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Ding PF, Liu XZ, Peng Z, Cui Y, Liu Y, Zhang JT, Zhu Q, Wang J, Zhou Y, Gao YY, Hang CH, Li W. miR-93-5p impairs autophagy-lysosomal pathway via TET3 after subarachnoid hemorrhage. Exp Neurol 2024; 380:114904. [PMID: 39094768 DOI: 10.1016/j.expneurol.2024.114904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/01/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024]
Abstract
Intact autophagy-lysosomal pathway (ALP) in neuronal survival is crucial. However, it remains unclear whether ALP is intact after subarachnoid hemorrhage (SAH). Ten-eleven translocation (TET) 3 primarily regulates genes related to autophagy in neurons in neurodegenerative diseases. This study aims to investigate the role of TET3 in the ALP following SAH. The results indicate that the ALP is impaired after SAH, with suppressed autophagic flux and an increase in autophagosomes. This is accompanied by a decrease in TET3 expression. Activation of TET3 by α-KG can improve ALP function and neural function to some extent. Silencing TET3 in neurons significantly inhibited the ALP function and increased apoptosis. Inhibition of miR-93-5p, which is elevated after SAH, promotes TET3 expression. This suggests that the downregulation of TET3 after SAH is, at least in part, due to elevated miR-93-5p. This study clarifies the key role of TET3 in the functional impairment of the ALP after SAH. The preliminary exploration revealed that miR-93-5p could lead to the downregulation of TET3, which could be a new target for neuroprotective therapy after SAH.
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Affiliation(s)
- Peng-Fei Ding
- Department of Neurosurgery, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China; Neurosurgical Institute, Nanjing University, Nanjing, China
| | - Xun-Zhi Liu
- Department of Neurosurgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China; Neurosurgical Institute, Nanjing University, Nanjing, China
| | - Zheng Peng
- Department of Neurosurgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China; Neurosurgical Institute, Nanjing University, Nanjing, China
| | - Yue Cui
- Department of Neurosurgery, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China; Neurosurgical Institute, Nanjing University, Nanjing, China
| | - Yang Liu
- Department of Neurosurgery, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China; Neurosurgical Institute, Nanjing University, Nanjing, China
| | - Jia-Tong Zhang
- Department of Neurosurgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China; Neurosurgical Institute, Nanjing University, Nanjing, China
| | - Qi Zhu
- Department of Neurosurgery, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China; Neurosurgical Institute, Nanjing University, Nanjing, China
| | - Jie Wang
- Department of Neurosurgery, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China; Neurosurgical Institute, Nanjing University, Nanjing, China
| | - Yan Zhou
- Department of Neurosurgery, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China; Department of Neurosurgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China; Department of Neurosurgery, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China; Neurosurgical Institute, Nanjing University, Nanjing, China
| | - Yong-Yue Gao
- Department of Neurosurgery, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China; Department of Neurosurgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China; Department of Neurosurgery, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China; Neurosurgical Institute, Nanjing University, Nanjing, China.
| | - Chun-Hua Hang
- Department of Neurosurgery, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China; Department of Neurosurgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China; Department of Neurosurgery, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China; Neurosurgical Institute, Nanjing University, Nanjing, China.
| | - Wei Li
- Department of Neurosurgery, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China; Department of Neurosurgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China; Department of Neurosurgery, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China; Neurosurgical Institute, Nanjing University, Nanjing, China.
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2
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Yang T, Wei Q, Pang D, Cheng Y, Huang J, Lin J, Xiao Y, Jiang Q, Wang S, Li C, Shang H. Clinical and genetic characteristics of ALS patients with variants in genes regulating DNA methylation. J Neurol 2024; 271:5556-5566. [PMID: 38907861 DOI: 10.1007/s00415-024-12508-9] [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: 03/25/2024] [Revised: 06/04/2024] [Accepted: 06/09/2024] [Indexed: 06/24/2024]
Abstract
BACKGROUND Aberrant DNA methylation alterations are implicated in amyotrophic lateral sclerosis (ALS). Nevertheless, the influence of genetic variants in genes regulating DNA methylation on ALS patients is not well understood. Therefore, we aim to provide a comprehensive variant profile of genes related to DNA methylation (DNMT1, DNMT3A, DNMT3B, DNMT3L) and demethylation (TET1, TET2, TET3, TDG) and to investigate the association of these variants with ALS. METHODS Variants were screened in a cohort of 2240 ALS patients from Southwest China, using controls from the Genome Aggregation Database (n = 9976) and the China Metabolic Analytics Project (n = 10,588). The over-representation of rare variants and their association with ALS risk were evaluated using Fisher's exact test with Bonferroni correction at both allele and gene levels. Kaplan-Meier analysis and Cox regression analysis were employed to explore the relationship between variants and survival. RESULTS A total of 210 variants meeting the criteria were identified. Gene-based burden analysis identified a significant increase in ALS risk associated with rare variants in the TET2 gene (OR = 1.95, 95% CI = 1.29-2.88, P = 0.001). Survival analysis demonstrated that patients carrying variants in demethylation-related genes had a higher risk of death compared to those with methylation-related gene variants (HR = 1.29, 95% CI = 1.03-1.86, P = 0.039). CONCLUSIONS This study provides a genetic variant profile of genes involved in DNA methylation and demethylation regulation, along with the clinical characteristics of ALS patients carrying these variants. The findings offer genetic evidence implicating disrupted DNA methylation dynamics in ALS.
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Affiliation(s)
- Tianmi Yang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Qianqian Wei
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Dejiang Pang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Yangfan Cheng
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Jingxuan Huang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Junyu Lin
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Yi Xiao
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Qirui Jiang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Shichan Wang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Chunyu Li
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China.
| | - Huifang Shang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China.
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3
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Yang Q, Cao Q, Yu Y, Lai X, Feng J, Li X, Jiang Y, Sun Y, Zhou ZW, Li X. Epigenetic and transcriptional landscapes during cerebral cortex development in a microcephaly mouse model. J Genet Genomics 2024; 51:419-432. [PMID: 37923173 DOI: 10.1016/j.jgg.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/07/2023]
Abstract
The cerebral cortex is a pivotal structure integral to advanced brain functions within the mammalian central nervous system. DNA methylation and hydroxymethylation play important roles in regulating cerebral cortex development. However, it remains unclear whether abnormal cerebral cortex development, such as microcephaly, could rescale the epigenetic landscape, potentially contributing to dysregulated gene expression during brain development. In this study, we characterize and compare the DNA methylome/hydroxymethylome and transcriptome profiles of the cerebral cortex across several developmental stages in wild-type (WT) mice and Mcph1 knockout (Mcph1-del) mice with severe microcephaly. Intriguingly, we discover a global reduction of 5'-hydroxymethylcytosine (5hmC) level, primarily in TET1-binding regions, in Mcph1-del mice compared to WT mice during juvenile and adult stages. Notably, genes exhibiting diminished 5hmC levels and concurrently decreased expression are essential for neurodevelopment and brain functions. Additionally, genes displaying a delayed accumulation of 5hmC in Mcph1-del mice are significantly associated with the establishment and maintenance of the nervous system during the adult stage. These findings reveal that aberrant cerebral cortex development in the early stages profoundly alters the epigenetic regulation program, which provides unique insights into the molecular mechanisms underpinning diseases related to cerebral cortex development.
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Affiliation(s)
- Qing Yang
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China; Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Qiang Cao
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yue Yu
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Xianxin Lai
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jiahao Feng
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Xinjie Li
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yinan Jiang
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yazhou Sun
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China; Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Zhong-Wei Zhou
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China.
| | - Xin Li
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China; Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China.
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4
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Caldwell BA, Li L. Epigenetic regulation of innate immune dynamics during inflammation. J Leukoc Biol 2024; 115:589-606. [PMID: 38301269 PMCID: PMC10980576 DOI: 10.1093/jleuko/qiae026] [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: 12/11/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/03/2024] Open
Abstract
Innate immune cells play essential roles in modulating both immune defense and inflammation by expressing a diverse array of cytokines and inflammatory mediators, phagocytizing pathogens to promote immune clearance, and assisting with the adaptive immune processes through antigen presentation. Rudimentary innate immune "memory" states such as training, tolerance, and exhaustion develop based on the nature, strength, and duration of immune challenge, thereby enabling dynamic transcriptional reprogramming to alter present and future cell behavior. Underlying transcriptional reprogramming are broad changes to the epigenome, or chromatin alterations above the level of DNA sequence. These changes include direct modification of DNA through cytosine methylation as well as indirect modifications through alterations to histones that comprise the protein core of nucleosomes. In this review, we will discuss recent advances in our understanding of how these epigenetic changes influence the dynamic behavior of the innate immune system during both acute and chronic inflammation, as well as how stable changes to the epigenome result in long-term alterations of innate cell behavior related to pathophysiology.
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Affiliation(s)
- Blake A. Caldwell
- Department of Biological Sciences, Virginia Tech, 970 Washington St. SW, Blacksburg, VA 24061-0910, USA
| | - Liwu Li
- Department of Biological Sciences, Virginia Tech, 970 Washington St. SW, Blacksburg, VA 24061-0910, USA
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5
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Wang Z, Ma H, Nasir A, Liu S, Li Z, Tao F, Bai Q. TET1-mediated epigenetic regulation of tumor necrosis factor-α in trigeminal ganglia contributes to chronic temporomandibular joint pain. Life Sci 2024; 336:122283. [PMID: 37993094 DOI: 10.1016/j.lfs.2023.122283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/15/2023] [Accepted: 11/19/2023] [Indexed: 11/24/2023]
Abstract
Chronic temporomandibular joint (TMJ) pain profoundly affects patients' quality of life. Trigeminal tumor necrosis factor-α (TNFα) plays a pivotal role in mediating TMJ pain in mice, yet the underlying epigenetic mechanisms remain enigmatic. To unravel these epigenetic intricacies, we employed a multifaceted approach. Hydroxymethylated DNA immunoprecipitation (hMeDIP) and chromatin immunoprecipitation (ChIP) followed by qPCR were employed to investigate the demethylation of TNFα gene (Tnfa) and its regulation by ten-eleven translocation methylcytosine dioxygenase 1 (TET1) in a chronic TMJ pain mouse model. The global levels of 5-hydroxymethylcytosine (5hmc) and percentage of 5hmc at the Tnfa promoter region were measured in the trigeminal ganglia (TG) and spinal trigeminal nucleus caudalis (Sp5C) following complete Freund's adjuvant (CFA) or saline treatment. TET1 knockdown and pain behavioral testing were conducted to ascertain the role of TET1-mediated epigenetic regulation of TNFα in the pathogenesis of chronic TMJ pain. Our finding revealed an increase in 5hmc at the Tnfa promoter region in both TG and Sp5C of CFA-treated mice. TET1 was upregulated in the mouse TG, and the ChIP result showed TET1 direct binding to the Tnfa promoter, with higher efficiency in the CFA-treated group. Immunofluorescence revealed the predominant expression of TET1 in trigeminal neurons. TET1 knockdown in the TG significantly reversed CFA-induced TNFα upregulation and alleviated chronic TMJ pain. In conclusion, our study implicates TET1 as a vital epigenetic regulator contributing to chronic inflammatory TMJ pain via trigeminal TNFα signaling. Targeting TET1 holds promise for epigenetic interventions in TMJ pain management.
