1
|
Majumdar C, Demir M, Merrill SR, Hashemian M, David SS. FSHing for DNA Damage: Key Features of MutY Detection of 8-Oxoguanine:Adenine Mismatches. Acc Chem Res 2024; 57:1019-1031. [PMID: 38471078 PMCID: PMC10993402 DOI: 10.1021/acs.accounts.3c00759] [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: 12/01/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 03/14/2024]
Abstract
Base excision repair (BER) enzymes are genomic superheroes that stealthily and accurately identify and remove chemically modified DNA bases. DNA base modifications erode the informational content of DNA and underlie many disease phenotypes, most conspicuously, cancer. The "OG" of oxidative base damage, 8-oxo-7,8-dihydroguanine (OG), is particularly insidious due to its miscoding ability that leads to the formation of rare, pro-mutagenic OG:A mismatches. Thwarting mutagenesis relies on the capture of OG:A mismatches prior to DNA replication and removal of the mis-inserted adenine by MutY glycosylases to initiate BER. The threat of OG and the importance of its repair are underscored by the association between inherited dysfunctional variants of the MutY human homologue (MUTYH) and colorectal cancer, known as MUTYH-associated polyposis (MAP). Our functional studies of the two founder MUTYH variants revealed that both have compromised activity and a reduced affinity for OG:A mismatches. Indeed, these studies underscored the challenge of the recognition of OG:A mismatches that are only subtly structurally different than T:A base pairs. Since the original discovery of MAP, many MUTYH variants have been reported, with most considered to be "variants of uncertain significance." To reveal features associated with damage recognition and adenine excision by MutY and MUTYH, we have developed a multipronged chemical biology approach combining enzyme kinetics, X-ray crystallography, single-molecule visualization, and cellular repair assays. In this review, we highlight recent work in our laboratory where we defined MutY structure-activity relationship (SAR) studies using synthetic analogs of OG and A in cellular and in vitro assays. Our studies revealed the 2-amino group of OG as the key distinguishing feature of OG:A mismatches. Indeed, the unique position of the 2-amino group in the major groove of OGsyn:Aanti mismatches provides a means for its rapid detection among a large excess of highly abundant and structurally similar canonical base pairs. Furthermore, site-directed mutagenesis and structural analysis showed that a conserved C-terminal domain β-hairpin "FSH'' loop is critical for OG recognition with the "His" serving as the lesion detector. Notably, MUTYH variants located within and near the FSH loop have been associated with different forms of cancer. Uncovering the role(s) of this loop in lesion recognition provided a detailed understanding of the search and repair process of MutY. Such insights are also useful to identify mutational hotspots and pathogenic variants, which may improve the ability of physicians to diagnose the likelihood of disease onset and prognosis. The critical importance of the "FSH" loop in lesion detection suggests that it may serve as a unique locus for targeting probes or inhibitors of MutY/MUTYH to provide new chemical biology tools and avenues for therapeutic development.
Collapse
Affiliation(s)
- Chandrima Majumdar
- Department of Chemistry, University
of California, Davis, California 95616, United States
| | - Merve Demir
- Department of Chemistry, University
of California, Davis, California 95616, United States
| | - Steven R. Merrill
- Department of Chemistry, University
of California, Davis, California 95616, United States
| | - Mohammad Hashemian
- Department of Chemistry, University
of California, Davis, California 95616, United States
| | - Sheila S. David
- Department of Chemistry, University
of California, Davis, California 95616, United States
| |
Collapse
|
2
|
Conlon S, Khuu C, Trasviña-Arenas CH, Xia T, Hamm ML, Raetz AG, David SS. Cellular Repair of Synthetic Analogs of Oxidative DNA Damage Reveals a Key Structure-Activity Relationship of the Cancer-Associated MUTYH DNA Repair Glycosylase. ACS CENTRAL SCIENCE 2024; 10:291-301. [PMID: 38435525 PMCID: PMC10906249 DOI: 10.1021/acscentsci.3c00784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 03/05/2024]
Abstract
The base excision repair glycosylase MUTYH prevents mutations associated with the oxidatively damaged base, 8-oxo-7,8-dihydroguanine (OG), by removing undamaged misincorporated adenines from OG:A mispairs. Defects in OG:A repair in individuals with inherited MUTYH variants are correlated with the colorectal cancer predisposition syndrome known as MUTYH-associated polyposis (MAP). Herein, we reveal key structural features of OG required for efficient repair by human MUTYH using structure-activity relationships (SAR). We developed a GFP-based plasmid reporter assay to define SAR with synthetically generated OG analogs in human cell lines. Cellular repair results were compared with kinetic parameters measured by adenine glycosylase assays in vitro. Our results show substrates lacking the 2-amino group of OG, such as 8OI:A (8OI = 8-oxoinosine), are not repaired in cells, despite being excellent substrates in in vitro adenine glycosylase assays, new evidence that the search and detection steps are critical factors in cellular MUTYH repair functionality. Surprisingly, modification of the O8/N7H of OG, which is the distinguishing feature of OG relative to G, was tolerated in both MUTYH-mediated cellular repair and in vitro adenine glycosylase activity. The lack of sensitivity to alterations at the O8/N7H in the SAR of MUTYH substrates is distinct from previous work with bacterial MutY, indicating that the human enzyme is much less stringent in its lesion verification. Our results imply that the human protein relies almost exclusively on detection of the unique major groove position of the 2-amino group of OG within OGsyn:Aanti mispairs to select contextually incorrect adenines for excision and thereby thwart mutagenesis. These results predict that MUTYH variants that exhibit deficiencies in OG:A detection will be severely compromised in a cellular setting. Moreover, the reliance of MUTYH on the interaction with the OG 2-amino group suggests that disrupting this interaction with small molecules may provide a strategy to develop potent and selective MUTYH inhibitors.
