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Faria JP, Assumpção JG, de Oliveira Matos L, Soardi FC, Bretz GPM, Friedman E, De Marco L. Spectrum of germline pathogenic variants in Brazilian hereditary breast/ovarian cancer cases. Breast Cancer Res Treat 2024:10.1007/s10549-024-07383-x. [PMID: 38874686 DOI: 10.1007/s10549-024-07383-x] [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: 04/01/2024] [Accepted: 05/19/2024] [Indexed: 06/15/2024]
Abstract
PURPOSE To define the spectrum of germline pathogenic variants (PVs) and copy number variant (CNV) in cancer susceptibility genes to the burden of breast and ovarian cancer (BC, OvC) in high-risk Brazilians in Minas Gerais with health insurance, southeast Brazil, undergoing multigene panel testing (MGPT). METHODS Genotyping eligible individuals with health insurance in the Brazilian healthcare system for Hereditary Breast and Ovarian Cancer Syndrome to undergo molecular testing for 44 or 141-gene panels, a decision that was insurance driven. RESULTS Overall, 701 individuals clinically defined as high BC/OvC risk, underwent MGPT from 1/2021 to 10/2022, with ~ 50% genotyped with a 44-gene panel and the rest with a 141-gene panel. Overall, 16.4% and 22.6% of genotyped individuals harbored PVs using 44-gene and the 141 gene panel, respectively. The most frequently mutated genes were: BRCA2 (3.7%); BRCA1 (3.6%) and monoallelic MUTYH (3.1%). CONCLUSION The rate of PVs detected in high-risk individuals in this study was twice the 10% threshold used in Brazilian health guidelines. MGPT doubled the detection rate of PVs in cancer susceptibility genes in high-risk individuals compared with BRCA1/BRCA2 genotyping alone. The spectrum of PVs in Southern Brazil is diverse, with few recurring variants such as TP53 (0.6%), suggesting regional founder effects. The use of MGPT in hereditary cancer in Minas Gerais significantly increased the detection rate of P/LPVs compared to existing guidelines and should be considered as the primary genotyping modality in assessing hereditary cancer risk in Brazil.
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Affiliation(s)
| | | | | | | | | | - Eitan Friedman
- The Preventive Personalized Medicine Center, Assuta Medical Center and the School of Medicine, Tel-Aviv, Israel
| | - Luiz De Marco
- Department of Surgery, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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2
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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.
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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
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3
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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.
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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
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4
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Dong G, Yin X, Liang Y, Chen J, Wang J, Jiang F, Wang C, Guo W, Wang Y. A novel AluYb8 insertion-associated non-coding RNA, lncMUTYH, impairs mitochondrial function and dampens the M2-like polarization of macrophages. Free Radic Res 2024; 58:27-42. [PMID: 38145459 DOI: 10.1080/10715762.2023.2299333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/06/2023] [Indexed: 12/26/2023]
Abstract
An inverted AluYb8 insertion in the MUTYH intron 15 (AluYb8MUTYH variant) has been reported to be associated with reduced MUTYH1 expression and mitochondrial dysfunction with age. However, the underlying mechanism remains unknown. In this study, we identified a novel transcript associated with the AluYb8MUTYH variant, which revealed that this transcript is about 780 nucleotides in length with a poly-A tail, lacks protein-coding potential, referred to as lncMUTYH. The results from the reporter gene system confirmed that the lncMUTYH down-regulates MUTYH1 expression at the translational level. Site-directed mutagenesis on the 5'-terminal exon sequences of α-MUTYH and lncMUTYH constructs revealed that lncMUTYH can act as a trans-regulator that depends on the partial base pairing between its exonized AluYb8 sequence and the 5'UTR of α-MUTYH to impede MUTYH 1 expression. Furthermore, we have demonstrated a correlation between decreased mitochondrion-localized MUTYH1 caused by lncMUTYH and lowered levels of mitochondrial biological function indicators, such as mtDNA content, mitochondrial regulatory gene expression, oxygen consumption rate, ATP product, and mitochondrial respiratory capacity. Notably, we found that lncMUTYH inhibited the M2-like polarization of macrophages, and CD68/CD206-positive cell fractions were significantly lower in lncMUTYH ectopically expressing cells. The results confirmed that the AluYb8MUTYH-associated lncMUTYH, derived from an AluYb8 insertion mutation, acts as a trans-regulatory factor that inhibits the MUTYH1 protein expression, leading to a progressive mitochondrial dysfunction that may disrupt macrophage differentiation. In summary, lncMUTYH can contribute to AluYb8MUTYH-associated mitochondrial dysfunction with age and hamper the macrophage polarization process, potentially increasing the risk of developing age-related diseases.
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Affiliation(s)
- Gaochao Dong
- Department of Medical Genetics, Medical School, Nanjing University, Nanjing, China
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
| | - Xuewen Yin
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
- Department of Pharmacy, Nanjing Stomatological Hospital, Medical School, Nanjing University, Nanjing, China
| | - Yingkuan Liang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
| | - Jingwen Chen
- Department of Medical Genetics, Medical School, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, China
| | - Jie Wang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
| | - Feng Jiang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
| | - Chaochen Wang
- ZJU-UoE Institute, Zhejiang University School of Medicine, International Campus, Zhejiang University, Zhejiang, China
| | - Wenwen Guo
- Department of Pathology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yaping Wang
- Department of Medical Genetics, Medical School, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, China
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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.
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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
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Lagniton PNP, Tam B, Wang SM. DARVIC: Dihedral angle-reliant variant impact classifier for functional prediction of missense VUS. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2023; 238:107596. [PMID: 37201251 DOI: 10.1016/j.cmpb.2023.107596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 04/19/2023] [Accepted: 05/10/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND Of the large number of genetic variants identified, the functional impact for most of them remains unknown. Mutations in DNA damage repair genes such as MUTYH, which is involved in repairing A:8-oxoG mismatches caused by reactive oxygen species, can cause a higher risk of cancer. Mutations happening in other key genes such as TP53 also pose huge health threats and risk of cancer. The interpretation of genetic variants' functional impact is a forefront issue that needs to be addressed. Many different in silico methods based on different principles have been developed and applied in interpreting genetic variants. However, a current challenge is that many existing methods tend to overpredict the pathogenicity of benign variants. A new approach is needed to tackle this issue to improve genetic variant interpretation through the use of in silico methods. METHODS In this study, we developed another protein structural-based approach called Dihedral angle-reliant variant impact classifier (DARVIC) to predict the deleterious impact of the coding-changing missense variants. DARVIC uses Ramachandran's principle of protein stereochemistry as the theoretical foundation and uses molecular dynamics simulations coupled with a supervised machine learning algorithm XGBoost to determine the functional impact of missense variants on protein structural stability. RESULTS We characterized the features of dihedral angles in dynamic protein structures. We also tested the performance of DARVIC in MUTYH and TP53 missense variants and achieved satisfactory results in reflecting the functional impacts of the variants on protein structure. The method achieved a balanced accuracy of 84% in a functionally validated MUTYH dataset containing both benign and pathogenic missense variants, higher than other existing in silico methods. Along with that, DARVIC was able to predict 119 (47%) deleterious variants from a dataset of 254 MUTYH VUS. Further application of DARVIC to a functionally validated TP53 dataset had a balanced accuracy of 94%, topping other methods, demonstrating DARVIC's robustness. CONCLUSION DARVIC provides a valuable tool to predict the functional impacts of missense variants based on their effects on protein structural stability and motion. At its current state, DARVIC performed well in predicting the functional impact of the missense variants both in MUTYH and TP53. We expect its high potential to predict functional impact for the missense variants in other genes.
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Affiliation(s)
- Philip Naderev P Lagniton
- Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Macao
| | - Benjamin Tam
- Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Macao
| | - San Ming Wang
- Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Macao; Senior Author, Macao.
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7
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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.
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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]
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MUTYH Actively Contributes to Microglial Activation and Impaired Neurogenesis in the Pathogenesis of Alzheimer's Disease. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:8635088. [PMID: 34970419 PMCID: PMC8714343 DOI: 10.1155/2021/8635088] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/29/2021] [Accepted: 11/19/2021] [Indexed: 12/12/2022]
Abstract
Oxidative stress is a major risk factor for Alzheimer's disease (AD), which is characterized by brain atrophy, amyloid plaques, neurofibrillary tangles, and loss of neurons. 8-Oxoguanine, a major oxidatively generated nucleobase highly accumulated in the AD brain, is known to cause neurodegeneration. In mammalian cells, several enzymes play essential roles in minimizing the 8-oxoguanine accumulation in DNA. MUTYH with adenine DNA glycosylase activity excises adenine inserted opposite 8-oxoguanine in DNA. MUTYH is reported to actively contribute to the neurodegenerative process in Parkinson and Huntington diseases and some mouse models of neurodegenerative diseases by accelerating neuronal dysfunction and microgliosis under oxidative conditions; however, whether or not MUTYH is involved in AD pathogenesis remains unclear. In the present study, we examined the contribution of MUTYH to the AD pathogenesis. Using postmortem human brains, we showed that various types of MUTYH transcripts and proteins are expressed in most hippocampal neurons and glia in both non-AD and AD brains. We further introduced MUTYH deficiency into App NL-G-F/NL-G-F knock-in AD model mice, which produce humanized toxic amyloid-β without the overexpression of APP protein, and investigated the effects of MUTYH deficiency on the behavior, pathology, gene expression, and neurogenesis. MUTYH deficiency improved memory impairment in App NL-G-F/NL-G-F mice, accompanied by reduced microgliosis. Gene expression profiling strongly suggested that MUTYH is involved in the microglial response pathways under AD pathology and contributes to the phagocytic activity of disease-associated microglia. We also found that MUTYH deficiency ameliorates impaired neurogenesis in the hippocampus, thus improving memory impairment. In conclusion, we propose that MUTYH, which is expressed in the hippocampus of AD patients as well as non-AD subjects, actively contributes to memory impairment by inducing microgliosis with poor neurogenesis in the preclinical AD phase and that MUTYH is a novel therapeutic target for AD, as its deficiency is highly beneficial for ameliorating AD pathogenesis.
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Dell'Elice A, Cini G, Fornasarig M, Armelao F, Barana D, Bianchi F, Casalis Cavalchini GC, Maffè A, Mammi I, Pedroni M, Percesepe A, Sorrentini I, Tibiletti M, Maestro R, Quaia M, Viel A. Filling the gap: A thorough investigation for the genetic diagnosis of unsolved polyposis patients with monoallelic MUTYH pathogenic variants. Mol Genet Genomic Med 2021; 9:e1831. [PMID: 34704405 PMCID: PMC8683633 DOI: 10.1002/mgg3.1831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/23/2021] [Accepted: 09/28/2021] [Indexed: 11/09/2022] Open
Abstract
Backgrounds MUTYH‐associated polyposis (MAP) is an autosomal recessive disease caused by biallelic pathogenic variants (PV) of the MUTYH gene. The aim of this study was to investigate the genetic causes of unexplained polyposis patients with monoallelic MUTYH PV. The analysis focused on 26 patients with suspected MAP, belonging to 23 families. Ten probands carried also one or more additional MUTYH variants of unknown significance. Methods Based on variant type and on the collected clinical and molecular data, these variants were reinterpreted by applying the ACMG/AMP rules. Moreover, supplementary analyses were carried out to investigate the presence of other variants and copy number variations in the coding and promoter regions of MUTYH, as well as other polyposis genes (APC, NTHL1, POLE, POLD1, MSH3, RNF43, and MCM9). Results We reclassified 4 out of 10 MUTYH variants as pathogenic or likely pathogenic, thus supporting the diagnosis of MAP in only four cases. Two other patients belonging to the same family showed a previously undetected deletion of the APC gene promoter. No PVs were found in the other investigated genes. However, 6 out of the 18 remaining families are still interesting MAP candidates, due to the co‐presence of a class 3 MUTYH variant that could be reinterpreted in the next future. Conclusion Several efforts are necessary to fully elucidate the genetic etiology of suspected MAP patients, especially those with the most severe polyposis/tumor phenotype. Clinical data, tumor molecular profile, family history, and polyposis inheritance mode may guide variant interpretation and address supplementary studies.
