
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, 87 Ding JiaQiao Road, Nanjing, 210009, China
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China
| | - He Cui
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, 87 Ding JiaQiao Road, Nanjing, 210009, China
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China
| | - Fengchang Qiao
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, 87 Ding JiaQiao Road, Nanjing, 210009, China
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China
| | - Ling Wang
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, 87 Ding JiaQiao Road, Nanjing, 210009, China
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China
| | - Jiaojiao Hu
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, 87 Ding JiaQiao Road, Nanjing, 210009, China
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China
| | - Huzhang Wu
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, 87 Ding JiaQiao Road, Nanjing, 210009, China
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China
| | - Wei Song
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, 87 Ding JiaQiao Road, Nanjing, 210009, China
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China
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20
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Haney SL, Hlady RA, Opavska J, Klinkebiel D, Pirruccello SJ, Dutta S, Datta K, Simpson MA, Wu L, Opavsky R. Methylation-independent repression of Dnmt3b contributes to oncogenic activity of Dnmt3a in mouse MYC-induced T-cell lymphomagenesis. Oncogene 2015; 34:5436-5446. [PMID: 25639876 PMCID: PMC4533871 DOI: 10.1038/onc.2014.472] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 10/28/2014] [Accepted: 11/25/2014] [Indexed: 12/16/2022]
Abstract
DNA methyltransferase 3A (DNMT3A) catalyzes cytosine methylation of mammalian genomic DNA. In addition to myeloid malignancies, mutations in DNMT3A have been recently reported in T-cell lymphoma and leukemia, implying a possible involvement in the pathogenesis of human diseases. However, the role of Dnmt3a in T-cell transformation in vivo is poorly understood. Here we analyzed the functional consequences of Dnmt3a inactivation in a mouse model of MYC-induced T-cell lymphomagenesis (MTCL). Loss of Dnmt3a delayed tumorigenesis by suppressing cellular proliferation during disease progression. Gene expression profiling and pathway analysis identified upregulation of 17 putative tumor suppressor genes, including DNA methyltransferase Dnmt3b, in Dnmt3a-deficient lymphomas as molecular events potentially responsible for the delayed lymphomagenesis in Dnmt3a(Δ/Δ) mice. Interestingly, promoter and gene body methylation of these genes was not substantially changed between control and Dnmt3a-deficient lymphomas, suggesting that Dnmt3a may inhibit their expression in a methylation-independent manner. Re-expression of both wild type and catalytically inactive Dnmt3a in Dnmt3a(Δ/Δ) lymphoma cells in vitro inhibited Dnmt3b expression, indicating that Dnmt3b upregulation may be directly repressed by Dnmt3a. Importantly, genetic inactivation of Dnmt3b accelerated lymphomagenesis in Dnmt3a(Δ/Δ) mice, demonstrating that upregulation of Dnmt3b is a relevant molecular change in Dnmt3a-deficient lymphomas that inhibits disease progression. Collectively, our data demonstrate an unexpected oncogenic role for Dnmt3a in MTCL through methylation-independent repression of Dnmt3b and possibly other tumor suppressor genes.
