1
|
Fahrer J, Christmann M. DNA Alkylation Damage by Nitrosamines and Relevant DNA Repair Pathways. Int J Mol Sci 2023; 24:ijms24054684. [PMID: 36902118 PMCID: PMC10003415 DOI: 10.3390/ijms24054684] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/17/2023] [Accepted: 02/24/2023] [Indexed: 03/04/2023] Open
Abstract
Nitrosamines occur widespread in food, drinking water, cosmetics, as well as tobacco smoke and can arise endogenously. More recently, nitrosamines have been detected as impurities in various drugs. This is of particular concern as nitrosamines are alkylating agents that are genotoxic and carcinogenic. We first summarize the current knowledge on the different sources and chemical nature of alkylating agents with a focus on relevant nitrosamines. Subsequently, we present the major DNA alkylation adducts induced by nitrosamines upon their metabolic activation by CYP450 monooxygenases. We then describe the DNA repair pathways engaged by the various DNA alkylation adducts, which include base excision repair, direct damage reversal by MGMT and ALKBH, as well as nucleotide excision repair. Their roles in the protection against the genotoxic and carcinogenic effects of nitrosamines are highlighted. Finally, we address DNA translesion synthesis as a DNA damage tolerance mechanism relevant to DNA alkylation adducts.
Collapse
Affiliation(s)
- Jörg Fahrer
- Division of Food Chemistry and Toxicology, Department of Chemistry, RPTU Kaiserslautern-Landau, Erwin-Schrödinger Strasse 52, D-67663 Kaiserslautern, Germany
- Correspondence: (J.F.); (M.C.); Tel.: +496312052974 (J.F.); Tel: +496131179066 (M.C.)
| | - Markus Christmann
- Department of Toxicology, University Medical Center Mainz, Obere Zahlbacher Strasse 67, D-55131 Mainz, Germany
- Correspondence: (J.F.); (M.C.); Tel.: +496312052974 (J.F.); Tel: +496131179066 (M.C.)
| |
Collapse
|
2
|
Tsao N, Brickner JR, Rodell R, Ganguly A, Wood M, Oyeniran C, Ahmad T, Sun H, Bacolla A, Zhang L, Lukinović V, Soll JM, Townley BA, Casanova AG, Tainer JA, He C, Vindigni A, Reynoird N, Mosammaparast N. Aberrant RNA methylation triggers recruitment of an alkylation repair complex. Mol Cell 2021; 81:4228-4242.e8. [PMID: 34686315 DOI: 10.1016/j.molcel.2021.09.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 07/18/2021] [Accepted: 09/21/2021] [Indexed: 12/13/2022]
Abstract
Central to genotoxic responses is their ability to sense highly specific signals to activate the appropriate repair response. We previously reported that the activation of the ASCC-ALKBH3 repair pathway is exquisitely specific to alkylation damage in human cells. Yet the mechanistic basis for the selectivity of this pathway was not immediately obvious. Here, we demonstrate that RNA but not DNA alkylation is the initiating signal for this process. Aberrantly methylated RNA is sufficient to recruit ASCC, while an RNA dealkylase suppresses ASCC recruitment during chemical alkylation. In turn, recruitment of ASCC during alkylation damage, which is mediated by the E3 ubiquitin ligase RNF113A, suppresses transcription and R-loop formation. We further show that alkylated pre-mRNA is sufficient to activate RNF113A E3 ligase in vitro in a manner dependent on its RNA binding Zn-finger domain. Together, our work identifies an unexpected role for RNA damage in eliciting a specific response to genotoxins.
Collapse
Affiliation(s)
- Ning Tsao
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Joshua R Brickner
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Rebecca Rodell
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Adit Ganguly
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Matthew Wood
- Division of Oncology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA; Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Clement Oyeniran
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Tanveer Ahmad
- Institute for Advanced Biosciences, Grenoble Alpes University, CNRS UMR5309, INSERM U1209, Grenoble, France
| | - Hua Sun
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Lisheng Zhang
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Institute for Biophysical Dynamics, University of Chicago, Chicago IL 60637, USA
| | - Valentina Lukinović
- Institute for Advanced Biosciences, Grenoble Alpes University, CNRS UMR5309, INSERM U1209, Grenoble, France
| | - Jennifer M Soll
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Brittany A Townley
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Alexandre G Casanova
- Institute for Advanced Biosciences, Grenoble Alpes University, CNRS UMR5309, INSERM U1209, Grenoble, France
| | - John A Tainer
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Chuan He
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Institute for Biophysical Dynamics, University of Chicago, Chicago IL 60637, USA; Howard Hughes Medical Institute, University of Chicago, Chicago IL 60637, USA
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Nicolas Reynoird
- Institute for Advanced Biosciences, Grenoble Alpes University, CNRS UMR5309, INSERM U1209, Grenoble, France
| | - Nima Mosammaparast
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA.