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Affiliation(s)
- Anastasia Dell'Elice
- Unit of Functional Oncogenomics and Genetics, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Giulia Cini
- Unit of Functional Oncogenomics and Genetics, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Mara Fornasarig
- Unit of Oncologic Gastroenterology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Franco Armelao
- U.O. Multizonale Gastroenterologia ed Endoscopia Digestiva, Ospedale Santa Chiara, Azienda Provinciale per i Servizi sanitari, Trento, Italy
| | - Daniela Barana
- Oncology Unit, Local Health and Social Care Unit, ULSS8 Berica, Montecchio Maggiore, Italy
| | - Francesca Bianchi
- Clinica Oncologica e Centro Regionale di Genetica Oncologica, Università Politecnica delle Marche, Azienda Ospedaliero-Universitaria Ospedali Riuniti, Ancona, Italy
| | | | - Antonella Maffè
- S.S. Genetica e Biologia Molecolare, S.C. Interaziendale Laboratorio Analisi Chimico Cliniche e Microbiologia, ASO S Croce e Carle, Cuneo, Italy
| | - Isabella Mammi
- Medical Genetics Unit, Dolo General Hospital, Venezia, Italy
| | - Monica Pedroni
- Dipartimento di Scienze Mediche e Chirurgiche Materno-Infantili e dell'Adulto, Università di Modena e Reggio Emilia, Modena, Italy
| | | | | | - Mariagrazia Tibiletti
- Department of Pathology, Circolo Hospital ASST Settelaghi, Varese, Italy.,Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Roberta Maestro
- Unit of Functional Oncogenomics and Genetics, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Michele Quaia
- Unit of Functional Oncogenomics and Genetics, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Alessandra Viel
- Unit of Functional Oncogenomics and Genetics, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
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Karamperis K, Tsoumpeli MT, Kounelis F, Koromina M, Mitropoulou C, Moutinho C, Patrinos GP. Genome-based therapeutic interventions for β-type hemoglobinopathies. Hum Genomics 2021; 15:32. [PMID: 34090531 PMCID: PMC8178887 DOI: 10.1186/s40246-021-00329-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 04/28/2021] [Indexed: 12/18/2022] Open
Abstract
For decades, various strategies have been proposed to solve the enigma of hemoglobinopathies, especially severe cases. However, most of them seem to be lagging in terms of effectiveness and safety. So far, the most prevalent and promising treatment options for patients with β-types hemoglobinopathies, among others, predominantly include drug treatment and gene therapy. Despite the significant improvements of such interventions to the patient's quality of life, a variable response has been demonstrated among different groups of patients and populations. This is essentially due to the complexity of the disease and other genetic factors. In recent years, a more in-depth understanding of the molecular basis of the β-type hemoglobinopathies has led to significant upgrades to the current technologies, as well as the addition of new ones attempting to elucidate these barriers. Therefore, the purpose of this article is to shed light on pharmacogenomics, gene addition, and genome editing technologies, and consequently, their potential use as direct and indirect genome-based interventions, in different strategies, referring to drug and gene therapy. Furthermore, all the latest progress, updates, and scientific achievements for patients with β-type hemoglobinopathies will be described in detail.
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Affiliation(s)
- Kariofyllis Karamperis
- Department of Pharmacy, School of Health Sciences, Laboratory of Pharmacogenomics and Individualized Therapy, University of Patras, Patras, Greece
- The Golden Helix Foundation, London, UK
| | - Maria T Tsoumpeli
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Fotios Kounelis
- Department of Computing, Group of Large-Scale Data & Systems, Imperial College London, London, UK
| | - Maria Koromina
- Department of Pharmacy, School of Health Sciences, Laboratory of Pharmacogenomics and Individualized Therapy, University of Patras, Patras, Greece
| | | | - Catia Moutinho
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, Australia
| | - George P Patrinos
- Department of Pharmacy, School of Health Sciences, Laboratory of Pharmacogenomics and Individualized Therapy, University of Patras, Patras, Greece.
- College of Medicine and Health Sciences, Department of Pathology, United Arab Emirates University, Al-Ain, United Arab Emirates.
- Zayed Center of Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.
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12
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Tone AA, McCuaig JM, Ricker N, Boghosian T, Romagnuolo T, Stickle N, Virtanen C, Zhang T, Kim RH, Ferguson SE, May T, Laframboise S, Armel S, Demsky R, Volenik A, Stuart-McEwan T, Shaw P, Oza A, Kamel-Reid S, Stockley T, Bernardini MQ. The Prevent Ovarian Cancer Program (POCP): Identification of women at risk for ovarian cancer using complementary recruitment approaches. Gynecol Oncol 2021; 162:97-106. [PMID: 33858678 DOI: 10.1016/j.ygyno.2021.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/09/2021] [Indexed: 11/17/2022]
Abstract
BACKGROUND Up to 20% of high-grade serous ovarian carcinomas (HGSOC) are hereditary; however, historical uptake of genetic testing is low. We used a unique combination of approaches to identify women in Ontario, Canada, with a first-degree relative (FDR) who died from HGSOC without prior genetic testing, and offer them multi-gene panel testing. METHODS From May 2015-Sept 2019, genetic counseling and testing was provided to eligible participants. Two recruitment strategies were employed, including self-identification in response to an outreach campaign and direct targeting of FDRs of deceased HGSOC patients treated at our institution. The rate of pathogenic variants (PV) in established/potential ovarian cancer risk genes and the benefits/challenges of each approach were assessed. RESULTS A total of 564 women enrolled in response to our outreach campaign (n = 473) or direct recruitment (n = 91). Mean age at consent was 52 years and 96% did not meet provincial testing criteria. Genetic results were provided to 528 individuals from 458 families. The rate of PVs in ovarian cancer risk genes was highest when FDRs were diagnosed with HGSOC <60 years (9.4% vs. 3.9% ≥ 60y, p = 0.0160). Participants in the outreach vs. direct recruitment cohort had a similar rate of PVs; however, uptake of genetic testing (97% vs. 89%; p = 0.0036) and study completion (95% vs. 87%; p = 0.0062) rates were higher in the former. Eleven participants with pathogenic variants have completed risk-reducing gynecologic surgery, with one stage I HGSOC and two breast cancers identified. CONCLUSION Overall PV rates in this large cohort were lower than expected; however, we provide evidence that genetic testing criteria in Ontario should include individuals with a deceased FDR diagnosed with HGSOC <60 years of age.
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Affiliation(s)
- Alicia A Tone
- Gynecologic Oncology, The University Health Network, Toronto, Canada; Ovarian Cancer Canada, Toronto, Canada
| | - Jeanna M McCuaig
- Gynecologic Oncology, The University Health Network, Toronto, Canada; Familial Cancer Clinic, The University Health Network, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Nicole Ricker
- Gynecologic Oncology, The University Health Network, Toronto, Canada
| | - Talin Boghosian
- Gynecologic Oncology, The University Health Network, Toronto, Canada
| | - Tina Romagnuolo
- Gynecologic Oncology, The University Health Network, Toronto, Canada
| | - Natalie Stickle
- Bioinformatics and HPC Core, The University Health Network, Toronto, Canada
| | - Carl Virtanen
- Bioinformatics and HPC Core, The University Health Network, Toronto, Canada
| | - Tong Zhang
- Advanced Molecular Diagnostics Laboratory, The University Health Network, Toronto, Canada
| | - Raymond H Kim
- Familial Cancer Clinic, The University Health Network, Toronto, Canada; Department of Medicine, University of Toronto, Toronto, Canada; Medical Oncology, The University Health Network, Toronto, Canada
| | - Sarah E Ferguson
- Gynecologic Oncology, The University Health Network, Toronto, Canada; Department of Obstetrics and Gynecology, University of Toronto, Toronto, Canada
| | - Taymaa May
- Gynecologic Oncology, The University Health Network, Toronto, Canada
| | | | - Susan Armel
- Familial Cancer Clinic, The University Health Network, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Rochelle Demsky
- Familial Cancer Clinic, The University Health Network, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Alexandra Volenik
- Familial Cancer Clinic, The University Health Network, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | | | - Patricia Shaw
- Gynecologic Pathology, The University Health Network, Toronto, Canada
| | - Amit Oza
- Medical Oncology, The University Health Network, Toronto, Canada
| | - Suzanne Kamel-Reid
- Advanced Molecular Diagnostics Laboratory, The University Health Network, Toronto, Canada; Clinical Laboratory Genetics, The University Health Network, Toronto, Canada
| | - Tracy Stockley
- Advanced Molecular Diagnostics Laboratory, The University Health Network, Toronto, Canada; Clinical Laboratory Genetics, The University Health Network, Toronto, Canada
| | - Marcus Q Bernardini
- Gynecologic Oncology, The University Health Network, Toronto, Canada; Department of Obstetrics and Gynecology, University of Toronto, Toronto, Canada.
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13
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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.
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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
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14
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Landrith T, Li B, Cass AA, Conner BR, LaDuca H, McKenna DB, Maxwell KN, Domchek S, Morman NA, Heinlen C, Wham D, Koptiuch C, Vagher J, Rivera R, Bunnell A, Patel G, Geurts JL, Depas MM, Gaonkar S, Pirzadeh-Miller S, Krukenberg R, Seidel M, Pilarski R, Farmer M, Pyrtel K, Milliron K, Lee J, Hoodfar E, Nathan D, Ganzak AC, Wu S, Vuong H, Xu D, Arulmoli A, Parra M, Hoang L, Molparia B, Fennessy M, Fox S, Charpentier S, Burdette J, Pesaran T, Profato J, Smith B, Haynes G, Dalton E, Crandall JRR, Baxter R, Lu HM, Tippin-Davis B, Elliott A, Chao E, Karam R. Splicing profile by capture RNA-seq identifies pathogenic germline variants in tumor suppressor genes. NPJ Precis Oncol 2020; 4:4. [PMID: 32133419 PMCID: PMC7039900 DOI: 10.1038/s41698-020-0109-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/30/2020] [Indexed: 12/12/2022] Open
Abstract
Germline variants in tumor suppressor genes (TSGs) can result in RNA mis-splicing and predisposition to cancer. However, identification of variants that impact splicing remains a challenge, contributing to a substantial proportion of patients with suspected hereditary cancer syndromes remaining without a molecular diagnosis. To address this, we used capture RNA-sequencing (RNA-seq) to generate a splicing profile of 18 TSGs (APC, ATM, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MLH1, MSH2, MSH6, MUTYH, NF1, PALB2, PMS2, PTEN, RAD51C, RAD51D, and TP53) in 345 whole-blood samples from healthy donors. We subsequently demonstrated that this approach can detect mis-splicing by comparing splicing profiles from the control dataset to profiles generated from whole blood of individuals previously identified with pathogenic germline splicing variants in these genes. To assess the utility of our TSG splicing profile to prospectively identify pathogenic splicing variants, we performed concurrent capture DNA and RNA-seq in a cohort of 1000 patients with suspected hereditary cancer syndromes. This approach improved the diagnostic yield in this cohort, resulting in a 9.1% relative increase in the detection of pathogenic variants, demonstrating the utility of performing simultaneous DNA and RNA genetic testing in a clinical context.
