1
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Ulschmid CM, Sun MR, Jabbarpour CR, Steward AC, Rivera-González KS, Cao J, Martin AA, Barnes M, Wicklund L, Madrid A, Papale LA, Joseph DB, Vezina CM, Alisch RS, Lipinski RJ. Disruption of DNA methylation-mediated cranial neural crest proliferation and differentiation causes orofacial clefts in mice. Proc Natl Acad Sci U S A 2024; 121:e2317668121. [PMID: 38194455 PMCID: PMC10801837 DOI: 10.1073/pnas.2317668121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/14/2023] [Indexed: 01/11/2024] Open
Abstract
Orofacial clefts of the lip and palate are widely recognized to result from complex gene-environment interactions, but inadequate understanding of environmental risk factors has stymied development of prevention strategies. We interrogated the role of DNA methylation, an environmentally malleable epigenetic mechanism, in orofacial development. Expression of the key DNA methyltransferase enzyme DNMT1 was detected throughout palate morphogenesis in the epithelium and underlying cranial neural crest cell (cNCC) mesenchyme, a highly proliferative multipotent stem cell population that forms orofacial connective tissue. Genetic and pharmacologic manipulations of DNMT activity were then applied to define the tissue- and timing-dependent requirement of DNA methylation in orofacial development. cNCC-specific Dnmt1 inactivation targeting initial palate outgrowth resulted in OFCs, while later targeting during palatal shelf elevation and elongation did not. Conditional Dnmt1 deletion reduced cNCC proliferation and subsequent differentiation trajectory, resulting in attenuated outgrowth of the palatal shelves and altered development of cNCC-derived skeletal elements. Finally, we found that the cellular mechanisms of cleft pathogenesis observed in vivo can be recapitulated by pharmacologically reducing DNA methylation in multipotent cNCCs cultured in vitro. These findings demonstrate that DNA methylation is a crucial epigenetic regulator of cNCC biology, define a critical period of development in which its disruption directly causes OFCs, and provide opportunities to identify environmental influences that contribute to OFC risk.
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Affiliation(s)
- Caden M. Ulschmid
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
| | - Miranda R. Sun
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
| | - Christopher R. Jabbarpour
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
| | - Austin C. Steward
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
| | - Kenneth S. Rivera-González
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
- Molecular and Environmental Toxicology Training Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI53706
| | - Jocelyn Cao
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
| | - Alexander A. Martin
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
| | - Macy Barnes
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
| | - Lorena Wicklund
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
| | - Andy Madrid
- Neurological Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI53706
| | - Ligia A. Papale
- Neurological Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI53706
| | - Diya B. Joseph
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
| | - Chad M. Vezina
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
- Molecular and Environmental Toxicology Training Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI53706
| | - Reid S. Alisch
- Neurological Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI53706
| | - Robert J. Lipinski
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
- Molecular and Environmental Toxicology Training Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI53706
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2
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Xu D, Yan S, Jin H, Chen C, Tang X, Wang X, Li Y, Fei F, Yang A. Integration of RRBS and RNA-seq unravels the regulatory role of DNMT3A in porcine Sertoli cell proliferation. Front Genet 2024; 14:1302351. [PMID: 38264208 PMCID: PMC10803568 DOI: 10.3389/fgene.2023.1302351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/20/2023] [Indexed: 01/25/2024] Open
Abstract
DNMT3A participates in de novo methylation, yet its impact on the proliferation of testicular Sertoli cells remains unclear. Development-specific methylation has been proven to be associated with cellular development. Therefore, in this study, we simulated DNMT3A expression pattern during testicular development by DNMT3A interference. Then, RRBS and RNA-seq were used to decipher DNMT3A regulatory mechanisms on Sertoli cell proliferation. Immunofluorescence staining revealed the expression of DNMT3A in the Sertoli cells of the prepubertal testis. DNMT3A was demonstrated to inhibit the cell cycle and proliferation of Sertoli cells, while promoting cell apoptosis. After transfected with DNMT3A interference, a total of 560 DEGs and 2,091 DMGs produced by DNMT3A interference were identified between two treated groups, respectively. Integrating the results from RRBS and RNA-seq, the overlapping genes between DMGs and DEGs were found to be enriched in the Gene Ontology (GO) terms related to cellular development and the Apelin signaling pathway. The present study demonstrated the impact of DNMT3A on the proliferation of porcine testicular Sertoli cells, suggesting that DNMT3A primarily acts through the Apelin signaling pathway. These findings provide valuable insights into how DNMT3A influences testicular development and health, offering new perspectives.
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Affiliation(s)
- Dong Xu
- Department of Biological and Environmental Engineering, Yueyang Vocational Technical College, Yueyang, Hunan, China
| | - Saina Yan
- School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Huimin Jin
- School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Chujie Chen
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Xiangwei Tang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Xu Wang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Yonghong Li
- Department of Biological and Environmental Engineering, Yueyang Vocational Technical College, Yueyang, Hunan, China
| | - Fang Fei
- Department of Biological and Environmental Engineering, Yueyang Vocational Technical College, Yueyang, Hunan, China
| | - Anqi Yang
- School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, China
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3
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Bassal MA. The Interplay between Dysregulated Metabolism and Epigenetics in Cancer. Biomolecules 2023; 13:944. [PMID: 37371524 DOI: 10.3390/biom13060944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/21/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Cellular metabolism (or energetics) and epigenetics are tightly coupled cellular processes. It is arguable that of all the described cancer hallmarks, dysregulated cellular energetics and epigenetics are the most tightly coregulated. Cellular metabolic states regulate and drive epigenetic changes while also being capable of influencing, if not driving, epigenetic reprogramming. Conversely, epigenetic changes can drive altered and compensatory metabolic states. Cancer cells meticulously modify and control each of these two linked cellular processes in order to maintain their tumorigenic potential and capacity. This review aims to explore the interplay between these two processes and discuss how each affects the other, driving and enhancing tumorigenic states in certain contexts.
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Affiliation(s)
- Mahmoud Adel Bassal
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
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4
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Ramini D, Latini S, Giuliani A, Matacchione G, Sabbatinelli J, Mensà E, Bacalini MG, Garagnani P, Rippo MR, Bronte G, Bonafè M, Cardelli M, Olivieri F. Replicative Senescence-Associated LINE1 Methylation and LINE1-Alu Expression Levels in Human Endothelial Cells. Cells 2022; 11:cells11233799. [PMID: 36497059 PMCID: PMC9739197 DOI: 10.3390/cells11233799] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/22/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022] Open
Abstract
One of the main challenges of current research on aging is to identify the complex epigenetic mechanisms involved in the acquisition of the cellular senescent phenotype. Despite some evidence suggested that epigenetic changes of DNA repetitive elements, including transposable elements (TE) sequences, are associated with replicative senescence of fibroblasts, data on different types of cells are scarce. We previously analysed genome-wide DNA methylation of young and replicative senescent human endothelial cells (HUVECs), highlighting increased levels of demethylated sequences in senescent cells. Here, we aligned the most significantly demethylated single CpG sites to the reference genome and annotated their localization inside TE sequences and found a significant hypomethylation of sequences belonging to the Long-Interspersed Element-1 (LINE-1 or L1) subfamilies L1M, L1P, and L1HS. To verify the hypothesis that L1 demethylation could be associated with increased transcription/activation of L1s and/or Alu elements (non-autonomous retroelements that usually depend on L1 sequences for reverse transcription and retrotransposition), we quantified the RNA expression levels of both L1 (generic L1 elements or site-specific L1PA2 on chromosome 14) and Alu elements in young and senescent HUVECs and human dermal fibroblasts (NHDFs). The RNA expression of Alu and L1 sequences was significantly increased in both senescent HUVECs and NHDFs, whereas the RNA transcript of L1PA2 on chromosome 14 was not significantly modulated in senescent cells. Moreover, we found an increased amount of TE DNA copies in the cytoplasm of senescent HUVECs and NHDFs. Our results support the hypothesis that TE, which are significantly increased in senescent cells, could be retrotranscribed to DNA sequences.