Collapse
Affiliation(s)
- Savannah
G. Conlon
- Department
of Chemistry, University of California,
Davis, One Shields Avenue, Davis, California 95616, United States
- Graduate
Program in Chemistry and Chemical Biology, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Cindy Khuu
- Department
of Chemistry, University of California,
Davis, One Shields Avenue, Davis, California 95616, United States
- Biochemistry,
Molecular, Cellular and Developmental Biology Graduate Group, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Carlos H. Trasviña-Arenas
- Department
of Chemistry, University of California,
Davis, One Shields Avenue, Davis, California 95616, United States
| | - Tian Xia
- Department
of Chemistry, University of California,
Davis, One Shields Avenue, Davis, California 95616, United States
- Graduate
Program in Chemistry and Chemical Biology, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Michelle L. Hamm
- Department
of Chemistry, University of Richmond, 410 Westhampton Way, Richmond, Virginia 23173, United States
| | - Alan G. Raetz
- Department
of Chemistry, University of California,
Davis, One Shields Avenue, Davis, California 95616, United States
- Biochemistry,
Molecular, Cellular and Developmental Biology Graduate Group, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Sheila S. David
- Department
of Chemistry, University of California,
Davis, One Shields Avenue, Davis, California 95616, United States
- Graduate
Program in Chemistry and Chemical Biology, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
- Biochemistry,
Molecular, Cellular and Developmental Biology Graduate Group, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| |
Collapse
|
3
|
Paller CJ, Tukachinsky H, Maertens A, Decker B, Sampson JR, Cheadle JP, Antonarakis ES. Pan-Cancer Interrogation of MUTYH Variants Reveals Biallelic Inactivation and Defective Base Excision Repair Across a Spectrum of Solid Tumors. JCO Precis Oncol 2024; 8:e2300251. [PMID: 38394468 PMCID: PMC10901435 DOI: 10.1200/po.23.00251] [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: 05/21/2023] [Revised: 11/22/2023] [Accepted: 12/11/2023] [Indexed: 02/25/2024] Open
Abstract
PURPOSE Biallelic germline pathogenic variants of the base excision repair (BER) pathway gene MUTYH predispose to colorectal cancer (CRC) and other cancers. The possible association of heterozygous variants with broader cancer susceptibility remains uncertain. This study investigated the prevalence and consequences of pathogenic MUTYH variants and MUTYH loss of heterozygosity (LOH) in a large pan-cancer analysis. MATERIALS AND METHODS Data from 354,366 solid tumor biopsies that were sequenced as part of routine clinical care were analyzed using a validated algorithm to distinguish germline from somatic MUTYH variants. RESULTS Biallelic germline pathogenic MUTYH variants were identified in 119 tissue biopsies. Most were CRCs and showed increased tumor mutational burden (TMB) and a mutational signature consistent with defective BER (COSMIC Signature SBS18). Germline heterozygous pathogenic variants were identified in 5,991 biopsies and their prevalence was modestly elevated in some cancer types. About 12% of these cancers (738 samples: including adrenal gland cancers, pancreatic islet cell tumors, nonglioma CNS tumors, GI stromal tumors, and thyroid cancers) showed somatic LOH for MUTYH, higher rates of chromosome 1p loss (where MUTYH is located), elevated genomic LOH, and higher COSMIC SBS18 signature scores, consistent with BER deficiency. CONCLUSION This analysis of MUTYH alterations in a large set of solid cancers suggests that in addition to the established role of biallelic pathogenic MUTYH variants in cancer predisposition, a broader range of cancers may possibly arise in MUTYH heterozygotes via a mechanism involving somatic LOH at the MUTYH locus and defective BER. However, the effect is modest and requires confirmation in additional studies before being clinically actionable.
Collapse
Affiliation(s)
- Channing J Paller
- Johns Hopkins University School of Medicine, Oncology, Baltimore, MD
| | | | - Alexandra Maertens
- Johns Hopkins University, Bloomberg School of Public Health, Center for Alternatives to Animal Testing (CAAT), Baltimore, MD
| | | | - Julian R Sampson
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Jeremy P Cheadle
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Emmanuel S Antonarakis
- University of Minnesota Masonic Cancer Center, Division of Hematology, Oncology and Transplantation, Minneapolis, MN
| |
Collapse
|
4
|
Sugiyama T, Sanyal MR. Biochemical analysis of H 2O 2-induced mutation spectra revealed that multiple damages were involved in the mutational process. DNA Repair (Amst) 2024; 134:103617. [PMID: 38154332 PMCID: PMC10842480 DOI: 10.1016/j.dnarep.2023.103617] [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: 06/06/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 12/30/2023]
Abstract
Reactive oxygen species (ROS) are a major threat to genomic integrity and believed to be one of the etiologies of cancers. Here we developed a cell-free system to analyze ROS-induced mutagenesis, in which DNA was exposed to H2O2 and then subjected to translesion DNA synthesis by various DNA polymerases. Then, frequencies of mutations on the DNA products were determined by using next-generation sequencing technology. The majority of observed mutations were either C>A or G>A, caused by dAMP insertion at G and C residues, respectively. These mutations showed similar spectra to COSMIC cancer mutational signature 18 and 36, which are proposed to be caused by ROS. The in vitro mutations can be produced by replicative DNA polymerases (yeast DNA polymerase δ and ε), suggesting that ordinary DNA replication is sufficient to produce them. Very little G>A mutation was observed immediately after exposure to H2O2, but the frequency was increased during the 24 h after the ROS was removed, indicating that the initial oxidation product of cytosine needs to be maturated into a mutagenic lesion. Glycosylase-sensitivities of these mutations suggest that the C>A were made on 8-oxoguanine or Fapy-guanine, and that G>A were most likely made on 5-hydroxycytosine modification.
Collapse
Affiliation(s)
- Tomohiko Sugiyama
- Department of Biological Sciences, Ohio University, Athens, OH 45701, USA; Molecular and Cellular Biology Graduate Program, Ohio University, Athens, OH 45701, USA.
| | - Mahima R Sanyal
- Department of Biological Sciences, Ohio University, Athens, OH 45701, USA; Molecular and Cellular Biology Graduate Program, Ohio University, Athens, OH 45701, USA
| |
Collapse
|
5
|
Diao W, Farrell JD, Wang B, Ye F, Wang Z. Preorganized Internal Electric Field Promotes a Double-Displacement Mechanism for the Adenine Excision Reaction by Adenine DNA Glycosylase. J Phys Chem B 2023; 127:8551-8564. [PMID: 37782825 DOI: 10.1021/acs.jpcb.3c04928] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Adenine DNA glycosylase (MutY) is a monofunctional glycosylase, removing adenines (A) misinserted opposite 8-oxo-7,8-dihydroguanine (OG), a common product of oxidative damage to DNA. Through multiscale calculations, we decipher a detailed adenine excision mechanism of MutY that is consistent with all available experimental data, involving an initial protonation step and two nucleophilic displacement steps. During the first displacement step, N-glycosidic bond cleavage is accompanied by the attack of the carboxylate group of residue Asp144 at the anomeric carbon (C1'), forming a covalent glycosyl-enzyme intermediate to stabilize the fleeting oxocarbenium ion. After departure of the excised base, water nucleophiles can be recruited to displace Asp144, completing the catalytic cycle with retention of stereochemistry at the C1' position. The two displacement reactions are found to mostly involve the movement of the oxocarbenium ion, occurring with large charge reorganization and thus sensitive to the internal electric field (IEF) exerted by the polar protein environment. Intriguingly, we find that the negatively charged carboxylate group is a good nucleophile for the oxocarbenium ion, yet an unactivated water molecule is not, and that the electric field catalysis strategy is used by the enzyme to enable its unique double-displacement reaction mechanism. A strong IEF, pointing toward 5' direction of the substrate sugar ring, greatly facilitates the second displacement reaction at the expense of elevating the barrier of the first one, thereby allowing both reactions to occur. These findings not only increase our understanding of the strategies used by DNA glycosylases to repair DNA lesions, but also have important implications for how internal/external electric field can be applied to modulate chemical reactions.