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Affiliation(s)
| | - Bing Li
- Ambry Genetics, Aliso Viejo, CA USA
| | | | | | | | | | | | | | | | | | - Deborah Wham
- Aurora St. Luke’s Medical Center, Milwaukee, WI USA
| | | | | | - Ragene Rivera
- Texas Oncology, El Paso, Fort Worth, and Austin, TX USA
| | - Ann Bunnell
- Texas Oncology, El Paso, Fort Worth, and Austin, TX USA
| | - Gayle Patel
- Texas Oncology, El Paso, Fort Worth, and Austin, TX USA
| | | | | | | | | | | | | | - Robert Pilarski
- Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH USA
| | - Meagan Farmer
- University of Alabama at Birmingham, Birmingham, AL USA
| | | | | | - John Lee
- Cedars-Sinai Medical Center, Los Angeles, CA USA
| | | | | | | | - Sitao Wu
- Ambry Genetics, Aliso Viejo, CA USA
| | | | - Dong Xu
- Ambry Genetics, Aliso Viejo, CA USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Elizabeth Chao
- Ambry Genetics, Aliso Viejo, CA USA
- University of California at Irvine, Irvine, CA USA
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15
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Abduljaleel Z, Athar M, Al-Allaf FA, Al-Dehlawi S, Vazquez JR. Association of functional variants and protein-to-protein physical interactions of human MutY homolog linked with familial adenomatous polyposis and colorectal cancer syndrome. Noncoding RNA Res 2020; 4:155-173. [PMID: 32072083 PMCID: PMC7012779 DOI: 10.1016/j.ncrna.2019.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/26/2019] [Accepted: 11/19/2019] [Indexed: 11/26/2022] Open
Abstract
The human gene MUTYH codes for a DNA glycosylase involved in the repair of oxidative DNA damage. Faulty MUTYH protein activity causes the accumulation of G→T transversions due to unrepaired 8-oxoG:A mismatches. MUTYH germ-line mutations in humans are linked with a recessive form of Familial Adenomatous Polyposis (FAP) and colorectal cancer predisposition. We studied the repair capacity of variants identified in MUTYH-associated polyposis (MAP) patients. MAP is inherited in an autosomal recessive type due to mutations in MUTYH (Y165C, G382D, P54S, A22V, Q63R, G45D, S136P and N43S), indicating that both copies of the gene become inactivated. However, the parents of an individual with an autosomal recessive condition may serve as carriers, each harboring one copy of the mutated gene without showing signs or symptoms of MAP. Six protein partners have been associated with MUTYH, four via direct physical interactions, namely, hMSH6, hPCNA, hRPA1, and hAPEX1. We examined, for the first time, specific interactions of these protein partners with MAP-associated MUTYH mutants using molecular dynamics simulations. The approach provided tools for exploration of the conformational energy landscape accessible to protein partners. The investigation also determined the impact before and after energy minimization of protein-protein interactions and binding affinities of MUTYH wild type and mutant forms, as well as the interactions with other proteins. Taken together, this study provided new insights into the role of MUTYH and its interacting proteins in MAP.
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Affiliation(s)
- Zainularifeen Abduljaleel
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O.Box: 715, Makkah 21955, Saudi Arabia.,Science and Technology Unit, Umm Al-Qura University, P.O. Box: 715, Makkah 21955, Saudi Arabia.,Bircham University, Av. Sierra, 2, 28691 Villanueva de la Canada, Madrid, Spain
| | - Mohammad Athar
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O.Box: 715, Makkah 21955, Saudi Arabia.,Science and Technology Unit, Umm Al-Qura University, P.O. Box: 715, Makkah 21955, Saudi Arabia
| | - Faisal A Al-Allaf
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O.Box: 715, Makkah 21955, Saudi Arabia.,Science and Technology Unit, Umm Al-Qura University, P.O. Box: 715, Makkah 21955, Saudi Arabia
| | - Saied Al-Dehlawi
- The Regional Laboratory, Ministry of Health (MOH), P.O. Box: 6251, Makkah, Saudi Arabia
| | - Jose R Vazquez
- Bircham University, Av. Sierra, 2, 28691 Villanueva de la Canada, Madrid, Spain
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16
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Wang J, Jia N, Lin Q, Huang Y, Li J, Jiang Q, Liu W, Xu J, Hou Y, Liu J, Li M, Lu W, Zhou Y, Zhang Y, Tong H. Clinicopathological and molecular characteristics of abdominal desmoid tumors in the Chinese population: A single-center report of 15 cases. Oncol Lett 2019; 18:6443-6450. [PMID: 31807167 PMCID: PMC6876325 DOI: 10.3892/ol.2019.11038] [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: 02/07/2019] [Accepted: 09/24/2019] [Indexed: 12/05/2022] Open
Abstract
Desmoid tumors (DTs), derived from the abdomen, are a type of rare and aggressive borderline tumor exhibiting high recurrence and malignant potential. The aim of the present study was to investigate the clinicopathological and molecular characteristics of abdominal DT in a Chinese population and to provide clues for selecting the optimal treatment strategy for different types of abdominal DT. The clinicopathological data of 15 consecutive patients with DT was collected. Matched fresh-frozen tumor tissues and peripheral blood samples were used to detect mutations of adenomatous polyposis coli gene (APC), β-catenin (CTNNB1) and MutY DNA glycosylase (MUTYH) using Sanger sequencing. Pearson's test was conducted to analyze the differences between sporadic DT and familial adenomatous polyposis (FAP) associated with DT. Time to progress (TTP) and overall survival curves were estimated using the Kaplan-Meier method and compared using the log-rank test. A review of the patient clinicopathological characteristics revealed that FAP-associated DT exhibited a higher rate of abdominal surgery history (P=0.011), with no significant differences in any other characteristics. Sequencing revealed that mutations in the APC, CTNNB1 and MUTYH genes were common in DT, and only one patient harbored no mutations in these genes. Survival analyses revealed that patients with FAP exhibited shorter TTP (P=0.030). Log-rank test demonstrated a tendency towards shorter TTP in the cases where an R2 resection was performed (P=0.072) and a tendency towards poor prognosis in the cases of DT associated with FAP (P=0.087). In conclusion, Abdominal DTs were prone to occur in patients with FAP with a history of abdominal surgery. Mutations in the APC, CTNNB1 and MUTYH genes were detected in patients with DTs. To the best of our knowledge, this is the first study of abdominal DT occurrence in patients with MUTYH-associated FAP. The prognosis of DT associated with FAP may be worse compared with that of sporadic DT.
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Affiliation(s)
- Jiongyuan Wang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Ning Jia
- Laboratory of Molecular Biology, Department of Biochemistry, An Hui Medical University, Hefei, Anhui 230032, P.R. China
| | - Qiaowei Lin
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Yuan Huang
- Endoscopy Center, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Jinglei Li
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Quan Jiang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Wenshuai Liu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Jing Xu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Ju Liu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Ming Li
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, P.R. China
| | - Weiqi Lu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Yuhong Zhou
- Department of Oncology, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Yong Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Hanxing Tong
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
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17
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Boldinova EO, Khairullin RF, Makarova AV, Zharkov DO. Isoforms of Base Excision Repair Enzymes Produced by Alternative Splicing. Int J Mol Sci 2019; 20:ijms20133279. [PMID: 31277343 PMCID: PMC6651865 DOI: 10.3390/ijms20133279] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 06/29/2019] [Accepted: 07/02/2019] [Indexed: 02/07/2023] Open
Abstract
Transcripts of many enzymes involved in base excision repair (BER) undergo extensive alternative splicing, but functions of the corresponding alternative splice variants remain largely unexplored. In this review, we cover the studies describing the common alternatively spliced isoforms and disease-associated variants of DNA glycosylases, AP-endonuclease 1, and DNA polymerase beta. We also discuss the roles of alternative splicing in the regulation of their expression, catalytic activities, and intracellular transport.
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Affiliation(s)
| | - Rafil F Khairullin
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 9 Parizhskoy Kommuny Str., 420012 Kazan, Russia
| | - Alena V Makarova
- RAS Institute of Molecular Genetics, 2 Kurchatova Sq., 123182 Moscow, Russia.
| | - Dmitry O Zharkov
- Novosibirsk State University, 1 Pirogova St., 630090 Novosibirsk, Russia.
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia.
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18
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Raetz AG, David SS. When you're strange: Unusual features of the MUTYH glycosylase and implications in cancer. DNA Repair (Amst) 2019; 80:16-25. [PMID: 31203172 DOI: 10.1016/j.dnarep.2019.05.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 05/23/2019] [Accepted: 05/29/2019] [Indexed: 02/06/2023]
Abstract
MUTYH is a base-excision repair glycosylase that removes adenine opposite 8-oxoguanine (OG). Variants of MUTYH defective in functional activity lead to MUTYH-associated polyposis (MAP), which progresses to cancer with very high penetrance. Whole genome and whole exome sequencing studies have found MUTYH deficiencies in an increasing number of cancer types. While the canonical OG:A repair activity of MUTYH is well characterized and similar to bacterial MutY, here we review more recent evidence that MUTYH has activities independent of OG:A repair and appear centered on the interdomain connector (IDC) region of MUTYH. We summarize evidence that MUTYH is involved in rapid DNA damage response (DDR) signaling, including PARP activation, 9-1-1 and ATR signaling, and SIRT6 activity. MUTYH alters survival and DDR to a wide variety of DNA damaging agents in a time course that is not consistent with the formation of OG:A mispairs. Studies that suggest MUTYH inhibits the repair of alkyl-DNA damage and cyclopyrimidine dimers (CPDs) is reviewed, and evidence of a synthetic lethal interaction with mismatch repair (MMR) is summarized. Based on these studies we suggest that MUTYH has evolved from an OG:A mispair glycosylase to a multifunctional scaffold for DNA damage response signaling.
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Affiliation(s)
- Alan G Raetz
- Department of Chemistry, University of California, Davis, Davis, CA, USA.
| | - Sheila S David
- Department of Chemistry, University of California, Davis, Davis, CA, USA.
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19
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Araujo LF, Molfetta GA, Vincenzi OC, Huber J, Teixeira LA, Ferraz VE, Silva WA. Molecular basis of familial adenomatous polyposis in the southeast of Brazil: identification of six novel mutations. Int J Biol Markers 2019; 34:80-89. [PMID: 30852976 DOI: 10.1177/1724600818814462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
BACKGROUND The goal of this study was to screen point mutations and deletions in APC and MUTYH genes in patients suspected of familial adenomatous polyposis (FAP) in a Brazilian cohort. METHODS We used high-resolution melting, Sanger direct sequencing and multiplex ligation-dependent probe association (MLPA) assays to identify point mutations, and large genomic variations within the coding regions of APC and MUTYH genes. RESULTS We identified 19 causative mutations in 40 Brazilian patients from 20 different families. Four novel mutations were identified in the APC gene and two in the MUTYH gene. We also found a high intra- and inter-familial diversity regarding extracolonic manifestations, and gastric polyps were the most common manifestation found in our cohort. CONCLUSION We believe that the FAP mutational spectrum can be population-specific and screening FAP patients in different populations can improve pre-clinical diagnosis and improve clinical conduct.