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Affiliation(s)
- Zhitao Wang
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Heng Ma
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Abdul Nasir
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China; Medical Research Center, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Sufang Liu
- Department of Biomedical Sciences, Texas A&M University College of Dentistry, Dallas, TX, USA
| | - Zhisong Li
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Feng Tao
- Department of Biomedical Sciences, Texas A&M University College of Dentistry, Dallas, TX, USA.
| | - Qian Bai
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China; Medical Research Center, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
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6
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Zhang XJ, Han BB, Shao ZY, Yan R, Gao J, Liu T, Jin ZY, Lai W, Xu ZM, Wang CH, Zhang F, Gu C, Wang Y, Wang H, Walsh CP, Guo F, Xu GL, Du YR. Auto-suppression of Tet dioxygenases protects the mouse oocyte genome from oxidative demethylation. Nat Struct Mol Biol 2024; 31:42-53. [PMID: 38177668 DOI: 10.1038/s41594-023-01125-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 09/14/2023] [Indexed: 01/06/2024]
Abstract
DNA cytosine methylation plays a vital role in repressing retrotransposons, and such derepression is linked with developmental failure, tumorigenesis and aging. DNA methylation patterns are formed by precisely regulated actions of DNA methylation writers (DNA methyltransferases) and erasers (TET, ten-eleven translocation dioxygenases). However, the mechanisms underlying target-specific oxidation of 5mC by TET dioxygenases remain largely unexplored. Here we show that a large low-complexity domain (LCD), located in the catalytic part of Tet enzymes, negatively regulates the dioxygenase activity. Recombinant Tet3 lacking LCD is shown to be hyperactive in converting 5mC into oxidized species in vitro. Endogenous expression of the hyperactive Tet3 mutant in mouse oocytes results in genome-wide 5mC oxidation. Notably, the occurrence of aberrant 5mC oxidation correlates with a consequent loss of the repressive histone mark H3K9me3 at ERVK retrotransposons. The erosion of both 5mC and H3K9me3 causes ERVK derepression along with upregulation of their neighboring genes, potentially leading to the impairment of oocyte development. These findings suggest that Tet dioxygenases use an intrinsic auto-regulatory mechanism to tightly regulate their enzymatic activity, thus achieving spatiotemporal specificity of methylome reprogramming, and highlight the importance of methylome integrity for development.
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Affiliation(s)
- Xiao-Jie Zhang
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Bin-Bin Han
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhen-Yu Shao
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Rui Yan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Juan Gao
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ting Liu
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Zi-Yang Jin
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Weiyi Lai
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Zhi-Mei Xu
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chao-Han Wang
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fengjuan Zhang
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chan Gu
- Changping Laboratory, Beijing, China
| | - Yin Wang
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Chinese Academy of Medical Sciences (RU069) and Zhongshan-Xuhui Hospital, Medical College of Fudan University, Shanghai, China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Colum P Walsh
- Genomic Medicine Research Group, Biomedical Sciences, Ulster University, Coleraine, UK
- Department of Cell Biology, Institute for Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Fan Guo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Guo-Liang Xu
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Chinese Academy of Medical Sciences (RU069) and Zhongshan-Xuhui Hospital, Medical College of Fudan University, Shanghai, China.
| | - Ya-Rui Du
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
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7
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Kaplánek R, Kejík Z, Hajduch J, Veselá K, Kučnirová K, Skaličková M, Venhauerová A, Hosnedlová B, Hromádka R, Dytrych P, Novotný P, Abramenko N, Antonyová V, Hoskovec D, Babula P, Masařík M, Martásek P, Jakubek M. TET protein inhibitors: Potential and limitations. Biomed Pharmacother 2023; 166:115324. [PMID: 37598475 DOI: 10.1016/j.biopha.2023.115324] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/31/2023] [Accepted: 08/10/2023] [Indexed: 08/22/2023] Open
Abstract
TET proteins (methylcytosine dioxygenases) play an important role in the regulation of gene expression. Dysregulation of their activity is associated with many serious pathogenic states such as oncological diseases. Regulation of their activity by specific inhibitors could represent a promising therapeutic strategy. Therefore, this review describes various types of TET protein inhibitors in terms of their inhibitory mechanism and possible applicability. The potential and possible limitations of this approach are thoroughly discussed in the context of TET protein functionality in living systems. Furthermore, possible therapeutic strategies based on the inhibition of TET proteins are presented and evaluated, especially in the field of oncological diseases.
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Affiliation(s)
- Robert Kaplánek
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Zdeněk Kejík
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Jan Hajduch
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Kateřina Veselá
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Kateřina Kučnirová
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Markéta Skaličková
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Anna Venhauerová
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Božena Hosnedlová
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Róbert Hromádka
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Petr Dytrych
- 1st Department of Surgery-Department of Abdominal, Thoracic Surgery and Traumatology, First Faculty of Medicine, Charles University and General University Hospital, U Nemocnice 2, 121 08 Prague, Czech Republic
| | - Petr Novotný
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Nikita Abramenko
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Veronika Antonyová
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - David Hoskovec
- 1st Department of Surgery-Department of Abdominal, Thoracic Surgery and Traumatology, First Faculty of Medicine, Charles University and General University Hospital, U Nemocnice 2, 121 08 Prague, Czech Republic
| | - Petr Babula
- Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Michal Masařík
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Pavel Martásek
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic.
| | - Milan Jakubek
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic.
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8
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Wołowiec A, Wołowiec Ł, Grześk G, Jaśniak A, Osiak J, Husejko J, Kozakiewicz M. The Role of Selected Epigenetic Pathways in Cardiovascular Diseases as a Potential Therapeutic Target. Int J Mol Sci 2023; 24:13723. [PMID: 37762023 PMCID: PMC10531432 DOI: 10.3390/ijms241813723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/03/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Epigenetics is a rapidly developing science that has gained a lot of interest in recent years due to the correlation between characteristic epigenetic marks and cardiovascular diseases (CVDs). Epigenetic modifications contribute to a change in gene expression while maintaining the DNA sequence. The analysis of these modifications provides a thorough insight into the cardiovascular system from its development to its further functioning. Epigenetics is strongly influenced by environmental factors, including known cardiovascular risk factors such as smoking, obesity, and low physical activity. Similarly, conditions affecting the local microenvironment of cells, such as chronic inflammation, worsen the prognosis in cardiovascular diseases and additionally induce further epigenetic modifications leading to the consolidation of unfavorable cardiovascular changes. A deeper understanding of epigenetics may provide an answer to the continuing strong clinical impact of cardiovascular diseases by improving diagnostic capabilities, personalized medical approaches and the development of targeted therapeutic interventions. The aim of the study was to present selected epigenetic pathways, their significance in cardiovascular diseases, and their potential as a therapeutic target in specific medical conditions.
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Affiliation(s)
- Anna Wołowiec
- Department of Geriatrics, Division of Biochemistry and Biogerontology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Łukasz Wołowiec
- Department of Cardiology and Clinical Pharmacology, Faculty of Health Sciences, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Grzegorz Grześk
- Department of Cardiology and Clinical Pharmacology, Faculty of Health Sciences, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Albert Jaśniak
- Department of Cardiology and Clinical Pharmacology, Faculty of Health Sciences, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Joanna Osiak
- Department of Cardiology and Clinical Pharmacology, Faculty of Health Sciences, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Jakub Husejko
- Department of Cardiology and Clinical Pharmacology, Faculty of Health Sciences, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Mariusz Kozakiewicz
- Department of Geriatrics, Division of Biochemistry and Biogerontology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
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9
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Halawani D, Wang Y, Ramakrishnan A, Estill M, He X, Shen L, Friedel RH, Zou H. Circadian clock regulator Bmal1 gates axon regeneration via Tet3 epigenetics in mouse sensory neurons. Nat Commun 2023; 14:5165. [PMID: 37620297 PMCID: PMC10449865 DOI: 10.1038/s41467-023-40816-7] [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: 10/25/2022] [Accepted: 08/11/2023] [Indexed: 08/26/2023] Open
Abstract
Axon regeneration of dorsal root ganglia (DRG) neurons after peripheral axotomy involves reconfiguration of gene regulatory circuits to establish regenerative gene programs. However, the underlying mechanisms remain unclear. Here, through an unbiased survey, we show that the binding motif of Bmal1, a central transcription factor of the circadian clock, is enriched in differentially hydroxymethylated regions (DhMRs) of mouse DRG after peripheral lesion. By applying conditional deletion of Bmal1 in neurons, in vitro and in vivo neurite outgrowth assays, as well as transcriptomic profiling, we demonstrate that Bmal1 inhibits axon regeneration, in part through a functional link with the epigenetic factor Tet3. Mechanistically, we reveal that Bmal1 acts as a gatekeeper of neuroepigenetic responses to axonal injury by limiting Tet3 expression and restricting 5hmC modifications. Bmal1-regulated genes not only concern axon growth, but also stress responses and energy homeostasis. Furthermore, we uncover an epigenetic rhythm of diurnal oscillation of Tet3 and 5hmC levels in DRG neurons, corresponding to time-of-day effect on axon growth potential. Collectively, our studies demonstrate that targeting Bmal1 enhances axon regeneration.
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Affiliation(s)
- Dalia Halawani
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yiqun Wang
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Orthopedics, Second Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Aarthi Ramakrishnan
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Molly Estill
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xijing He
- Department of Orthopedics, Second Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
- Department of Orthopedics, Xi'an International Medical Center Hospital, Xi'an, China
| | - Li Shen
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Roland H Friedel
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hongyan Zou
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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10
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Cui W, Huang Z, Jin SG, Johnson J, Lau KH, Hostetter G, Pfeifer GP. Deficiency of the Polycomb Protein RYBP and TET Methylcytosine Oxidases Promotes Extensive CpG Island Hypermethylation and Malignant Transformation. Cancer Res 2023; 83:2480-2495. [PMID: 37272752 PMCID: PMC10391329 DOI: 10.1158/0008-5472.can-23-0269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/24/2023] [Accepted: 05/31/2023] [Indexed: 06/06/2023]
Abstract
Hypermethylation of CpG islands (CGI) is a common feature of cancer cells and predominantly affects Polycomb-associated genomic regions. Elucidating the underlying mechanisms leading to DNA hypermethylation in human cancer could help identify chemoprevention strategies. Here, we evaluated the role of Polycomb complexes and 5-methylcytosine (5mC) oxidases in protecting CGIs from DNA methylation and observed that four genes coding for components of Polycomb repressive complex 1 (PRC1) are downregulated in tumors. Inactivation of RYBP, a key activator of variant PRC1 complexes, in combination with all three 5mC oxidases (TET proteins) in nontumorigenic bronchial epithelial cells led to widespread hypermethylation of Polycomb-marked CGIs affecting almost 4,000 target genes, which closely resembled the DNA hypermethylation landscape observed in human squamous cell lung tumors. The RYBP- and TET-deficient cells showed methylation-associated aberrant regulation of cancer-relevant pathways, including defects in the Hippo tumor suppressor network. Notably, the quadruple knockout cells acquired a transformed phenotype, including anchorage-independent growth and formation of squamous cell carcinomas in mice. This work provides a mechanism promoting hypermethylation of CGIs and shows that such hypermethylation can lead to cell transformation. The breakdown of a two-pronged protection mechanism can be a route towards genome-wide hypermethylation of CGIs in tumors. SIGNIFICANCE Dysfunction of the Polycomb component RYBP in combination with loss of 5-methylcytosine oxidases promotes widespread hypermethylation of CpG islands in bronchial cells and induces tumorigenesis, resembling changes seen in human lung tumors.