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Affiliation(s)
- Deborah Ramini
- Clinic of Laboratory and Precision Medicine, IRCCS INRCA, 60121 Ancona, Italy
| | - Silvia Latini
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
| | - Angelica Giuliani
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
- Correspondence: ; Tel.: +39-071-220-6243
| | - Giulia Matacchione
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
| | - Jacopo Sabbatinelli
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
- Laboratory Medicine Unit, Azienda Ospedaliero Universitaria delle Marche, 60126 Ancona, Italy
| | - Emanuela Mensà
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
| | | | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126 Bologna, Italy
- Applied Biomedical Research Center (CRBA), S. Orsola-Malpighi Polyclinic, 40126 Bologna, Italy
- CNR Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”-Unit of Bologna, 40126 Bologna, Italy
- Department of Laboratory Medicine, Clinical Chemistry, Karolinska Institutet, Karolinska University Hospital, 141 86 Huddinge, Sweden
| | - Maria Rita Rippo
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
| | - Giuseppe Bronte
- Clinic of Laboratory and Precision Medicine, IRCCS INRCA, 60121 Ancona, Italy
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
| | - Massimiliano Bonafè
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126 Bologna, Italy
| | - Maurizio Cardelli
- Advanced Technology Center for Aging Research, IRCCS INRCA, 60121 Ancona, Italy
| | - Fabiola Olivieri
- Clinic of Laboratory and Precision Medicine, IRCCS INRCA, 60121 Ancona, Italy
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
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5
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Xu L, Peng B, Wu H, Zheng Y, Yu Q, Fang S. METTL7B contributes to the malignant progression of glioblastoma by inhibiting EGR1 expression. Metab Brain Dis 2022; 37:1133-1143. [PMID: 35254598 DOI: 10.1007/s11011-022-00925-6] [Citation(s) in RCA: 4] [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] [Received: 07/09/2021] [Accepted: 01/31/2022] [Indexed: 11/26/2022]
Abstract
Glioblastoma (GBM), a predominant central nervous system (CNS) malignancy, is correlated with high mortality and severe morbidity. Mammalian methyltransferase-like 7B (METTL7B) as a methyltransferase has been identified to participate in cancer progression. However, its function in GBM is elusive. Accordingly, we aimed to explore the effect of METTL7B on GBM. The expression of METTL7B and EGR2 in GBM patients and GBM cells were detected by qPCR, western blots and immunohistochemical staining. Cell viability was assessed by CCK-8 assays. Cell proliferation was determined by EdU, colony formation, and tumor sphere formation assays. METTL7B shRNA was injected into the Balb/c nude mice. The size and weight of isolated tumor was measured. And the expression levels of Ki67, METTL7B and EGR1 were examined by immunohistochemical staining. METTL7B was significantly elevated, while EGR1 was downregulated in clinical GBM tissues. METTL7B upregulation was associated with the low overall survival of GBM patients. Moreover, METTL7B depletion remarkably attenuated GBM cell proliferation. Mechanistically, METTL7B overexpression inhibited EGR1 expression in GBM cells. EGR1 knockdown rescued the inhibitory effect of METTL7B depletion on GBM cell proliferation. Meanwhile, METTL7B depletion arrested more GBM cells at the G0/G1, but fewer cells at the S phase, which EGR1 knockdown reversed these effects. Furthermore, tumorigenicity analysis revealed that METTL7B promotes tumor growth of GBM cells in vivo. METTL7B contributes to the malignant progression of GBM by inhibiting EGR1 expression. METTL7B and EGR1 may be utilized as the treatment targets for GBM therapy.
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Affiliation(s)
- Li Xu
- Department of Neurosurgery, Central People's Hospital of Zhanjiang, No.236 Yuanzhu Road, Chikan District, Zhanjiang City, Guangdong Province, 524045, People's Republic of China.
| | - Biao Peng
- Deparment of Neurosurgery, the Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou City, Guangdong Province, 510080, People's Republic of China
| | - Haiqiang Wu
- Department of Neurosurgery, Central People's Hospital of Zhanjiang, No.236 Yuanzhu Road, Chikan District, Zhanjiang City, Guangdong Province, 524045, People's Republic of China
| | - Yike Zheng
- Department of Neurosurgery, Central People's Hospital of Zhanjiang, No.236 Yuanzhu Road, Chikan District, Zhanjiang City, Guangdong Province, 524045, People's Republic of China
| | - Qingwen Yu
- Department of Neurosurgery, Central People's Hospital of Zhanjiang, No.236 Yuanzhu Road, Chikan District, Zhanjiang City, Guangdong Province, 524045, People's Republic of China
| | - Shuiqiao Fang
- Department of Neurosurgery, Central People's Hospital of Zhanjiang, No.236 Yuanzhu Road, Chikan District, Zhanjiang City, Guangdong Province, 524045, People's Republic of China
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6
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Ruan X, Zhang R, Zhu H, Ye C, Wang Z, Dong E, Li R, Cheng Z, Peng H. Research progress on epigenetics of small B-cell lymphoma. Clin Transl Oncol 2022; 24:1501-1514. [PMID: 35334078 DOI: 10.1007/s12094-022-02820-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 02/26/2022] [Indexed: 10/18/2022]
Abstract
Small B-cell lymphoma is the classification of B-cell chronic lymphoproliferative disorders that include chronic lymphocytic leukaemia/small lymphocytic lymphoma, follicular lymphoma, mantle cell lymphoma, marginal zone lymphoma, lymphoplasmacytic lymphoma/Waldenstrom macroglobulinemia. The clinical presentation is somewhat heterogeneous, and its occurrence and development mechanisms are not yet precise and may involve epigenetic changes. Epigenetic alterations mainly include DNA methylation, histone modification, and non-coding RNA, which are essential for genetic detection, early diagnosis, and assessment of treatment resistance in small B-cell lymphoma. As chronic lymphocytic leukemia/small lymphocytic lymphoma has already been reported in the literature, this article focuses on small B-cell lymphomas such as follicular lymphoma, mantle cell lymphoma, marginal zone lymphoma, and Waldenstrom macroglobulinemia. It discusses recent developments in epigenetic research to diagnose and treat this group of lymphomas. This review provides new ideas for the treatment and prognosis assessment of small B-cell lymphoma by exploring the connection between small B-cell lymphoma and epigenetics.
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Affiliation(s)
- Xueqin Ruan
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Engineering Research Center of Targeted Therapy for Hematopoietic Malignancies, Changsha, Hunan, China.,Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Rong Zhang
- Division of Cancer Immunotherapy, National Cancer Center Exploratory Oncology Research & Clinical Trial Center, Chiba, Japan
| | - Hongkai Zhu
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Engineering Research Center of Targeted Therapy for Hematopoietic Malignancies, Changsha, Hunan, China.,Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Can Ye
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Engineering Research Center of Targeted Therapy for Hematopoietic Malignancies, Changsha, Hunan, China.,Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Zhihua Wang
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Engineering Research Center of Targeted Therapy for Hematopoietic Malignancies, Changsha, Hunan, China.,Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - En Dong
- Blood Center, Changsha, Hunan, China
| | - Ruijuan Li
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China. .,Hunan Engineering Research Center of Targeted Therapy for Hematopoietic Malignancies, Changsha, Hunan, China. .,Institute of Molecular Hematology, Central South University, Changsha, Hunan, China.
| | - Zhao Cheng
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China. .,Hunan Engineering Research Center of Targeted Therapy for Hematopoietic Malignancies, Changsha, Hunan, China. .,Institute of Molecular Hematology, Central South University, Changsha, Hunan, China.
| | - Hongling Peng
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Engineering Research Center of Targeted Therapy for Hematopoietic Malignancies, Changsha, Hunan, China.,Institute of Molecular Hematology, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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7
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Mierziak J, Kostyn K, Boba A, Czemplik M, Kulma A, Wojtasik W. Influence of the Bioactive Diet Components on the Gene Expression Regulation. Nutrients 2021; 13:3673. [PMID: 34835928 PMCID: PMC8619229 DOI: 10.3390/nu13113673] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 02/07/2023] Open
Abstract
Diet bioactive components, in the concept of nutrigenetics and nutrigenomics, consist of food constituents, which can transfer information from the external environment and influence gene expression in the cell and thus the function of the whole organism. It is crucial to regard food not only as the source of energy and basic nutriments, crucial for living and organism development, but also as the factor influencing health/disease, biochemical mechanisms, and activation of biochemical pathways. Bioactive components of the diet regulate gene expression through changes in the chromatin structure (including DNA methylation and histone modification), non-coding RNA, activation of transcription factors by signalling cascades, or direct ligand binding to the nuclear receptors. Analysis of interactions between diet components and human genome structure and gene activity is a modern approach that will help to better understand these relations and will allow designing dietary guidances, which can help maintain good health.