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Affiliation(s)
- Luiza Ferreira Araujo
- 1 Departament of Genetics, Ribeirão Preto Medical School, University of São Paulo, Brazil.,3 Center for Cell-Based Therapy CEPID/FAPESP, and Regional Blood Center of Ribeirão Preto, Brazil.,5 Medical Genomics Laboratory, AC Camargo Cancer Center, Brazil
| | - Greice Andreotti Molfetta
- 1 Departament of Genetics, Ribeirão Preto Medical School, University of São Paulo, Brazil.,2 Center for Medical Genomics at Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, Brazil.,3 Center for Cell-Based Therapy CEPID/FAPESP, and Regional Blood Center of Ribeirão Preto, Brazil
| | - Otavio Costa Vincenzi
- 2 Center for Medical Genomics at Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, Brazil.,3 Center for Cell-Based Therapy CEPID/FAPESP, and Regional Blood Center of Ribeirão Preto, Brazil.,4 Medical Genetics Unit, Clinical Hospital of the Medical School of Ribeirão Preto, University of São Paulo, Brazil
| | - Jair Huber
- 4 Medical Genetics Unit, Clinical Hospital of the Medical School of Ribeirão Preto, University of São Paulo, Brazil
| | - Lorena Alves Teixeira
- 4 Medical Genetics Unit, Clinical Hospital of the Medical School of Ribeirão Preto, University of São Paulo, Brazil
| | - Victor Evangelista Ferraz
- 1 Departament of Genetics, Ribeirão Preto Medical School, University of São Paulo, Brazil.,2 Center for Medical Genomics at Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, Brazil.,4 Medical Genetics Unit, Clinical Hospital of the Medical School of Ribeirão Preto, University of São Paulo, Brazil
| | - Wilson Araujo Silva
- 1 Departament of Genetics, Ribeirão Preto Medical School, University of São Paulo, Brazil.,2 Center for Medical Genomics at Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, Brazil.,3 Center for Cell-Based Therapy CEPID/FAPESP, and Regional Blood Center of Ribeirão Preto, Brazil.,4 Medical Genetics Unit, Clinical Hospital of the Medical School of Ribeirão Preto, University of São Paulo, Brazil
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Köger N, Brieger A, Hinrichsen IM, Zeuzem S, Plotz G. Analysis of MUTYH alternative transcript expression, promoter function, and the effect of human genetic variants. Hum Mutat 2019; 40:472-482. [PMID: 30653782 DOI: 10.1002/humu.23709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 12/14/2018] [Accepted: 01/14/2019] [Indexed: 01/07/2023]
Abstract
The human DNA repair gene MUTYH, whose mutational loss causes a colorectal polyposis and cancer predisposition, contains three alternative first exons. In order to analyze alternative transcription and the effect of genetic alterations found in humans, we established a cell-based minigene experimental model supporting transcription and splicing and thoroughly verified its functionality. We identified highly conserved promoter areas and inactivated them in the minigene, and also introduced six human variants. Moreover, the potential contribution of CpG island methylation and specific transcription factors on MUTYH transcription was addressed. The findings allowed to attribute regulatory roles to three conserved motifs in the promoter: an M4 motif, a transcription factor IIB recognition element, and a GC box. Moreover, the data showed that three patient variants compromised MUTYH expression and therefore have the potential to cause pathogenic effects. We did not find evidence for a biologically relevant contribution of CpG island methylation or a direct transcriptional activation by DNA damage. Besides insight into the regulation of MUTYH transcription, the work therefore provides a functional MUTYH minigene experimental system suitable as a diagnostic tool for analyzing patient variants, and a functional map of the promotor that also can facilitate pathogenicity classifications of human variants.
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Affiliation(s)
- Nicole Köger
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinikum, Frankfurt, Germany
| | - Angela Brieger
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinikum, Frankfurt, Germany
| | - Inga M Hinrichsen
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinikum, Frankfurt, Germany
| | - Stefan Zeuzem
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinikum, Frankfurt, Germany
| | - Guido Plotz
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinikum, Frankfurt, Germany
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21
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Nuñez NN, Khuu C, Babu CS, Bertolani SJ, Rajavel AN, Spear JE, Armas JA, Wright JD, Siegel JB, Lim C, David SS. The Zinc Linchpin Motif in the DNA Repair Glycosylase MUTYH: Identifying the Zn 2+ Ligands and Roles in Damage Recognition and Repair. J Am Chem Soc 2018; 140:13260-13271. [PMID: 30208271 PMCID: PMC6443246 DOI: 10.1021/jacs.8b06923] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The DNA base excision repair (BER) glycosylase MUTYH prevents DNA mutations by catalyzing adenine (A) excision from inappropriately formed 8-oxoguanine (8-oxoG):A mismatches. The importance of this mutation suppression activity in tumor suppressor genes is underscored by the association of inherited variants of MUTYH with colorectal polyposis in a hereditary colorectal cancer syndrome known as MUTYH-associated polyposis, or MAP. Many of the MAP variants encompass amino acid changes that occur at positions surrounding the two-metal cofactor-binding sites of MUTYH. One of these cofactors, found in nearly all MUTYH orthologs, is a [4Fe-4S]2+ cluster coordinated by four Cys residues located in the N-terminal catalytic domain. We recently uncovered a second functionally relevant metal cofactor site present only in higher eukaryotic MUTYH orthologs: a Zn2+ ion coordinated by three Cys residues located within the extended interdomain connector (IDC) region of MUTYH that connects the N-terminal adenine excision and C-terminal 8-oxoG recognition domains. In this work, we identified a candidate for the fourth Zn2+ coordinating ligand using a combination of bioinformatics and computational modeling. In addition, using in vitro enzyme activity assays, fluorescence polarization DNA binding assays, circular dichroism spectroscopy, and cell-based rifampicin resistance assays, the functional impact of reduced Zn2+ chelation was evaluated. Taken together, these results illustrate the critical role that the "Zn2+ linchpin motif" plays in MUTYH repair activity by providing for proper engagement of the functional domains on the 8-oxoG:A mismatch required for base excision catalysis. The functional importance of the Zn2+ linchpin also suggests that adjacent MAP variants or exposure to environmental chemicals may compromise Zn2+ coordination, and ability of MUTYH to prevent disease.
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Affiliation(s)
- Nicole N. Nuñez
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California, 95616, USA
| | - Cindy Khuu
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California, 95616, USA
- Biochemistry, Molecular, Cellular and Developmental Graduate Group, University of California, Davis, 95616, USA
| | - C. Satheesan Babu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan R. O. C
| | - Steve J. Bertolani
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California, 95616, USA
- Genome Center, University of California, Davis, One Shields Avenue, Davis, California, 95616, USA
| | - Anisha N. Rajavel
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California, 95616, USA
| | - Jensen E. Spear
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California, 95616, USA
| | - Jeremy A. Armas
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California, 95616, USA
| | - Jon D. Wright
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan R. O. C
| | - Justin B. Siegel
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California, 95616, USA
- Genome Center, University of California, Davis, One Shields Avenue, Davis, California, 95616, USA
- Department of Biochemistry and Molecular Medicine, University of California, Davis, One Shields Avenue, Davis, California, 95616, USA
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan R. O. C
| | - Sheila S. David
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California, 95616, USA
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22
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McDonnell KJ, Chemler JA, Bartels PL, O'Brien E, Marvin ML, Ortega J, Stern RH, Raskin L, Li GM, Sherman DH, Barton JK, Gruber SB. A human MUTYH variant linking colonic polyposis to redox degradation of the [4Fe4S] 2+ cluster. Nat Chem 2018; 10:873-880. [PMID: 29915346 PMCID: PMC6060025 DOI: 10.1038/s41557-018-0068-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 04/20/2018] [Indexed: 12/26/2022]
Abstract
The human DNA repair enzyme MUTYH excises mispaired adenine residues in oxidized DNA. Homozygous MUTYH mutations underlie the autosomal, recessive cancer syndrome MUTYH-associated polyposis. We report a MUTYH variant, p.C306W (c.918C>G), with a tryptophan residue in place of native cysteine, that ligates the [4Fe4S] cluster in a patient with colonic polyposis and family history of early age colon cancer. In bacterial MutY, the [4Fe4S] cluster is redox active, allowing rapid localization to target lesions by long-range, DNA-mediated signalling. In the current study, using DNA electrochemistry, we determine that wild-type MUTYH is similarly redox-active, but MUTYH C306W undergoes rapid oxidative degradation of its cluster to [3Fe4S]+, with loss of redox signalling. In MUTYH C306W, oxidative cluster degradation leads to decreased DNA binding and enzyme function. This study confirms redox activity in eukaryotic DNA repair proteins and establishes MUTYH C306W as a pathogenic variant, highlighting the essential role of redox signalling by the [4Fe4S] cluster.
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Affiliation(s)
- Kevin J McDonnell
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Joseph A Chemler
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Phillip L Bartels
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Elizabeth O'Brien
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Monica L Marvin
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Janice Ortega
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ralph H Stern
- Division of Molecular Medicine and Genetics, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Guo-Min Li
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.
- Departments of Medicinal Chemistry, Chemistry and Microbiology & Immunology, University of Michigan, Ann Arbor, MI, USA.
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Stephen B Gruber
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA.
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Wachnowsky C, Fidai I, Cowan JA. Iron-sulfur cluster biosynthesis and trafficking - impact on human disease conditions. Metallomics 2018; 10:9-29. [PMID: 29019354 PMCID: PMC5783746 DOI: 10.1039/c7mt00180k] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Iron-sulfur clusters (Fe-S) are one of the most ancient, ubiquitous and versatile classes of metal cofactors found in nature. Proteins that contain Fe-S clusters constitute one of the largest families of proteins, with varied functions that include electron transport, regulation of gene expression, substrate binding and activation, radical generation, and, more recently discovered, DNA repair. Research during the past two decades has shown that mitochondria are central to the biogenesis of Fe-S clusters in eukaryotic cells via a conserved cluster assembly machinery (ISC assembly machinery) that also controls the synthesis of Fe-S clusters of cytosolic and nuclear proteins. Several key steps for synthesis and trafficking have been determined for mitochondrial Fe-S clusters, as well as the cytosol (CIA - cytosolic iron-sulfur protein assembly), but detailed mechanisms of cluster biosynthesis, transport, and exchange are not well established. Genetic mutations and the instability of certain steps in the biosynthesis and maturation of mitochondrial, cytosolic and nuclear Fe-S cluster proteins affects overall cellular iron homeostasis and can lead to severe metabolic, systemic, neurological and hematological diseases, often resulting in fatality. In this review we briefly summarize the current molecular understanding of both mitochondrial ISC and CIA assembly machineries, and present a comprehensive overview of various associated inborn human disease states.
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Affiliation(s)
- C Wachnowsky
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA.
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24
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Characteristics of MUTYH variants in Japanese colorectal polyposis patients. Int J Clin Oncol 2018; 23:497-503. [PMID: 29330641 DOI: 10.1007/s10147-017-1234-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/20/2017] [Indexed: 12/21/2022]
Abstract
BACKGROUND The base excision repair gene MUTYH is the causative gene of colorectal polyposis syndrome, which is an autosomal recessive disorder associated with a high risk of colorectal cancer. Since few studies have investigated the genotype-phenotype association in Japanese patients with MUTYH variants, the aim of this study was to clarify the clinicopathological findings in Japanese patients with MUTYH gene variants who were detected by screening causative genes associated with hereditary colorectal polyposis. METHODS After obtaining informed consent, genetic testing was performed using target enrichment sequencing of 26 genes, including MUTYH. RESULTS Of the 31 Japanese patients with suspected hereditary colorectal polyposis, eight MUTYH variants were detected in five patients. MUTYH hotspot variants known for Caucasians, namely p.G396D and p.Y179D, were not among the detected variants.Of five patients, two with biallelic MUTYH variants were diagnosed with MUTYH-associated polyposis, while two others had monoallelic MUTYH variants. One patient had the p.P18L and p.G25D variants on the same allele; however, supportive data for considering these two variants 'pathogenic' were lacking. CONCLUSIONS Two patients with biallelic MUTYH variants and two others with monoallelic MUTYH variants were identified among Japanese colorectal polyposis patients. Hotspot variants of the MUTYH gene for Caucasians were not hotspots for Japanese patients.
