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Ma J, Qi R, Harcourt EM, Chen YT, Barbosa GM, Peng Z, Howarth S, Delaney S, Li D. 3,N4-Etheno-5-methylcytosine blocks TET1-3 oxidation but is repaired by ALKBH2, 3 and FTO. Nucleic Acids Res 2024:gkae818. [PMID: 39315710 DOI: 10.1093/nar/gkae818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 09/04/2024] [Accepted: 09/11/2024] [Indexed: 09/25/2024] Open
Abstract
5-Methyldeoxycytidine (5mC) is a major epigenetic marker that regulates cellular functions in mammals. Endogenous lipid peroxidation can convert 5mC into 3,N4-etheno-5-methylcytosine (ϵ5mC). ϵ5mC is structurally similar to the mutagenic analog 3,N4-ethenocytosine (ϵC), which is repaired by AlkB family enzymes in the direct reversal repair (DRR) pathway and excised by DNA glycosylases in the base excision repair (BER) pathway. However, the repair of ϵ5mC has not been reported. Here, we examined the activities against ϵ5mC by DRR and BER enzymes and TET1-3, enzymes that modify the 5-methyl group in 5mC. We found that the etheno modification of 5mC blocks oxidation by TET1-3. Conversely, three human homologs in the AlkB family, ALKBH2, 3 and FTO were able to repair ϵ5mC to 5mC, which was subsequently modified by TET1 to 5-hydroxymethylcytosine. We also demonstrated that ALKBH2 likely repairs ϵ5mC in MEF cells. Another homolog, ALKBH5, could not repair ϵ5mC. Also, ϵ5mC is not a substrate for BER glycosylases SMUG1, AAG, or TDG. These findings indicate DRR committed by ALKBH2, 3 and FTO could reduce the detrimental effects of ϵ5mC in genetics and epigenetics and may work together with TET enzymes to modulate epigenetic regulations.
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Affiliation(s)
- Jian Ma
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston RI 02881, USA
| | - Rui Qi
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston RI 02881, USA
| | - Emily M Harcourt
- Department of Chemistry, Le Moyne College, Syracuse, NY 13214, USA
| | - Yi-Tzai Chen
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston RI 02881, USA
| | | | - Zhiyuan Peng
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston RI 02881, USA
| | - Samuel Howarth
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston RI 02881, USA
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, RI 02912, USA
| | - Deyu Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston RI 02881, USA
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Wang H, Xie L, Guo H, Li L, Chen S, Fan Y, Tian J, Xu L, Kong X, Xuan A. m 1A demethylase Alkbh3 regulates neurogenesis through m 1A demethylation of Mmp15 mRNA. Cell Biosci 2024; 14:92. [PMID: 39004750 PMCID: PMC11246583 DOI: 10.1186/s13578-024-01275-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 07/10/2024] [Indexed: 07/16/2024] Open
Abstract
BACKGROUND N1-Methyladenosine (m1A) is an abundant modification of transcripts regulating mRNA structure and translation efficiency. However, the characteristics and biological functions of mRNA m1A modification in adult hippocampal neurogenesis remain enigmatic. RESULTS We found that m1A demethylase Alkbh3 was dramatically enriched in neurons and neuronal genesis. Functionally, depletion of Alkbh3 in neural stem cells (NSCs) significantly decreased m1A modification, neuronal differentiation and proliferation coupling with increasing gliogenesis, whereas overexpressing Alkbh3 facilitated neuronal differentiation and proliferation. Mechanistically, the m1A demethylation of Mmp15 mRNA by Alkbh3 improved its RNA stability and translational efficacy, which promoted neurogenesis. Therapeutically, the silencing of Alkbh3 reduced hippocampal neurogenesis and impaired spatial memory in the adult mice. CONCLUSIONS We reveal a novel function of m1A demethylation on Mmp15 mRNA in Alkbh3-mediated neurogenesis, which shed light on advancing Alkbh3 regulation of neurogenesis as a novel neurotherapeutic strategy.