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Affiliation(s)
- Staci L. Haney
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Ryan A. Hlady
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Jana Opavska
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - David Klinkebiel
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Samuel J. Pirruccello
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Samikshan Dutta
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Kaustubh Datta
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Melanie A. Simpson
- Department of Biochemistry, University of Nebraska, Lincoln, Nebraska, USA
| | - Lizhao Wu
- Department of Microbiology and Molecular Genetics, Rutgers New Jersey Medical School-Cancer Center, Newark, NJ, USA
| | - Rene Opavsky
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, USA
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA
- Center for Lymphoma and Leukemia Research, University of Nebraska Medical Center, Omaha, Nebraska, USA
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21
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Computational fishing of new DNA methyltransferase inhibitors from natural products. J Mol Graph Model 2015; 60:43-54. [PMID: 26099696 DOI: 10.1016/j.jmgm.2015.04.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/28/2015] [Accepted: 04/22/2015] [Indexed: 12/31/2022]
Abstract
DNA methyltransferase inhibitors (DNMTis) have become an alternative for cancer therapies. However, only two DNMTis have been approved as anticancer drugs, although with some restrictions. Natural products (NPs) are a promising source of drugs. In order to find NPs with novel chemotypes as DNMTis, 47 compounds with known activity against these enzymes were used to build a LDA-based QSAR model for active/inactive molecules (93% accuracy) based on molecular descriptors. This classifier was employed to identify potential DNMTis on 800 NPs from NatProd Collection. 447 selected compounds were docked on two human DNA methyltransferase (DNMT) structures (PDB codes: 3SWR and 2QRV) using AutoDock Vina and Surflex-Dock, prioritizing according to their score values, contact patterns at 4 Å and molecular diversity. Six consensus NPs were identified as virtual hits against DNMTs, including 9,10-dihydro-12-hydroxygambogic, phloridzin, 2',4'-dihydroxychalcone 4'-glucoside, daunorubicin, pyrromycin and centaurein. This method is an innovative computational strategy for identifying DNMTis, useful in the identification of potent and selective anticancer drugs.
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22
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Hamm CA, Costa FF. Epigenomes as therapeutic targets. Pharmacol Ther 2015; 151:72-86. [PMID: 25797698 DOI: 10.1016/j.pharmthera.2015.03.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 03/06/2015] [Indexed: 12/19/2022]
Abstract
Epigenetics is a molecular phenomenon that pertains to heritable changes in gene expression that do not involve changes in the DNA sequence. Epigenetic modifications in a whole genome, known as the epigenome, play an essential role in the regulation of gene expression in both normal development and disease. Traditional epigenetic changes include DNA methylation and histone modifications. Recent evidence reveals that other players, such as non-coding RNAs, may have an epigenetic regulatory role. Aberrant epigenetic signaling is becoming to be known as a central component of human disease, and the reversible nature of the epigenetic modifications provides an exciting opportunity for the development of clinically relevant therapeutics. Current epigenetic therapies provide a clinical benefit through disrupting DNA methyltransferases or histone deacetylases. However, the emergence of next-generation epigenetic therapies provides an opportunity to more effectively disrupt epigenetic disease states. Novel epigenetic therapies may improve drug targeting and drug delivery, optimize dosing schedules, and improve the efficacy of preexisting treatment modalities (chemotherapy, radiation, and immunotherapy). This review discusses the epigenetic mechanisms that contribute to the disease, available epigenetic therapies, epigenetic therapies currently in development, and the potential future use of epigenetic therapeutics in a clinical setting.
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Affiliation(s)
- Christopher A Hamm
- Cancer Biology and Epigenomics Program, Ann & Robert H Lurie Children's Hospital of Chicago Research Center and Department of Pediatrics, Northwestern University's Feinberg School of Medicine, 225 E. Chicago Avenue, Box 220, Chicago, IL 60611-2605, USA.
| | - Fabricio F Costa
- Cancer Biology and Epigenomics Program, Ann & Robert H Lurie Children's Hospital of Chicago Research Center and Department of Pediatrics, Northwestern University's Feinberg School of Medicine, 225 E. Chicago Avenue, Box 220, Chicago, IL 60611-2605, USA; StartUp Health Academy, 2000 Broadway St, 18th Floor, New York, NY 10.023, USA; Genomic Enterprise, 2405 N. Sheffield Av., # 14088, Chicago, IL 60.614, USA; Genomic Sciences and Biotechnology Program, UCB - Brasilia, SGAN 916 Modulo B, Bloco C, 70.790-160 Brasilia, Brazil.
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23
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Rodríguez-Rodero S, Delgado-Álvarez E, Fernández AF, Fernández-Morera JL, Menéndez-Torre E, Fraga MF. Epigenetic alterations in endocrine-related cancer. Endocr Relat Cancer 2014; 21:R319-30. [PMID: 24898948 DOI: 10.1530/erc-13-0070] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Aberrant epigenetics is a hallmark of cancer, and endocrine-related tumors are no exception. Recent research has been identifying an ever-growing number of epigenetic alterations in both genomic DNA methylation and histone post-translational modification in tumors of the endocrine system. Novel microarray and ultra-deep sequencing technologies have allowed the identification of genome-wide epigenetic patterns in some tumor types such as adrenocortical, parathyroid, and breast carcinomas. However, in other cancer types, such as the multiple endocrine neoplasia syndromes and thyroid cancer, tumor information is limited to candidate genes alone. Future research should fill this gap and deepen our understanding of the functional role of these alterations in cancer, as well as defining their possible clinical uses.