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25
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Majumdar C, Nuñez NN, Raetz AG, Khuu C, David SS. Cellular Assays for Studying the Fe-S Cluster Containing Base Excision Repair Glycosylase MUTYH and Homologs. Methods Enzymol 2018; 599:69-99. [PMID: 29746250 DOI: 10.1016/bs.mie.2017.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Many DNA repair enzymes, including the human adenine glycosylase MUTYH, require iron-sulfur (Fe-S) cluster cofactors for DNA damage recognition and subsequent repair. MUTYH prokaryotic and eukaryotic homologs are a family of adenine (A) glycosylases that cleave A when mispaired with the oxidatively damaged guanine lesion, 8-oxo-7,8-dihydroguanine (OG). Faulty OG:A repair has been linked to the inheritance of missense mutations in the MUTYH gene. These inherited mutations can result in the onset of a familial colorectal cancer disorder known as MUTYH-associated polyposis (MAP). While in vitro studies can be exceptional at unraveling how MutY interacts with its OG:A substrate, cell-based assays are needed to provide a cellular context to these studies. In addition, strategic comparison of in vitro and in vivo studies can provide exquisite insight into the search, selection, excision process, and the coordination with protein partners, required to mediate full repair of the lesion. A commonly used assay is the rifampicin resistance assay that provides an indirect evaluation of the intrinsic mutation rate in Escherichia coli (E. coli or Ec), read out as antibiotic-resistant cell growth. Our laboratory has also developed a bacterial plasmid-based assay that allows for direct evaluation of repair of a defined OG:A mispair. This assay provides a means to assess the impact of catalytic defects in affinity and excision on overall repair. Finally, a mammalian GFP-based reporter assay has been developed that more accurately models features of mammalian cells. Taken together, these assays provide a cellular context to the repair activity of MUTYH and its homologs that illuminates the role these enzymes play in preventing mutations and disease.
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Affiliation(s)
| | - Nicole N Nuñez
- University of California, Davis, Davis, CA, United States
| | - Alan G Raetz
- University of California, Davis, Davis, CA, United States
| | - Cindy Khuu
- University of California, Davis, Davis, CA, United States
| | - Sheila S David
- University of California, Davis, Davis, CA, United States.
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26
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Banda DM, Nuñez NN, Burnside MA, Bradshaw KM, David SS. Repair of 8-oxoG:A mismatches by the MUTYH glycosylase: Mechanism, metals and medicine. Free Radic Biol Med 2017; 107:202-215. [PMID: 28087410 PMCID: PMC5457711 DOI: 10.1016/j.freeradbiomed.2017.01.008] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 01/01/2017] [Accepted: 01/04/2017] [Indexed: 12/12/2022]
Abstract
Reactive oxygen and nitrogen species (RONS) may infringe on the passing of pristine genetic information by inducing DNA inter- and intra-strand crosslinks, protein-DNA crosslinks, and chemical alterations to the sugar or base moieties of DNA. 8-Oxo-7,8-dihydroguanine (8-oxoG) is one of the most prevalent DNA lesions formed by RONS and is repaired through the base excision repair (BER) pathway involving the DNA repair glycosylases OGG1 and MUTYH in eukaryotes. MUTYH removes adenine (A) from 8-oxoG:A mispairs, thus mitigating the potential of G:C to T:A transversion mutations from occurring in the genome. The paramount role of MUTYH in guarding the genome is well established in the etiology of a colorectal cancer predisposition syndrome involving variants of MUTYH, referred to as MUTYH-associated polyposis (MAP). In this review, we highlight recent advances in understanding how MUTYH structure and related function participate in the manifestation of human disease such as MAP. Here we focus on the importance of MUTYH's metal cofactor sites, including a recently discovered "Zinc linchpin" motif, as well as updates to the catalytic mechanism. Finally, we touch on the insight gleaned from studies with MAP-associated MUTYH variants and recent advances in understanding the multifaceted roles of MUTYH in the cell, both in the prevention of mutagenesis and tumorigenesis.
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Affiliation(s)
- Douglas M Banda
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Nicole N Nuñez
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Michael A Burnside
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Katie M Bradshaw
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Sheila S David
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States.
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27
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Gonzalez RS, Washington K, Shi C. Current applications of molecular pathology in colorectal carcinoma. ACTA ACUST UNITED AC 2017. [DOI: 10.1186/s41241-017-0020-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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28
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Lv XP. Gastrointestinal tract cancers: Genetics, heritability and germ line mutations. Oncol Lett 2017; 13:1499-1508. [PMID: 28454282 PMCID: PMC5403708 DOI: 10.3892/ol.2017.5629] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 11/21/2016] [Indexed: 12/18/2022] Open
Abstract
Gastrointestinal (GI) tract cancers that arise due to genetic mutations affect a large number of individuals worldwide. Even though many of the GI tract cancers arise sporadically, few of these GI tract cancers harboring a hereditary predisposition are now recognized and well characterized. These include Cowden syndrome, MUTYH-associated polyposis, hereditary pancreatic cancer, Lynch syndrome, Peutz-Jeghers syndrome, familial adenomatous polyposis (FAP), attenuated FAP, serrated polyposis syndrome, and hereditary gastric cancer. Molecular characterization of the genes that are involved in these syndromes was useful in the development of genetic testing for diagnosis and also facilitated understanding of the genetic basis of GI cancers. Current knowledge on the genetics of GI cancers with emphasis on heritability and germ line mutations forms the basis of the present review.
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Affiliation(s)
- Xiao-Peng Lv
- Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical College, The Affiliated Xuzhou Hospital of Medical College of Southeast University, Xuzhou, Jiangsu 221009, P.R. China
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29
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Taki K, Sato Y, Nomura S, Ashihara Y, Kita M, Tajima I, Sugano K, Arai M. Mutation analysis of MUTYH in Japanese colorectal adenomatous polyposis patients. Fam Cancer 2016; 15:261-5. [PMID: 26684191 DOI: 10.1007/s10689-015-9857-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Germline MUTYH mutations were investigated in 14 Japanese colorectal polyposis patients without germ line adenomatous polyposis coli (APC) gene mutations. Three patients had a heterozygous IVS10-2A>G MUTYH mutation. The onset of MUTYH-associated polyposis (MAP) occurs later than that of familial adenomatous polyposis with germline APC mutation. Thus, we compared the carrier frequency of MUTYH IVS10-2A>G heterozygote in the APC mutation negative cases with that in 115 controls over 70 years of age who showed no apparent clinical manifestations of cancer and claimed that they had no history of cancer at the time of enrollment. The frequency of IVS10-2A>G heterozygote in APC germline mutation negative polyposis patients was significantly higher than control subject (p = 0.012, Chi square test). Although the sample size is still too small to conclude, the IVS10-2A>G MUTYH heterozygote might add to the risk of developing germline APC mutation negative polyposis.
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Affiliation(s)
- Keiko Taki
- Clinical Genetic Oncology, Cancer Institute Hospital of Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
- Division of Bioresources, Chemical Resources Laboratory, Tokyo Institute of Technology, Yokohama, Japan
| | - Yuri Sato
- Clinical Genetic Oncology, Cancer Institute Hospital of Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Sachio Nomura
- Clinical Genetic Oncology, Cancer Institute Hospital of Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
- Department of Clinical Research, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yuumi Ashihara
- Clinical Genetic Oncology, Cancer Institute Hospital of Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Mizuho Kita
- Clinical Genetic Oncology, Cancer Institute Hospital of Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | | | - Kokichi Sugano
- Oncogene Research Unit/Cancer Prevention Unit, Tochigi Cancer Center Research Institute, Tochigi, Japan
| | - Masami Arai
- Clinical Genetic Oncology, Cancer Institute Hospital of Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan.
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30
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Ricci MT, Miccoli S, Turchetti D, Bondavalli D, Viel A, Quaia M, Giacomini E, Gismondi V, Sanchez-Mete L, Stigliano V, Martayan A, Mazzei F, Bignami M, Bonelli L, Varesco L. Type and frequency of MUTYH variants in Italian patients with suspected MAP: a retrospective multicenter study. J Hum Genet 2016; 62:309-315. [PMID: 27829682 DOI: 10.1038/jhg.2016.132] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/12/2016] [Accepted: 10/04/2016] [Indexed: 12/12/2022]
Abstract
To determine prevalence, spectrum and genotype-phenotype correlations of MUTYH variants in Italian patients with suspected MAP (MUTYH-associated polyposis), a retrospective analysis was conducted to identify patients who had undergone MUTYH genetic testing from September 2002 to February 2014. Results of genetic testing and patient clinical characteristics were collected (gender, number of polyps, age at polyp diagnosis, presence of colorectal cancer (CRC) and/or other cancers, family data). The presence of large rearrangements of the MUTYH gene was evaluated by Multiplex Ligation-dependent Probe Amplification analysis. In all, 299 patients with colorectal neoplasia were evaluated: 61.2% were males, the median age at polyps or cancer diagnosis was 50 years (16-80 years), 65.2% had <100 polyps and 51.8% had CRC. A total of 36 different MUTYH variants were identified: 13 (36.1%) were classified as pathogenetic, whereas 23 (63.9%) were variants of unknown significance (VUS). Two pathogenetic variants were observed in 78 patients (26.1%). A large homozygous deletion of exon 15 was found in one patient (<1.0%). MAP patients were younger than those with negative MUTYH testing at polyps diagnosis (P<0.0001) and at first cancer diagnosis (P=0.007). MAP patients carrying the p.Glu480del variant presented with a younger age at polyp diagnosis as compared to patients carrying p.Gly396Asp and p.Tyr179Cys variants. A high heterogeneity of MUTYH variants and a high rate of VUS were identified in a cohort of Italian patients with suspected MAP. Genotype-phenotype analysis suggests that the p.Glu480del variant is associated with a severe phenotype.
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Affiliation(s)
| | - Sara Miccoli
- Research Center on Hereditary Cancer, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Daniela Turchetti
- Research Center on Hereditary Cancer, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | | | - Alessandra Viel
- Funcional Onco-genomics and Genetics, CRO Aviano National Cancer Institute, Aviano (PN), Italy
| | - Michele Quaia
- Funcional Onco-genomics and Genetics, CRO Aviano National Cancer Institute, Aviano (PN), Italy
| | - Elisa Giacomini
- Funcional Onco-genomics and Genetics, CRO Aviano National Cancer Institute, Aviano (PN), Italy
| | - Viviana Gismondi
- Unit of Hereditary Cancer, IRCCS AOU San Martino-IST, Genoa, Italy
| | - Lupe Sanchez-Mete
- Division of Gastroenterology and Digestive Endoscopy, Regina Elena National Cancer Institute-IRCCS, Rome, Italy
| | - Vittoria Stigliano
- Division of Gastroenterology and Digestive Endoscopy, Regina Elena National Cancer Institute-IRCCS, Rome, Italy
| | - Aline Martayan
- Clinical Pathology Unit, Regina Elena National Cancer Institute-IRCCS, Rome, Italy
| | - Filomena Mazzei
- Unit of Experimental and Computational Carcinogenesis, Istituto Superiore di Sanità, Rome, Italy
| | - Margherita Bignami
- Unit of Experimental and Computational Carcinogenesis, Istituto Superiore di Sanità, Rome, Italy
| | - Luigina Bonelli
- Unit of Clinical Epidemiology, IRCCS AOU San Martino-IST, Genoa, Italy
| | - Liliana Varesco
- Unit of Hereditary Cancer, IRCCS AOU San Martino-IST, Genoa, Italy
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31
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Abstract
Familial adenomatous polyposis (FAP) is a colorectal cancer predisposition syndrome with considerable genetic and phenotypic heterogeneity, defined by the development of multiple adenomas throughout the colorectum. FAP is caused either by monoallelic mutations in the adenomatous polyposis coli gene APC, or by biallelic germline mutations of MUTYH, this latter usually presenting with milder phenotype. The aim of the present study was to characterize the genotype and phenotype of Hungarian FAP patients. Mutation screening of 87 unrelated probands from FAP families (21 of them presented as the attenuated variant of the disease, showing <100 polyps) was performed using DNA sequencing and multiplex ligation-dependent probe amplification. Twenty-four different pathogenic mutations in APC were identified in 65 patients (75 %), including nine cases (37.5 %) with large genomic alterations. Twelve of the point mutations were novel. In addition, APC-negative samples were also tested for MUTYH mutations and we were able to identify biallelic pathogenic mutations in 23 % of these cases (5/22). Correlations between the localization of APC mutations and the clinical manifestations of the disease were observed, cases with a mutation in the codon 1200-1400 region showing earlier age of disease onset (p < 0.003). There were only a few, but definitive dissimilarities between APC- and MUTYH-associated FAP in our cohort: the age at onset of polyposis was significantly delayed for biallelic MUTYH mutation carriers as compared to patients with an APC mutation. Our data represent the first comprehensive study delineating the mutation spectra of both APC and MUTYH in Hungarian FAP families, and underscore the overlap between the clinical characteristics of APC- and MUTYH-associated phenotypes, necessitating a more appropriate clinical characterization of FAP families.