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Affiliation(s)
- Huan Wang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Linjie Xie
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Haomin Guo
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Lishi Li
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Shuwei Chen
- School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Ye Fan
- Scientific Research Center of Guangzhou Medical University, Guangzhou, 511436, China
| | - Jingyuan Tian
- Scientific Research Center of Guangzhou Medical University, Guangzhou, 511436, China
| | - Liping Xu
- Scientific Research Center of Guangzhou Medical University, Guangzhou, 511436, China.
- The Affiliated TCM Hospital of Guangzhou Medical University, Guangzhou, 510645, China.
| | - Xuejian Kong
- Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, 511518, China.
| | - Aiguo Xuan
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China.
- School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 511436, China.
- Scientific Research Center of Guangzhou Medical University, Guangzhou, 511436, China.
- Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, 511518, China.
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Guilbaud A, Ghanegolmohammadi F, Wang Y, Leng J, Kreymerman A, Gamboa Varela J, Garbern J, Elwell H, Cao F, Ricci-Blair E, Liang C, Balamkundu S, Vidoudez C, DeMott M, Bedi K, Margulies K, Bennett D, Palmer A, Barkley-Levenson A, Lee R, Dedon P. Discovery adductomics provides a comprehensive portrait of tissue-, age- and sex-specific DNA modifications in rodents and humans. Nucleic Acids Res 2023; 51:10829-10845. [PMID: 37843128 PMCID: PMC10639045 DOI: 10.1093/nar/gkad822] [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: 04/20/2023] [Revised: 08/27/2023] [Accepted: 09/27/2023] [Indexed: 10/17/2023] Open
Abstract
DNA damage causes genomic instability underlying many diseases, with traditional analytical approaches providing minimal insight into the spectrum of DNA lesions in vivo. Here we used untargeted chromatography-coupled tandem mass spectrometry-based adductomics (LC-MS/MS) to begin to define the landscape of DNA modifications in rat and human tissues. A basis set of 114 putative DNA adducts was identified in heart, liver, brain, and kidney in 1-26-month-old rats and 111 in human heart and brain by 'stepped MRM' LC-MS/MS. Subsequent targeted analysis of these species revealed species-, tissue-, age- and sex-biases. Structural characterization of 10 selected adductomic signals as known DNA modifications validated the method and established confidence in the DNA origins of the signals. Along with strong tissue biases, we observed significant age-dependence for 36 adducts, including N2-CMdG, 5-HMdC and 8-Oxo-dG in rats and 1,N6-ϵdA in human heart, as well as sex biases for 67 adducts in rat tissues. These results demonstrate the potential of adductomics for discovering the true spectrum of disease-driving DNA adducts. Our dataset of 114 putative adducts serves as a resource for characterizing dozens of new forms of DNA damage, defining mechanisms of their formation and repair, and developing them as biomarkers of aging and disease.