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Affiliation(s)
- Justyna Mierziak
- Faculty of Biotechnology, University of Wrocław, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland; (A.B.); (M.C.); (A.K.)
| | - Kamil Kostyn
- Department of Genetics, Plant Breeding & Seed Production, Faculty of Life Sciences and Technology, Wroclaw University of Environmental and Life Sciences, pl. Grunwaldzki 24A, 50-363 Wroclaw, Poland;
| | - Aleksandra Boba
- Faculty of Biotechnology, University of Wrocław, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland; (A.B.); (M.C.); (A.K.)
| | - Magdalena Czemplik
- Faculty of Biotechnology, University of Wrocław, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland; (A.B.); (M.C.); (A.K.)
| | - Anna Kulma
- Faculty of Biotechnology, University of Wrocław, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland; (A.B.); (M.C.); (A.K.)
| | - Wioleta Wojtasik
- Faculty of Biotechnology, University of Wrocław, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland; (A.B.); (M.C.); (A.K.)
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8
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Li TH, Qin C, Zhao BB, Cao HT, Yang XY, Wang YY, Li ZR, Zhou XT, Wang WB. Identification METTL18 as a Potential Prognosis Biomarker and Associated With Immune Infiltrates in Hepatocellular Carcinoma. Front Oncol 2021; 11:665192. [PMID: 34123827 PMCID: PMC8187872 DOI: 10.3389/fonc.2021.665192] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 05/06/2021] [Indexed: 12/20/2022] Open
Abstract
Methyltransferase-like 18 (METTL18), a METTL family member, is abundant in hepatocellular carcinoma (HCC). Studies have indicated the METTL family could regulate the progress of diverse malignancies while the role of METTL18 in HCC remains unclear. Data of HCC patients were acquired from the cancer genome atlas (TCGA) and gene expression omnibus (GEO). The expression level of METTL18 in HCC patients was compared with normal liver tissues by Wilcoxon test. Then, the logistic analysis was used to estimate the correlation between METTL18 and clinicopathological factors. Besides, Gene Ontology (GO), Gene Set Enrichment Analysis (GSEA), and single-sample Gene Set Enrichment Analysis (ssGSEA) were used to explore relevant functions and quantify the degree of immune infiltration for METTL18. Univariate and Multivariate Cox analyses and Kaplan-Meier analysis were used to estimate the association between METTL18 and prognosis. Besides, by cox multivariate analysis, a nomogram was conducted to forecast the influence of METTL18 on survival rates. METTL18-high was associated with Histologic grade, T stage, Pathologic stage, BMI, Adjacent hepatic tissue inflammation, AFP, Vascular invasion, and TP53 status (P < 0.05). HCC patients with METTL18-high had a poor Overall-Survival [OS; hazard ratio (HR): 1.87, P < 0.001), Disease-Specific Survival (DSS, HR: 1.76, P = 0.015), and Progression-Free Interval (PFI, HR: 1.51, P = 0.006). Multivariate analysis demonstrated that METTL18 was an independent factor for OS (HR: 2.093, P < 0.001), DSS (HR: 2.404, P = 0.015), and PFI (HR: 1.133, P = 0.006). Based on multivariate analysis, the calibration plots and C-indexes of nomograms showed an efficacious predictive effect for HCC patients. GSEA demonstrated that METTL18-high could activate G2M checkpoint, E2F targets, KRAS signaling pathway, and Mitotic Spindle. There was a positive association between the METTL18 and abundance of innate immunocytes (T helper 2 cells) and a negative relation to the abundance of adaptive immunocytes (Dendritic cells, Cytotoxic cells etc.). Finally, we uncovered knockdown of METTL18 significantly suppressed the proliferation, invasion, and migration of HCC cells in vitro. This research indicates that METTL18 could be a novel biomarker to evaluate HCC patients' prognosis and an important regulator of immune responses in HCC.
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Affiliation(s)
- Tian-Hao Li
- Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.,Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Cheng Qin
- Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.,Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Bang-Bo Zhao
- Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.,Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Hong-Tao Cao
- Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.,Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Xiao-Ying Yang
- Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.,Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yuan-Yang Wang
- Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.,Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Ze-Ru Li
- Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.,Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Xing-Tong Zhou
- Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.,Department of Breast Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Wei-Bin Wang
- Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.,Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
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9
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Dixon G, Pan H, Yang D, Rosen BP, Jashari T, Verma N, Pulecio J, Caspi I, Lee K, Stransky S, Glezer A, Liu C, Rivas M, Kumar R, Lan Y, Torregroza I, He C, Sidoli S, Evans T, Elemento O, Huangfu D. QSER1 protects DNA methylation valleys from de novo methylation. Science 2021; 372:eabd0875. [PMID: 33833093 PMCID: PMC8185639 DOI: 10.1126/science.abd0875] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 02/23/2021] [Indexed: 12/12/2022]
Abstract
DNA methylation is essential to mammalian development, and dysregulation can cause serious pathological conditions. Key enzymes responsible for deposition and removal of DNA methylation are known, but how they cooperate to regulate the methylation landscape remains a central question. Using a knockin DNA methylation reporter, we performed a genome-wide CRISPR-Cas9 screen in human embryonic stem cells to discover DNA methylation regulators. The top screen hit was an uncharacterized gene, QSER1, which proved to be a key guardian of bivalent promoters and poised enhancers of developmental genes, especially those residing in DNA methylation valleys (or canyons). We further demonstrate genetic and biochemical interactions of QSER1 and TET1, supporting their cooperation to safeguard transcriptional and developmental programs from DNMT3-mediated de novo methylation.
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Affiliation(s)
- Gary Dixon
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
| | - Heng Pan
- Department of Physiology and Biophysics, Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Dapeng Yang
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
| | - Bess P Rosen
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
| | - Therande Jashari
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
| | - Nipun Verma
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
- Weill Graduate School of Medical Sciences at Cornell University-The Rockefeller University-Sloan Kettering Institute Tri-Institutional M.D.-Ph.D. Program, New York, NY 10065, USA
| | - Julian Pulecio
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
| | - Inbal Caspi
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
| | - Kihyun Lee
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Abigail Glezer
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
| | - Chang Liu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Marco Rivas
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Ritu Kumar
- Department of Surgery, Weill Cornell Medicine, New York, NY 10065, USA
| | - Yahui Lan
- Department of Surgery, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ingrid Torregroza
- Department of Surgery, Weill Cornell Medicine, New York, NY 10065, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Todd Evans
- Department of Surgery, Weill Cornell Medicine, New York, NY 10065, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA.
| | - Danwei Huangfu
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA.
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Li J, Deng Q, Fan W, Zeng Q, He H, Huang F. Melatonin-induced suppression of DNA methylation promotes odontogenic differentiation in human dental pulp cells. Bioengineered 2020; 11:829-840. [PMID: 32718272 PMCID: PMC8291816 DOI: 10.1080/21655979.2020.1795425] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/09/2020] [Accepted: 07/09/2020] [Indexed: 02/07/2023] Open
Abstract
Differentiation potency of human dental pulp cells (hDPCs) is essential for dentin regeneration. DNA methylation is one of the major epigenetic mechanisms and is suggested to involve in differentiation of hDPCs, the machinery of which includes DNA methyltransferase enzymes (DNMTs) and methyl-CpG-binding domain proteins (MBDs). Our previous study has found that melatonin (MT) promoted hDPC differentiation, but its mechanism remains elusive. We aimed to investigate the role of DNA methylation in the promotion of MT to differentiation of hDPCs in vitro. hDPCs were cultured in basal growth medium (CO) or odontogenic medium (OM) exposed to MT at different concentrations (0, 10-12, 10-10, 10-8, 10-6, 10-4 M). The cell growth was analyzed using Cell Counting Kit-8 assay, and mineralized tissue formation was measured using Alizarin red staining. The expression of the 10 genes (DNMT1, DNMT3A, DNMT3B, MBD1-6, MeCP2) was determined using real-time qPCR and western blotting. The abundance of MeCP2 in the nuclei was evaluated using immunofluorescence analysis. Global methylation level was tested using ELISA. We found that mineralized tissue formation significantly increased in OM with MT at 10-4 M, while the levels of MeCP2 and global DNA methylation level declined. The expression of MBD1, MBD3, and MBD4 significantly increased in OM alone, and the expession of DNMT1 and MBD2 was decreased. These results indicate that MT promotes odontogenic differentiation of hDPCs in vitro by regulating the levels of DNMT1, MeCP2, and global DNA methylation, suggesting that MT-induced DNA methylation machinery may play an important role in tooth regeneration.