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Affiliation(s)
- Wei Cui
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
| | - Zhijun Huang
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
| | - Seung-Gi Jin
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
| | - Jennifer Johnson
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
| | - Kin H. Lau
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, Michigan
| | - Galen Hostetter
- Pathology and Biorepository Core, Van Andel Institute, Grand Rapids, Michigan
| | - Gerd P. Pfeifer
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
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11
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Zhou J, Horton JR, Kaur G, Chen Q, Li X, Mendoza F, Wu T, Blumenthal RM, Zhang X, Cheng X. Biochemical and structural characterization of the first-discovered metazoan DNA cytosine-N4 methyltransferase from the bdelloid rotifer Adineta vaga. J Biol Chem 2023; 299:105017. [PMID: 37414145 PMCID: PMC10406627 DOI: 10.1016/j.jbc.2023.105017] [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: 05/26/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023] Open
Abstract
Much is known about the generation, removal, and roles of 5-methylcytosine (5mC) in eukaryote DNA, and there is a growing body of evidence regarding N6-methyladenine, but very little is known about N4-methylcytosine (4mC) in the DNA of eukaryotes. The gene for the first metazoan DNA methyltransferase generating 4mC (N4CMT) was reported and characterized recently by others, in tiny freshwater invertebrates called bdelloid rotifers. Bdelloid rotifers are ancient, apparently asexual animals, and lack canonical 5mC DNA methyltransferases. Here, we characterize the kinetic properties and structural features of the catalytic domain of the N4CMT protein from the bdelloid rotifer Adineta vaga. We find that N4CMT generates high-level methylation at preferred sites, (a/c)CG(t/c/a), and low-level methylation at disfavored sites, exemplified by ACGG. Like the mammalian de novo 5mC DNA methyltransferase 3A/3B (DNMT3A/3B), N4CMT methylates CpG dinucleotides on both DNA strands, generating hemimethylated intermediates and eventually fully methylated CpG sites, particularly in the context of favored symmetric sites. In addition, like DNMT3A/3B, N4CMT methylates non-CpG sites, mainly CpA/TpG, though at a lower rate. Both N4CMT and DNMT3A/3B even prefer similar CpG-flanking sequences. Structurally, the catalytic domain of N4CMT closely resembles the Caulobacter crescentus cell cycle-regulated DNA methyltransferase. The symmetric methylation of CpG, and similarity to a cell cycle-regulated DNA methyltransferase, together suggest that N4CMT might also carry out DNA synthesis-dependent methylation following DNA replication.
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Affiliation(s)
- Jujun Zhou
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Gundeep Kaur
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Qin Chen
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xuwen Li
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Fabian Mendoza
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Tao Wu
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA.
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
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12
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5-hydroxymethylcytosine stabilizes transcription by preventing aberrant initiation in gene bodies. Nat Genet 2023; 55:2-3. [PMID: 36593302 DOI: 10.1038/s41588-022-01253-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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13
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Arroyo M, Hastert FD, Zhadan A, Schelter F, Zimbelmann S, Rausch C, Ludwig AK, Carell T, Cardoso MC. Isoform-specific and ubiquitination dependent recruitment of Tet1 to replicating heterochromatin modulates methylcytosine oxidation. Nat Commun 2022; 13:5173. [PMID: 36056023 PMCID: PMC9440122 DOI: 10.1038/s41467-022-32799-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/15/2022] [Indexed: 01/26/2023] Open
Abstract
Oxidation of the epigenetic DNA mark 5-methylcytosine by Tet dioxygenases is an established route to diversify the epigenetic information, modulate gene expression and overall cellular (patho-)physiology. Here, we demonstrate that Tet1 and its short isoform Tet1s exhibit distinct nuclear localization during DNA replication resulting in aberrant cytosine modification levels in human and mouse cells. We show that Tet1 is tethered away from heterochromatin via its zinc finger domain, which is missing in Tet1s allowing its targeting to these regions. We find that Tet1s interacts with and is ubiquitinated by CRL4(VprBP). The ubiquitinated Tet1s is then recognized by Uhrf1 and recruited to late replicating heterochromatin. This leads to spreading of 5-methylcytosine oxidation to heterochromatin regions, LINE 1 activation and chromatin decondensation. In summary, we elucidate a dual regulation mechanism of Tet1, contributing to the understanding of how epigenetic information can be diversified by spatio-temporal directed Tet1 catalytic activity.
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Affiliation(s)
- María Arroyo
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Florian D. Hastert
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany ,grid.425396.f0000 0001 1019 0926Section AIDS and newly emerging pathogens, Paul Ehrlich Institute, Paul-Ehrlich-Str. 51-59, 63225 Langen, Germany
| | - Andreas Zhadan
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Florian Schelter
- grid.5252.00000 0004 1936 973XDepartment of Chemistry, Ludwig Maximilians University, Butenandstr. 5-13, 81377 Munich, Germany
| | - Susanne Zimbelmann
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Cathia Rausch
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany ,grid.16008.3f0000 0001 2295 9843Present Address: Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6, avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Anne K. Ludwig
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany ,grid.5253.10000 0001 0328 4908Present Address: Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
| | - Thomas Carell
- grid.5252.00000 0004 1936 973XDepartment of Chemistry, Ludwig Maximilians University, Butenandstr. 5-13, 81377 Munich, Germany
| | - M. Cristina Cardoso
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
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14
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Early Expression of Tet1 and Tet2 in Mouse Zygotes Altered DNA Methylation Status and Affected Embryonic Development. Int J Mol Sci 2022; 23:ijms23158495. [PMID: 35955629 PMCID: PMC9369288 DOI: 10.3390/ijms23158495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 02/01/2023] Open
Abstract
Ten-eleven translocation (Tet) dioxygenases can induce DNA demethylation by catalyzing 5-methylcytosine(5mC) to 5-hydroxymethylcytosine(5hmC), and play important roles during mammalian development. In mouse, Tet1 and Tet2 are not expressed in pronucleus-staged embryos and are not involved in the genomic demethylation of early zygotes. Here, we investigated the influence of Tet1 and Tet2 on methylation of parental genomes by ectopically expressing Tet1 and Tet2 in zygotes. Immunofluorescence staining showed a marked 5hmC increase in the maternal pronucleus after injection of Tet1 or Tet2 mRNA into zygotes. Whole-genome bisulfite sequencing further revealed that Tet2 greatly enhanced the global demethylation of both parental genomes, while Tet1 only promoted the paternal demethylation. Tet1 and Tet2 overexpression altered the DNA methylation across genomes, including various genic elements and germline-specific differently methylated regions. Tet2 exhibited overall stronger demethylation activity than Tet1. Either Tet1 or Tet2 overexpression impaired preimplantation embryonic development. These results demonstrated that early expression of Tet1 and Tet2 could substantially alter the zygotic methylation landscape and damage embryonic development. These findings provide new insights into understanding the function of Tet dioxygenases and the mechanism of DNA methylation in relation to embryogenesis.
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15
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Qi J, Cui D, Wu QN, Zhao Q, Chen ZH, Li L, Birchmeier W, Yu Y, Tao R. Targeting Wnt/β-Catenin Signaling by TET1/FOXO4 Inhibits Metastatic Spreading and Self-Renewal of Cancer Stem Cells in Gastric Cancer. Cancers (Basel) 2022; 14:cancers14133232. [PMID: 35805009 PMCID: PMC9264907 DOI: 10.3390/cancers14133232] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 12/19/2022] Open
Abstract
Simple Summary Metastasis is the main cause of death for patients suffering gastric cancer. Epithelial-mesenchymal transition (EMT) and cancer stem cells (CSC) are critical attributes of metastasis, both of which are regulated tightly by DNA methylation and Wnt/β-catenin signaling. In this study, we unveiled a novel TET1-FOXO4-β-catenin signaling cascade, in which TET1 inhibits β-catenin activity and its nuclear translocation through transactivating FOXO4 expression. TET1 expression can significantly inhibit EMT and stemness properties of gastric cancer cells, while knocking-down endogenous TET1 induces metastasis and enhances self-renewal of CSCs by activating canonical Wnt signaling, which could be fully rescued by modulating FOXO4 expression. Our data also showed that low expression of TET1 or FOXO4 predicts poor survival of gastric cancer patients, suggesting reactivation of TET1 or FOXO4 might be a novel therapeutic approach to prevent gastric cancer metastasis. Abstract Metastasis is the main cause of death for patients suffering gastric cancer. Epithelial-mesenchymal transition (EMT) and cancer stem cells (CSC) are critical attributes of metastasis, both of which are regulated tightly by DNA methylation and Wnt/β-catenin signaling. Here, we studied the functions of DNA dioxygenase TET1 in regulating Wnt signaling and in gastric cancer metastasis. Knocking-down and overexpressing TET1 in gastric cancer cells promoted and inhibited metastatic spreading to the liver in immune-deficient mice, respectively. TET1 showed inhibitory effects on metastasis-related features -EMT and CSC, which were reversed by interfering with Wnt/β-catenin signaling. RNA-sequencing identified FOXO4 as a direct transactivating target of TET1. FOXO4 directly interacted with β-catenin and recruited it in the cytoplasm, so as to inhibit β-catenin-mediated transcription of Wnt target genes, including CSC marker EpCAM. Moreover, modulation of FOXO4 could reverse the effects of TET1 manipulation on EMT and self-renewal of CSCs. The analysis with clinical samples confirmed the value of FOXO4 as an independent prognostic predictor of patients’ overall survival. Taken together, regulation of Wnt signaling by TET1/FOXO4 is essential for metastasis-associated cellular properties, and targeting TET1/FOXO4/β-catenin pathway may serve as promising therapeutics in the prevention and treatment of gastric cancer metastasis.
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Affiliation(s)
- Jingjing Qi
- General Surgery, Cancer Center, Department of Hepatobiliary & Pancreatic Surgery and Minimally Invasive Surgery, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou 310014, China; (J.Q.); (D.C.); (L.L.)
- Tumor Epigenetics Laboratory, Johannes Kepler University Linz, Altenbergerstraße 69, 4040 Linz, Austria
| | - Di Cui
- General Surgery, Cancer Center, Department of Hepatobiliary & Pancreatic Surgery and Minimally Invasive Surgery, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou 310014, China; (J.Q.); (D.C.); (L.L.)
- Cancer Center, Department of Gastroenterology, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou 310014, China
| | - Qi-Nian Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; (Q.-N.W.); (Q.Z.)
| | - Qi Zhao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; (Q.-N.W.); (Q.Z.)
| | - Zhan-Hong Chen
- Department of Oncology, The Third Affiliated Hospital of Sun Yat-sen University, 600 Tianhe Road, Guangzhou 510630, China;
| | - Lianjie Li
- General Surgery, Cancer Center, Department of Hepatobiliary & Pancreatic Surgery and Minimally Invasive Surgery, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou 310014, China; (J.Q.); (D.C.); (L.L.)
| | - Walter Birchmeier
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany;
| | - Yong Yu
- Tumor Epigenetics Laboratory, Johannes Kepler University Linz, Altenbergerstraße 69, 4040 Linz, Austria
- Correspondence: (Y.Y.); (R.T.); Tel.: +43-732-24688875 (Y.Y.); +86-133-0191-9116 (R.T.)
| | - Ran Tao
- General Surgery, Cancer Center, Department of Hepatobiliary & Pancreatic Surgery and Minimally Invasive Surgery, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou 310014, China; (J.Q.); (D.C.); (L.L.)
- Cancer Center, Department of Gastroenterology, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou 310014, China
- Correspondence: (Y.Y.); (R.T.); Tel.: +43-732-24688875 (Y.Y.); +86-133-0191-9116 (R.T.)