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Affiliation(s)
- Axel Guilbaud
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Farzan Ghanegolmohammadi
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Yijun Wang
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jiapeng Leng
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Alexander Kreymerman
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Jacqueline Gamboa Varela
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jessica Garbern
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Hannah Elwell
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Fang Cao
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Elisabeth M Ricci-Blair
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Cui Liang
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore
| | - Seetharamsing Balamkundu
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore
| | - Charles Vidoudez
- Harvard Center for Mass Spectrometry, Harvard University, Cambridge, MA 02138, USA
| | - Michael S DeMott
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Kenneth Bedi
- University of Pennsylvania Cardiovascular Institute, Philadelphia, PA, USA
| | | | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | | | - Richard T Lee
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore
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4
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Peng Z, Ma J, Christov CZ, Karabencheva-Christova T, Lehnert N, Li D. Kinetic Studies on the 2-Oxoglutarate/Fe(II)-Dependent Nucleic Acid Modifying Enzymes from the AlkB and TET Families. DNA 2023; 3:65-84. [PMID: 38698914 PMCID: PMC11065319 DOI: 10.3390/dna3020005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Nucleic acid methylations are important genetic and epigenetic biomarkers. The formation and removal of these markers is related to either methylation or demethylation. In this review, we focus on the demethylation or oxidative modification that is mediated by the 2-oxoglutarate (2-OG)/Fe(II)-dependent AlkB/TET family enzymes. In the catalytic process, most enzymes oxidize 2-OG to succinate, in the meantime oxidizing methyl to hydroxymethyl, leaving formaldehyde and generating demethylated base. The AlkB enzyme from Escherichia coli has nine human homologs (ALKBH1-8 and FTO) and the TET family includes three members, TET1 to 3. Among them, some enzymes have been carefully studied, but for certain enzymes, few studies have been carried out. This review focuses on the kinetic properties of those 2-OG/Fe(II)-dependent enzymes and their alkyl substrates. We also provide some discussions on the future directions of this field.
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Affiliation(s)
- Zhiyuan Peng
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Jian Ma
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Christo Z. Christov
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA
| | | | - Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Deyu Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
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5
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Li Q, Zhu Q. The role of demethylase AlkB homologs in cancer. Front Oncol 2023; 13:1153463. [PMID: 37007161 PMCID: PMC10060643 DOI: 10.3389/fonc.2023.1153463] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/03/2023] [Indexed: 03/18/2023] Open
Abstract
The AlkB family (ALKBH1-8 and FTO), a member of the Fe (II)- and α-ketoglutarate-dependent dioxygenase superfamily, has shown the ability to catalyze the demethylation of a variety of substrates, including DNA, RNA, and histones. Methylation is one of the natural organisms’ most prevalent forms of epigenetic modifications. Methylation and demethylation processes on genetic material regulate gene transcription and expression. A wide variety of enzymes are involved in these processes. The methylation levels of DNA, RNA, and histones are highly conserved. Stable methylation levels at different stages can coordinate the regulation of gene expression, DNA repair, and DNA replication. Dynamic methylation changes are essential for the abilities of cell growth, differentiation, and division. In some malignancies, the methylation of DNA, RNA, and histones is frequently altered. To date, nine AlkB homologs as demethylases have been identified in numerous cancers’ biological processes. In this review, we summarize the latest advances in the research of the structures, enzymatic activities, and substrates of the AlkB homologs and the role of these nine homologs as demethylases in cancer genesis, progression, metastasis, and invasion. We provide some new directions for the AlkB homologs in cancer research. In addition, the AlkB family is expected to be a new target for tumor diagnosis and treatment.
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Affiliation(s)
- Qiao Li
- Department of Orthopedic Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
- Department of Spine Surgery, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Qingsan Zhu
- Department of Orthopedic Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
- *Correspondence: Qingsan Zhu,
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6
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Li X, Cao G, Liu X, Tang TS, Guo C, Liu H. Polymerases and DNA Repair in Neurons: Implications in Neuronal Survival and Neurodegenerative Diseases. Front Cell Neurosci 2022; 16:852002. [PMID: 35846567 PMCID: PMC9279898 DOI: 10.3389/fncel.2022.852002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/23/2022] [Indexed: 12/22/2022] Open
Abstract
Most of the neurodegenerative diseases and aging are associated with reactive oxygen species (ROS) or other intracellular damaging agents that challenge the genome integrity of the neurons. As most of the mature neurons stay in G0/G1 phase, replication-uncoupled DNA repair pathways including BER, NER, SSBR, and NHEJ, are pivotal, efficient, and economic mechanisms to maintain genomic stability without reactivating cell cycle. In these progresses, polymerases are prominent, not only because they are responsible for both sensing and repairing damages, but also for their more diversified roles depending on the cell cycle phase and damage types. In this review, we summarized recent knowledge on the structural and biochemical properties of distinct polymerases, including DNA and RNA polymerases, which are known to be expressed and active in nervous system; the biological relevance of these polymerases and their interactors with neuronal degeneration would be most graphically illustrated by the neurological abnormalities observed in patients with hereditary diseases associated with defects in DNA repair; furthermore, the vicious cycle of the trinucleotide repeat (TNR) and impaired DNA repair pathway is also discussed. Unraveling the mechanisms and contextual basis of the role of the polymerases in DNA damage response and repair will promote our understanding about how long-lived postmitotic cells cope with DNA lesions, and why disrupted DNA repair contributes to disease origin, despite the diversity of mutations in genes. This knowledge may lead to new insight into the development of targeted intervention for neurodegenerative diseases.