Collapse
Affiliation(s)
- Wenwen Diao
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - James D Farrell
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Fangfu Ye
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang 325000, China
| | - Zhanfeng Wang
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
| |
Collapse
|
6
|
Osifová Z, Šála M, Dračínský M. Hydrogen-Bonding Interactions of 8-Substituted Purine Derivatives. ACS OMEGA 2023; 8:25538-25548. [PMID: 37483191 PMCID: PMC10357537 DOI: 10.1021/acsomega.3c03244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/21/2023] [Indexed: 07/25/2023]
Abstract
Hydrogen bonding between nucleobases is a crucial noncovalent interaction for life on Earth. Canonical nucleobases form base pairs according to two main geometries: Watson-Crick pairing, which enables the static functions of nucleic acids, such as the storing of genetic information; and Hoogsteen pairing, which facilitates the dynamic functions of these biomacromolecules. This precisely tuned system can be affected by oxidation or substitution of nucleobases, leading to changes in their hydrogen-bonding patterns. This paper presents an investigation into the intermolecular interactions of various 8-substituted purine derivatives with their hydrogen-bonding partners. The systems were analyzed using nuclear magnetic resonance spectroscopy and density functional theory calculations. Our results demonstrate that the stability of hydrogen-bonded complexes, or base pairs, depends primarily on the number of intermolecular H-bonds and their donor-acceptor alternation. No strong preferences for a particular geometry, either Watson-Crick or Hoogsteen, were found.
Collapse
Affiliation(s)
- Zuzana Osifová
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague 6, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 2030, 128 00 Prague, Czech Republic
| | - Michal Šála
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague 6, Czech Republic
| | - Martin Dračínský
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague 6, Czech Republic
| |
Collapse
|
7
|
Nischwitz E, Schoonenberg VA, Fradera-Sola A, Dejung M, Vydzhak O, Levin M, Luke B, Butter F, Scheibe M. DNA damage repair proteins across the Tree of Life. iScience 2023; 26:106778. [PMID: 37250769 PMCID: PMC10220248 DOI: 10.1016/j.isci.2023.106778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/27/2023] [Accepted: 04/25/2023] [Indexed: 05/31/2023] Open
Abstract
Genome maintenance is orchestrated by a highly regulated DNA damage response with specific DNA repair pathways. Here, we investigate the phylogenetic diversity in the recognition and repair of three well-established DNA lesions, primarily repaired by base excision repair (BER) and ribonucleotide excision repair (RER): (1) 8-oxoguanine, (2) abasic site, and (3) incorporated ribonucleotide in DNA in 11 species: Escherichia coli, Bacillus subtilis, Halobacterium salinarum, Trypanosoma brucei, Tetrahymena thermophila, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Caenorhabditis elegans, Homo sapiens, Arabidopsis thaliana, and Zea mays. Using quantitative mass spectrometry, we identified 337 binding proteins across these species. Of these proteins, 99 were previously characterized to be involved in DNA repair. Through orthology, network, and domain analysis, we linked 44 previously unconnected proteins to DNA repair. Our study presents a resource for future study of the crosstalk and evolutionary conservation of DNA damage repair across all domains of life.
Collapse
Affiliation(s)
| | | | | | - Mario Dejung
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Olga Vydzhak
- Institute of Developmental Biology and Neurobiology (IDN), Johannes-Gutenberg-University, 55128 Mainz, Germany
| | - Michal Levin
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Brian Luke
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
- Institute of Developmental Biology and Neurobiology (IDN), Johannes-Gutenberg-University, 55128 Mainz, Germany
| | - Falk Butter
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Marion Scheibe
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| |
Collapse
|
8
|
De Rosa M, Barnes RP, Nyalapatla PR, Wipf P, Opresko PL. OGG1 and MUTYH repair activities promote telomeric 8-oxoguanine induced cellular senescence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.10.536247. [PMID: 37090589 PMCID: PMC10120708 DOI: 10.1101/2023.04.10.536247] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Telomeres are prone to formation of the common oxidative lesion 8-oxoguanine (8oxoG), and the acute production of 8oxoG damage at telomeres is sufficient to drive rapid cellular senescence. OGG1 and MUTYH glycosylases initiate base excision repair (BER) at 8oxoG sites to remove the lesion or prevent mutation. Here, we show OGG1 loss or inhibition, or MUTYH loss, partially rescues telomeric 8oxoG-induced senescence, and loss of both glycosylases results in a near complete rescue. Loss of these glycosylases also suppresses 8oxoG-induced telomere fragility and dysfunction, indicating that single-stranded break (SSB) intermediates arising downstream of glycosylase activity impair telomere replication. The failure to initiate BER in glycosylase-deficient cells suppresses PARylation at SSB intermediates and confers resistance to the synergistic effects of PARP inhibitors on damage-induced senescence. Our studies reveal that inefficient completion of 8oxoG BER at telomeres triggers cellular senescence via SSB intermediates which impair telomere replication and stability.
Collapse
Affiliation(s)
- Mariarosaria De Rosa
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Ryan P. Barnes
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | | | - Peter Wipf
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Deparment of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Patricia L. Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| |
Collapse
|
9
|
Bowhead NEIL1: molecular cloning, characterization, and enzymatic properties. Biochimie 2023; 206:136-149. [PMID: 36334646 DOI: 10.1016/j.biochi.2022.10.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/19/2022] [Accepted: 10/25/2022] [Indexed: 11/08/2022]
Abstract
Nei Like DNA Glycosylase 1 (NEIL1) is a DNA glycosylase, which specifically processes oxidative DNA damage by initiating base excision repair. NEIL1 recognizes and removes bases, primarily oxidized pyrimidines, which have been damaged by endogenous oxidation or exogenous mutagenic agents. NEIL1 functions through a combined glycosylase/AP (apurinic/apyrimidinic)-lyase activity, whereby it cleaves the N-glycosylic bond between the DNA backbone and the damaged base via its glycosylase activity and hydrolysis of the DNA backbone through beta-delta elimination due to its AP-lyase activity. In our study we investigated our hypothesis proposing that the cancer resistance of the bowhead whale can be associated with a better DNA repair with NEIL1 being upregulated or more active. Here, we report the molecular cloning and characterization of three transcript variants of bowhead whale NEIL1 of which two were homologous to human transcripts. In addition, a novel NEIL1 transcript variant was found. A differential expression of NEIL mRNA was detected in bowhead eye, liver, kidney, and muscle. The A-to-I editing of NEIL1 mRNA was shown to be conserved in the bowhead and two adenosines in the 242Lys codon were subjected to editing. A mass spectroscopy analysis of liver and eye tissue failed to demonstrate the existence of a NEIL1 isoform originating from RNA editing. Recombinant bowhead and human NEIL1 were expressed in E. coli and assayed for enzymatic activity. Both bowhead and human recombinant NEIL1 catalyzed, with similar efficiency, the removal of a 5-hydroxyuracil lesion in a DNA bubble structure. Hence, these results do not support our hypothesis but do not refute the hypothesis either.