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32
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Rosner G, Bercovich D, Daniel YE, Strul H, Fliss-Isakov N, Ben-Yehoiada M, Santo E, Halpern Z, Kariv R. Increased risk for colorectal adenomas and cancer in mono-allelic MUTYH mutation carriers: results from a cohort of North-African Jews. Fam Cancer 2016; 14:427-36. [PMID: 25822476 DOI: 10.1007/s10689-015-9799-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Bi-allelic MUTYH gene mutations are associated with a clinical phenotype of multiple colorectal adenomas and an increased risk for colorectal cancer (CRC). It is unclear whether mono-allelic MUTYH gene carriers (heterozygotes) are also at increased risk for even few adenomas or cancer. In order to clarify an association between MUTYH heterozygotes and adenomas, we evaluated the frequency and types of MUTYH mutations and variants in 72 North-African Jews having few (≥3) colorectal adenomas with or without early onset (<50 years) CRC compared to 29 healthy controls. Germ-line DNA was analyzed for a panel of 6 MUTYH mutations and variants, and Sanger sequencing of the entire MUTYH gene was performed for mono-allelic MUTYH mutation carriers. APC gene mutations and Lynch syndrome were excluded in the relevant cases according to accepted clinical criteria. Twenty-two of the 72 adenoma subjects (30.5%) had MUTYH mutations or variants. Nine were homozygotes or compound heterozygotes: all had >10 adenomas and one had CRC. Thirteen others were mono-allelic carriers (heterozygotes) of a single MUTYH mutation: six had more than ten adenomas and seven had less than ten adenomas; of these 13 mono-allelic carriers, six had a neoplasm: three CRCs and three extra-intestinal tumors. Eleven of the thirteen mono-allelic carriers with adenomas had a family history of cancer in first or second degree relatives. A multivariable model showed positive correlation between G396D, Y179C and 1186 ins GG mutations and number of adenomas (OR 8.6, 10.2 and 14.4, respectively). The Q324H variant was negatively associated with the number of adenomatous polyps (OR -5.23). In conclusion, MUTYH mutations are prevalent among Jews of North-African origin with colorectal adenomas with or without early onset CRC. Mono-allelic MUTYH carriers with a family history of cancer had a clinical phenotype that varied from having only few adenomas to multiple (>10) adenomas. These findings support MUTYH testing in patients with even few adenomas and suggest the consideration of increased surveillance in mono-allelic carriers with a family history of cancer.
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Affiliation(s)
- Guy Rosner
- Departmant of Gastroenterology, Tel-Aviv Sourasky Medical Center, 6 Weizmann St., 64239, Tel Aviv, Israel,
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Komine K, Shimodaira H, Takao M, Soeda H, Zhang X, Takahashi M, Ishioka C. Functional Complementation Assay for 47 MUTYH Variants in a MutY-Disrupted Escherichia coli Strain. Hum Mutat 2016; 36:704-11. [PMID: 25820570 PMCID: PMC4682456 DOI: 10.1002/humu.22794] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 03/25/2015] [Indexed: 12/27/2022]
Abstract
MUTYH-associated polyposis (MAP) is an adenomatous polyposis transmitted in an autosomal-recessive pattern, involving biallelic inactivation of the MUTYH gene. Loss of a functional MUTYH protein will result in the accumulation of G:T mismatched DNA caused by oxidative damage. Although p.Y179C and p.G396D are the two most prevalent MUTYH variants, more than 200 missense variants have been detected. It is difficult to determine whether these variants are disease-causing mutations or single-nucleotide polymorphisms. To understand the functional consequences of these variants, we generated 47 MUTYH gene variants via site-directed mutagenesis, expressed the encoded proteins in MutY-disrupted Escherichia coli, and assessed their abilities to complement the functional deficiency in the E. coli by monitoring spontaneous mutation rates. Although the majority of variants exhibited intermediate complementation relative to the wild type, some variants severely interfered with this complementation. However, some variants retained functioning similar to the wild type. In silico predictions of functional effects demonstrated a good correlation. Structural prediction of MUTYH based on the MutY protein structure allowed us to interpret effects on the protein stability or catalytic activity. These data will be useful for evaluating the functional consequences of missense MUTYH variants detected in patients with suspected MAP.
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Affiliation(s)
- Keigo Komine
- Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Aoba-ku, Sendai, Japan.,Department of Clinical Oncology, Tohoku University Hospital, Aoba-ku, Sendai, Japan
| | - Hideki Shimodaira
- Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Aoba-ku, Sendai, Japan.,Department of Clinical Oncology, Tohoku University Hospital, Aoba-ku, Sendai, Japan
| | - Masashi Takao
- Department of Molecular Genetics, Institute of Development, Aging and Cancer, Tohoku University, Aoba-ku, Sendai, Japan
| | - Hiroshi Soeda
- Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Aoba-ku, Sendai, Japan.,Department of Clinical Oncology, Tohoku University Hospital, Aoba-ku, Sendai, Japan
| | - Xiaofei Zhang
- Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Aoba-ku, Sendai, Japan
| | - Masanobu Takahashi
- Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Aoba-ku, Sendai, Japan.,Department of Clinical Oncology, Tohoku University Hospital, Aoba-ku, Sendai, Japan
| | - Chikashi Ishioka
- Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Aoba-ku, Sendai, Japan.,Department of Clinical Oncology, Tohoku University Hospital, Aoba-ku, Sendai, Japan
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Distinct functional consequences of MUTYH variants associated with colorectal cancer: Damaged DNA affinity, glycosylase activity and interaction with PCNA and Hus1. DNA Repair (Amst) 2015; 34:39-51. [PMID: 26377631 DOI: 10.1016/j.dnarep.2015.08.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 08/03/2015] [Indexed: 12/13/2022]
Abstract
MUTYH is a base excision repair (BER) enzyme that prevents mutations in DNA associated with 8-oxoguanine (OG) by catalyzing the removal of adenine from inappropriately formed OG:A base-pairs. Germline mutations in the MUTYH gene are linked to colorectal polyposis and a high risk of colorectal cancer, a syndrome referred to as MUTYH-associated polyposis (MAP). There are over 300 different MUTYH mutations associated with MAP and a large fraction of these gene changes code for missense MUTYH variants. Herein, the adenine glycosylase activity, mismatch recognition properties, and interaction with relevant protein partners of human MUTYH and five MAP variants (R295C, P281L, Q324H, P502L, and R520Q) were examined. P281L MUTYH was found to be severely compromised both in DNA binding and base excision activity, consistent with the location of this variation in the iron-sulfur cluster (FCL) DNA binding motif of MUTYH. Both R295C and R520Q MUTYH were found to have low fractions of active enzyme, compromised affinity for damaged DNA, and reduced rates for adenine excision. In contrast, both Q324H and P502L MUTYH function relatively similarly to WT MUTYH in both binding and glycosylase assays. However, P502L and R520Q exhibited reduced affinity for PCNA (proliferation cell nuclear antigen), consistent with their location in the PCNA-binding motif of MUTYH. Whereas, only Q324H, and not R295C, was found to have reduced affinity for Hus1 of the Rad9-Hus1-Rad1 complex, despite both being localized to the same region implicated for interaction with Hus1. These results underscore the diversity of functional consequences due to MUTYH variants that may impact the progression of MAP.
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Guo W, Zheng B, Guo D, Cai Z, Wang Y. Association of AluYb8 insertion/deletion polymorphism in the MUTYH gene with mtDNA maintain in the type 2 diabetes mellitus patients. Mol Cell Endocrinol 2015; 409:33-40. [PMID: 25829257 DOI: 10.1016/j.mce.2015.03.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 03/16/2015] [Accepted: 03/23/2015] [Indexed: 12/15/2022]
Abstract
A common AluYb8-element insertion/deletion polymorphism of the MUTYH gene (AluYb8MUTYH) is a novel genetic risk factor for type 2 diabetes mellitus (T2DM). In the present study, mtDNA sequencing analysis indicated that the mtDNA sequence heteroplasmy was not associated with AluYb8MUTYH polymorphism. To better understand the genetic risk for T2DM, we investigated the association of this polymorphism with mtDNA content, mtDNA breakage and mtDNA transcription in the leukocytes of T2DM patients. The mtDNA content and unbroken mtDNA were significantly increased in the mutant patients than in the wild-type patients (P <0.05, respectively). However, no association between mtDNA transcription and AluYb8MUTYH variant was observed. The results suggested that the AluYb8MUTYH variant was associated with an altered mtDNA maintain in T2DM patients. The high level of mtDNA content observed in the mutant patients may have resulted from inefficient base excision repair of mitochondrial MUTYH and a compensatory mechanism that is triggered by elevated oxidative stress.
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Affiliation(s)
- Wenwen Guo
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, No.22 HanKou Road, Nanjing 210093, China; Department of Medical Genetics, Nanjing University School of Medicine, No.22 HanKou Road, Nanjing 210093, China; Clinical Molecular Diagnostic Center, Second Hospital, Nanjing Medical University, No.121 Jiangjiayuan Road, Nanjing 210011, China
| | - Bixia Zheng
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, No.22 HanKou Road, Nanjing 210093, China; Department of Medical Genetics, Nanjing University School of Medicine, No.22 HanKou Road, Nanjing 210093, China
| | - Dong Guo
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, No.22 HanKou Road, Nanjing 210093, China; Department of Medical Genetics, Nanjing University School of Medicine, No.22 HanKou Road, Nanjing 210093, China
| | - Zhenming Cai
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, No.22 HanKou Road, Nanjing 210093, China; Department of Medical Genetics, Nanjing University School of Medicine, No.22 HanKou Road, Nanjing 210093, China
| | - Yaping Wang
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, No.22 HanKou Road, Nanjing 210093, China; Department of Medical Genetics, Nanjing University School of Medicine, No.22 HanKou Road, Nanjing 210093, China.
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Errichiello E, Balsamo A, Cerni M, Venesio T. Mitochondrial variants in MT-CO2 and D-loop instability are involved in MUTYH-associated polyposis. J Mol Med (Berl) 2015; 93:1271-81. [PMID: 26138249 DOI: 10.1007/s00109-015-1312-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 05/28/2015] [Accepted: 06/16/2015] [Indexed: 12/21/2022]
Abstract
UNLABELLED Mitochondrial DNA alterations have been widely reported in different human tumours, including colorectal carcinoma, but their mutational spectrum and pathogenic role in specific subsets of patients with polyposis syndromes have been poorly investigated. We compared the breadth of somatic variants across the mitochondrial genome of MUTYH-associated polyposis (MAP) patients with homogeneous groups of classical/attenuated familial adenomatous polyposis (FAP/AFAP) and sporadic cases. Overall, we screened 121 adenomas and seven adenocarcinomas and their corresponding germinal controls, for mitochondrial genes with a crucial role in oxidative phosphorylation and translation (MT-CO1, MT-CO2, MT-CO3, MT-TD, MT-TS1, MT-ATP6) as well as a hypervariable sequence (HV-II) within the control region displacement loop (D-loop), a marker of hypermutability and clonal expansion. The sequencing analysis revealed the presence of 17 variants, mostly causing non-synonymous changes in conserved amino acid residues, typically distributed in the MT-CO2 gene of MAP patients (P < 0.0001), who frequently carried the hot spot m.7763G>A variant. Accordingly, D-loop instability was also significantly associated with variants grouped inside the MT-CO2 gene (P = 0.0061). This is the first report showing a locus-specific distribution of mitochondrial DNA alterations in a subtype of colorectal tumourigenesis. In addition, our findings suggest that MT-CO2 variants, representing early molecular events in MAP tumorigenesis, might be a potential prognostic biomarker for the cancer-risk assessment of patients affected by this syndrome. KEY MESSAGES We compared the frequencies of mtDNA variants in MAP vs. FAP/AFAP/sporadic patients. We found a gene-specific (MT-CO2) distribution of mtDNA variants in MAP cases. Most mtDNA variants caused non-synonymous changes in conserved amino acid residues. D-loop instability was significantly associated with variants grouped inside MT-CO2. MT-CO2 variants might be a potential prognostic biomarker in MAP patients.