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Affiliation(s)
- Sandra Rodríguez-Rodero
- Endocrinology and Nutrition ServiceHospital Universitario Central de Asturias, Av. Julian Clavería s/n, 33006 Oviedo, SpainCancer Epigenetics LaboratoryInstituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33006 Oviedo, SpainDepartment of Immunology and OncologyNational Center for Biotechnology, CNB-CSIC, Cantoblanco, Madrid E-28049, SpainEndocrinology and Nutrition ServiceHospital Universitario Central de Asturias, Av. Julian Clavería s/n, 33006 Oviedo, SpainCancer Epigenetics LaboratoryInstituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33006 Oviedo, SpainDepartment of Immunology and OncologyNational Center for Biotechnology, CNB-CSIC, Cantoblanco, Madrid E-28049, Spain
| | - Elías Delgado-Álvarez
- Endocrinology and Nutrition ServiceHospital Universitario Central de Asturias, Av. Julian Clavería s/n, 33006 Oviedo, SpainCancer Epigenetics LaboratoryInstituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33006 Oviedo, SpainDepartment of Immunology and OncologyNational Center for Biotechnology, CNB-CSIC, Cantoblanco, Madrid E-28049, Spain
| | - Agustín F Fernández
- Endocrinology and Nutrition ServiceHospital Universitario Central de Asturias, Av. Julian Clavería s/n, 33006 Oviedo, SpainCancer Epigenetics LaboratoryInstituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33006 Oviedo, SpainDepartment of Immunology and OncologyNational Center for Biotechnology, CNB-CSIC, Cantoblanco, Madrid E-28049, Spain
| | - Juan L Fernández-Morera
- Endocrinology and Nutrition ServiceHospital Universitario Central de Asturias, Av. Julian Clavería s/n, 33006 Oviedo, SpainCancer Epigenetics LaboratoryInstituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33006 Oviedo, SpainDepartment of Immunology and OncologyNational Center for Biotechnology, CNB-CSIC, Cantoblanco, Madrid E-28049, Spain
| | - Edelmiro Menéndez-Torre
- Endocrinology and Nutrition ServiceHospital Universitario Central de Asturias, Av. Julian Clavería s/n, 33006 Oviedo, SpainCancer Epigenetics LaboratoryInstituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33006 Oviedo, SpainDepartment of Immunology and OncologyNational Center for Biotechnology, CNB-CSIC, Cantoblanco, Madrid E-28049, Spain
| | - Mario F Fraga
- Endocrinology and Nutrition ServiceHospital Universitario Central de Asturias, Av. Julian Clavería s/n, 33006 Oviedo, SpainCancer Epigenetics LaboratoryInstituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33006 Oviedo, SpainDepartment of Immunology and OncologyNational Center for Biotechnology, CNB-CSIC, Cantoblanco, Madrid E-28049, SpainEndocrinology and Nutrition ServiceHospital Universitario Central de Asturias, Av. Julian Clavería s/n, 33006 Oviedo, SpainCancer Epigenetics LaboratoryInstituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33006 Oviedo, SpainDepartment of Immunology and OncologyNational Center for Biotechnology, CNB-CSIC, Cantoblanco, Madrid E-28049, Spain
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24
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Chen BF, Chan WY. The de novo DNA methyltransferase DNMT3A in development and cancer. Epigenetics 2014; 9:669-77. [PMID: 24589714 DOI: 10.4161/epi.28324] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
DNA methylation, one of the best-characterized epigenetic modifications, plays essential roles in development, aging and diseases. The de novo DNA methyltransferase DNMT3A is responsible for the establishment of de novo genomic DNA methylation patterns and, as such, involved in normal development as well as in many diseases including cancer. In recent years, our understanding of this important protein has made significant progress, which was facilitated by stunning development in the analysis of the DNA methylome of multiple organs and cell types. In this review, recent developments in the characterization of DNMT3A were discussed with special emphasis on the roles of DNMT3A in development and cancer.