| |
Collapse
|
3
|
Fang S, Eriyagama D, Yuan Y, Shahsavari S, Chen J, Lin X, Halami B. Dim and Dmoc Protecting Groups for Oligodeoxynucleotide Synthesis. ACTA ACUST UNITED AC 2021; 82:e111. [PMID: 32628352 DOI: 10.1002/cpnc.111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This protocol provides details for the preparation of nucleoside phosphoramidites with 1,3-dithian-2-yl-methyl (Dim) and 1,3-dithian-2-yl-methoxycarbonyl (Dmoc) as protecting groups, and a linker with Dmoc as the cleavable function, then using them for solid phase synthesis of sensitive oligodeoxynucleotides (ODNs). Using these Dim-Dmoc phosphoramidites and Dmoc linker, ODN synthesis can be achieved under typical conditions using phosphoramidite chemistry with slight modifications, and ODN deprotection and cleavage can be achieved under mild conditions involving oxidation with sodium periodate at pH 4 followed by aniline at pH 8. Under the mild deprotection and cleavage conditions, many sensitive functional groups including but not limited to esters, thioesters, alkyl halides, N-aryl amides, and α-chloroamides-which cannot survive the basic and nucleophilic deprotection and cleavage conditions such as concentrated ammonium hydroxide and dilute potassium methoxide used in typical ODN synthesis technologies-can survive. Thus, it is expected that the Dim-Dmoc ODN synthesis technology will find applications in the synthesis of ODNs that contain a wide range of sensitive functional groups. © 2020 Wiley Periodicals LLC. Basic Protocol: Synthesis, deprotection, cleavage, and purification of sensitive oligodeoxynucleotides Support Protocol 1: Synthesis of Dim-Dmoc nucleoside phosphoramidites Support Protocol 2: Preparation of CPG with a Dmoc linker Support Protocol 3: Synthesis of a phosphoramidite containing a sensitive alkyl ester group.
Collapse
Affiliation(s)
- Shiyue Fang
- Department of Chemistry, Michigan Technological University, Houghton, Michigan
| | | | - Yinan Yuan
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan
| | - Shahien Shahsavari
- Department of Chemistry, Michigan Technological University, Houghton, Michigan
| | - Jinsen Chen
- Department of Chemistry, Michigan Technological University, Houghton, Michigan
| | - Xi Lin
- Department of Chemistry, Michigan Technological University, Houghton, Michigan
| | - Bhaskar Halami
- Department of Chemistry, Michigan Technological University, Houghton, Michigan
| |
Collapse
|
4
|
Yang Y, Xu X. Identification of key genes in coronary artery disease: an integrative approach based on weighted gene co-expression network analysis and their correlation with immune infiltration. Aging (Albany NY) 2021; 13:8306-8319. [PMID: 33686958 PMCID: PMC8034924 DOI: 10.18632/aging.202638] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/29/2021] [Indexed: 12/04/2022]
Abstract
This study aimed to identify key genes related to coronary artery disease (CAD) and its association with immune cells infiltration. GSE20680 and GSE20681 were downloaded from GEO. We identified red and pink modules in WGCNA analysis and found 104 genes in these two modules. Next, least absolute shrinkage and selection operator (LASSO) logistic regression was used to screen and verify the diagnostic markers of CAD. We identified ASCC2, LRRC18, and SLC25A37 as the key genes in CAD diagnosis. We further studied the immune cells infiltration in CAD patients with CIBERSORT, and the correlation between key genes and infiltrating immune cells was analyzed. We also found immune cells, including macrophages M0, mast cells resting and T cells CD8, were associated with ASCC2, LRRC18 and SLC25A37. Gene enrichment analysis indicated that these genes mainly enriched in apoptotic signaling pathway for biological pathway analysis, riboflavin metabolism for KEGG analysis. The diagnostic efficiency of these key genes measured by AUC in the training set, testing set and validation cohort was 0.92, 0.96 and 0.83, respectively. In conclusion, ASCC2, LRRC18 and SLC25A37 can be used as diagnostic markers of CAD, and immune cell infiltration plays an important role in the onset and development of CAD.
Collapse
Affiliation(s)
- Yang Yang
- Fourth Affiliated Hospital of China Medical University, Huanggu, Shenyang 110032, Liaoning, China
| | - Xiangshan Xu
- Fourth Affiliated Hospital of China Medical University, Huanggu, Shenyang 110032, Liaoning, China
| |
Collapse
|
5
|
Peng Y, Pei H. DNA alkylation lesion repair: outcomes and implications in cancer chemotherapy. J Zhejiang Univ Sci B 2021; 22:47-62. [PMID: 33448187 DOI: 10.1631/jzus.b2000344] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Alkylated DNA lesions, induced by both exogenous chemical agents and endogenous metabolites, represent a major form of DNA damage in cells. The repair of alkylation damage is critical in all cells because such damage is cytotoxic and potentially mutagenic. Alkylation chemotherapy is a major therapeutic modality for many tumors, underscoring the importance of the repair pathways in cancer cells. Several different pathways exist for alkylation repair, including base excision and nucleotide excision repair, direct reversal by methyl-guanine methyltransferase (MGMT), and dealkylation by the AlkB homolog (ALKBH) protein family. However, maintaining a proper balance between these pathways is crucial for the favorable response of an organism to alkylating agents. Here, we summarize the progress in the field of DNA alkylation lesion repair and describe the implications for cancer chemotherapy.
Collapse
Affiliation(s)
- Yihan Peng
- Department of Biochemistry and Molecular Medicine, the George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA.,GW Cancer Center, the George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
| | - Huadong Pei
- Department of Biochemistry and Molecular Medicine, the George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA. .,GW Cancer Center, the George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA.
| |
Collapse
|