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16
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Uh K, Lee K. TET3 CXXC domain is critical for post-fertilization demethylation and expression of pluripotency genes in pig embryos. Biol Reprod 2022; 107:1205-1216. [PMID: 35766395 DOI: 10.1093/biolre/ioac129] [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: 02/16/2022] [Revised: 06/01/2022] [Accepted: 06/18/2022] [Indexed: 11/12/2022] Open
Abstract
Enzymes of the Ten-eleven translocation (TET) family are considered to play an important role in the regulation of DNA methylation patterns by converting 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Known as a maternal transcript enriched in mature oocytes, TET3 has been suggested to initiate DNA demethylation of the paternal genome in zygotes. Previous studies in mouse cells indicate that the N-terminal CXXC domain of TET3 is important in catalyzing the oxidation of 5mC through its potential DNA binding ability; however, it is not clear whether the DNA binding capacity of CXXC domain is required for the 5hmC conversion in mammalian embryos. Here, we identified TET3 isoforms in porcine oocytes and investigated the role of the oocyte specific TET3 isoform (pTET3L) in controlling postfertilization demethylation in porcine embryos. The pTET3L possessed sequences representing a known DNA binding domain, the CXXC, and injection of the TET3 CXXC fused with GFP into mature porcine oocytes resulted in exclusive localization of the GFP-CXXC in the pronuclei. The CXXC overexpression reduced the 5mC level in zygotes and enhanced the DNA demethylation of the NANOG promoter in 2-cell stage embryos. Furthermore, there was an increase in the transcript abundance of NANOG and ESRRB in blastocysts developed from GFP-CXXC injected oocytes. Targeted knockdown of pTET3L resulted in the downregulation of pluripotency genes in subsequently developed blastocysts. The findings indicate that the CXXC domain of TET3 serves as a critical component for the postfertilization demethylation of porcine embryos and coordinates proper expression of pluripotency related genes in blastocysts. Summary sentence: TET3 isoform containing CXXC domain is the predominant isoform in porcine oocytes and orchestrates post-fertilization demethylation and proper expression of pluripotency genes in porcine embryos.
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Affiliation(s)
- Kyungjun Uh
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65201, USA
| | - Kiho Lee
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65201, USA
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17
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Joshi K, Liu S, Breslin S J P, Zhang J. Mechanisms that regulate the activities of TET proteins. Cell Mol Life Sci 2022; 79:363. [PMID: 35705880 DOI: 10.1007/s00018-022-04396-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/16/2022] [Accepted: 05/23/2022] [Indexed: 02/08/2023]
Abstract
The ten-eleven translocation (TET) family of dioxygenases consists of three members, TET1, TET2, and TET3. All three TET enzymes have Fe+2 and α-ketoglutarate (α-KG)-dependent dioxygenase activities, catalyzing the 1st step of DNA demethylation by converting 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), and further oxidize 5hmC to 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Gene knockout studies demonstrated that all three TET proteins are involved in the regulation of fetal organ generation during embryonic development and normal tissue generation postnatally. TET proteins play such roles by regulating the expression of key differentiation and fate-determining genes via (1) enzymatic activity-dependent DNA methylation of the promoters and enhancers of target genes; and (2) enzymatic activity-independent regulation of histone modification. Interacting partner proteins and post-translational regulatory mechanisms regulate the activities of TET proteins. Mutations and dysregulation of TET proteins are involved in the pathogenesis of human diseases, specifically cancers. Here, we summarize the research on the interaction partners and post-translational modifications of TET proteins. We also discuss the molecular mechanisms by which these partner proteins and modifications regulate TET functioning and target gene expression. Such information will help in the design of medications useful for targeted therapy of TET-mutant-related diseases.
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Affiliation(s)
- Kanak Joshi
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA
| | - Shanhui Liu
- School of Life Sciences, Lanzhou University Second Hospital, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Peter Breslin S J
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA.,Departments of Molecular/Cellular Physiology and Biology, Loyola University Medical Center and Loyola University Chicago, Chicago, IL, 60660, USA
| | - Jiwang Zhang
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA. .,Departments of Pathology and Radiation Oncology, Loyola University Medical Center, Maywood, IL, 60153, USA.
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18
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Role of main RNA modifications in cancer: N 6-methyladenosine, 5-methylcytosine, and pseudouridine. Signal Transduct Target Ther 2022; 7:142. [PMID: 35484099 PMCID: PMC9051163 DOI: 10.1038/s41392-022-01003-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 12/16/2022] Open
Abstract
Cancer is one of the major diseases threatening human life and health worldwide. Epigenetic modification refers to heritable changes in the genetic material without any changes in the nucleic acid sequence and results in heritable phenotypic changes. Epigenetic modifications regulate many biological processes, such as growth, aging, and various diseases, including cancer. With the advancement of next-generation sequencing technology, the role of RNA modifications in cancer progression has become increasingly prominent and is a hot spot in scientific research. This review studied several common RNA modifications, such as N6-methyladenosine, 5-methylcytosine, and pseudouridine. The deposition and roles of these modifications in coding and noncoding RNAs are summarized in detail. Based on the RNA modification background, this review summarized the expression, function, and underlying molecular mechanism of these modifications and their regulators in cancer and further discussed the role of some existing small-molecule inhibitors. More in-depth studies on RNA modification and cancer are needed to broaden the understanding of epigenetics and cancer diagnosis, treatment, and prognosis.
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19
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Non-Psychotropic Cannabinoids as Inhibitors of TET1 Protein. Bioorg Chem 2022; 124:105793. [DOI: 10.1016/j.bioorg.2022.105793] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 03/30/2022] [Accepted: 04/03/2022] [Indexed: 12/18/2022]
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20
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Laurent A, Madigou T, Bizot M, Turpin M, Palierne G, Mahé E, Guimard S, Métivier R, Avner S, Le Péron C, Salbert G. TET2-mediated epigenetic reprogramming of breast cancer cells impairs lysosome biogenesis. Life Sci Alliance 2022; 5:5/7/e202101283. [PMID: 35351824 PMCID: PMC8963717 DOI: 10.26508/lsa.202101283] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 11/24/2022] Open
Abstract
TET2-mediated oxidation of 5-methylcytosine establishes an antiviral state and contributes to MYC-dependent down-regulation of genes involved in lysosome biogenesis and function in breast cancer cells. Methylation and demethylation of cytosines in DNA are believed to act as keystones of cell-specific gene expression by controlling the chromatin structure and accessibility to transcription factors. Cancer cells have their own transcriptional programs, and we sought to alter such a cancer-specific program by enforcing expression of the catalytic domain (CD) of the methylcytosine dioxygenase TET2 in breast cancer cells. The TET2 CD decreased the tumorigenic potential of cancer cells through both activation and repression of a repertoire of genes that, interestingly, differed in part from the one observed upon treatment with the hypomethylating agent decitabine. In addition to promoting the establishment of an antiviral state, TET2 activated 5mC turnover at thousands of MYC-binding motifs and down-regulated a panel of known MYC-repressed genes involved in lysosome biogenesis and function. Thus, an extensive cross-talk between TET2 and the oncogenic transcription factor MYC establishes a lysosomal storage disease–like state that contributes to an exacerbated sensitivity to autophagy inducers.
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Affiliation(s)
- Audrey Laurent
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Thierry Madigou
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Maud Bizot
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Marion Turpin
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Gaëlle Palierne
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Elise Mahé
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Sarah Guimard
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Raphaël Métivier
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Stéphane Avner
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Christine Le Péron
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Gilles Salbert
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
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21
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DNA Methylation Malleability and Dysregulation in Cancer Progression: Understanding the Role of PARP1. Biomolecules 2022; 12:biom12030417. [PMID: 35327610 PMCID: PMC8946700 DOI: 10.3390/biom12030417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/28/2022] [Accepted: 03/04/2022] [Indexed: 02/05/2023] Open
Abstract
Mammalian genomic DNA methylation represents a key epigenetic modification and its dynamic regulation that fine-tunes the gene expression of multiple pathways during development. It maintains the gene expression of one generation of cells; particularly, the mitotic inheritance of gene-expression patterns makes it the key governing mechanism of epigenetic change to the next generation of cells. Convincing evidence from recent discoveries suggests that the dynamic regulation of DNA methylation is accomplished by the enzymatic action of TET dioxygenase, which oxidizes the methyl group of cytosine and activates transcription. As a result of aberrant DNA modifications, genes are improperly activated or inhibited in the inappropriate cellular context, contributing to a plethora of inheritable diseases, including cancer. We outline recent advancements in understanding how DNA modifications contribute to tumor suppressor gene silencing or oncogenic-gene stimulation, as well as dysregulation of DNA methylation in cancer progression. In addition, we emphasize the function of PARP1 enzymatic activity or inhibition in the maintenance of DNA methylation dysregulation. In the context of cancer remediation, the impact of DNA methylation and PARP1 pharmacological inhibitors, and their relevance as a combination therapy are highlighted.
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22
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Lejart A, Zentout S, Chapuis C, D'Augustin O, Smith R, Salbert G, Huet S. The N-terminal domain of TET1 promotes the formation of dense chromatin regions refractory to transcription. Chromosoma 2022; 131:47-58. [PMID: 35235010 DOI: 10.1007/s00412-022-00769-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 01/24/2022] [Accepted: 01/31/2022] [Indexed: 11/03/2022]
Abstract
TET (ten-eleven translocation) enzymes initiate active cytosine demethylation via the oxidation of 5-methylcytosine. TET1 is composed of a C-terminal domain, which bears the catalytic activity of the enzyme, and a N-terminal region that is less well characterized except for the CXXC domain responsible for the targeting to CpG islands. While cytosine demethylation induced by TET1 promotes transcription, this protein also interacts with chromatin-regulating factors that rather silence this process, the coordination between these two opposite functions of TET1 being unclear. In the present work, we uncover a new function of the N-terminal part of the TET1 protein in the regulation of the chromatin architecture. This domain of the protein promotes the establishment of a compact chromatin architecture displaying reduced exchange rate of core histones and partial dissociation of the histone linker. This chromatin reorganization process, which does not rely on the CXXC domain, is associated with a global shutdown of transcription and an increase in heterochromatin-associated histone epigenetic marks. Based on these findings, we propose that the dense chromatin organization generated by the N-terminal domain of TET1 could contribute to restraining the transcription enhancement induced by the DNA demethylation activity of this enzyme.
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Affiliation(s)
- Audrey Lejart
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, 35000, Rennes, France
| | - Siham Zentout
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, 35000, Rennes, France
| | - Catherine Chapuis
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, 35000, Rennes, France
| | - Ostiane D'Augustin
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, 35000, Rennes, France
- Institut de Biologie François Jacob, Institute of Cellular and Molecular Radiobiology, Université Paris-Saclay, Université de Paris, CEA, 92265, Fontenay-aux-Roses, France
| | - Rebecca Smith
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, 35000, Rennes, France
| | - Gilles Salbert
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, 35000, Rennes, France.
| | - Sébastien Huet
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, 35000, Rennes, France.
- Institut Universitaire de France, Paris, France.