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Affiliation(s)
- Jingzhou Li
- Department of Pediatric Dentistry, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Qianyi Deng
- Paediatric Dentistry and Orthodontics, Faculty of Dentistry, The University of Hong Kong, Hong Kong, China
| | - Wenguo Fan
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
- Department of Oral Anatomy and Physiology, Hospital of Stomatology,Guanghua School of Stomatology,Sun Yat-sen University, Guangzhou, China
| | - Qi Zeng
- Department of Pediatric Dentistry, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Hongwen He
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
- Department of Oral Anatomy and Physiology, Hospital of Stomatology,Guanghua School of Stomatology,Sun Yat-sen University, Guangzhou, China
| | - Fang Huang
- Department of Pediatric Dentistry, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
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11
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Kumari A, Bhawal S, Kapila S, Yadav H, Kapila R. Health-promoting role of dietary bioactive compounds through epigenetic modulations: a novel prophylactic and therapeutic approach. Crit Rev Food Sci Nutr 2020; 62:619-639. [PMID: 33081489 DOI: 10.1080/10408398.2020.1825286] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The epigenome is an overall epigenetic state of an organism, which is as important as that of the genome for normal development and functioning of an individual. Epigenetics involves heritable but reversible changes in gene expression through alterations in DNA methylation, histone modifications and regulation of non-coding RNAs in cells, without any change in the DNA sequence. Epigenetic changes are owned by various environmental factors including pollution, microbiota and diet, which have profound effects on epigenetic modifiers. The bioactive compounds present in the diet mainly include curcumin, resveratrol, catechins, quercetin, genistein, sulforaphane, epigallocatechin-3-gallate, alkaloids, vitamins, and peptides. Bioactive compounds released during fermentation by the action of microbes also have a significant effect on the host epigenome. Besides, recent studies have explored the new insights in vitamin's functions through epigenetic regulation. These bioactive compounds exert synergistic, preventive and therapeutic effects when combined as well as when used with chemotherapeutic agents. Therefore, these compounds have potential of therapeutic agents that could be used as "Epidrug" to treat many inflammatory diseases and various cancers where chemotherapy results have many side effects. In this review, the effect of diet derived bioactive compounds through epigenetic modulations on in vitro and in vivo models is discussed.
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Affiliation(s)
- Ankita Kumari
- Animal Biochemistry Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Shalaka Bhawal
- Animal Biochemistry Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Suman Kapila
- Animal Biochemistry Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Hariom Yadav
- Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Rajeev Kapila
- Animal Biochemistry Division, ICAR-National Dairy Research Institute, Karnal, India
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12
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曹 圆, 许 凯, 陈 玢, 王 奕, 李 炳, 李 朝, 徐 鹏. [Expression of DNMT3b in human bladder cancer tissue and its correlation with clinical prognosis]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2020; 40:1295-1300. [PMID: 32990224 PMCID: PMC7544589 DOI: 10.12122/j.issn.1673-4254.2020.09.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Indexed: 12/24/2022]
Abstract
OBJECTIVE To investigate the expression of DNMT3b in human bladder cancer tissues and its correlation with postoperative survival of patients with bladder cancer. METHODS Thirty-eight pairs of surgically resected human bladder cancer tissues and adjacent bladder tissues were detected by immunohistochemistry for DNMT3b expression, and the correlations of DNMT3b expression level were analyzed with the patients'age, gender, pathological grade, tumor size, T stage, lymph node metastasis and TNM stages. Kaplan-Meier survival analysis was performed to assess the effect of DNMT3b expression on survival outcomes of the patients. RESULTS High DNMT3b protein expression was detected in 63.16% of the bladder cancer tissues and in 13.16% of the adjacent tissues (P < 0.05). The expression level of DNMT3b was associated with the pathological grade (P=0.002), tumor size (P < 0.001), T stage (P < 0.001), lymphatic metastasis (P=0.039) and TNM stage (P < 0.001), but not with gender or age of the patients. Multivariate logistic regression analysis showed that the protein expression level of DNMT3b was correlated with tumor size (P=0.008) and TNM grades of the tumor (P=0.042). Kaplan-Meier analysis showed that the patients with a high DNMT3b expression had a significantly shorter overall survival than those with a low DNMT3b expression (P=0.021). CONCLUSIONS DNMT3b overexpression in bladder cancer is closely related to such clinicopathological factors as pathological grade, tumor size, T stage, lymphatic metastasis, and TNM stage and a shorter overall survival of the patients, suggesting the potential value of DNMT3b as a prognostic marker and a new therapeutic target for bladder cancer.
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Affiliation(s)
- 圆 曹
- />南方医科大学珠江医院泌尿外科,广东 广州 510282Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - 凯 许
- />南方医科大学珠江医院泌尿外科,广东 广州 510282Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - 玢屾 陈
- />南方医科大学珠江医院泌尿外科,广东 广州 510282Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - 奕铭 王
- />南方医科大学珠江医院泌尿外科,广东 广州 510282Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - 炳坤 李
- />南方医科大学珠江医院泌尿外科,广东 广州 510282Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - 朝明 李
- />南方医科大学珠江医院泌尿外科,广东 广州 510282Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - 鹏 徐
- />南方医科大学珠江医院泌尿外科,广东 广州 510282Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
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13
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Liu Y, Feng Y, Li Y, Hu Y, Zhang Q, Huang Y, Shi K, Ran C, Hou J, Zhou G, Wang X. Chlorogenic Acid Decreases Malignant Characteristics of Hepatocellular Carcinoma Cells by Inhibiting DNMT1 Expression. Front Pharmacol 2020; 11:867. [PMID: 32655395 PMCID: PMC7325898 DOI: 10.3389/fphar.2020.00867] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 05/26/2020] [Indexed: 12/15/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is the most common malignant tumor of the adult liver, exhibiting rapid progression and poor prognosis. Chlorogenic acid (CGA), a polyphenol, has several biological activities, including the suppression of liver cancer cell invasion and metastasis. Increased levels or alterations in the function of DNMT1 are associated with the inactivation of tumor suppressor genes. However, the CGA-affected DNMT1 expression mediated mechanism is still unclear. Methods The human hepatocellular carcinoma (HCC) HepG2 cells were treated with a positive control drug (5-AZA) or varying doses of CGA. DNA methyltransferase 1 (DNMT1) protein levels and other relevant proteins were evaluated using Western blotting and immunocytochemistry. Cell-cycle analysis was performed by flow cytometry-based PI staining, and cell viability was assessed using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The transwell invasion and wound healing assays were used to evaluate cell migration and invasion. In vivo proliferation of the HCC cells was detected. We investigated the expression of DNMT1, p53, p21, p-ERK, MMP-2, and MMP-9 in tumors using immunohistochemical analysis. Results Our results showed that CGA inhibited the proliferation, colony formation, invasion, and metastasis of HepG2 cells both in vitro and in vivo by down-regulating DNMT1 protein expression, which enhanced p53 and p21 activity, and resulting in a significant reduction in cell proliferation and metastasis. Moreover, CGA inactivated ERK1/2 and reduced MMP-2 and MMP-9 expression in HepG2 cells. Conclusions CGA can suppress liver cancer cell proliferation, invasion, and metastasis through several pathways. CGA could serve as a candidate chemopreventive agent for HCC.