Collapse
|
10
|
Evolutionary Origin of Germline Pathogenic MUTYH Variations in Modern Humans. Biomolecules 2023; 13:biom13030429. [PMID: 36979362 PMCID: PMC10046817 DOI: 10.3390/biom13030429] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/30/2022] [Accepted: 01/04/2023] [Indexed: 03/02/2023] Open
Abstract
MUTYH plays an essential role in preventing oxidation-caused DNA damage. Pathogenic germline variations in MUTYH damage its function, causing intestinal polyposis and colorectal cancer. Determination of the evolutionary origin of the variation is essential to understanding the etiological relationship between MUTYH variation and cancer development. In this study, we analyzed the origins of pathogenic germline variants in human MUTYH. Using a phylogenic approach, we searched pathogenic MUTYH variants in modern humans in the MUTYH of 99 vertebrates across eight clades. We did not find pathogenic variants shared between modern humans and the non-human vertebrates following the evolutionary tree, ruling out the possibility of cross-species conservation as the origin of human pathogenic variants in MUTYH. We then searched the variants in the MUTYH of 5031 ancient humans and extinct Neanderthals and Denisovans. We identified 24 pathogenic variants in 42 ancient humans dated between 30,570 and 480 years before present (BP), and three pathogenic variants in Neanderthals dated between 65,000 and 38,310 years BP. Data from our study revealed that human pathogenic MUTYH variants mostly arose in recent human history and were partially inherited from Neanderthals.
Collapse
|
11
|
Demir M, Russelburg LP, Lin WJ, Trasviña-Arenas C, Huang B, Yuen P, Horvath M, David S. Structural snapshots of base excision by the cancer-associated variant MutY N146S reveal a retaining mechanism. Nucleic Acids Res 2023; 51:1034-1049. [PMID: 36631987 PMCID: PMC9943663 DOI: 10.1093/nar/gkac1246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/18/2022] [Accepted: 12/16/2022] [Indexed: 01/13/2023] Open
Abstract
DNA glycosylase MutY plays a critical role in suppression of mutations resulted from oxidative damage, as highlighted by cancer-association of the human enzyme. MutY requires a highly conserved catalytic Asp residue for excision of adenines misinserted opposite 8-oxo-7,8-dihydroguanine (OG). A nearby Asn residue hydrogen bonds to the catalytic Asp in structures of MutY and its mutation to Ser is an inherited variant in human MUTYH associated with colorectal cancer. We captured structural snapshots of N146S Geobacillus stearothermophilus MutY bound to DNA containing a substrate, a transition state analog and enzyme-catalyzed abasic site products to provide insight into the base excision mechanism of MutY and the role of Asn. Surprisingly, despite the ability of N146S to excise adenine and purine (P) in vitro, albeit at slow rates, N146S-OG:P complex showed a calcium coordinated to the purine base altering its conformation to inhibit hydrolysis. We obtained crystal structures of N146S Gs MutY bound to its abasic site product by removing the calcium from crystals of N146S-OG:P complex to initiate catalysis in crystallo or by crystallization in the absence of calcium. The product structures of N146S feature enzyme-generated β-anomer abasic sites that support a retaining mechanism for MutY-catalyzed base excision.
Collapse
Affiliation(s)
- Merve Demir
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - L Peyton Russelburg
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Wen-Jen Lin
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | | | - Beili Huang
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Philip K Yuen
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Martin P Horvath
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Sheila S David
- Department of Chemistry, University of California, Davis, CA 95616, USA
| |
Collapse
|
12
|
Downie JM, Riaz M, Xie J, Lee M, Chan AT, Gibbs P, Orchard SG, Mahady SE, Sebra RP, Murray AM, Macrae F, Schadt E, Woods RL, McNeil JJ, Lacaze P, Gala M. Incident Cancer Risk and Signatures Among Older MUTYH Carriers: Analysis of Population-Based and Genomic Cohorts. Cancer Prev Res (Phila) 2022; 15:509-519. [PMID: 35609203 PMCID: PMC9356994 DOI: 10.1158/1940-6207.capr-22-0080] [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: 02/17/2022] [Revised: 03/31/2022] [Accepted: 05/10/2022] [Indexed: 02/03/2023]
Abstract
MUTYH carriers have an increased colorectal cancer risk in case-control studies, with loss of heterozygosity (LOH) as the presumed mechanism. We evaluated cancer risk among carriers in a prospective, population-based cohort of older adults. In addition, we assessed if cancers from carriers demonstrated mutational signatures (G:C>T:A transversions) associated with early LOH. We calculated incident risk of cancer and colorectal cancer among 13,131 sequenced study participants of the ASPirin in Reducing Events in the Elderly cohort, stratified by sex and adjusting for age, smoking, alcohol use, BMI, polyp history, history of cancer, and aspirin use. MUTYH carriers were identified among 13,033 participants in The Cancer Genome Atlas and International Cancer Genome Consortium, and somatic signatures of cancers were analyzed. Male MUTYH carriers demonstrated an increased risk for overall cancer incidence [multivariable HR, 1.66; 95% confidence interval (CI), 1.03-2.68; P = 0.038] driven by increased colorectal cancer incidence (multivariable HR, 3.55; 95% CI, 1.42-8.78; P = 0.007), as opposed to extracolonic cancer incidence (multivariable HR, 1.40; 95% CI, 0.81-2.44; P = 0.229). Female carriers did not demonstrate increased risk of cancer, colorectal cancer, or extracolonic cancers. Analysis of mutation signatures from cancers of MUTYH carriers revealed no significant contribution toward early mutagenesis from widespread G:C>T:A transversions among gastrointestinal epithelial cancers. Among cancers from carriers, somatic transversions associated with base-excision repair deficiency are uncommon, suggestive of diverse mechanisms of carcinogenesis in carriers compared with those who inherit biallelic MUTYH mutations. PREVENTION RELEVANCE Despite absence of loss of heterozygosity in colorectal cancers, elderly male MUTYH carriers appeared to be at increased of colorectal cancer.