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23
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Schmidl D, Jonasson NSW, Menke A, Schneider S, Daumann L. Spectroscopic and in vitro investigations of Fe2+/α-Ketoglutarate-dependent enzymes involved in nucleic acid repair and modification. Chembiochem 2022; 23:e202100605. [PMID: 35040547 PMCID: PMC9401043 DOI: 10.1002/cbic.202100605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/14/2022] [Indexed: 11/08/2022]
Abstract
The activation of molecular oxygen for the highly selective functionalization and repair of DNA and RNA nucleobases is achieved by α-ketoglutarate (α-KG)/iron-dependent dioxygenases. Enzymes of special interest are the human homologs AlkBH of Escherichia coli EcAlkB and ten-eleven translocation (TET) enzymes. These enzymes are involved in demethylation or dealkylation of DNA and RNA, although additional physiological functions are continuously being revealed. Given their importance, studying enzyme-substrate interactions, turnover and kinetic parameters is pivotal for the understanding of the mode of action of these enzymes. Diverse analytical methods, including X-ray crystallography, UV/Vis absorption, electron paramagnetic resonance (EPR), circular dichroism (CD) and NMR spectroscopy have been employed to study the changes in the active site and the overall enzyme structure upon substrate, cofactor and inhibitor addition. Several methods are now available to assess activity of these enzymes. By discussing limitations and possibilities of these techniques for EcAlkB, AlkBH and TET we aim to give a comprehensive synopsis from a bioinorganic point of view, addressing researchers from different disciplines working in the highly interdisciplinary and rapidly evolving field of epigenetic processes and DNA/RNA repair and modification.
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Affiliation(s)
- David Schmidl
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Niko S W Jonasson
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Annika Menke
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Sabine Schneider
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Lena Daumann
- Ludwig-Maximilians-Universität München, Department of Chemistry, Butenandtstr. 5-13, 81377, München, GERMANY
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24
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Onodera A, Kiuchi M, Kokubo K, Nakayama T. Epigenetic regulation of inflammation by CxxC domain‐containing proteins*. Immunol Rev 2022. [DOI: 10.1111/imr.13056
expr 964170082 + 969516512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Affiliation(s)
- Atsushi Onodera
- Department of Immunology Graduate School of Medicine Chiba University Chiba Japan
- Institute for Global Prominent Research Chiba University Chiba Japan
| | - Masahiro Kiuchi
- Department of Immunology Graduate School of Medicine Chiba University Chiba Japan
| | - Kota Kokubo
- Department of Immunology Graduate School of Medicine Chiba University Chiba Japan
| | - Toshinori Nakayama
- Department of Immunology Graduate School of Medicine Chiba University Chiba Japan
- AMED‐CREST, AMED Chiba Japan
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25
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Onodera A, Kiuchi M, Kokubo K, Nakayama T. Epigenetic regulation of inflammation by CxxC domain-containing proteins. Immunol Rev 2021; 305:137-151. [PMID: 34935162 DOI: 10.1111/imr.13056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/03/2021] [Accepted: 11/12/2021] [Indexed: 12/14/2022]
Abstract
Epigenetic regulation of gene transcription in the immune system is important for proper control of protective and pathogenic inflammation. Aberrant epigenetic modifications are often associated with dysregulation of the immune cells, including lymphocytes and macrophages, leading to pathogenic inflammation and autoimmune diseases. Two classical epigenetic markers-histone modifications and DNA cytosine methylation, the latter is the 5 position of the cytosine base in the context of CpG dinucleotides-play multiple roles in the immune system. CxxC domain-containing proteins, which basically bind to the non-methylated CpG (i.e., epigenetic "readers"), often function as "writers" of the epigenetic markers via their catalytic domain within the proteins or by interacting with other epigenetic modifiers. We herein report the most recent advances in our understanding of the functions of CxxC domain-containing proteins in the immune system and inflammation, mainly focusing on T cells and macrophages.
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Affiliation(s)
- Atsushi Onodera
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Institute for Global Prominent Research, Chiba University, Chiba, Japan
| | - Masahiro Kiuchi
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kota Kokubo
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Toshinori Nakayama
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan.,AMED-CREST, AMED, Chiba, Japan
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26
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Sapozhnikov DM, Szyf M. Unraveling the functional role of DNA demethylation at specific promoters by targeted steric blockage of DNA methyltransferase with CRISPR/dCas9. Nat Commun 2021; 12:5711. [PMID: 34588447 PMCID: PMC8481236 DOI: 10.1038/s41467-021-25991-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/07/2021] [Indexed: 01/10/2023] Open
Abstract
Despite four decades of research to support the association between DNA methylation and gene expression, the causality of this relationship remains unresolved. Here, we reaffirm that experimental confounds preclude resolution of this question with existing strategies, including recently developed CRISPR/dCas9 and TET-based epigenetic editors. Instead, we demonstrate a highly effective method using only nuclease-dead Cas9 and guide RNA to physically block DNA methylation at specific targets in the absence of a confounding flexibly-tethered enzyme, thereby enabling the examination of the role of DNA demethylation per se in living cells, with no evidence of off-target activity. Using this method, we probe a small number of inducible promoters and find the effect of DNA demethylation to be small, while demethylation of CpG-rich FMR1 produces larger changes in gene expression. This method could be used to reveal the extent and nature of the contribution of DNA methylation to gene regulation.
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Affiliation(s)
- Daniel M Sapozhnikov
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC, Canada.
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27
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DNA Demethylation in the Processes of Repair and Epigenetic Regulation Performed by 2-Ketoglutarate-Dependent DNA Dioxygenases. Int J Mol Sci 2021; 22:ijms221910540. [PMID: 34638881 PMCID: PMC8508711 DOI: 10.3390/ijms221910540] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 12/05/2022] Open
Abstract
Site-specific DNA methylation plays an important role in epigenetic regulation of gene expression. Chemical methylation of DNA, including the formation of various methylated nitrogenous bases, leads to the formation of genotoxic modifications that impair DNA functions. Despite the fact that different pathways give rise to methyl groups in DNA, the main pathway for their removal is oxidative demethylation, which is catalyzed by nonheme Fe(II)/α-ketoglutarate–dependent DNA dioxygenases. DNA dioxygenases share a common catalytic mechanism of the oxidation of the alkyl groups on nitrogenous bases in nucleic acids. This review presents generalized data on the catalytic mechanism of action of DNA dioxygenases and on the participation of typical representatives of this superfamily, such as prokaryotic enzyme AlkB and eukaryotic enzymes ALKBH1–8 and TET1–3, in both processes of direct repair of alkylated DNA adducts and in the removal of an epigenetic mark (5-methylcytosine).
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28
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Wu J, Liu LL, Cao M, Hu A, Hu D, Luo Y, Wang H, Zhong JN. DNA methylation plays important roles in retinal development and diseases. Exp Eye Res 2021; 211:108733. [PMID: 34418429 DOI: 10.1016/j.exer.2021.108733] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 12/16/2022]
Abstract
DNA methylation is important in developing and post-mitotic cells in various tissues. Recent studies have shown that DNA methylation is highly dynamic, and plays important roles during retinal development and aging. In addition, the dynamic regulation of DNA methylation is involved in the occurrence and development of age-related macular degeneration and diabetic retinopathy and shows potential in disease diagnoses and prognoses. This review introduces the epigenetic concepts of DNA methylation and demethylation with an emphasis on their regulatory roles in retinal development and related diseases. Moreover, we propose exciting ideas such as its crosstalk with other epigenetic modifications and retinal regeneration, to provide a potential direction for understanding retinal diseases from the epigenetic perspective.
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Affiliation(s)
- Jing Wu
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China; Department of Ophthalmology, Lishui Municipal Central Hospital, Lishui, 323000, Zhejiang Province, China
| | - Lin-Lin Liu
- Department of Ophthalmology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China
| | - Miao Cao
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China; Department of Ophthalmology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China
| | - Ang Hu
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China
| | - Die Hu
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China; Department of Ophthalmology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China
| | - Yan Luo
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China
| | - Hui Wang
- Department of Ophthalmology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China.
| | - Jia-Ning Zhong
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China.
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29
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Ravel-Godreuil C, Massiani-Beaudoin O, Mailly P, Prochiantz A, Joshi RL, Fuchs J. Perturbed DNA methylation by Gadd45b induces chromatin disorganization, DNA strand breaks and dopaminergic neuron death. iScience 2021; 24:102756. [PMID: 34278264 PMCID: PMC8264156 DOI: 10.1016/j.isci.2021.102756] [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: 01/22/2021] [Revised: 05/14/2021] [Accepted: 06/17/2021] [Indexed: 12/13/2022] Open
Abstract
Age is a major risk factor for neurodegenerative diseases like Parkinson's disease, but few studies have explored the contribution of key hallmarks of aging, namely DNA methylation changes and heterochromatin destructuration, in the neurodegenerative process. Here, we investigated the consequences of viral overexpression of Gadd45b, a multifactorial protein involved in DNA demethylation, in the mouse midbrain. Gadd45b overexpression induced global and stable changes in DNA methylation, particularly in introns of genes related to neuronal functions, as well as on LINE-1 transposable elements. This was paralleled by disorganized heterochromatin, increased DNA damage, and vulnerability to oxidative stress. LINE-1 de-repression, a potential source of DNA damage, preceded Gadd45b-induced neurodegeneration, whereas prolonged Gadd45b expression deregulated expression of genes related to heterochromatin maintenance, DNA methylation, or Parkinson's disease. Our data indicates that aging-related alterations contribute to dopaminergic neuron degeneration with potential implications for Parkinson's disease.
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Affiliation(s)
- Camille Ravel-Godreuil
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Olivia Massiani-Beaudoin
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Philippe Mailly
- Orion Imaging Facility, Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Labex Memolife, Université PSL, Paris, France
| | - Alain Prochiantz
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Rajiv L. Joshi
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Julia Fuchs
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
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30
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Dick A, Chen A. The role of TET proteins in stress-induced neuroepigenetic and behavioural adaptations. Neurobiol Stress 2021; 15:100352. [PMID: 34189192 PMCID: PMC8220100 DOI: 10.1016/j.ynstr.2021.100352] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 05/21/2021] [Accepted: 06/05/2021] [Indexed: 12/27/2022] Open
Abstract
Over the past decade, critical, non-redundant roles of the ten-eleven translocation (TET) family of dioxygenase enzymes have been identified in the brain during developmental and postnatal stages. Specifically, TET-mediated active demethylation, involving the iterative oxidation of 5-methylcytosine to 5-hydroxymethylcytosine and subsequent oxidative derivatives, is dynamically regulated in response to environmental stimuli such as neuronal activity, learning and memory processes, and stressor exposure. Such changes may therefore perpetuate stable and dynamic transcriptional patterns within neuronal populations required for neuroplasticity and behavioural adaptation. In this review, we will highlight recent evidence supporting a role of TET protein function and active demethylation in stress-induced neuroepigenetic and behavioural adaptations. We further explore potential mechanisms by which TET proteins may mediate both the basal and pathological embedding of stressful life experiences within the brain of relevance to stress-related psychiatric disorders.
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Affiliation(s)
- Alec Dick
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
- Corresponding author.
| | - Alon Chen
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
- The Ruhman Family Laboratory for Research on the Neurobiology of Stress, Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
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31
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Morris-Blanco KC, Chokkalla AK, Bertogliat MJ, Vemuganti R. TET3 regulates DNA hydroxymethylation of neuroprotective genes following focal ischemia. J Cereb Blood Flow Metab 2021; 41:590-603. [PMID: 32380888 PMCID: PMC7922754 DOI: 10.1177/0271678x20912965] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The 5-hydroxymethylcytosine (5hmC) epigenetic modification is highly enriched in the CNS and a critical modulator of neuronal function and development. We found that cortical 5hmC was enhanced from 5 min to three days of reperfusion following focal ischemia in adult mice. Blockade of the 5hmC-producing enzyme ten-eleven translocase 3 (TET3) increased edema, infarct volume, and motor function impairments. To determine the mechanism by which TET3 provides ischemic neuroprotection, we assessed the genomic regions where TET3 modulates 5hmC. Genome-wide sequencing analysis of differentially hydroxymethylated regions (DhMRs) revealed that focal ischemia robustly increased 5hmC at the promoters of thousands of genes in a TET3-dependent manner. TET3 inhibition reduced 5hmC at the promoters of neuroprotective genes involved in cell survival, angiogenesis, neurogenesis, antioxidant defense, DNA repair, and metabolism demonstrating a role for TET3 in endogenous protection against stroke. The mRNA expression of several genes with known involvement in ischemic neuroprotection were also reduced with TET3 knockdown in both male and female mice, establishing a correlation between decreased promoter 5hmC levels and decreased gene expression. Collectively, our results indicate that TET3 globally increases 5hmC at regulatory regions and overwhelmingly modulates 5hmC in several neuroprotective pathways that may improve outcome after ischemic injury.