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Affiliation(s)
- Yao Liu
- Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Ying Feng
- Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Yuxin Li
- Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Ying Hu
- Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Qun Zhang
- Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Yunyi Huang
- Department of Gastroenterology, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Ke Shi
- Department of Gastroenterology, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Chongping Ran
- Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Jie Hou
- Department of Gastroenterology, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Guiqin Zhou
- Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Xianbo Wang
- Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing, China
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14
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Liu D, Li W, Zhong F, Yin J, Zhou W, Li S, Sun X, Xu J, Li G, Wen Y, Wang J, Hong M, Cheng Z, Yuan J, Dai L, Sun J, Wang J, Qiu C, Wang G, Zou C. METTL7B Is Required for Cancer Cell Proliferation and Tumorigenesis in Non-Small Cell Lung Cancer. Front Pharmacol 2020; 11:178. [PMID: 32180726 PMCID: PMC7059849 DOI: 10.3389/fphar.2020.00178] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/10/2020] [Indexed: 11/13/2022] Open
Abstract
Lung cancer remains a leading cause of cancer-associated mortality worldwide, however, molecular mechanisms underlying lung cancer tumorigenesis and progression remain unknown. Here, we report evidence showing that one member of the mammalian methyltransferase-like family (METTL), METTL7B, is a potential molecular target for treatment of non-small cell lung cancer (NSCLC). METTL7B expression was elevated in the majority of NSCLC comparing to normal tissues. Increased expression of METTL7B contributed to advanced stages of tumor development and poor survival in NSCLC patients. Lentivirus-mediated shRNA silencing of METTL7B suppressed proliferation and tumorigenesis of cancer cells in vitro and in vivo. Investigation on gene expression profiles of NSCLC cells revealed that abundant cell cycle related genes were downregulated in the absence of METTL7B. Pathway enrichment analysis indicated that METTL7B participated in cell cycle regulation. Notably, CCND1, a key regulator for G1/S transition, was significantly decreased with the depletion of METTL7B, resulting in G0/G1 arrest, indicating that METTL7B is critical for cell cycle progression. Taken together, our findings implicate that METTL7B is essential for NSCLC development and progression. METTL7B might serve as a potential therapeutic target for NSCLC.
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Affiliation(s)
- Dongcheng Liu
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, the First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, China.,Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, China
| | - Wei Li
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, the First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, China.,Shenzhen Public Service Platform on Tumor Precision Medicine and Molecular Diagnosis, the Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China
| | - Fuhua Zhong
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, the First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, China
| | - Jianhua Yin
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Wei Zhou
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, the First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, China
| | - Shixuan Li
- Department of Thoracic Surgery, the First Affiliated Hospital of Southern University of Sciences and Technology, Shenzhen People's Hospital, Shenzhen, China
| | - Xuefeng Sun
- Department of Thoracic Surgery, the First Affiliated Hospital of Southern University of Sciences and Technology, Shenzhen People's Hospital, Shenzhen, China
| | - Jing Xu
- Department of Pathology, the First Affiliated Hospital of Southern University of Sciences and Technology, Shenzhen People's Hospital, Shenzhen, China
| | - Guofeng Li
- Department of Thoracic Surgery, the First Affiliated Hospital of Southern University of Sciences and Technology, Shenzhen People's Hospital, Shenzhen, China
| | - Yuxin Wen
- Department of Thoracic Surgery, the First Affiliated Hospital of Southern University of Sciences and Technology, Shenzhen People's Hospital, Shenzhen, China
| | - Jiaqing Wang
- Department of Thoracic Surgery, the First Affiliated Hospital of Southern University of Sciences and Technology, Shenzhen People's Hospital, Shenzhen, China
| | - Malin Hong
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, the First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, China
| | - Zhiqiang Cheng
- Shenzhen Public Service Platform on Tumor Precision Medicine and Molecular Diagnosis, the Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China.,Department of Pathology, the First Affiliated Hospital of Southern University of Sciences and Technology, Shenzhen People's Hospital, Shenzhen, China
| | - Jimin Yuan
- The Second Clinical Medical College of Jinan University, the First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, China
| | - Lingyun Dai
- The Second Clinical Medical College of Jinan University, the First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, China
| | - Jichao Sun
- The Second Clinical Medical College of Jinan University, the First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, China
| | - Jigang Wang
- The Second Clinical Medical College of Jinan University, the First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, China
| | - Chen Qiu
- Department of Respiratory and Critical Medicine, Shenzhen People's Hospital, Second Clinical Medical College, Jinan University, Shenzhen, China
| | - Guangsuo Wang
- Department of Thoracic Surgery, the First Affiliated Hospital of Southern University of Sciences and Technology, Shenzhen People's Hospital, Shenzhen, China
| | - Chang Zou
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, the First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, China.,Shenzhen Public Service Platform on Tumor Precision Medicine and Molecular Diagnosis, the Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China
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15
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The Pattern and Function of DNA Methylation in Fungal Plant Pathogens. Microorganisms 2020; 8:microorganisms8020227. [PMID: 32046339 PMCID: PMC7074731 DOI: 10.3390/microorganisms8020227] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/06/2020] [Accepted: 02/06/2020] [Indexed: 01/05/2023] Open
Abstract
To successfully infect plants and trigger disease, fungal plant pathogens use various strategies that are dependent on characteristics of their biology and genomes. Although pathogenic fungi are different from animals and plants in the genomic heritability, sequence feature, and epigenetic modification, an increasing number of phytopathogenic fungi have been demonstrated to share DNA methyltransferases (MTases) responsible for DNA methylation with animals and plants. Fungal plant pathogens predominantly possess four types of DNA MTase homologs, including DIM-2, DNMT1, DNMT5, and RID. Numerous studies have indicated that DNA methylation in phytopathogenic fungi mainly distributes in transposable elements (TEs), gene promoter regions, and the repetitive DNA sequences. As an important and heritable epigenetic modification, DNA methylation is associated with silencing of gene expression and transposon, and it is responsible for a wide range of biological phenomena in fungi. This review highlights the relevant reports and insights into the important roles of DNA methylation in the modulation of development, pathogenicity, and secondary metabolism of fungal plant pathogens. Recent evidences prove that there are massive links between DNA and histone methylation in fungi, and they commonly regulate fungal development and mycotoxin biosynthesis.
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16
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Feng L, Zhou J, Xia B, Tian BF. The Positive Effect of TET2 on the Osteogenic Differentiation of Human Adipose-Derived Mesenchymal Stem Cells. Cell Reprogram 2020; 22:3-13. [PMID: 31829736 DOI: 10.1089/cell.2019.0045] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Li Feng
- Department of Traumatic Orthopedics, Jining No. 1 People's Hospital, Jining, China
| | - Jing Zhou
- Department of Gynecology, Jining No. 1 People's Hospital, Jining, China
| | - Bo Xia
- Department of Traumatic Orthopedics, Jining No. 1 People's Hospital, Jining, China
| | - Bao-Fang Tian
- Department of Traumatic Orthopedics, Jining No. 1 People's Hospital, Jining, China
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17
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Ma TM, Sun LP, Dong NN, Sun MJ, Yuan Y. Protein expression trends of DNMT1 in gastrointestinal diseases: From benign to precancerous lesions to cancer. World J Gastrointest Oncol 2019; 11:1141-1150. [PMID: 31908719 PMCID: PMC6937440 DOI: 10.4251/wjgo.v11.i12.1141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 09/04/2019] [Accepted: 09/13/2019] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND In recent years, the incidence of gastrointestinal (GI) cancer in China has increased annually. Early detection and appropriate therapy are considered to be the key to treat GI cancer. DNMT1 takes an active part in the advancement of GI cancer, which will change as the disease progresses. But its expression characteristics in the dynamic variations of GI carcinogenesis are still unclear.
AIM To investigate the expression characteristics of DNMT1 in different GI diseases.
METHODS We detected the expression of DNMT1 in 650 cases of different GI diseases by immunohistochemistry, including 90 cases of chronic superficial gastritis (CSG), 72 cases of atrophic gastritis with intestinal metaplasia (AG/GIM), 54 cases of low-grade intraepithelial neoplasia (GLIN), 66 cases of high-grade intraepithelial neoplasia (GHIN), 71 cases of early gastric cancer (EGC), 90 cases of normal intestinal mucosa (NIM), 54 cases of intestinal low-grade intraepithelial neoplasia (ILIN), 71 cases of intestinal high-grade intraepithelial neoplasia (IHIN), and 82 cases of early colorectal cancer (ECRC).