Collapse
Affiliation(s)
- Jonathan M. Downie
- Gastrointestinal Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Moeen Riaz
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Jing Xie
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Minyi Lee
- Gastrointestinal Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- MD-Ph.D. Program, Boston University School of Medicine, Boston, MA
| | - Andrew T. Chan
- Gastrointestinal Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Peter Gibbs
- Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Oncology, Western Health, Melbourne, Australia
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Suzanne G. Orchard
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Suzanne E. Mahady
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
- Department of Gastroenterology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Robert P. Sebra
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Anne M. Murray
- Berman Center for Outcomes and Clinical Research, Hennepin Healthcare Research Institute, Hennepin Healthcare, Minneapolis, MN, USA
| | - Finlay Macrae
- Department of Genomic Medicine; Family Cancer Clinic, Department of Medicine, Department of Pathology, Royal Melbourne Hospital, University of Melbourne, Parkville, VIC, Australia
| | - Eric Schadt
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Robyn L. Woods
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - John J. McNeil
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Paul Lacaze
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Manish Gala
- Gastrointestinal Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| |
Collapse
|
13
|
Torgasheva NA, Diatlova EA, Grin IR, Endutkin AV, Mechetin GV, Vokhtantsev IP, Yudkina AV, Zharkov DO. Noncatalytic Domains in DNA Glycosylases. Int J Mol Sci 2022; 23:ijms23137286. [PMID: 35806289 PMCID: PMC9266487 DOI: 10.3390/ijms23137286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 02/04/2023] Open
Abstract
Many proteins consist of two or more structural domains: separate parts that have a defined structure and function. For example, in enzymes, the catalytic activity is often localized in a core fragment, while other domains or disordered parts of the same protein participate in a number of regulatory processes. This situation is often observed in many DNA glycosylases, the proteins that remove damaged nucleobases thus initiating base excision DNA repair. This review covers the present knowledge about the functions and evolution of such noncatalytic parts in DNA glycosylases, mostly concerned with the human enzymes but also considering some unique members of this group coming from plants and prokaryotes.
Collapse
Affiliation(s)
- Natalia A. Torgasheva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, 630090 Novosibirsk, Russia; (N.A.T.); (E.A.D.); (I.R.G.); (A.V.E.); (G.V.M.); (I.P.V.); (A.V.Y.)
| | - Evgeniia A. Diatlova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, 630090 Novosibirsk, Russia; (N.A.T.); (E.A.D.); (I.R.G.); (A.V.E.); (G.V.M.); (I.P.V.); (A.V.Y.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Street, 630090 Novosibirsk, Russia
| | - Inga R. Grin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, 630090 Novosibirsk, Russia; (N.A.T.); (E.A.D.); (I.R.G.); (A.V.E.); (G.V.M.); (I.P.V.); (A.V.Y.)
| | - Anton V. Endutkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, 630090 Novosibirsk, Russia; (N.A.T.); (E.A.D.); (I.R.G.); (A.V.E.); (G.V.M.); (I.P.V.); (A.V.Y.)
| | - Grigory V. Mechetin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, 630090 Novosibirsk, Russia; (N.A.T.); (E.A.D.); (I.R.G.); (A.V.E.); (G.V.M.); (I.P.V.); (A.V.Y.)
| | - Ivan P. Vokhtantsev
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, 630090 Novosibirsk, Russia; (N.A.T.); (E.A.D.); (I.R.G.); (A.V.E.); (G.V.M.); (I.P.V.); (A.V.Y.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Street, 630090 Novosibirsk, Russia
| | - Anna V. Yudkina
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, 630090 Novosibirsk, Russia; (N.A.T.); (E.A.D.); (I.R.G.); (A.V.E.); (G.V.M.); (I.P.V.); (A.V.Y.)
| | - Dmitry O. Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, 630090 Novosibirsk, Russia; (N.A.T.); (E.A.D.); (I.R.G.); (A.V.E.); (G.V.M.); (I.P.V.); (A.V.Y.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Street, 630090 Novosibirsk, Russia
- Correspondence:
| |
Collapse
|
14
|
MUTYH-associated tumor syndrome: The other face of MAP. Oncogene 2022; 41:2531-2539. [DOI: 10.1038/s41388-022-02304-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/23/2022] [Accepted: 03/29/2022] [Indexed: 12/13/2022]
|
15
|
Unusual structures and unknown roles of FeS clusters in metalloenzymes seen from a resonance Raman spectroscopic perspective. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214287] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
16
|
Sahin I, Saat H. New Perspectives on the Recurrent Monoallelic Germline Mutations of DNA Repair and Checkpoint Genes and Clinical Variability. Genet Test Mol Biomarkers 2022; 26:17-25. [PMID: 35089076 DOI: 10.1089/gtmb.2021.0108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background: Inherited cancers account for ∼10% of cancer cases. Many hereditary cancers are associated with mutations in DNA repair and checkpoint genes making their clinical surveillance important. Methods: We screened 900 patients using a comprehensive cancer gene panel with the following diagnoses: familial (n = 537, 59.6%), colorectal (n = 117, 13%), breast-ovarian (n = 215, 23.8%), endometrium (n = 12, 1.3%), gastric (n = 11, 1.2%), and thyroid (n = 8, 0.8%). Results: The most commonly mutated genes identified were ATM, MSH6, MUTYH, CHEK2, APC, MLH1, RAD50, PALB2, MSH2, CDH1, and PMS2. The most prevalent heterozygous was MUTYH: c.884C>T(P295L), which was predominant in the breast-ovarian group. Notably, the MUTYH, MSH6, and MSH2 variants showed a higher incidence of extracolonic malignancy. Among the DNA mismatch repair (MMR) genes, MSH6 mutations were the most common, followed by mutations in MLH1, MSH2, PMS2, and EPCAM. Conclusion: These findings offer a new perspective and suggest that, beyond ATM, CHEK2, and PALB2, patients with germline monoallelic mutations in MUTYH, MSH6, APC, CDH1, MHS2, and PMS2 may present with a hereditary breast-ovarian cancer phenotype. Continued developments in assessing and researching new variants of known cancer candidate genes will play an important role in improving individual risk prediction, therapy, and prognosis for familial cancers.