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Affiliation(s)
- Kahlilia C Morris-Blanco
- Department of Neurological Surgery, University of Wisconsin-Madison, Madison, WI, USA.,Department of Research, William S. Middleton Veterans Administration Hospital, Madison, WI, USA
| | - Anil K Chokkalla
- Department of Neurological Surgery, University of Wisconsin-Madison, Madison, WI, USA.,Cellular and Molecular Pathology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Mario J Bertogliat
- Department of Neurological Surgery, University of Wisconsin-Madison, Madison, WI, USA
| | - Raghu Vemuganti
- Department of Neurological Surgery, University of Wisconsin-Madison, Madison, WI, USA.,Department of Research, William S. Middleton Veterans Administration Hospital, Madison, WI, USA.,Cellular and Molecular Pathology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
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32
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Broome R, Chernukhin I, Jamieson S, Kishore K, Papachristou EK, Mao SQ, Tejedo CG, Mahtey A, Theodorou V, Groen AJ, D'Santos C, Balasubramanian S, Farcas AM, Siersbæk R, Carroll JS. TET2 is a component of the estrogen receptor complex and controls 5mC to 5hmC conversion at estrogen receptor cis-regulatory regions. Cell Rep 2021; 34:108776. [PMID: 33626359 PMCID: PMC7921846 DOI: 10.1016/j.celrep.2021.108776] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 01/05/2021] [Accepted: 01/29/2021] [Indexed: 01/10/2023] Open
Abstract
Estrogen receptor-α (ER) drives tumor development in ER-positive (ER+) breast cancer. The transcription factor GATA3 has been closely linked to ER function, but its precise role in this setting remains unclear. Quantitative proteomics was used to assess changes to the ER complex in response to GATA3 depletion. Unexpectedly, few proteins were lost from the ER complex in the absence of GATA3, with the only major change being depletion of the dioxygenase TET2. TET2 binding constituted a near-total subset of ER binding in multiple breast cancer models, with loss of TET2 associated with reduced activation of proliferative pathways. TET2 knockdown did not appear to change global methylated cytosine (5mC) levels; however, oxidation of 5mC to 5-hydroxymethylcytosine (5hmC) was significantly reduced, and these events occurred at ER enhancers. These findings implicate TET2 in the maintenance of 5hmC at ER sites, providing a potential mechanism for TET2-mediated regulation of ER target genes.
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Affiliation(s)
- Rebecca Broome
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Igor Chernukhin
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Stacey Jamieson
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; Merck Sharp & Dohme (UK) Limited, 120 Moorgate, London EC2M 6UR, UK
| | - Kamal Kishore
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | | | - Shi-Qing Mao
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | | | - Areeb Mahtey
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Vasiliki Theodorou
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology - Hellas Nikolaou Plastira 100, 70013 Heraklion, Crete, Greece
| | - Arnoud J Groen
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Clive D'Santos
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Shankar Balasubramanian
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Anca Madalina Farcas
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; Bioscience, Oncology R&D, AstraZeneca, Cambridge CB2 0RE, UK.
| | - Rasmus Siersbæk
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK.
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33
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An all-to-all approach to the identification of sequence-specific readers for epigenetic DNA modifications on cytosine. Nat Commun 2021; 12:795. [PMID: 33542217 PMCID: PMC7862700 DOI: 10.1038/s41467-021-20950-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/14/2020] [Indexed: 12/31/2022] Open
Abstract
Epigenetic modifications of DNA play important roles in many biological processes. Identifying readers of these epigenetic marks is a critical step towards understanding the underlying mechanisms. Here, we present an all-to-all approach, dubbed digital affinity profiling via proximity ligation (DAPPL), to simultaneously profile human TF-DNA interactions using mixtures of random DNA libraries carrying different epigenetic modifications (i.e., 5-methylcytosine, 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine) on CpG dinucleotides. Many proteins that recognize consensus sequences carrying these modifications in symmetric and/or hemi-modified forms are identified. We further demonstrate that the modifications in different sequence contexts could either enhance or suppress TF binding activity. Moreover, many modifications can affect TF binding specificity. Furthermore, symmetric modifications show a stronger effect in either enhancing or suppressing TF-DNA interactions than hemi-modifications. Finally, in vivo evidence suggests that USF1 and USF2 might regulate transcription via hydroxymethylcytosine-binding activity in weak enhancers in human embryonic stem cells. Identifying readers of epigenetic marks is a critical step for understanding the role of epigenetic marks in biology. Here, the authors applied DAPPL, an all-to-all approach to profile the interactions between TFs and epigenetic modified DNA libraries.
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34
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Tsagaratou A. Deciphering the multifaceted roles of TET proteins in T-cell lineage specification and malignant transformation. Immunol Rev 2021; 300:22-36. [PMID: 33410200 DOI: 10.1111/imr.12940] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/23/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022]
Abstract
TET proteins are DNA demethylases that can oxidize 5-methylcytosine (5mC) to generate 5-hydroxymethylcytosine (5hmC) and other oxidized mC bases (oxi-mCs). Importantly, TET proteins govern cell fate decisions during development of various cell types by activating a cell-specific gene expression program. In this review, we focus on the role of TET proteins in T-cell lineage specification. We explore the multifaceted roles of TET proteins in regulating gene expression in the contexts of T-cell development, lineage specification, function, and disease. Finally, we discuss the future directions and experimental strategies required to decipher the precise mechanisms employed by TET proteins to fine-tune gene expression and safeguard cell identity.
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Affiliation(s)
- Ageliki Tsagaratou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Center of Translational Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Institute of Inflammatory Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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35
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Xu X, Zeisberg EM. High-Fidelity CRISPR/Cas9-Based Gene-Specific Hydroxymethylation. Methods Mol Biol 2021; 2272:195-206. [PMID: 34009615 DOI: 10.1007/978-1-0716-1294-1_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Aberrant promoter hypermethylation leads to gene silencing and is associated with various pathologies including cancer and organ fibrosis. Active DNA demethylation is mediated by TET enzymes: TET1, TET2, and TET3, which convert 5-methylcytosine to 5-hydroxymethylcytosine. Induction of gene-specific hydroxymethylation via CRISPR/Cas9 gene technology provides an opportunity to reactivate a single target gene silenced in pathological conditions. We utilized a spCas9 variant fused with TET3 catalytic domain to mediate gene-specific hydroxymethylation with subsequent gene reactivation which holds promise for gene therapy. Here, we present guidelines for gene-specific hydroxymethylation targeting with a specific focus on designing sgRNA and functional assessments in vitro.
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Affiliation(s)
- Xingbo Xu
- Department of Cardiology and Pneumology, University Medical Center of Göttingen, Georg-August University, Göttingen, Germany.
- DZHK (German Centre for Cardiovascular Research, Partner Site), Göttingen, Germany.
| | - Elisabeth M Zeisberg
- Department of Cardiology and Pneumology, University Medical Center of Göttingen, Georg-August University, Göttingen, Germany
- DZHK (German Centre for Cardiovascular Research, Partner Site), Göttingen, Germany
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36
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Montibus B, Cercy J, Bouschet T, Charras A, Maupetit-Méhouas S, Nury D, Gonthier-Guéret C, Chauveau S, Allegre N, Chariau C, Hong CC, Vaillant I, Marques CJ, Court F, Arnaud P. TET3 controls the expression of the H3K27me3 demethylase Kdm6b during neural commitment. Cell Mol Life Sci 2021; 78:757-768. [PMID: 32405722 PMCID: PMC9644380 DOI: 10.1007/s00018-020-03541-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 04/21/2020] [Accepted: 04/24/2020] [Indexed: 01/03/2023]
Abstract
The acquisition of cell identity is associated with developmentally regulated changes in the cellular histone methylation signatures. For instance, commitment to neural differentiation relies on the tightly controlled gain or loss of H3K27me3, a hallmark of polycomb-mediated transcriptional gene silencing, at specific gene sets. The KDM6B demethylase, which removes H3K27me3 marks at defined promoters and enhancers, is a key factor in neurogenesis. Therefore, to better understand the epigenetic regulation of neural fate acquisition, it is important to determine how Kdm6b expression is regulated. Here, we investigated the molecular mechanisms involved in the induction of Kdm6b expression upon neural commitment of mouse embryonic stem cells. We found that the increase in Kdm6b expression is linked to a rearrangement between two 3D configurations defined by the promoter contact with two different regions in the Kdm6b locus. This is associated with changes in 5-hydroxymethylcytosine (5hmC) levels at these two regions, and requires a functional ten-eleven-translocation (TET) 3 protein. Altogether, our data support a model whereby Kdm6b induction upon neural commitment relies on an intronic enhancer the activity of which is defined by its TET3-mediated 5-hmC level. This original observation reveals an unexpected interplay between the 5-hmC and H3K27me3 pathways during neural lineage commitment in mammals. It also questions to which extent KDM6B-mediated changes in H3K27me3 level account for the TET-mediated effects on gene expression.
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Affiliation(s)
- Bertille Montibus
- Université Clermont Auvergne, CNRS, Inserm, GReD, 63000, Clermont-Ferrand, France
- King's College, London, UK
| | - Jil Cercy
- Université Clermont Auvergne, CNRS, Inserm, GReD, 63000, Clermont-Ferrand, France
| | - Tristan Bouschet
- Institut de Génomique Fonctionnelle (IGF), University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Amandine Charras
- Université Clermont Auvergne, CNRS, Inserm, GReD, 63000, Clermont-Ferrand, France
- Department of Women's and Children's Health, Institute of Lifecourse and Medical Sciences, Liverpool University, Liverpool, UK
| | | | - David Nury
- Université Clermont Auvergne, CNRS, Inserm, GReD, 63000, Clermont-Ferrand, France
| | | | - Sabine Chauveau
- Université Clermont Auvergne, CNRS, Inserm, GReD, 63000, Clermont-Ferrand, France
| | - Nicolas Allegre
- Université Clermont Auvergne, CNRS, Inserm, GReD, 63000, Clermont-Ferrand, France
| | - Caroline Chariau
- Nantes Université, CHU Nantes, SFR Santé, FED4203, Inserm UMS 016, CNRS UMS 3556, 44000, Nantes, France
| | - Charles C Hong
- Vanderbilt University School of Medicine Nashville, Nashville, USA
| | - Isabelle Vaillant
- Université Clermont Auvergne, CNRS, Inserm, GReD, 63000, Clermont-Ferrand, France
| | - C Joana Marques
- Life and Health Sciences Research Institute (ICVS), University of Minho, Campus de Gualtar, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga, Portugal
- Department of Genetics, Faculty of Medicine, University of Porto (FMUP), Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Porto, Portugal
| | - Franck Court
- Université Clermont Auvergne, CNRS, Inserm, GReD, 63000, Clermont-Ferrand, France.
| | - Philippe Arnaud
- Université Clermont Auvergne, CNRS, Inserm, GReD, 63000, Clermont-Ferrand, France.