RESULTS In the CSG group, all cases showed weakly positive or negative expression of DNMT1. However, in other four groups (AG/GIM, GLIN, GHIN, and EGC), the positive expression rate gradually increased with the severity of the diseases; the negative or weakly positive cases accounted for 55.56% (40/72), 38.89% (21/54), 1.52% (1/66), and 1.41% (1/71), respectively. Besides, the moderately positive cases were 44.44% (32/72), 57.41% (31/54), 80.30% (53/66), and 43.66% (31/71), respectively. The strongly positive cases only existed in the GLIN (3.70%, 2/54), GHIN (18.18%, 12/66), and EGC (54.93%, 39/71) groups. The differences between any two groups were statistically significant (P < 0.05). Similarly, in the NIM group, cases with weakly positive expression of DNMT1 were predominant (91.11%, 82/90), and the rest were moderately positive cases (8.89%, 8/90). In the ILIN, IHIN, and ECRC groups, the rates of cases with weak or negative expression of DNMT1 were 46.30% (25/54), 12.68% (9/71), and 4.88% (4/82), respectively; with moderately positive expression were 53.70% (29/54), 71.83% (51/71), and 34.15% (28/82), respectively; and with strongly positive expression were 0.00% (0/54), 15.49% (11/71), and 60.98% (50/82), respectively. The differences between any two groups were also statistically significant (P < 0.05).
CONCLUSION The overexpression of DNMT1 protein could effectively predict early GI cancers and severe precancerous lesions, which may have potential clinical application value.
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Affiliation(s)
- Tian-Miao Ma
- Department of Gastroenterology, the First Hospital of China Medical University, Shenyang 110001, Liaoning Province, China
| | - Li-Ping Sun
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang 110001, Liaoning Province, China
| | - Nan-Nan Dong
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang 110001, Liaoning Province, China
| | - Ming-Jun Sun
- Department of Gastroenterology, the First Hospital of China Medical University, Shenyang 110001, Liaoning Province, China
| | - Yuan Yuan
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang 110001, Liaoning Province, China
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18
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Veland N, Lu Y, Hardikar S, Gaddis S, Zeng Y, Liu B, Estecio MR, Takata Y, Lin K, Tomida MW, Shen J, Saha D, Gowher H, Zhao H, Chen T. DNMT3L facilitates DNA methylation partly by maintaining DNMT3A stability in mouse embryonic stem cells. Nucleic Acids Res 2019; 47:152-167. [PMID: 30321403 PMCID: PMC6326784 DOI: 10.1093/nar/gky947] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/05/2018] [Indexed: 12/12/2022] Open
Abstract
DNMT3L (DNMT3-like), a member of the DNMT3 family, has no DNA methyltransferase activity but regulates de novo DNA methylation. While biochemical studies show that DNMT3L is capable of interacting with both DNMT3A and DNMT3B and stimulating their enzymatic activities, genetic evidence suggests that DNMT3L is essential for DNMT3A-mediated de novo methylation in germ cells but is dispensable for de novo methylation during embryogenesis, which is mainly mediated by DNMT3B. How DNMT3L regulates DNA methylation and what determines its functional specificity are not well understood. Here we show that DNMT3L-deficient mouse embryonic stem cells (mESCs) exhibit downregulation of DNMT3A, especially DNMT3A2, the predominant DNMT3A isoform in mESCs. DNA methylation analysis of DNMT3L-deficient mESCs reveals hypomethylation at many DNMT3A target regions. These results confirm that DNMT3L is a positive regulator of DNA methylation, contrary to a previous report that, in mESCs, DNMT3L regulates DNA methylation positively or negatively, depending on genomic regions. Mechanistically, DNMT3L forms a complex with DNMT3A2 and prevents DNMT3A2 from being degraded. Restoring the DNMT3A protein level in DNMT3L-deficient mESCs partially recovers DNA methylation. Thus, our work uncovers a role for DNMT3L in maintaining DNMT3A stability, which contributes to the effect of DNMT3L on DNMT3A-dependent DNA methylation.
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Affiliation(s)
- Nicolas Veland
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Swanand Hardikar
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Sally Gaddis
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Yang Zeng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Bigang Liu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Marcos R Estecio
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Yoko Takata
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Kevin Lin
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Mary W Tomida
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Debapriya Saha
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA.,Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA.,Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Hongbo Zhao
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Hospital and Institute of Obstetrics and Gynecology, Fudan University, Shanghai, People's Republic of China
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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19
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Xu L, Hao H, Hao Y, Wei G, Li G, Ma P, Xu L, Ding N, Ma S, Chen AF, Jiang Y. Aberrant MFN2 transcription facilitates homocysteine-induced VSMCs proliferation via the increased binding of c-Myc to DNMT1 in atherosclerosis. J Cell Mol Med 2019; 23:4611-4626. [PMID: 31104361 PMCID: PMC6584594 DOI: 10.1111/jcmm.14341] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 02/28/2019] [Accepted: 04/05/2019] [Indexed: 12/19/2022] Open
Abstract
It is well‐established that homocysteine (Hcy) is an independent risk factor for atherosclerosis. Hcy can promote vascular smooth muscle cell (VSMC) proliferation, it plays a key role in neointimal formation and thus contribute to arteriosclerosis. However, the molecular mechanism on VSMCs proliferation underlying atherosclerosis is not well elucidated. Mitofusin‐2 (MFN2) is an important transmembrane GTPase in the mitochondrial outer membrane and it can block cells in the G0/G1 stage of the cell cycle. To investigate the contribution of aberrant MFN2 transcription in Hcy‐induced VSMCs proliferation and the underlying mechanisms. Cell cycle analysis revealed a decreased proportion of VSMCs in G0/G1 and an increased proportion in S phase in atherosclerotic plaque of APOE−/− mice with hyperhomocystinaemia (HHcy) as well as in VSMCs exposed to Hcy in vitro. The DNA methylation level of MFN2 promoter was obviously increased in VSMCs treated with Hcy, leading to suppressed promoter activity and low expression of MFN2. In addition, we found that the expression of c‐Myc was increased in atherosclerotic plaque and VSMCs treated with Hcy. Further study showed that c‐Myc indirectly regulates MFN2 expression is duo to the binding of c‐Myc to DNMT1 promoter up‐regulates DNMT1 expression leading to DNA hypermethylation of MFN2 promoter, thereby inhibits MFN2 expression in VSMCs treated with Hcy. In conclusion, our study demonstrated that Hcy‐induced hypermethylation of MFN2 promoter inhibits the transcription of MFN2, leading to VSMCs proliferation in plaque formation, and the increased binding of c‐Myc to DNMT1 promoter is a new and relevant molecular mechanism.
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Affiliation(s)
- Long Xu
- Ningxia Vascular Injury and Repair Research Key Laboratory, Ningxia Medical University, Yinchuan, China.,School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Hongyi Hao
- The People's Hospital in Ningxia Hui Autonomous Region, Yinchuan, China
| | - Yinju Hao
- The People's Hospital in Ningxia Hui Autonomous Region, Yinchuan, China
| | - Guo Wei
- Ningxia Vascular Injury and Repair Research Key Laboratory, Ningxia Medical University, Yinchuan, China.,School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Guizhong Li
- Ningxia Vascular Injury and Repair Research Key Laboratory, Ningxia Medical University, Yinchuan, China.,School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Pengjun Ma
- Ningxia Vascular Injury and Repair Research Key Laboratory, Ningxia Medical University, Yinchuan, China.,Department of Clinical Medicine, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Lingbo Xu
- Ningxia Vascular Injury and Repair Research Key Laboratory, Ningxia Medical University, Yinchuan, China.,School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Ning Ding
- Ningxia Vascular Injury and Repair Research Key Laboratory, Ningxia Medical University, Yinchuan, China.,School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Shengchao Ma
- Ningxia Vascular Injury and Repair Research Key Laboratory, Ningxia Medical University, Yinchuan, China.,School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Alex F Chen
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Yideng Jiang
- Ningxia Vascular Injury and Repair Research Key Laboratory, Ningxia Medical University, Yinchuan, China.,School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia, China
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20
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Laisné M, Gupta N, Kirsh O, Pradhan S, Defossez PA. Mechanisms of DNA Methyltransferase Recruitment in Mammals. Genes (Basel) 2018; 9:genes9120617. [PMID: 30544749 PMCID: PMC6316769 DOI: 10.3390/genes9120617] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 11/30/2018] [Accepted: 12/05/2018] [Indexed: 12/11/2022] Open
Abstract
DNA methylation is an essential epigenetic mark in mammals. The proper distribution of this mark depends on accurate deposition and maintenance mechanisms, and underpins its functional role. This, in turn, depends on the precise recruitment and activation of de novo and maintenance DNA methyltransferases (DNMTs). In this review, we discuss mechanisms of recruitment of DNMTs by transcription factors and chromatin modifiers—and by RNA—and place these mechanisms in the context of biologically meaningful epigenetic events. We present hypotheses and speculations for future research, and underline the fundamental and practical benefits of better understanding the mechanisms that govern the recruitment of DNMTs.