Collapse
Affiliation(s)
- Ibrahim Sahin
- Department of Medical Genetics, University of Health Sciences, Dışkapı Yıldırım Beyazıt Training and Research Hospital, Ankara, Turkey
| | - Hanife Saat
- Department of Medical Genetics, University of Health Sciences, Dışkapı Yıldırım Beyazıt Training and Research Hospital, Ankara, Turkey
| |
Collapse
|
17
|
Trasviña-Arenas CH, Demir M, Lin WJ, David SS. Structure, function and evolution of the Helix-hairpin-Helix DNA glycosylase superfamily: Piecing together the evolutionary puzzle of DNA base damage repair mechanisms. DNA Repair (Amst) 2021; 108:103231. [PMID: 34649144 DOI: 10.1016/j.dnarep.2021.103231] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 10/20/2022]
Abstract
The Base Excision Repair (BER) pathway is a highly conserved DNA repair system targeting chemical base modifications that arise from oxidation, deamination and alkylation reactions. BER features lesion-specific DNA glycosylases (DGs) which recognize and excise modified or inappropriate DNA bases to produce apurinic/apyrimidinic (AP) sites and coordinate AP-site hand-off to subsequent BER pathway enzymes. The DG superfamilies identified have evolved independently to cope with a wide variety of nucleobase chemical modifications. Most DG superfamilies recognize a distinct set of structurally related lesions. In contrast, the Helix-hairpin-Helix (HhH) DG superfamily has the remarkable ability to act upon structurally diverse sets of base modifications. The versatility in substrate recognition of the HhH-DG superfamily has been shaped by motif and domain acquisitions during evolution. In this paper, we review the structural features and catalytic mechanisms of the HhH-DG superfamily and draw a hypothetical reconstruction of the evolutionary path where these DGs developed diverse and unique enzymatic features.
Collapse
Affiliation(s)
| | - Merve Demir
- Department of Chemistry, University of California, Davis, CA 95616, U.S.A
| | - Wen-Jen Lin
- Department of Chemistry, University of California, Davis, CA 95616, U.S.A
| | - Sheila S David
- Department of Chemistry, University of California, Davis, CA 95616, U.S.A..
| |
Collapse
|
18
|
Hutchcraft ML, Gallion HH, Kolesar JM. MUTYH as an Emerging Predictive Biomarker in Ovarian Cancer. Diagnostics (Basel) 2021; 11:84. [PMID: 33419231 PMCID: PMC7825630 DOI: 10.3390/diagnostics11010084] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 12/28/2020] [Accepted: 01/05/2021] [Indexed: 12/15/2022] Open
Abstract
Approximately 18% of ovarian cancers have an underlying genetic predisposition and many of the genetic alterations have become intervention and therapy targets. Although mutations in MutY homolog (MUTYH) are best known for MUTYH associated polyposis and colorectal cancer, it plays a role in the development of ovarian cancer. In this review, we discuss the function of the MUTYH gene, mutation epidemiology, and its mechanism for carcinogenesis. We additionally examine its emerging role in the development of ovarian cancer and how it may be used as a predictive and targetable biomarker. MUTYH mutations may confer the risk of ovarian cancer by the failure of its well-known base excision repair mechanism or by failure to induce cell death. Biallelic germline MUTYH mutations confer a 14% risk of ovarian cancer by age 70. A monoallelic germline mutation in conjunction with a somatic MUTYH mutation may also contribute to the development of ovarian cancer. Resistance to platinum-based chemotherapeutic agents may be seen in tumors with monoallelic mutations, but platinum sensitivity in the biallelic setting. As MUTYH is intimately associated with targetable molecular partners, therapeutic options for MUTYH driven ovarian cancers include programed-death 1/programed-death ligand-1 inhibitors and poly-adenosine diphosphate ribose polymerase inhibitors. Understanding the function of MUTYH and its associated partners is critical for determining screening, risk reduction, and therapeutic approaches for MUTYH-driven ovarian cancers.
Collapse
Affiliation(s)
- Megan L. Hutchcraft
- Division of Gynecologic Oncology, Department of Obstetrics & Gynecology, University of Kentucky Markey Cancer Center, 800 Rose Street, Lexington, KY 40536-0263, USA; (M.L.H.); (H.H.G.)
| | - Holly H. Gallion
- Division of Gynecologic Oncology, Department of Obstetrics & Gynecology, University of Kentucky Markey Cancer Center, 800 Rose Street, Lexington, KY 40536-0263, USA; (M.L.H.); (H.H.G.)
| | - Jill M. Kolesar
- Division of Gynecologic Oncology, Department of Obstetrics & Gynecology, University of Kentucky Markey Cancer Center, 800 Rose Street, Lexington, KY 40536-0263, USA; (M.L.H.); (H.H.G.)
- Department of Pharmacy Practice & Science, University of Kentucky College of Pharmacy, 567 Todd Building, 789 South Limestone Street, Lexington, KY 40539-0596, USA
| |
Collapse
|
19
|
Majumdar C, McKibbin PL, Krajewski AE, Manlove AH, Lee JK, David SS. Unique Hydrogen Bonding of Adenine with the Oxidatively Damaged Base 8-Oxoguanine Enables Specific Recognition and Repair by DNA Glycosylase MutY. J Am Chem Soc 2020; 142:20340-20350. [PMID: 33202125 DOI: 10.1021/jacs.0c06767] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The DNA glycosylase MutY prevents deleterious mutations resulting from guanine oxidation by recognition and removal of adenine (A) misincorporated opposite 8-oxo-7,8-dihydroguanine (OG). Correct identification of OG:A is crucial to prevent improper and detrimental MutY-mediatedadenine excision from G:A or T:A base pairs. Here we present a structure-activity relationship (SAR) study using analogues of A to probe the basis for OG:A specificity of MutY. We correlate observed in vitro MutY activity on A analogue substrates with their experimental and calculated acidities to provide mechanistic insight into the factors influencing MutY base excision efficiency. These data show that H-bonding and electrostatic interactions of the base within the MutY active site modulate the lability of the N-glycosidic bond. A analogues that were not excised from duplex DNA as efficiently as predicted by calculations provided insight into other required structural features, such as steric fit and H-bonding within the active site for proper alignment with MutY catalytic residues. We also determined MutY-mediated repair of A analogues paired with OG within the context of a DNA plasmid in bacteria. Remarkably, the magnitudes of decreased in vitro MutY excision rates with different A analogue duplexes do not correlate with the impact on overall MutY-mediated repair. The feature that most strongly correlated with facile cellular repair was the ability of the A analogues to H-bond with the Hoogsteen face of OG. Notably, base pairing of A with OG uniquely positions the 2-amino group of OG in the major groove and provides a means to indirectly select only these inappropriately placed adenines for excision. This highlights the importance of OG lesion detection for efficient MutY-mediated cellular repair. The A analogue SARs also highlight the types of modifications tolerated by MutY and will guide the development of specific probes and inhibitors of MutY.