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37
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Huang Z, Yu J, Cui W, Johnson BK, Kim K, Pfeifer GP. The chromosomal protein SMCHD1 regulates DNA methylation and the 2c-like state of embryonic stem cells by antagonizing TET proteins. SCIENCE ADVANCES 2021; 7:7/4/eabb9149. [PMID: 33523915 PMCID: PMC7817097 DOI: 10.1126/sciadv.abb9149] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 11/24/2020] [Indexed: 05/15/2023]
Abstract
5-Methylcytosine (5mC) oxidases, the ten-eleven translocation (TET) proteins, initiate DNA demethylation, but it is unclear how 5mC oxidation is regulated. We show that the protein SMCHD1 (structural maintenance of chromosomes flexible hinge domain containing 1) is found in complexes with TET proteins and negatively regulates TET activities. Removal of SMCHD1 from mouse embryonic stem (ES) cells induces DNA hypomethylation, preferentially at SMCHD1 target sites and accumulation of 5-hydroxymethylcytosine (5hmC), along with promoter demethylation and activation of the Dux double-homeobox gene. In the absence of SMCHD1, ES cells acquire a two-cell (2c) embryo-like state characterized by activation of an early embryonic transcriptome that is substantially imposed by Dux Using Smchd1/Tet1/Tet2/Tet3 quadruple-knockout cells, we show that DNA demethylation, activation of Dux, and other genes upon SMCHD1 loss depend on TET proteins. These data identify SMCHD1 as an antagonist of the 2c-like state of ES cells and of TET-mediated DNA demethylation.
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Affiliation(s)
- Zhijun Huang
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Jiyoung Yu
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
- Asan Medical Center, University of Ulsan, College of Medicine, Songpa, Seoul, South Korea
| | - Wei Cui
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Benjamin K Johnson
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Kyunggon Kim
- Asan Medical Center, University of Ulsan, College of Medicine, Songpa, Seoul, South Korea
| | - Gerd P Pfeifer
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
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38
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Abstract
The 5-methylcytosine (5mC) oxidation pathway mediated by TET proteins involves step-wise oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC and 5caC can be removed from DNA by base excision repair and the completion of this pathway results in "demethylation" of 5mC by converting the modified base back into cytosine. In vitro studies with TET proteins aimed at analyzing their DNA substrate specificities and their activity within defined chromatin templates are relatively limited. Here we describe purification methods for mammalian TET proteins based on expression in insect cells or in 293T cells. We also briefly summarize a method that can be used to monitor 5-methylcytosine oxidase activity of the purified TET proteins in vitro.
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Affiliation(s)
- Zhijun Huang
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Jiyoung Yu
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Asan Medical Center, University of Ulsan, College of Medicine, Seoul, South Korea
| | - Jennifer Johnson
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Seung-Gi Jin
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Gerd P Pfeifer
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
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39
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Guan Y, Hasipek M, Tiwari AD, Maciejewski JP, Jha BK. TET-dioxygenase deficiency in oncogenesis and its targeting for tumor-selective therapeutics. Semin Hematol 2021; 58:27-34. [PMID: 33509440 PMCID: PMC7938524 DOI: 10.1053/j.seminhematol.2020.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/04/2020] [Accepted: 12/19/2020] [Indexed: 02/08/2023]
Abstract
TET2 is one of the most frequently mutated genes in myeloid neoplasms. TET2 loss-of-function perturbs myeloid differentiation and causes clonal expansion. Despite extensive knowledge regarding biochemical mechanisms underlying distorted myeloid differentiation, targeted therapies are lagging. Here we review known biochemical mechanisms and candidate therapies that emerge from this. Specifically, we discuss the potential utility of vitamin C to compensate for TET-dioxygenase deficiency, to thereby restore the biochemical function. An alternative approach exploits the TET-deficient state for synthetic lethality, exploiting the fact that a minimum level of TET-dioxygenase activity is required for cell survival, rendering TET2-mutant malignant cells selectively vulnerable to inhibitors of TET-function.
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Affiliation(s)
- Yihong Guan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Metis Hasipek
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Anand D Tiwari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Babal K Jha
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH.
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40
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He C, Bozler J, Janssen KA, Wilusz JE, Garcia BA, Schorn AJ, Bonasio R. TET2 chemically modifies tRNAs and regulates tRNA fragment levels. Nat Struct Mol Biol 2020; 28:62-70. [PMID: 33230319 PMCID: PMC7855721 DOI: 10.1038/s41594-020-00526-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 09/28/2020] [Indexed: 12/16/2022]
Abstract
The ten-eleven translocation 2 (TET2) protein, which oxidizes 5-methylcytosine in DNA, can also bind RNA; however, the targets and function of TET2-RNA interactions in vivo are not fully understood. Using stringent affinity tags introduced at the Tet2 locus, we purified and sequenced TET2-crosslinked RNAs from mouse embryonic stem cells (mESCs) and found a high enrichment for tRNAs. RNA immunoprecipitation with an antibody against 5-hydroxymethylcytosine (hm5C) recovered tRNAs that overlapped with those bound to TET2 in cells. Mass spectrometry (MS) analyses revealed that TET2 is necessary and sufficient for the deposition of the hm5C modification on tRNA. Tet2 knockout in mESCs affected the levels of several small noncoding RNAs originating from TET2-bound tRNAs that were enriched by hm5C immunoprecipitation. Thus, our results suggest a new function of TET2 in promoting the conversion of 5-methylcytosine to hm5C on tRNA and regulating the processing or stability of different classes of tRNA fragments.
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Affiliation(s)
- Chongsheng He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, Hunan, P. R. China. .,Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA. .,Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | - Julianna Bozler
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kevin A Janssen
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Benjamin A Garcia
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Roberto Bonasio
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA. .,Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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41
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de Oliveira DT, Guerra-Sá R. Uncovering epigenetic landscape: a new path for biomarkers identification and drug development. Mol Biol Rep 2020; 47:9097-9122. [PMID: 33089404 DOI: 10.1007/s11033-020-05916-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/10/2020] [Indexed: 12/31/2022]
Abstract
Scientific advances in recent decades have revealed an incredible degree of plasticity in gene expression in response to various environmental, nutritional, physiological, pathological, and behavioral conditions. Epigenetics emerges in this sense, as the link between the internal (genetic) and external (environmental) factors underlying the expression of the phenotype. Methylation of DNA and histone post-translationa modifications are canonical epigenetic events. Additionally, noncoding RNAs molecules (microRNAs and lncRNAs) have also been proposed as another layer of epigenetic regulation. Together, these events are responsible for regulating gene expression throughout life, controlling cellular fate in both normal and pathological development. Despite being a relatively recent science, epigenetics has been arousing the interest of researchers from different segments of the life sciences and the general public. This review highlights the recent advances in the characterization of the epigenetic events and points promising use of these brands for the diagnosis, prognosis, and therapy of diseases. We also present several classes of epigenetic modifying compounds with therapeutic applications (so-call epidrugs) and their current status in clinical trials and approved by the FDA. In summary, hopefully, we provide the reader with theoretical bases for a better understanding of the epigenetic mechanisms and of the promising application of these marks and events in the medical clinic.
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Affiliation(s)
- Daiane Teixeira de Oliveira
- Programa de Pós-graduação em Ciências Farmacêuticas, Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil.
| | - Renata Guerra-Sá
- Programa de Pós-graduação em Ciências Farmacêuticas, Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil.,Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
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42
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Kharat SS, Ding X, Swaminathan D, Suresh A, Singh M, Sengodan SK, Burkett S, Marks H, Pamala C, He Y, Fox SD, Buehler EC, Muegge K, Martin SE, Sharan SK. Degradation of 5hmC-marked stalled replication forks by APE1 causes genomic instability. Sci Signal 2020; 13:13/645/eaba8091. [PMID: 32817374 DOI: 10.1126/scisignal.aba8091] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Synthetic lethality between poly(ADP-ribose) polymerase (PARP) inhibition and BRCA deficiency is exploited to treat breast and ovarian tumors. However, resistance to PARP inhibitors (PARPis) is common. To identify potential resistance mechanisms, we performed a genome-wide RNAi screen in BRCA2-deficient mouse embryonic stem cells and validation in KB2P1.21 mouse mammary tumor cells. We found that resistance to multiple PARPi emerged with reduced expression of TET2 (ten-eleven translocation), which promotes DNA demethylation by oxidizing 5-methylcytosine (5mC) to 5-hydroxymethycytosine (5hmC) and other products. TET2 knockdown in BRCA2-deficient cells protected stalled replication forks (RFs). Increasing 5hmC abundance induced the degradation of stalled RFs in KB2P1.21 and human cancer cells by recruiting the base excision repair-associated apurinic/apyrimidinic endonuclease APE1, independent of the BRCA2 status. TET2 loss did not affect the recruitment of the repair protein RAD51 to sites of double-strand breaks (DSBs) or the abundance of proteins associated with RF integrity. The loss of TET2, of its product 5hmC, and of APE1 recruitment to stalled RFs promoted resistance to the chemotherapeutic cisplatin. Our findings reveal a previously unknown role for the epigenetic mark 5hmC in maintaining the integrity of stalled RFs and a potential resistance mechanism to PARPi and cisplatin.
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Affiliation(s)
- Suhas S Kharat
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Xia Ding
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Divya Swaminathan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Akshey Suresh
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Manish Singh
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Satheesh K Sengodan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Sandra Burkett
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Hanna Marks
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Chinmayi Pamala
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Yafeng He
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Stephen D Fox
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Eugen C Buehler
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850, USA
| | - Kathrin Muegge
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.,Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Scott E Martin
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850, USA
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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43
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Shanak S, Helms V. DNA methylation and the core pluripotency network. Dev Biol 2020; 464:145-160. [PMID: 32562758 DOI: 10.1016/j.ydbio.2020.06.001] [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] [Received: 01/09/2020] [Revised: 05/01/2020] [Accepted: 06/04/2020] [Indexed: 01/06/2023]
Abstract
From the onset of fertilization, the genome undergoes cell division and differentiation. All of these developmental transitions and differentiation processes include cell-specific signatures and gradual changes of the epigenome. Understanding what keeps stem cells in the pluripotent state and what leads to differentiation are fascinating and biomedically highly important issues. Numerous studies have identified genes, proteins, microRNAs and small molecules that exert essential effects. Notably, there exists a core pluripotency network that consists of several transcription factors and accessory proteins. Three eminent transcription factors, OCT4, SOX2 and NANOG, serve as hubs in this core pluripotency network. They bind to the enhancer regions of their target genes and modulate, among others, the expression levels of genes that are associated with Gene Ontology terms related to differentiation and self-renewal. Also, much has been learned about the epigenetic rewiring processes during these changes of cell fate. For example, DNA methylation dynamics is pivotal during embryonic development. The main goal of this review is to highlight an intricate interplay of (a) DNA methyltransferases controlling the expression levels of core pluripotency factors by modulation of the DNA methylation levels in their enhancer regions, and of (b) the core pluripotency factors controlling the transcriptional regulation of DNA methyltransferases. We discuss these processes both at the global level and in atomistic detail based on information from structural studies and from computer simulations.
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Affiliation(s)
- Siba Shanak
- Faculty of Science, Arab-American University, Jenin, Palestine; Center for Bioinformatics, Saarland University, Saarbruecken, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbruecken, Germany.