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Affiliation(s)
- Marthe Laisné
- Epigenetics and Cell Fate, UMR7216 CNRS, University Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France.
| | - Nikhil Gupta
- Epigenetics and Cell Fate, UMR7216 CNRS, University Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France.
| | - Olivier Kirsh
- Epigenetics and Cell Fate, UMR7216 CNRS, University Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France.
| | | | - Pierre-Antoine Defossez
- Epigenetics and Cell Fate, UMR7216 CNRS, University Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France.
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21
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Burgos-Morón E, Calderón-Montaño JM, Pastor N, Höglund A, Ruiz-Castizo Á, Domínguez I, López-Lázaro M, Hajji N, Helleday T, Mateos S, Orta ML. The Cockayne syndrome protein B is involved in the repair of 5-AZA-2'-deoxycytidine-induced DNA lesions. Oncotarget 2018; 9:35069-35084. [PMID: 30416680 PMCID: PMC6205548 DOI: 10.18632/oncotarget.26189] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 09/10/2018] [Indexed: 12/21/2022] Open
Abstract
The Cockayne Syndrome Protein B (CSB) plays an essential role in Transcription-Coupled Nucleotide Excision Repair (TC-NER) by recruiting repair proteins once transcription is blocked with a DNA lesion. In fact, CSB-deficient cells are unable to recover from transcription-blocking DNA lesions. 5-Aza-2′-deoxycytidine (5-azadC) is a nucleoside analogue that covalently traps DNA methyltransferases (DNMTs) onto DNA. This anticancer drug has a double mechanism of action: it reverts aberrant hypermethylation in tumour-suppressor genes, and it induces DNA damage. We have recently reported that Homologous Recombination and XRCC1/PARP play an important role in the repair of 5-azadC-induced DNA damage. However, the mechanisms involved in the repair of the DNMT adducts induced by azadC remain poorly understood. In this paper, we show for the first time the importance of CSB in the repair of azadC-induced DNA lesions. We propose a model in which CSB initiates a signalling pathway to repair transcription blocks induced by incorporated 5-azadC. Indeed, CSB-deficient cells treated with 5-azadC show a delay in the repair of trapped DNMT1, increased levels of DNA damage and reduced survival.
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Affiliation(s)
- Estefanía Burgos-Morón
- Department of Pharmacology, Faculty of Pharmacy, University of Seville, 41012 Seville, Spain
| | | | - Nuria Pastor
- Department of Cell Biology, Faculty of Biology, University of Seville, 41012 Seville, Spain
| | - Andreas Höglund
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-171 21 Stockholm, Sweden.,Present address: Sprint Bioscience AB, 141 57 Huddinge, Sweden
| | - Ángel Ruiz-Castizo
- Department of Cell Biology, Faculty of Biology, University of Seville, 41012 Seville, Spain
| | - Inmaculada Domínguez
- Department of Cell Biology, Faculty of Biology, University of Seville, 41012 Seville, Spain
| | - Miguel López-Lázaro
- Department of Pharmacology, Faculty of Pharmacy, University of Seville, 41012 Seville, Spain
| | - Nabil Hajji
- Department of Medicine, Division of Experimental Medicine, Centre for Pharmacology & Therapeutics, Toxicology Unit, Imperial College London, Hammersmith Campus, London, W12 0NN UK
| | - Thomas Helleday
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-171 21 Stockholm, Sweden
| | - Santiago Mateos
- Department of Cell Biology, Faculty of Biology, University of Seville, 41012 Seville, Spain
| | - Manuel Luis Orta
- Department of Cell Biology, Faculty of Biology, University of Seville, 41012 Seville, Spain
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22
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Xiong J, Ding N, Gao T, Wang Y, Guo W, Zhang H, Ma X, Li F, Sun J, Yang X, Wu K, Zhang H, Jiang Y. Hypermethylation of endoplasmic reticulum disulfide oxidase 1α leads to trophoblast cell apoptosis through endoplasmic reticulum stress in preeclampsia. J Cell Biochem 2018; 119:8588-8599. [PMID: 30058081 DOI: 10.1002/jcb.27101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 04/27/2018] [Indexed: 12/16/2022]
Abstract
Abnormal trophoblast cell apoptosis is implicated in the pathogenesis of pregnancy-related disorders including preeclampsia (PE), and endoplasmic reticulum (ER) stress has been considered as a novel pathway in the regulation of cell apoptosis. In this study, we observed that both apoptosis and ER stress are triggered in trophoblast cells under hypoxia as well as in the placenta of PE rats. Quantitative polymerase chain reaction and Western blot analysis showed that the expression of endoplasmic reticulum disulfide oxidase 1α (ERO1α) is suppressed in trophoblast cells under hypoxia due to the hypermethylation of the ERO1α promoter region, and the inhibition of ERO1α expression plays an important role in ER stress and trophoblast cell apoptosis. Furthermore, we found that DNA methyltransferase 1 (DNMT1) is a key methyltransferase for DNA methylation in the regulation of ERO1α expression, and the binding level of DNMT1 to the ERO1α promoter is markedly elevated under hypoxia although DNMT1 expression is inhibited by hypoxia, suggesting that the binding level of DNMT1 to the ERO1α promoter region rather than the DNMT1 expression level contributes to the hypermethylation of ERO1α. Taken together, these results demonstrate that the hypermethylation of ERO1α mediated by increased binding of DNMT1 to the ERO1α promoter leads to trophoblast cell apoptosis through ER stress in the placenta of PE rats, which shed insight into the etiology of PE and might present a validated therapeutic target for the treatment of PE.
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Affiliation(s)
- Jiantuan Xiong
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Ning Ding
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia, China.,Ningxia Key Laboratory of Vascular Injury and Repair Research, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Tingting Gao
- Ningxia Key Laboratory of Vascular Injury and Repair Research, Ningxia Medical University, Yinchuan, Ningxia, China.,Department of Clinical Medicine, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Yanhua Wang
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia, China.,Ningxia Key Laboratory of Vascular Injury and Repair Research, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Wei Guo
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia, China.,Ningxia Key Laboratory of Vascular Injury and Repair Research, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Hui Zhang
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia, China.,Ningxia Key Laboratory of Vascular Injury and Repair Research, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Xiaoli Ma
- Ningxia Key Laboratory of Vascular Injury and Repair Research, Ningxia Medical University, Yinchuan, Ningxia, China.,Department of Clinical Medicine, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Fan Li
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia, China.,Ningxia Key Laboratory of Vascular Injury and Repair Research, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Jianmin Sun
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia, China.,Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Xiaoling Yang
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia, China.,Ningxia Key Laboratory of Vascular Injury and Repair Research, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Kai Wu
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Huiping Zhang
- Department of Prenatal Diagnosis Center, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
| | - Yideng Jiang
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia, China.,Ningxia Key Laboratory of Vascular Injury and Repair Research, Ningxia Medical University, Yinchuan, Ningxia, China
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23
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SanMiguel JM, Bartolomei MS. DNA methylation dynamics of genomic imprinting in mouse development. Biol Reprod 2018; 99:252-262. [PMID: 29462489 PMCID: PMC6044325 DOI: 10.1093/biolre/ioy036] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/31/2018] [Accepted: 02/07/2018] [Indexed: 01/05/2023] Open
Abstract
DNA methylation is an essential epigenetic mark crucial for normal mammalian development. This modification controls the expression of a unique class of genes, designated as imprinted, which are expressed monoallelically and in a parent-of-origin-specific manner. Proper parental allele-specific DNA methylation at imprinting control regions (ICRs) is necessary for appropriate imprinting. Processes that deregulate DNA methylation of imprinted loci cause disease in humans. DNA methylation patterns dramatically change during mammalian development: first, the majority of the genome, with the exception of ICRs, is demethylated after fertilization, and subsequently undergoes genome-wide de novo DNA methylation. Secondly, after primordial germ cells are specified in the embryo, another wave of demethylation occurs, with ICR demethylation occurring late in the process. Lastly, ICRs reacquire DNA methylation imprints in developing germ cells. We describe the past discoveries and current literature defining these crucial dynamics in relation to imprinted genes and the rest of the genome.