Collapse
Affiliation(s)
- Chandrima Majumdar
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Paige L McKibbin
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Allison E Krajewski
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08854, United States
| | - Amelia H Manlove
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Jeehiun K Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08854, United States
| | - Sheila S David
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| |
Collapse
|
20
|
Zhu RY, Majumdar C, Khuu C, De Rosa M, Opresko PL, David SS, Kool ET. Designer Fluorescent Adenines Enable Real-Time Monitoring of MUTYH Activity. ACS CENTRAL SCIENCE 2020; 6:1735-1742. [PMID: 33145410 PMCID: PMC7596860 DOI: 10.1021/acscentsci.0c00369] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Indexed: 05/04/2023]
Abstract
The human DNA base excision repair enzyme MUTYH (MutY homolog DNA glycosylase) excises undamaged adenine that has been misincorporated opposite the oxidatively damaged 8-oxoG, preventing transversion mutations and serving as an important defense against the deleterious effects of this damage. Mutations in the MUTYH gene predispose patients to MUTYH-associated polyposis and colorectal cancer, and MUTYH expression has been documented as a biomarker for pancreatic cancer. Measuring MUTYH activity is therefore critical for evaluating and diagnosing disease states as well as for testing this enzyme as a potential therapeutic target. However, current methods for measuring MUTYH activity rely on indirect electrophoresis and radioactivity assays, which are difficult to implement in biological and clinical settings. Herein, we synthesize and identify novel fluorescent adenine derivatives that can act as direct substrates for excision by MUTYH as well as bacterial MutY. When incorporated into synthetic DNAs, the resulting fluorescently modified adenine-release turn-on (FMART) probes report on enzymatic base excision activity in real time, both in vitro and in mammalian cells and human blood. We also employ the probes to identify several promising small-molecule modulators of MUTYH by employing FMART probes for in vitro screening.
Collapse
Affiliation(s)
- Ru-Yi Zhu
- Department
of Chemistry, ChEM-H Institute, and Stanford Cancer Institute, Stanford University, Stanford, California 94305, United States
| | - Chandrima Majumdar
- Department
of Chemistry, and Biochemistry, Molecular, Cellular and Developmental
Biology Graduate Group, University of California
at Davis, Davis, California 95616, United States
| | - Cindy Khuu
- Department
of Chemistry, and Biochemistry, Molecular, Cellular and Developmental
Biology Graduate Group, University of California
at Davis, Davis, California 95616, United States
| | - Mariarosaria De Rosa
- Department
of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania 15261, United States
- Hillman
Cancer Center, University of Pittsburgh
Medical Center, Pittsburgh, Pennsylvania 15261, United States
| | - Patricia L. Opresko
- Department
of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania 15261, United States
- Hillman
Cancer Center, University of Pittsburgh
Medical Center, Pittsburgh, Pennsylvania 15261, United States
| | - Sheila S. David
- Department
of Chemistry, and Biochemistry, Molecular, Cellular and Developmental
Biology Graduate Group, University of California
at Davis, Davis, California 95616, United States
| | - Eric T. Kool
- Department
of Chemistry, ChEM-H Institute, and Stanford Cancer Institute, Stanford University, Stanford, California 94305, United States
- E-mail:
| |
Collapse
|
21
|
Lee AJ, Majumdar C, Kathe SD, Van Ostrand RP, Vickery HR, Averill AM, Nelson SR, Manlove AH, McCord MA, David SS. Detection of OG:A Lesion Mispairs by MutY Relies on a Single His Residue and the 2-Amino Group of 8-Oxoguanine. J Am Chem Soc 2020; 142:13283-13287. [PMID: 32664726 DOI: 10.1021/jacs.0c04284] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
MutY glycosylase excises adenines misincorporated opposite the oxidatively damaged lesion, 8-oxo-7,8-dihydroguanine (OG), to initiate base excision repair and prevent G to T transversion mutations. Successful repair requires MutY recognition of the OG:A mispair amidst highly abundant and structurally similar undamaged DNA base pairs. Herein we use a combination of in vitro and bacterial cell repair assays with single-molecule fluorescence microscopy to demonstrate that both a C-terminal domain histidine residue and the 2-amino group of OG base are critical for MutY detection of OG:A sites. These studies are the first to directly link deficiencies in MutY lesion detection with incomplete cellular repair. These results suggest that defects in lesion detection of human MutY (MUTYH) variants may prove predictive of early-onset colorectal cancer known an MUTYH-associated polyposis. Furthermore, unveiling these specific molecular determinants for repair makes it possible to envision new MUTYH-specific cancer therapies.
Collapse
Affiliation(s)
- Andrea J Lee
- Department of Microbiology and Molecular Genetics, University of Vermont, 95 Carrigan Drive, Burlington, Vermont 05405, United States
| | - Chandrima Majumdar
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Scott D Kathe
- Department of Microbiology and Molecular Genetics, University of Vermont, 95 Carrigan Drive, Burlington, Vermont 05405, United States
| | - Robert P Van Ostrand
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Holly R Vickery
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - April M Averill
- Department of Microbiology and Molecular Genetics, University of Vermont, 95 Carrigan Drive, Burlington, Vermont 05405, United States
| | - Shane R Nelson
- Department of Molecular Physiology and Biophysics, University of Vermont, 149 Beaumont Avenue, Burlington, Vermont 05405, United States
| | - Amelia H Manlove
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Morgan A McCord
- Department of Microbiology and Molecular Genetics, University of Vermont, 95 Carrigan Drive, Burlington, Vermont 05405, United States
| | - Sheila S David
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| |
Collapse
|
22
|
Molecular Aspects of Colorectal Adenomas: The Interplay among Microenvironment, Oxidative Stress, and Predisposition. BIOMED RESEARCH INTERNATIONAL 2020; 2020:1726309. [PMID: 32258104 PMCID: PMC7102468 DOI: 10.1155/2020/1726309] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 12/23/2019] [Accepted: 12/30/2019] [Indexed: 12/11/2022]
Abstract
The development of colorectal cancer (CRC) is a multistep process initiated by a benign polyp that has the potential to evolve into in situ carcinoma through the interactions between environmental and genetic factors. CRC incidence rates are constantly increased for young adult patients presenting an advanced tumor stage. The majority of CRCs arise from colonic adenomas originating from aberrant cell proliferation of colon epithelium. Endoscopic polypectomy represents a tool for early detection and removal of polyps, although the occurrence of cancers after negative colonoscopy shows a significant incidence. It has long been recognized that the aberrant regulation of Wingless/It (Wnt)/β-Catenin signaling in the pathogenesis of colorectal cancer is supported by its critical role in the differentiation of stem cells in intestinal crypts and in the maintenance of intestinal homeostasis. For this review, we will focus on the development of adenomatous polyps through the interplay between renewal signaling in the colon epithelium and reactive oxygen species (ROS) production. The current knowledge of molecular pathology allows us to deepen the relationships between oxidative stress and other risk factors as lifestyle, microbiota, and predisposition. We underline that the chronic inflammation and ROS production in the colon epithelium can impair the Wnt/β-catenin and/or base excision repair (BER) pathways and predispose to polyp development. In fact, the coexistence of oxidative DNA damage and errors in DNA polymerase can foster C>T transitions in various types of cancer and adenomas, leading to a hypermutated phenotype of tumor cells. Moreover, the function of Adenomatous Polyposis Coli (APC) protein in regulating DNA repair is very important as therapeutic implication making DNA damaging chemotherapeutic agents more effective in CRC cells that tend to accumulate mutations. Additional studies will determine whether approaches based on Wnt inhibition would provide long-term therapeutic value in CRC, but it is clear that APC disruption plays a central role in driving and maintaining tumorigenesis.