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Affiliation(s)
- Xiaoling Li
- Nano-Biotechnology Key Lab of Hebei Province, Yanshan University, Qinhuangdao, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
- Xiaoling Li
| | - Guanghui Cao
- Nano-Biotechnology Key Lab of Hebei Province, Yanshan University, Qinhuangdao, China
| | - Xiaokang Liu
- Nano-Biotechnology Key Lab of Hebei Province, Yanshan University, Qinhuangdao, China
| | - Tie-Shan Tang
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Caixia Guo
- Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
- *Correspondence: Caixia Guo
| | - Hongmei Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Hongmei Liu
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7
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Cheng W, Ma J, Tao Q, Adeel K, Xiang L, Liu D, Zhang Z, Li J. Demethylation of m1A assisted degradation of the signal probe for rapid electrochemical detection of ALKBH3 activity with practical applications. Talanta 2021; 240:123151. [PMID: 34942472 DOI: 10.1016/j.talanta.2021.123151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 12/03/2021] [Accepted: 12/14/2021] [Indexed: 11/17/2022]
Abstract
ALKBH3 is an important marker for early diagnosis and histopathological grading of prostate cancer. However, the lack of a rapid and sensitive method to quantify the enzyme's activity in the current time necessitates the development of a new quantitative assay. Herein, we first tried to quantitative assay for ALKBH3 activity using an electrochemical method based on the degradation of the signal probe due to alkyl group of the m1A removal by ALKBH3. A strong electrochemical signal can be obtained when the ferrocene (Fc) labeled dsDNAs with 1-methyladenine are immobilized on the electrode. In the presence of ALKBH3, the 3' blunt of DNA can be formed because of the removal of alkyl group of the Fc-DNA probe, which can be recognized and degraded by Exonuclease III (Exo III). As a result, the electrochemical signal produced by Fc greatly decreases, and the activity of ALKBH3 can be easily detected via changes in electrochemical signal. Quantitative analysis of ALKBH3 activity showed a wide detection range (0.1 and 20 ng/mL) and low detection limit (0.04 ng/mL). Furthermore, the method can be applied to detect 1-methyladenine through ALKBH3 in cell lysates and tissue samples, providing a new method for clinical detection of prostate cancer.
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Affiliation(s)
- Wenting Cheng
- Department of Clinical Laboratory, Nanjing Gaochun People's Hospital, Nanjing, 211300, PR China
| | - Jiehua Ma
- Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, 210004, PR China
| | - Qinfang Tao
- Department of Clinical Laboratory, Nanjing Gaochun People's Hospital, Nanjing, 211300, PR China
| | - Khan Adeel
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210000, PR China
| | - Liangliang Xiang
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, 210003, PR China
| | - Duxian Liu
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, 210003, PR China
| | - Zhaoli Zhang
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, 210003, PR China
| | - Jinlong Li
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, 210003, PR China.