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Affiliation(s)
- Jennifer M SanMiguel
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Marisa S Bartolomei
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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24
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Xu Y, Su D, Zhu L, Zhang S, Ma S, Wu K, Yuan Q, Lin N. S-allylcysteine suppresses ovarian cancer cell proliferation by DNA methylation through DNMT1. J Ovarian Res 2018; 11:39. [PMID: 29759079 PMCID: PMC5952516 DOI: 10.1186/s13048-018-0412-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/03/2018] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The anti-tumor effects of S-allylcysteine (SAC), a water-soluble garlic derivative, on human ovarian cancer cells have been previous studied in vitro and in vivo models but the precise epigenetic molecular mechanisms are still unclear. This study aimed to investigate the epigenetic mechanism of SAC. METHODS Human epithelial ovarian cancer cell line A2780 was selected. Cell proliferation and cell cycle was analyzed. DNA methylation, DNA methyltransferase (DNMT) activity, tumor suppressor gene expressions, as well as protein expression were analyzed. RESULTS SAC could inhibit the proliferation of A2780 cells in dose- and time-dependent manners (the IC50 was 16.25 mmol/L and 5.25 mmol/L at 48 h and 72 h). Treatment of A2780 cells with SAC resulted in G1/S phase arrest. SAC treatment decreased global DNA methylation levels in A2780 cells in a dose-dependent manner. SAC decreased the levels of 5-methylcytosine, DNMT activity, messenger RNA (mRNA) and protein levels of DNMT1. Additionally, SAC treatment resulted in re-expression of the mRNA and proteins of silenced tumor suppressor gene CDKN1A accompany with reduced cell division control 2 expression. CONCLUSION Our data indicated the potential therapeutic effects of SAC on the human ovarian carcinoma cell line A2780 in vitro. The epigenetic mechanism of action of SAC may have important implications for epigenetic therapy.
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Affiliation(s)
- Yasi Xu
- Hangzhou Translational Medicine Research Center, Zhejiang Chinese Medical University, Hangzhou First People's Hospital, No.261 Huansha Road, Shangcheng District, Hangzhou, 310006, China.,College of Pharmaceutical Science, Zhejiang Chinese Medical University, No.548 Binwen Road, Binjiang District, Hangzhou, 310053, China
| | - Dan Su
- Department of Pathology, Zhejiang Cancer Hospital, No.38, Guangji Road, Hangzhou, 310022, China
| | - Lucheng Zhu
- Department of Oncology, Hangzhou Cancer Hospital, No.34, Yanguan Road, Hangzhou, 310002, China
| | - Shirong Zhang
- Hangzhou Translational Medicine Research Center, Zhejiang Chinese Medical University, Hangzhou First People's Hospital, No.261 Huansha Road, Shangcheng District, Hangzhou, 310006, China
| | - Shenglin Ma
- Hangzhou Translational Medicine Research Center, Zhejiang Chinese Medical University, Hangzhou First People's Hospital, No.261 Huansha Road, Shangcheng District, Hangzhou, 310006, China
| | - Kan Wu
- Department of Oncology, Hangzhou Cancer Hospital, No.34, Yanguan Road, Hangzhou, 310002, China
| | - Qiang Yuan
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, No.548 Binwen Road, Binjiang District, Hangzhou, 310053, China.
| | - Nengming Lin
- Hangzhou Translational Medicine Research Center, Zhejiang Chinese Medical University, Hangzhou First People's Hospital, No.261 Huansha Road, Shangcheng District, Hangzhou, 310006, China.
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25
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Zhang S, Li J, Li J, Yang Y, Kang X, Li Y, Wu X, Zhu Q, Zhou Y, Hu Y. Up-regulation of microRNA-203 in influenza A virus infection inhibits viral replication by targeting DR1. Sci Rep 2018; 8:6797. [PMID: 29717211 PMCID: PMC5931597 DOI: 10.1038/s41598-018-25073-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 04/13/2018] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNA molecules that play important roles in various biological processes. Much evidence shows that miRNAs are closely associated with numerous virus infections; however, involvement of cellular miRNAs in influenza A virus (IAV) infection is unclear. Here, we found that expression of miR-203 was up-regulated markedly via two different mechanisms during IAV infection. First, we examined the effects of type I interferon induced by IAV on direct activation of miR-203 expression. Next, we showed that DNA demethylation within the miR-203 promoter region in A549 cells induced its up-regulation, and that expression of DNA methyltransferase 1 was down-regulated following H5N1 virus infection. Ectopic expression of miR-203 in turn inhibited H5N1 virus replication by targeting down-regulator of transcription 1 (DR1), which was identified as a novel target of miR-203. Silencing DR1 in miR-203 knockout cells using a specific siRNA inhibited replication of the H5N1 virus, an effect similar to that of miR-203. In summary, the data show that host cell expression of miR-203 is up-regulated upon IAV infection, which increases antiviral responses by suppressing a novel target gene, DR1. Thus, we have identified a novel mechanism underlying the relationship between miR-203 and IAV infection.
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Affiliation(s)
- Sen Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Jing Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Junfeng Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Yinhui Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Xiaoping Kang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Yuchang Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Xiaoyan Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Qingyu Zhu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Yusen Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China.
| | - Yi Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China.
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26
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Cunningham CM, Eghbali M. An Introduction to Epigenetics in Cardiovascular Development, Disease, and Sexualization. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1065:31-47. [PMID: 30051375 DOI: 10.1007/978-3-319-77932-4_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Epigenetic regulation of gene expression is integral to cell differentiation, development, and disease. Modes of epigenetic regulation-including DNA methylation, histone modifications, and ncRNA-based regulation-alter chromatin structure, promotor accessibility, and contribute to posttranscriptional modifications. In the cardiovascular system, epigenetic regulation is necessary for proper cardiovascular development and homeostasis, while epigenetic dysfunction is associated with improper cardiac development and disease.Early sexualization of tissues, including X-inactivation in females and maternal and paternal imprinting, is also orchestrated through epigenetic mechanisms. Furthermore, sex chromosomes encode various sex-specific genes involved in epigenetic regulation, while sex hormones can act as regulatory cofactors that may predispose or protect males and females against developing diseases with a marked sex bias.The following book chapter summarizes the field of epigenetics in the context of cardiovascular development and disease while also highlighting the role of epigenetic regulation as a powerful source of sex differences within the cardiovascular system.
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Affiliation(s)
- Christine M Cunningham
- Department of Anesthesiology and Perioperative Medicine, Division of Molecular Medicine, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA, USA
| | - Mansoureh Eghbali
- Department of Anesthesiology and Perioperative Medicine, Division of Molecular Medicine, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA, USA.
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DNMT1 overexpression predicting gastric carcinogenesis, subsequent progression and prognosis: a meta and bioinformatic analysis. Oncotarget 2017; 8:96396-96408. [PMID: 29221215 PMCID: PMC5707109 DOI: 10.18632/oncotarget.21480] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 09/20/2017] [Indexed: 02/07/2023] Open
Abstract
DNMT1 is important in maintaining DNA methylation, and participates in the oncogenesis via up- or down-regulation leading to hyper-methylation or hypo-methylation. In the meta and bioinformatic analysis, we found that DNMT1 expression was higher in gastric cancer, compared with normal (p < 0.00001), para-cancerous (p = 0.0004) and dysplasia (p < 0.00001) tissues. DNMT1 up-regulation was associated with gender (OR = 2.27, p = 0.006), differentiation (OR = 0.21, p = 0.01) and TNM stage (OR = 0.31, p = 0.0005). Through TCGA database, DNMT1 overexpression increased gastric cancer risk, but unrelated with clinicopathological parameters and prognosis. Kaplan-Meier plotter showed, an increasing expression of DNMT1 was positive for overall survival rates of patients with stage III and IV (P = 0.044; P = 0.047), N2 and N1-3 phases of lymph node metastasis (P = 0.023; P = 0.032), as well as those with or without distant metastasis (P = 0.0052; P = 0.021). For DNMT1 negative patients, the progression-free survival rates was better in patients with Her2+ or Her2- than positive ones (P = 0.00015; P = 0.031). Besides, surgery alone was effective for the overall survival rates in patients with DNMT1 high expression (P = 0.035), while 5-Fu was useful for those with low expression (P < 0.05). In conclusion, these findings provided evidence that DNMT1 expression might be employed as a potential marker to indicate gastric carcinogenesis and subsequent progression, even prognosis.
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