Collapse
|
23
|
Raetz AG, Banda DM, Ma X, Xu G, Rajavel AN, McKibbin PL, Lebrilla CB, David SS. The DNA repair enzyme MUTYH potentiates cytotoxicity of the alkylating agent MNNG by interacting with abasic sites. J Biol Chem 2020; 295:3692-3707. [PMID: 32001618 DOI: 10.1074/jbc.ra119.010497] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 01/22/2020] [Indexed: 11/06/2022] Open
Abstract
Higher expression of the human DNA repair enzyme MUTYH has previously been shown to be strongly associated with reduced survival in a panel of 24 human lymphoblastoid cell lines exposed to the alkylating agent N-methyl-N'-nitro-N-nitrosoguanidine (MNNG). The molecular mechanism of MUTYH-enhanced MNNG cytotoxicity is unclear, because MUTYH has a well-established role in the repair of oxidative DNA lesions. Here, we show in mouse embryonic fibroblasts (MEFs) that this MNNG-dependent phenotype does not involve oxidative DNA damage and occurs independently of both O6-methyl guanine adduct cytotoxicity and MUTYH-dependent glycosylase activity. We found that blocking of abasic (AP) sites abolishes higher survival of Mutyh-deficient (Mutyh -/-) MEFs, but this blockade had no additive cytotoxicity in WT MEFs, suggesting the cytotoxicity is due to MUTYH interactions with MNNG-induced AP sites. We found that recombinant mouse MUTYH tightly binds AP sites opposite all four canonical undamaged bases and stimulated apurinic/apyrimidinic endonuclease 1 (APE1)-mediated DNA incision. Consistent with these observations, we found that stable expression of WT, but not catalytically-inactive MUTYH, enhances MNNG cytotoxicity in Mutyh -/- MEFs and that MUTYH expression enhances MNNG-induced genomic strand breaks. Taken together, these results suggest that MUTYH enhances the rapid accumulation of AP-site intermediates by interacting with APE1, implicating MUTYH as a factor that modulates the delicate process of base-excision repair independently of its glycosylase activity.
Collapse
Affiliation(s)
- Alan G Raetz
- Department of Chemistry, University of California, Davis, California 95616
| | - Douglas M Banda
- Department of Chemistry, University of California, Davis, California 95616
| | - Xiaoyan Ma
- Department of Chemistry, University of California, Davis, California 95616
| | - Gege Xu
- Department of Chemistry, University of California, Davis, California 95616
| | - Anisha N Rajavel
- Department of Chemistry, University of California, Davis, California 95616
| | - Paige L McKibbin
- Department of Chemistry, University of California, Davis, California 95616
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, California 95616
| | - Sheila S David
- Department of Chemistry, University of California, Davis, California 95616.
| |
Collapse
|
24
|
Fleming AM, Burrows CJ. Interplay of Guanine Oxidation and G-Quadruplex Folding in Gene Promoters. J Am Chem Soc 2020; 142:1115-1136. [PMID: 31880930 PMCID: PMC6988379 DOI: 10.1021/jacs.9b11050] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Living in an oxygen atmosphere demands an ability to thrive in the presence of reactive oxygen species (ROS). Aerobic organisms have successfully found solutions to the oxidative threats imposed by ROS by evolving an elaborate detoxification system, upregulating ROS during inflammation, and utilizing ROS as messenger molecules. In this Perspective, recent studies are discussed that demonstrate ROS as signaling molecules for gene regulation by combining two emergent properties of the guanine (G) heterocycle in DNA, namely, oxidation sensitivity and a propensity for G-quadruplex (G4) folding, both of which depend upon sequence context. In human gene promoters, this results from an elevated 5'-GG-3' dinucleotide frequency and GC enrichment near transcription start sites. Oxidation of DNA by ROS drives conversion of G to 8-oxo-7,8-dihydroguanine (OG) to mark target promoters for base excision repair initiated by OG-glycosylase I (OGG1). Sequence-dependent mechanisms for gene activation are available to OGG1 to induce transcription. Either OGG1 releases OG to yield an abasic site driving formation of a non-canonical fold, such as a G4, to be displayed to apurinic/apyrimidinic 1 (APE1) and stalling on the fold to recruit activating factors, or OGG1 binds OG and facilitates activator protein recruitment. The mechanisms described drive induction of stress response, DNA repair, or estrogen-induced genes, and these pathways are novel potential anticancer targets for therapeutic intervention. Chemical concepts provide a framework to discuss the regulatory or possible epigenetic potential of the OG modification in DNA, in which DNA "damage" and non-canonical folds collaborate to turn on or off gene expression. The next steps for scientific discovery in this growing field are discussed.
Collapse
Affiliation(s)
- Aaron M. Fleming
- 315 South 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT 84112-0850, USA
| | - Cynthia J. Burrows
- 315 South 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT 84112-0850, USA
| |
Collapse
|
25
|
Russelburg LP, O’Shea Murray VL, Demir M, Knutsen KR, Sehgal SL, Cao S, David SS, Horvath MP. Structural Basis for Finding OG Lesions and Avoiding Undamaged G by the DNA Glycosylase MutY. ACS Chem Biol 2020; 15:93-102. [PMID: 31829624 DOI: 10.1021/acschembio.9b00639] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The adenine glycosylase MutY selectively initiates repair of OG:A lesions and, by comparison, avoids G:A mispairs. The ability to distinguish these closely related substrates relies on the C-terminal domain of MutY, which structurally resembles MutT. To understand the mechanism for substrate specificity, we crystallized MutY in complex with DNA containing G across from the high-affinity azaribose transition state analogue. Our structure shows that G is accommodated by the OG site and highlights the role of a serine residue in OG versus G discrimination. The functional significance of Ser308 and its neighboring residues was evaluated by mutational analysis, revealing the critical importance of a β loop in the C-terminal domain for mutation suppression in cells, and biochemical performance in vitro. This loop comprising residues Phe307, Ser308, and His309 (Geobacillus stearothermophilus sequence positions) is conserved in MutY but absent in MutT and other DNA repair enzymes and may therefore serve as a MutY-specific target exploitable by chemical biological probes.
Collapse
Affiliation(s)
- L. Peyton Russelburg
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Valerie L. O’Shea Murray
- Department of Chemistry, University of California, Davis, California 95616, United States
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Merve Demir
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Kyle R. Knutsen
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Sonia L. Sehgal
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Sheng Cao
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Sheila S. David
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Martin P. Horvath
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, Utah 84112, United States
| |
Collapse
|