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44
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Rao VK, Swarnaseetha A, Tham GH, Lin WQ, Han BB, Benoukraf T, Xu GL, Ong CT. Phosphorylation of Tet3 by cdk5 is critical for robust activation of BRN2 during neuronal differentiation. Nucleic Acids Res 2020; 48:1225-1238. [PMID: 31807777 PMCID: PMC7026633 DOI: 10.1093/nar/gkz1144] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 11/20/2019] [Accepted: 11/27/2019] [Indexed: 12/27/2022] Open
Abstract
Tet3 regulates the dynamic balance between 5-methylcyotsine (5mC) and 5-hydroxymethylcytosine (5hmC) in DNA during brain development and homeostasis. However, it remains unclear how its functions are modulated in a context-dependent manner during neuronal differentiation. Here, we show that cyclin-dependent kinase 5 (cdk5) phosphorylates Tet3 at the highly conserved serine 1310 and 1379 residues within its catalytic domain, changing its in vitro dioxygenase activity. Interestingly, when stably expressed in Tet1, 2, 3 triple-knockout mouse embryonic stem cells (ESCs), wild-type Tet3 induces higher level of 5hmC and concomitant expression of genes associated with neurogenesis whereas phosphor-mutant (S1310A/S1379A) Tet3 causes elevated 5hmC and expression of genes that are linked to metabolic processes. Consistent with this observation, Tet3-knockout mouse ESCs rescued with wild-type Tet3 have higher level of 5hmC at the promoter of neuron-specific gene BRN2 when compared to cells that expressed phosphor-mutant Tet3. Wild-type and phosphor-mutant Tet3 also exhibit differential binding affinity to histone variant H2A.Z. The differential 5hmC enrichment and H2A.Z occupancy at BRN2 promoter is correlated with higher gene expression and more efficient neuronal differentiation of ESCs that expressed wild-type Tet3. Taken together, our results suggest that cdk5-mediated phosphorylation of Tet3 is required for robust activation of neuronal differentiation program.
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Affiliation(s)
- Vinay Kumar Rao
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Adusumalli Swarnaseetha
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Guo-Hong Tham
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Wei-Qi Lin
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Bin-Bin Han
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Touati Benoukraf
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.,Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL A1B 3V6, Canada
| | - Guo-Liang Xu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chin-Tong Ong
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
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45
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Wright EP, Abdelhamid MAS, Ehiabor MO, Grigg MC, Irving K, Smith NM, Waller ZAE. Epigenetic modification of cytosines fine tunes the stability of i-motif DNA. Nucleic Acids Res 2020; 48:55-62. [PMID: 31777919 PMCID: PMC6943138 DOI: 10.1093/nar/gkz1082] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 10/29/2019] [Accepted: 11/25/2019] [Indexed: 01/17/2023] Open
Abstract
i-Motifs are widely used in nanotechnology, play a part in gene regulation and have been detected in human nuclei. As these structures are composed of cytosine, they are potential sites for epigenetic modification. In addition to 5-methyl- and 5-hydroxymethylcytosine modifications, recent evidence has suggested biological roles for 5-formylcytosine and 5-carboxylcytosine. Herein the human telomeric i-motif sequence was used to examine how these four epigenetic modifications alter the thermal and pH stability of i-motifs. Changes in melting temperature and transitional pH depended on both the type of modification and its position within the i-motif forming sequence. The cytosines most sensitive to modification were next to the first and third loops within the structure. Using previously described i-motif forming sequences, we screened the MCF-7 and MCF-10A methylomes to map 5-methylcytosine and found the majority of sequences were differentially methylated in MCF7 (cancerous) and MCF10A (non-cancerous) cell lines. Furthermore, i-motif forming sequences stable at neutral pH were significantly more likely to be epigenetically modified than traditional acidic i-motif forming sequences. This work has implications not only in the epigenetic regulation of DNA, but also allows discreet tunability of i-motif stability for nanotechnological applications.
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Affiliation(s)
- Elisé P Wright
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Mahmoud A S Abdelhamid
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.,Centre for Molecular and Structural Biochemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Michelle O Ehiabor
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Melanie C Grigg
- School of Molecular Sciences, University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
| | - Kelly Irving
- School of Molecular Sciences, University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
| | - Nicole M Smith
- School of Molecular Sciences, University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
| | - Zoë A E Waller
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.,Centre for Molecular and Structural Biochemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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46
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Liu K, Min J. Structural Basis for the Recognition of Non-methylated DNA by the CXXC Domain. J Mol Biol 2020:S0022-2836(19)30591-1. [DOI: 10.1016/j.jmb.2019.09.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 02/07/2023]
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47
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Schneider M, Trummer C, Stengl A, Zhang P, Szwagierczak A, Cardoso MC, Leonhardt H, Bauer C, Antes I. Systematic analysis of the binding behaviour of UHRF1 towards different methyl- and carboxylcytosine modification patterns at CpG dyads. PLoS One 2020; 15:e0229144. [PMID: 32084194 PMCID: PMC7034832 DOI: 10.1371/journal.pone.0229144] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 01/30/2020] [Indexed: 01/24/2023] Open
Abstract
The multi-domain protein UHRF1 is essential for DNA methylation maintenance and binds DNA via a base-flipping mechanism with a preference for hemi-methylated CpG sites. We investigated its binding to hemi- and symmetrically modified DNA containing either 5-methylcytosine (mC), 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), or 5-carboxylcytosine (caC). Our experimental results indicate that UHRF1 binds symmetrically carboxylated and hybrid methylated/carboxylated CpG dyads in addition to its previously reported substrates. Complementary molecular dynamics simulations provide a possible mechanistic explanation of how the protein could differentiate between modification patterns. First, we observe different local binding modes in the nucleotide binding pocket as well as the protein's NKR finger. Second, both DNA modification sites are coupled through key residues within the NKR finger, suggesting a communication pathway affecting protein-DNA binding for carboxylcytosine modifications. Our results suggest a possible additional function of the hemi-methylation reader UHRF1 through binding of carboxylated CpG sites. This opens the possibility of new biological roles of UHRF1 beyond DNA methylation maintenance and of oxidised methylcytosine derivates in epigenetic regulation.
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Affiliation(s)
- Markus Schneider
- Center for Integrated Protein Science Munich at the TUM School of Life Sciences, Technische Universität München, Freising, Germany
| | - Carina Trummer
- Center for Integrated Protein Science Munich at the Department of Biology II, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Andreas Stengl
- Center for Integrated Protein Science Munich at the Department of Biology II, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Peng Zhang
- Center for Integrated Protein Science Munich at the Department of Biology II, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
- Cell Biology and Epigenetics at the Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Aleksandra Szwagierczak
- Center for Integrated Protein Science Munich at the Department of Biology II, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics at the Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Heinrich Leonhardt
- Center for Integrated Protein Science Munich at the Department of Biology II, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Christina Bauer
- Center for Integrated Protein Science Munich at the Department of Biology II, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Iris Antes
- Center for Integrated Protein Science Munich at the TUM School of Life Sciences, Technische Universität München, Freising, Germany
- * E-mail:
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48
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Mahmood AM, Dunwell JM. Evidence for novel epigenetic marks within plants. AIMS GENETICS 2019; 6:70-87. [PMID: 31922011 PMCID: PMC6949463 DOI: 10.3934/genet.2019.4.70] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 12/07/2019] [Indexed: 12/21/2022]
Abstract
Variation in patterns of gene expression can result from modifications in the genome that occur without a change in the sequence of the DNA; such modifications include methylation of cytosine to generate 5-methylcytosine (5mC) resulting in the generation of heritable epimutation and novel epialleles. This type of non-sequence variation is called epigenetics. The enzymes responsible for generation of such DNA modifications in mammals are named DNA methyltransferases (DNMT) including DNMT1, DNMT2 and DNMT3. The later stages of oxidations to these modifications are catalyzed by Ten Eleven Translocation (TET) proteins, which contain catalytic domains belonging to the 2-oxoglutarate dependent dioxygenase family. In various mammalian cells/tissues including embryonic stem cells, cancer cells and brain tissues, it has been confirmed that these proteins are able to induce the stepwise oxidization of 5-methyl cytosine to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and finally 5-carboxylcytosine (5caC). Each stage from initial methylation until the end of the DNA demethylation process is considered as a specific epigenetic mark that may regulate gene expression. This review discusses controversial evidence for the presence of such oxidative products, particularly 5hmC, in various plant species. Whereas some reports suggest no evidence for enzymatic DNA demethylation, other reports suggest that the presence of oxidative products is followed by the active demethylation and indicate the contribution of possible TET-like proteins in the regulation of gene expression in plants. The review also summarizes the results obtained by expressing the human TET conserved catalytic domain in transgenic plants.
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Affiliation(s)
- Asaad M Mahmood
- Department of Biology, College of Education, University of Garmian, Kalar, KRG/Iraq
| | - Jim M Dunwell
- School of School of Agriculture, Policy and Development, University of Reading, Reading, Berkshire, UK
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49
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DNA Modification Readers and Writers and Their Interplay. J Mol Biol 2019:S0022-2836(19)30718-1. [PMID: 31866298 DOI: 10.1016/j.jmb.2019.12.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 11/28/2019] [Accepted: 12/05/2019] [Indexed: 12/15/2022]
Abstract
Genomic DNA is modified in a postreplicative manner and several modifications, the enzymes responsible for their deposition as well as proteins that read these modifications, have been described. Here, we focus on the impact of DNA modifications on the DNA helix and review the writers and readers of cytosine modifications and how they interplay to shape genome composition, stability, and function.
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50
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Yang J, Horton JR, Li J, Huang Y, Zhang X, Blumenthal RM, Cheng X. Structural basis for preferential binding of human TCF4 to DNA containing 5-carboxylcytosine. Nucleic Acids Res 2019; 47:8375-8387. [PMID: 31081034 PMCID: PMC6895265 DOI: 10.1093/nar/gkz381] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 04/27/2019] [Accepted: 04/30/2019] [Indexed: 12/11/2022] Open
Abstract
The psychiatric risk-associated transcription factor 4 (TCF4) is linked to schizophrenia. Rare TCF4 coding variants are found in individuals with Pitt-Hopkins syndrome-an intellectual disability and autism spectrum disorder. TCF4 contains a C-terminal basic-helix-loop-helix (bHLH) DNA binding domain which recognizes the enhancer-box (E-box) element 5'-CANNTG-3' (where N = any nucleotide). A subset of the TCF4-occupancy sites have the expanded consensus binding specificity 5'-C(A/G)-CANNTG-3', with an added outer Cp(A/G) dinucleotide; for example in the promoter for CNIH3, a gene involved in opioid dependence. In mammalian genomes, particularly brain, the CpG and CpA dinucleotides can be methylated at the 5-position of cytosine (5mC), and then may undergo successive oxidations to the 5-hydroxymethyl (5hmC), 5-formyl (5fC), and 5-carboxyl (5caC) forms. We find that, in the context of 5'-0CG-1CA-2CG-3TG-3'(where the numbers indicate successive dinucleotides), modification of the central E-box 2CG has very little effect on TCF4 binding, E-box 1CA modification has a negative influence on binding, while modification of the flanking 0CG, particularly carboxylation, has a strong positive impact on TCF4 binding to DNA. Crystallization of TCF4 in complex with unmodified or 5caC-modified oligonucleotides revealed that the basic region of bHLH domain adopts multiple conformations, including an extended loop going through the DNA minor groove, or the N-terminal portion of a long helix binding in the DNA major groove. The different protein conformations enable arginine 576 (R576) to interact, respectively, with a thymine in the minor groove, a phosphate group of DNA backbone, or 5caC in the major groove. The Pitt-Hopkins syndrome mutations affect five arginine residues in the basic region, two of them (R569 and R576) involved in 5caC recognition. Our analyses indicate, and suggest a structural basis for, the preferential recognition of 5caC by a transcription factor centrally important in brain development.
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Affiliation(s)
- Jie Yang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John R Horton
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jia Li
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Yun Huang
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Xing Zhang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xiaodong Cheng
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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