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Affiliation(s)
- Edoardo Errichiello
- Molecular Pathology Laboratory, Unit of Pathology, Institute for Cancer Research and Treatment, FPO-IRCCS, Strada Provinciale 142, 10060, Candiolo, Torino, Italy
| | - Antonella Balsamo
- Molecular Pathology Laboratory, Unit of Pathology, Institute for Cancer Research and Treatment, FPO-IRCCS, Strada Provinciale 142, 10060, Candiolo, Torino, Italy
| | - Marianna Cerni
- Molecular Pathology Laboratory, Unit of Pathology, Institute for Cancer Research and Treatment, FPO-IRCCS, Strada Provinciale 142, 10060, Candiolo, Torino, Italy
| | - Tiziana Venesio
- Molecular Pathology Laboratory, Unit of Pathology, Institute for Cancer Research and Treatment, FPO-IRCCS, Strada Provinciale 142, 10060, Candiolo, Torino, Italy.
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Leoz ML, Carballal S, Moreira L, Ocaña T, Balaguer F. The genetic basis of familial adenomatous polyposis and its implications for clinical practice and risk management. APPLICATION OF CLINICAL GENETICS 2015; 8:95-107. [PMID: 25931827 PMCID: PMC4404874 DOI: 10.2147/tacg.s51484] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Familial adenomatous polyposis (FAP) is an inherited disorder that represents the most common gastrointestinal polyposis syndrome. Germline mutations in the APC gene were initially identified as responsible for FAP, and later, several studies have also implicated the MUTYH gene as responsible for this disease, usually referred to as MUTYH-associated polyposis (MAP). FAP and MAP are characterized by the early onset of multiple adenomatous colorectal polyps, a high lifetime risk of colorectal cancer (CRC), and in some patients the development of extracolonic manifestations. The goal of colorectal management in these patients is to prevent CRC mortality through endoscopic and surgical approaches. Individuals with FAP and their relatives should receive appropriate genetic counseling and join surveillance programs when indicated. This review is focused on the description of the main clinical and genetic aspects of FAP associated with germline APC mutations and MAP.
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Affiliation(s)
- Maria Liz Leoz
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBERehd), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain
| | - Sabela Carballal
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBERehd), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain
| | - Leticia Moreira
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBERehd), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain
| | - Teresa Ocaña
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBERehd), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain
| | - Francesc Balaguer
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBERehd), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain
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The MUTYH hotspot mutations p.G396D and p.Y179C do not cause substantial genetic susceptibility to biliary cancer. Fam Cancer 2015; 13:243-7. [PMID: 24420788 DOI: 10.1007/s10689-014-9699-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Inflammation-associated oxidative stress and DNA damage are involved in malignant transformation of cholangiocytes. Defective DNA repair mechanisms may predispose to cholangiocarcinoma (CCA) formation, and an elevated CCA risk for MutY human homologue (MUTYH) germline mutation carriers has been proposed previously. The aim of this study was to re-evaluate the MUTYH hotspot mutations p.Y179C (rs34612342) and p.G396D (rs36053993) as genetic susceptibility factors in a large CCA cohort. The study population consisted of 219 Caucasian CCA patients (66.2 ± 11.9 years, 130 males, 89 females; 43 intrahepatic and 176 extrahepatic tumours; tissue diagnosis in 77.6 %) and 355 healthy controls (61.0 ± 11.0 years; 158 males, 197 females). MUTYH hotspot variants were genotyped using TaqMan assays. Four CCA patients were monoallelic mutation carriers (3 p.G396D; 1 p.Y179C) whereas 6 control subjects were heterozygotes (5 p.G396D; 1 p.Y179C). None of the patients carried a biallelic hotspot mutation. The observed allele frequencies did not differ significantly between cases and controls (p > 0.05) and association tests did not provide evidence for an involvement of p.Y179C (OR 1.6 [95 % CI 0.1-26.0]) or p.G396D (OR 1.0 [95 % CI 0.2-4.1]) in the susceptibility to CCA. Power analysis identified a sufficient power only for large effect sizes (>90 % for OR > 5.8 for p.G396D and OR > 18.5 for p.Y179C). Monoallelic MUTYH hotspot mutations do not act as major genetic susceptibility factors causing a substantial CCA risk in the Caucasian population. Due to the low statistical power for the identification of small effect sizes, much larger studies will be needed to detect such effects of minor clinical significance.
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Grandval P, Fabre AJ, Gaildrat P, Baert-Desurmont S, Blayau M, Buisine MP, Coulet F, Maugard C, Pinson S, Remenieras A, Rouleau E, Uhrhammer N, Beroud C, Olschwang S. Genomic variations integrated database for MUTYH-associated adenomatous polyposis. J Med Genet 2014; 52:25-7. [PMID: 25368107 DOI: 10.1136/jmedgenet-2014-102752] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Philippe Grandval
- INSERM UMR_S910, Marseille, France Departments of medical Genetics and Gastroenterology, AP-HM La Timone, Marseille, France
| | - Aurélie J Fabre
- INSERM UMR_S910, Marseille, France Departments of medical Genetics and Gastroenterology, AP-HM La Timone, Marseille, France
| | | | | | - Martine Blayau
- Medical Genetics Department, CHU Pontchaillou, Rennes, France
| | | | - Florence Coulet
- Medical Genetics Department, AP-HP Pitié-Salpétrière, Paris, France
| | | | - Stéphane Pinson
- Medical Genetics Department, Edouard Herriot Hospital, Lyon, France
| | - Audrey Remenieras
- Medical Genetics Department, Institut Paoli-Calmettes, Marseille, France
| | | | - Nancy Uhrhammer
- Medical Genetics Department, Centre Jean Perrin, Clermont-Ferrand, France
| | - Christophe Beroud
- INSERM UMR_S910, Marseille, France Departments of medical Genetics and Gastroenterology, AP-HM La Timone, Marseille, France Aix-Marseille Université, Marseille, France
| | - Sylviane Olschwang
- INSERM UMR_S910, Marseille, France Departments of medical Genetics and Gastroenterology, AP-HM La Timone, Marseille, France Gastroenterology Department, European Hospital, Marseille, France Oncology Department, Clairval Hospital, Marseille, France The first two authors contributed equally to this work
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Oka S, Leon J, Tsuchimoto D, Sakumi K, Nakabeppu Y. MUTYH, an adenine DNA glycosylase, mediates p53 tumor suppression via PARP-dependent cell death. Oncogenesis 2014; 3:e121. [PMID: 25310643 PMCID: PMC4216901 DOI: 10.1038/oncsis.2014.35] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/15/2014] [Accepted: 08/25/2014] [Indexed: 12/12/2022] Open
Abstract
p53-regulated caspase-independent cell death has been implicated in suppression of tumorigenesis, however, the regulating mechanisms are poorly understood. We previously reported that 8-oxoguanine (8-oxoG) accumulation in nuclear DNA (nDNA) and mitochondrial DNA triggers two distinct caspase-independent cell death through buildup of single-strand DNA breaks by MutY homolog (MUTYH), an adenine DNA glycosylase. One pathway depends on poly-ADP-ribose polymerase (PARP) and the other depends on calpains. Deficiency of MUTYH causes MUTYH-associated familial adenomatous polyposis. MUTYH thereby suppresses tumorigenesis not only by avoiding mutagenesis, but also by inducing cell death. Here, we identified the functional p53-binding site in the human MUTYH gene and demonstrated that MUTYH is transcriptionally regulated by p53, especially in the p53/DNA mismatch repair enzyme, MLH1-proficient colorectal cancer-derived HCT116+Chr3 cells. MUTYH-small interfering RNA, an inhibitor for p53 or PARP suppressed cell death without an additive effect, thus revealing that MUTYH is a potential mediator of p53 tumor suppression, which is known to be upregulated by MLH1. Moreover, we found that the p53-proficient, mismatch repair protein, MLH1-proficient colorectal cancer cell line express substantial levels of MUTYH in nuclei but not in mitochondria, suggesting that 8-oxoG accumulation in nDNA triggers MLH1/PARP-dependent cell death. These results provide new insights on the molecular mechanism of tumorigenesis and potential new strategies for cancer therapies.
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Affiliation(s)
- S Oka
- 1] Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan [2] Research Center for Nucleotide Pool, Kyushu University, Fukuoka, Japan
| | - J Leon
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - D Tsuchimoto
- 1] Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan [2] Research Center for Nucleotide Pool, Kyushu University, Fukuoka, Japan
| | - K Sakumi
- 1] Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan [2] Research Center for Nucleotide Pool, Kyushu University, Fukuoka, Japan
| | - Y Nakabeppu
- 1] Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan [2] Research Center for Nucleotide Pool, Kyushu University, Fukuoka, Japan
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Valle L. Genetic predisposition to colorectal cancer: Where we stand and future perspectives. World J Gastroenterol 2014; 20:9828-9849. [PMID: 25110415 PMCID: PMC4123366 DOI: 10.3748/wjg.v20.i29.9828] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 02/10/2014] [Accepted: 04/03/2014] [Indexed: 02/06/2023] Open
Abstract
The development of colorectal cancer (CRC) can be influenced by genetic factors in both familial cases and sporadic cases. Familial CRC has been associated with genetic changes in high-, moderate- and low-penetrance susceptibility genes. However, despite the availability of current gene-identification techniques, the genetic causes of a considerable proportion of hereditary cases remain unknown. Genome-wide association studies of CRC have identified a number of common low-penetrance alleles associated with a slightly increased or decreased risk of CRC. The accumulation of low-risk variants may partly explain the familial risk of CRC, and some of these variants may modify the risk of cancer in patients with mutations in high-penetrance genes. Understanding the predisposition to develop CRC will require investigators to address the following challenges: the identification of genes that cause uncharacterized hereditary cases of CRC such as familial CRC type X and serrated polyposis; the classification of variants of unknown significance in known CRC-predisposing genes; and the identification of additional cancer risk modifiers that can be used to perform risk assessments for individual mutation carriers. We performed a comprehensive review of the genetically characterized and uncharacterized hereditary CRC syndromes and of low- and moderate-penetrance loci and variants identified through genome-wide association studies and candidate-gene approaches. Current challenges and future perspectives in the field of CRC predisposition are also discussed.
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Ran X, Cai WJ, Huang XF, Liu Q, Lu F, Qu J, Wu J, Jin ZB. 'RetinoGenetics': a comprehensive mutation database for genes related to inherited retinal degeneration. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau047. [PMID: 24939193 PMCID: PMC4060621 DOI: 10.1093/database/bau047] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Inherited retinal degeneration (IRD), a leading cause of human blindness worldwide, is exceptionally heterogeneous with clinical heterogeneity and genetic variety. During the past decades, tremendous efforts have been made to explore the complex heterogeneity, and massive mutations have been identified in different genes underlying IRD with the significant advancement of sequencing technology. In this study, we developed a comprehensive database, ‘RetinoGenetics’, which contains informative knowledge about all known IRD-related genes and mutations for IRD. ‘RetinoGenetics’ currently contains 4270 mutations in 186 genes, with detailed information associated with 164 phenotypes from 934 publications and various types of functional annotations. Then extensive annotations were performed to each gene using various resources, including Gene Ontology, KEGG pathways, protein–protein interaction, mutational annotations and gene–disease network. Furthermore, by using the search functions, convenient browsing ways and intuitive graphical displays, ‘RetinoGenetics’ could serve as a valuable resource for unveiling the genetic basis of IRD. Taken together, ‘RetinoGenetics’ is an integrative, informative and updatable resource for IRD-related genetic predispositions. Database URL:http://www.retinogenetics.org/.