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8
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Yao L, Yin H, Hong M, Wang Y, Yu T, Teng Y, Li T, Wu Q. RNA methylation in hematological malignancies and its interactions with other epigenetic modifications. Leukemia 2021; 35:1243-1257. [PMID: 33767371 DOI: 10.1038/s41375-021-01225-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 02/12/2021] [Accepted: 03/11/2021] [Indexed: 01/18/2023]
Abstract
Hematological malignancies are a class of malignant neoplasms attributed to abnormal differentiation of hematopoietic stem cells (HSCs). The systemic involvement, poor prognosis, chemotherapy resistance, and recurrence common in hematological malignancies urge researchers to look for novel treatment targets and mechanisms. In recent years, epigenetic abnormalities have been shown to play a vital role in tumorigenesis and progression in hematological malignancies. In addition to DNA methylation and histone modifications, which are most studied, RNA methylation has become increasingly significant. In this review, we elaborate recent advances in the understanding of RNA modification in the pathogenesis, diagnosis and molecular targeted therapies of hematological malignancies and discuss its intricate interactions with other epigenetic modifications, including DNA methylation, histone modifications and noncoding RNAs.
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Affiliation(s)
- Lan Yao
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hua Yin
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mei Hong
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Yajun Wang
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tingting Yu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yao Teng
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tingting Li
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qiuling Wu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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9
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He X, Wang P, Wang Y. Mitochondrial Transcription Factor A Binds to and Promotes Mutagenic Transcriptional Bypass of O4-Alkylthymidine Lesions. Anal Chem 2021; 93:1161-1169. [PMID: 33290046 PMCID: PMC7904241 DOI: 10.1021/acs.analchem.0c04224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
O2- and O4-alkylated thymidine lesions are known to be poorly repaired and persist in mammalian tissues. To understand how mammalian cells sense the presence and regulate the repair of these lesions, we employed a quantitative proteomic method to discover regioisomeric O2- and O4-n-butylthymidine (O2- and O4-nBudT)-binding proteins. We were able to identify 21 and 74 candidate DNA damage recognition proteins for O2-nBudT- and O4-nBudT-bearing DNA probes, respectively. Among these proteins, DDB1 and DDB2 selectively bind to O2-nBudT-containing DNA, whereas three high-mobility group (HMG) proteins (i.e., HMGB1, HMGB2, and mitochondrial transcription factor A (TFAM)) exhibit preferential binding to O4-nBudT-bearing DNA. We further demonstrated that TFAM binds directly and selectively with O4-alkyldT-harboring DNA, and the binding capacity depends mainly on the HMG box-A domain of TFAM. We also found that TFAM promotes transcriptional mutagenesis of O4-nBudT and O4-pyridyloxobutylthymidine, which is a DNA adduct induced by tobacco-specific N-nitrosamines, in vitro and in human cells. Together, we explored, for the first time, the interaction proteomes of O-alkyldT lesions, and our study expanded the functions of TFAM by revealing its capability in the recognition of O4-alkyldT-bearing DNA and uncovering its modulation of transcriptional mutagenesis of these lesions in human cells.
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Affiliation(s)
- Xiaomei He
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Pengcheng Wang
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
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10
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Xu B, Liu D, Wang Z, Tian R, Zuo Y. Multi-substrate selectivity based on key loops and non-homologous domains: new insight into ALKBH family. Cell Mol Life Sci 2021; 78:129-141. [PMID: 32642789 PMCID: PMC11072825 DOI: 10.1007/s00018-020-03594-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/24/2020] [Accepted: 07/03/2020] [Indexed: 12/16/2022]
Abstract
AlkB homologs (ALKBH) are a family of specific demethylases that depend on Fe2+ and α-ketoglutarate to catalyze demethylation on different substrates, including ssDNA, dsDNA, mRNA, tRNA, and proteins. Previous studies have made great progress in determining the sequence, structure, and molecular mechanism of the ALKBH family. Here, we first review the multi-substrate selectivity of the ALKBH demethylase family from the perspective of sequence and structural evolution. The construction of the phylogenetic tree and the comparison of key loops and non-homologous domains indicate that the paralogs with close evolutionary relationship have similar domain compositions. The structures show that the lack and variations of four key loops change the shape of clefts to cause the differences in substrate affinity, and non-homologous domains may be related to the compatibility of multiple substrates. We anticipate that the new insights into selectivity determinants of the ALKBH family are useful for understanding the demethylation mechanisms.