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Affiliation(s)
- Bi-Feng Chen
- Chinese University of Hong Kong-Shandong University Joint Laboratory on Reproductive Genetics; School of Biomedical Sciences; Shenzhen Research Institute; the Chinese University of Hong Kong; Hong Kong SAR, PR China
| | - Wai-Yee Chan
- Chinese University of Hong Kong-Shandong University Joint Laboratory on Reproductive Genetics; School of Biomedical Sciences; Shenzhen Research Institute; the Chinese University of Hong Kong; Hong Kong SAR, PR China
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25
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Wu LY, Wen B, Hu FL, Liu JY, Fu DS. DNMTs are differentially expressed in tissues at different distances from colorectal cancer lesions. Shijie Huaren Xiaohua Zazhi 2013; 21:2515-2521. [DOI: 10.11569/wcjd.v21.i25.2515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To detect the expression of DNA methyltransferases (DNMTs) in tissues at different distances from colorectal cancer lesions.
METHODS: Immunohistochemistry and Western blot were used to detect the expression of DNMTs in 25 colorectal cancer specimens and matched tumor-adjacent tissues (> 5 cm apart from the tumor and 2 cm apart from the tumor) and normal tissues (> 10 cm apart from the tumor). None of the patients received preoperative treatments such as radiotherapy or chemotherapy.
RESULTS: The corrected absorbance of DNMT1 detected by immunohistochemistry in tissues > 10, > 5 and 2 cm apart from the tumor was 0.359484 ± 0.037511, 0.460941 ± 0.032146 and 0.498767 ± 0.021143, respectively, showing an upward-trend (P < 0.05). The corresponding relative expression levels of DNMT1detected by Western blot were 0.7173, 0.7418 and 0.8296. Expression of DNMT3A in tissues > 5 and > 10 cm apart from the tumor was significantly higher than that in tissues 2 cm apart from the tumor (both P < 0. 05), although expression of DNMT3A showed no significant difference between tissues > 5 and > 10 cm apart from the tumor (P > 0. 05). Expression of DNMT3B in the above tissues was similar to that of DNMT3A.
CONCLUSION: Up-regulation of DNMT1, DNMT3A and DNMT3B may play a significant role in the occurrence of colorectal carcinoma.
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Essential role for Dnmt1 in the prevention and maintenance of MYC-induced T-cell lymphomas. Mol Cell Biol 2013; 33:4321-33. [PMID: 24001767 DOI: 10.1128/mcb.00776-13] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
DNA cytosine methylation is an epigenetic modification involved in the transcriptional repression of genes controlling a variety of physiological processes, including hematopoiesis. DNA methyltransferase 1 (Dnmt1) is a key enzyme involved in the somatic inheritance of DNA methylation and thus plays a critical role in epigenomic stability. Aberrant methylation contributes to the pathogenesis of human cancer and of hematologic malignancies in particular. To gain deeper insight into the function of Dnmt1 in lymphoid malignancies, we genetically inactivated Dnmt1 in a mouse model of MYC-induced T-cell lymphomagenesis. We show that loss of Dnmt1 delays lymphomagenesis by suppressing normal hematopoiesis and impairing tumor cell proliferation. Acute inactivation of Dnmt1 in primary lymphoma cells rapidly induced apoptosis, indicating that Dnmt1 is required to sustain T-cell lymphomas. Using high-resolution genome-wide profiling, we identified differentially methylated regions between control and Dnmt1-deficient lymphomas, demonstrating a locus-specific function for Dnmt1 in both maintenance and de novo promoter methylation. Dnmt1 activity is independent of the presence of Dnmt3a or Dnmt3b in de novo promoter methylation of the H2-Ab1 gene. Collectively, these data show for the first time that Dnmt1 is critical for the prevention and maintenance of T-cell lymphomas and contributes to aberrant methylation by both de novo and maintenance methylation.