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Affiliation(s)
- Baofang Xu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Dongyang Liu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zerong Wang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Ruixia Tian
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yongchun Zuo
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
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11
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Xiao MZ, Liu JM, Xian CL, Chen KY, Liu ZQ, Cheng YY. Therapeutic potential of ALKB homologs for cardiovascular disease. Biomed Pharmacother 2020; 131:110645. [PMID: 32942149 DOI: 10.1016/j.biopha.2020.110645] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/05/2020] [Accepted: 08/16/2020] [Indexed: 02/06/2023] Open
Abstract
Cardiovascular diseases (CVDs) are the leading causes of human death. Recently, ALKB homologs, including ALKBH1-8 and FTO, have been found to have a variety of biological functions, such as histone demethylation, RNA demethylation, and DNA demethylation. These functions may regulate the physiological and pathological processes of CVDs, including inflammation, oxidative stress, cell apoptosis, and mitochondrial, endothelial, and fat metabolism dysfunction. In the present review, we summarize the biological functions of ALKB homologs and the relationship between the ALKB homologs and CVDs. Importantly, we discuss the roles of ALKB homologs in the regulation of oxidative stress, inflammation, autophagy, and DNA damage in CVDs, as well as the practical applications of ALKB homologs inhibitors or agonists in treating CVDs. In conclusion, the ALKBH family might be a promising target for CVDs therapy.
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Affiliation(s)
- Ming-Zhu Xiao
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China; School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Jia-Ming Liu
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China; School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Cui-Ling Xian
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China; School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Keng-Yu Chen
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China; The Second Affiliated Hospital of Guangdong Pharmaceutical University, Yunfu, 527300, China
| | - Zhong-Qiu Liu
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China.
| | - Yuan-Yuan Cheng
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China.
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12
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Affiliation(s)
- Yang Yu
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
| | - Pengcheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Yuxiang Cui
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
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13
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Wu J, Wang P, Li L, Williams NL, Ji D, Zahurancik WJ, You C, Wang J, Suo Z, Wang Y. Replication studies of carboxymethylated DNA lesions in human cells. Nucleic Acids Res 2017; 45:7276-7284. [PMID: 28531304 PMCID: PMC5499590 DOI: 10.1093/nar/gkx442] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 05/04/2017] [Indexed: 12/11/2022] Open
Abstract
Metabolic activation of some N-nitroso compounds (NOCs), an important class of DNA damaging agents, can induce the carboxymethylation of nucleobases in DNA. Very little was previously known about how the carboxymethylated DNA lesions perturb DNA replication in human cells. Here, we investigated the effects of five carboxymethylated DNA lesions, i.e. O6-CMdG, N6-CMdA, N4-CMdC, N3-CMdT and O4-CMdT on the efficiency and fidelity of DNA replication in HEK293T human embryonic kidney cells. We found that, while neither N6-CMdA nor N4-CMdC blocked DNA replication or induced mutations, N3-CMdT, O4-CMdT and O6-CMdG moderately blocked DNA replication and induced substantial frequencies of T→A (81%), T→C (68%) and G→A (6.4%) mutations, respectively. In addition, our results revealed that CRISPR-Cas9-mediated depletion of Pol η resulted in significant drops in bypass efficiencies of N4-CMdC and N3-CMdT. Diminution in bypass efficiencies was also observed for N6-CMdA and O6-CMdG upon depletion of Pol κ, and for O6-CMdG upon removal of Pol ζ. Together, our study provided molecular-level insights into the impacts of the carboxymethylated DNA lesions on DNA replication in human cells, revealed the roles of individual translesion synthesis DNA polymerases in bypassing these lesions, and suggested the contributions of O6-CMdG, N3-CMdT and O4-CMdT to the mutations found in p53 gene of human gastrointestinal cancers.