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27
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Vidaki A, Daniel B, Court DS. Forensic DNA methylation profiling—Potential opportunities and challenges. Forensic Sci Int Genet 2013; 7:499-507. [DOI: 10.1016/j.fsigen.2013.05.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 05/14/2013] [Indexed: 11/26/2022]
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28
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Stepanenko AA, Vassetzky YS, Kavsan VM. Antagonistic functional duality of cancer genes. Gene 2013; 529:199-207. [PMID: 23933273 DOI: 10.1016/j.gene.2013.07.047] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 05/08/2013] [Accepted: 07/09/2013] [Indexed: 12/21/2022]
Abstract
Cancer evolution is a stochastic process both at the genome and gene levels. Most of tumors contain multiple genetic subclones, evolving in either succession or in parallel, either in a linear or branching manner, with heterogeneous genome and gene alterations, extensively rewired signaling networks, and addicted to multiple oncogenes easily switching with each other during cancer progression and medical intervention. Hundreds of discovered cancer genes are classified according to whether they function in a dominant (oncogenes) or recessive (tumor suppressor genes) manner in a cancer cell. However, there are many cancer "gene-chameleons", which behave distinctly in opposite way in the different experimental settings showing antagonistic duality. In contrast to the widely accepted view that mutant NADP(+)-dependent isocitrate dehydrogenases 1/2 (IDH1/2) and associated metabolite 2-hydroxyglutarate (R)-enantiomer are intrinsically "the drivers" of tumourigenesis, mutant IDH1/2 inhibited, promoted or had no effect on cell proliferation, growth and tumorigenicity in diverse experiments. Similar behavior was evidenced for dozens of cancer genes. Gene function is dependent on genetic network, which is defined by the genome context. The overall changes in karyotype can result in alterations of the role and function of the same genes and pathways. The diverse cell lines and tumor samples have been used in experiments for proving gene tumor promoting/suppressive activity. They all display heterogeneous individual karyotypes and disturbed signaling networks. Consequently, the effect and function of gene under investigation can be opposite and versatile in cells with different genomes that may explain antagonistic duality of cancer genes and the cell type- or the cellular genetic/context-dependent response to the same protein. Antagonistic duality of cancer genes might contribute to failure of chemotherapy. Instructive examples of unexpected activity of cancer genes and "paradoxical" effects of different anticancer drugs depending on the cellular genetic context/signaling network are discussed.
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Affiliation(s)
- A A Stepanenko
- State Key Laboratory of Molecular and Cellular Biology, Institute of Molecular Biology and Genetics, 150 Zabolotnogo Street, Kyiv 03680, Ukraine.
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29
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Graur D, Zheng Y, Price N, Azevedo RBR, Zufall RA, Elhaik E. On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol 2013; 5:578-90. [PMID: 23431001 PMCID: PMC3622293 DOI: 10.1093/gbe/evt028] [Citation(s) in RCA: 302] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2013] [Indexed: 12/11/2022] Open
Abstract
A recent slew of ENCyclopedia Of DNA Elements (ENCODE) Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according to which the fraction of the genome that is evolutionarily conserved through purifying selection is less than 10%. Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80 - 10 = 70% of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these "functional" regions or because no mutation in these regions can ever be deleterious. This absurd conclusion was reached through various means, chiefly by employing the seldom used "causal role" definition of biological function and then applying it inconsistently to different biochemical properties, by committing a logical fallacy known as "affirming the consequent," by failing to appreciate the crucial difference between "junk DNA" and "garbage DNA," by using analytical methods that yield biased errors and inflate estimates of functionality, by favoring statistical sensitivity over specificity, and by emphasizing statistical significance rather than the magnitude of the effect. Here, we detail the many logical and methodological transgressions involved in assigning functionality to almost every nucleotide in the human genome. The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten.
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Affiliation(s)
- Dan Graur
- Department of Biology and Biochemistry, University of Houston, TX, USA.
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