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Affiliation(s)
- Jun Wu
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Pengcheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA
| | - Lin Li
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Nicole L Williams
- Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA
| | - Debin Ji
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Walter J Zahurancik
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Changjun You
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Jianshuang Wang
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Zucai Suo
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA 92521, USA.,Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA
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14
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Ignatov A, Bondarenko K, Makarova A. Non-bulky Lesions in Human DNA: the Ways of Formation, Repair, and Replication. Acta Naturae 2017; 9:12-26. [PMID: 29104772 PMCID: PMC5662270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Indexed: 11/06/2022] Open
Abstract
DNA damage is a major cause of replication interruption, mutations, and cell death. DNA damage is removed by several types of repair processes. The involvement of specialized DNA polymerases in replication provides an important mechanism that helps tolerate persistent DNA damage. Specialized DNA polymerases incorporate nucleotides opposite lesions with high efficiency but demonstrate low accuracy of DNA synthesis. In this review, we summarize the types and mechanisms of formation and repair of non-bulky DNA lesions, and we provide an overview of the role of specialized DNA polymerases in translesion DNA synthesis.
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Affiliation(s)
- A.V. Ignatov
- Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, Moscow, 123182 , Russia
- Department of Molecular Biology, Faculty of Biology, Moscow State University, Leninskie Gory 1, bldg. 12, Moscow, 119991, Russia
| | - K.A. Bondarenko
- Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, Moscow, 123182 , Russia
| | - A.V. Makarova
- Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, Moscow, 123182 , Russia
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15
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Yu Y, Wang J, Wang P, Wang Y. Quantification of Azaserine-Induced Carboxymethylated and Methylated DNA Lesions in Cells by Nanoflow Liquid Chromatography-Nanoelectrospray Ionization Tandem Mass Spectrometry Coupled with the Stable Isotope-Dilution Method. Anal Chem 2016; 88:8036-42. [PMID: 27441891 PMCID: PMC5038140 DOI: 10.1021/acs.analchem.6b01349] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Humans are exposed to N-nitroso compounds through environmental exposure and endogenous metabolism. Some N-nitroso compounds can be metabolically activated to yield diazoacetate, which is known to induce DNA carboxymethylation. DNA lesion measurement remains one of the core tasks in toxicology and in evaluating human health risks associated with carcinogen exposure. In this study, we developed a highly sensitive nanoflow liquid chromatography-nanoelectrospray ionization-multistage tandem mass spectrometry (nLC-nESI-MS(3)) method for the simultaneous quantification of O(6)-carboxymethyl-2'-deoxyguanosine (O(6)-CMdG), O(6)-methyl-2'-deoxyguanosine (O(6)-MedG), and N(6)-carboxymethyl-2'-deoxyadenosine (N(6)-CMdA). We were able to measure the levels of these three lesions with the use of low-microgram quantities of DNA from cultured human skin fibroblasts and human colorectal carcinoma cells treated with azaserine, a DNA carboxymethylating agent. Our results revealed that the levels of O(6)-CMdG and O(6)-MedG increased when the dose of azaserine was increased from 0 to 450 μM. We, however, did not observe an apparent dose-dependent induction of N(6)-CMdA, suggesting the presence of repair mechanism(s) for the rapid clearance of this lesion in cells. This is the first report about the application of nLC-nESI-MS(3) technique for the simultaneous quantification of O(6)-CMdG, O(6)-MedG, and N(6)-CMdA. The method reported here will be useful for future investigations about the repair of the carboxymethylated DNA lesions and about the implications of these lesions in carcinogenesis.
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Affiliation(s)
- Yang Yu
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
| | - Jianshuang Wang
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Pengcheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
- Department of Chemistry, University of California, Riverside, California 92521, United States
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