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Affiliation(s)
- Xia Ran
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325027, China, Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, The Eye Hospital of Wenzhou Medical University, Wenzhou 325027, China and The State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health People's Republic of China, Wenzhou 325027, China
| | - Wei-Jun Cai
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325027, China, Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, The Eye Hospital of Wenzhou Medical University, Wenzhou 325027, China and The State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health People's Republic of China, Wenzhou 325027, ChinaInstitute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325027, China, Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, The Eye Hospital of Wenzhou Medical University, Wenzhou 325027, China and The State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health People's Republic of China, Wenzhou 325027, China
| | - Xiu-Feng Huang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325027, China, Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, The Eye Hospital of Wenzhou Medical University, Wenzhou 325027, China and The State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health People's Republic of China, Wenzhou 325027, ChinaInstitute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325027, China, Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, The Eye Hospital of Wenzhou Medical University, Wenzhou 325027, China and The State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health People's Republic of China, Wenzhou 325027, China
| | - Qi Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325027, China, Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, The Eye Hospital of Wenzhou Medical University, Wenzhou 325027, China and The State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health People's Republic of China, Wenzhou 325027, China
| | - Fan Lu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325027, China, Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, The Eye Hospital of Wenzhou Medical University, Wenzhou 325027, China and The State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health People's Republic of China, Wenzhou 325027, ChinaInstitute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325027, China, Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, The Eye Hospital of Wenzhou Medical University, Wenzhou 325027, China and The State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health People's Republic of China, Wenzhou 325027, China
| | - Jia Qu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325027, China, Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, The Eye Hospital of Wenzhou Medical University, Wenzhou 325027, China and The State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health People's Republic of China, Wenzhou 325027, ChinaInstitute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325027, China, Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, The Eye Hospital of Wenzhou Medical University, Wenzhou 325027, China and The State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health People's Republic of China, Wenzhou 325027, China
| | - Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325027, China, Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, The Eye Hospital of Wenzhou Medical University, Wenzhou 325027, China and The State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health People's Republic of China, Wenzhou 325027, China
| | - Zi-Bing Jin
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325027, China, Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, The Eye Hospital of Wenzhou Medical University, Wenzhou 325027, China and The State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health People's Republic of China, Wenzhou 325027, ChinaInstitute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325027, China, Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, The Eye Hospital of Wenzhou Medical University, Wenzhou 325027, China and The State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health People's Republic of China, Wenzhou 325027, China
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Grandval P, Blayau M, Buisine MP, Coulet F, Maugard C, Pinson S, Remenieras A, Tinat J, Uhrhammer N, Béroud C, Olschwang S. The UMD-APC database, a model of nation-wide knowledge base: update with data from 3,581 variations. Hum Mutat 2014; 35:532-6. [PMID: 24599579 DOI: 10.1002/humu.22539] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 02/21/2014] [Indexed: 12/13/2022]
Abstract
Familial adenomatous polyposis (FAP) is a rare autosomal-inherited disease that highly predisposes to colorectal cancer, characterized by a diffuse duodenal and colorectal polyposis associated with various extradigestive tumors and linked to germline mutations within the APC gene. A French consortium of laboratories involved in APC mutation screening has progressively improved the description of the variation spectrum, inferred functional significance of nontruncating variations, and delineated phenotypic characteristics of the disease. The current version of the UMD-APC database is described here. The total number of variations has risen to 5,453 representing 1,473 distinct variations. The published records initially registered into the database were extended with 3,581 germline variations found through genetic testing performed by the eight licensed laboratories belonging to the French APC network. Sixty six of 149 variations of previously unknown significance have now been classified as (likely) causal or neutral. The database is available on the Internet (http://www.umd.be/APC/) and updated twice per year according to the consensus rules of the network. The UMD-APC database is thus expected to facilitate functional classification of rare synonymous, nonsynonymous, and intronic mutations and consequently improve genetic counseling and medical care in FAP families.
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Affiliation(s)
- Philippe Grandval
- UMR_S910, INSERM, Marseille, France; AP-HM La Timone, Gastroenterology Department, Marseille, France
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Borras E, Taggart MW, Lynch PM, Vilar E. Establishing a diagnostic road map for MUTYH-associated polyposis. Clin Cancer Res 2014; 20:1061-3. [PMID: 24486588 DOI: 10.1158/1078-0432.ccr-13-3295] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The analysis of MUTYH-associated polyposis cases of the EPIPOLIP cohort confirms the importance of including serrated polyps in the diagnostic work-up of patients with oligopolyposis, suggests a role for screening polyps for the somatic c.34G>T KRAS mutation, and allows the implementation of a genetic testing strategy based on population data.
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Affiliation(s)
- Ester Borras
- Authors' Affiliations: Departments of Clinical Cancer Prevention, Pathology, and Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Picelli S, Lorenzo Bermejo J, Chang-Claude J, Hoffmeister M, Fernández-Rozadilla C, Carracedo A, Castells A, Castellví-Bel S, Naccarati A, Pardini B, Vodickova L, Müller H, Talseth-Palmer BA, Stibbard G, Peterlongo P, Nici C, Veneroni S, Li L, Casey G, Tenesa A, Farrington SM, Tomlinson I, Moreno V, van Wezel T, Wijnen J, Dunlop M, Radice P, Scott RJ, Vodicka P, Ruiz-Ponte C, Brenner H, Buch S, Völzke H, Hampe J, Schafmayer C, Lindblom A. Meta-analysis of mismatch repair polymorphisms within the cogent consortium for colorectal cancer susceptibility. PLoS One 2013; 8:e72091. [PMID: 24039736 PMCID: PMC3765450 DOI: 10.1371/journal.pone.0072091] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 07/06/2013] [Indexed: 11/22/2022] Open
Abstract
In the last four years, Genome-Wide Association Studies (GWAS) have identified sixteen low-penetrance polymorphisms on fourteen different loci associated with colorectal cancer (CRC). Due to the low risks conferred by known common variants, most of the 35% broad-sense heritability estimated by twin studies remains unexplained. Recently our group performed a case-control study for eight Single Nucleotide Polymorphisms (SNPs) in 4 CRC genes. The present investigation is a follow-up of that study. We have genotyped six SNPs that showed a positive association and carried out a meta-analysis based on eight additional studies comprising in total more than 8000 cases and 6000 controls. The estimated recessive odds ratio for one of the SNPs, rs3219489 (MUTYH Q338H), decreased from 1.52 in the original Swedish study, to 1.18 in the Swedish replication, and to 1.08 in the initial meta-analysis. Since the corresponding summary probability value was 0.06, we decided to retrieve additional information for this polymorphism. The incorporation of six further studies resulted in around 13000 cases and 13000 controls. The newly updated OR was 1.03. The results from the present large, multicenter study illustrate the possibility of decreasing effect sizes with increasing samples sizes. Phenotypic heterogeneity, differential environmental exposures, and population specific linkage disequilibrium patterns may explain the observed difference of genetic effects between Sweden and the other investigated cohorts.
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Affiliation(s)
- Simone Picelli
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden ; Ludwig Institute for Cancer Research - Stockholm branch, Stockholm, Sweden
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Guo W, Zheng B, Cai Z, Xu L, Guo D, Cao L, Wang Y. The polymorphic AluYb8 insertion in the MUTYH gene is associated with reduced type 1 protein expression and reduced mitochondrial DNA content. PLoS One 2013; 8:e70718. [PMID: 23936466 PMCID: PMC3735632 DOI: 10.1371/journal.pone.0070718] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 06/26/2013] [Indexed: 12/13/2022] Open
Abstract
The human mutY homolog (MUTYH) participates in base excision repair (BER), which is critical for repairing oxidized DNA bases and maintaining DNA replication fidelity. The polymorphic AluYb8 insertion in the 15th intron of the MUTYH gene (AluYb8MUTYH) has been shown to associate with an aggregated 8-hydroxy-2′-deoxyguanosine (8-OH-dG) lesion in genomic DNA and to serve as a risk factor for age-related diseases. In this work, we demonstrate that this variant is associated with a significant reduction of the type 1 MUTYH protein that localizes to mitochondria. Notably, this variant affects mitochondrial DNA (mtDNA) maintenance and functional mitochondrial mass in individuals homozygous for the AluYb8MUTYH variant. These findings provide evidence for an association between the AluYb8MUTYH variant and decreased mitochondrial homeostasis and, consequently, contribute to elucidating the roles of the AluYb8MUTYH variant in impairing the mitochondrial base excision repair (mtBER) system and increasing the risk of acquiring an age-related disease.
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Affiliation(s)
- Wenwen Guo
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, China
- The State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Bixia Zheng
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, China
| | - Zhenming Cai
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, China
| | - Lizhi Xu
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, China
| | - Dong Guo
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, China
| | - Lili Cao
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, China
| | - Yaping Wang
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, China
- The State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
- * E-mail:
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MUTYH-associated colorectal cancer and adenomatous polyposis. Surg Today 2013; 44:593-600. [PMID: 23605219 DOI: 10.1007/s00595-013-0592-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 03/04/2013] [Indexed: 12/28/2022]
Abstract
MUTYH-associated polyposis (MAP) was first described in 2002. MUTYH is a component of a base excision repair system that protects the genomic information from oxidative damage. When the MUTYH gene product is impaired by bi-allelic germline mutation, it leads to the mutation of cancer-related genes, such as the APC and/or the KRAS genes, via G to T transversion. MAP is a hereditary colorectal cancer syndrome inherited in an autosomal-recessive fashion. The clinical features of MAP include the presence of 10-100 adenomatous polyps in the colon, and early onset of colorectal cancer. Ethnic and geographical differences in the pattern of the MUTYH gene mutations have been suggested. In Caucasian patients, c.536A>G (Y179C) and c.1187G>A (G396D) mutations are frequently detected. In the Asian population, Y179C and G396D are uncommon, whereas other variants are suggested to be the major causes of MAP. We herein review the literature on MUTYH-associated colorectal cancer and adenomatous polyposis.
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Torrezan GT, da Silva FCC, Santos EMM, Krepischi ACV, Achatz MIW, Aguiar S, Rossi BM, Carraro DM. Mutational spectrum of the APC and MUTYH genes and genotype-phenotype correlations in Brazilian FAP, AFAP, and MAP patients. Orphanet J Rare Dis 2013; 8:54. [PMID: 23561487 PMCID: PMC3623842 DOI: 10.1186/1750-1172-8-54] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 03/27/2013] [Indexed: 01/01/2023] Open
Abstract
Background Patients with multiple colorectal adenomas are currently screened for germline mutations in two genes, APC and MUTYH. APC-mutated patients present classic or attenuated familial adenomatous polyposis (FAP/AFAP), while patients carrying biallelic MUTYH mutations exhibit MUTYH-associated polyposis (MAP). The spectrum of mutations as well as the genotype-phenotype correlations in polyposis syndromes present clinical impact and can be population specific, making important to obtain genetic and clinical data from different populations. Methods DNA sequencing of the complete coding region of the APC and MUTYH genes was performed in 23 unrelated Brazilian polyposis patients. In addition, mutation-negative patients were screened for large genomic rearrangements by multiplex ligation-dependent probe amplification, array-comparative genomic hybridization, and duplex quantitative PCR. Biallelic MUTYH mutations were confirmed by allele-specific PCR. Clinical data of the index cases and their affected relatives were used to assess genotype–phenotype correlations. Results Pathogenic mutations were identified in 20 of the 23 probands (87%): 14 in the APC gene and six in the MUTYH gene; six of them (30%) were described for the first time in this series. Genotype-phenotype correlations revealed divergent results compared with those described in other studies, particularly regarding the extent of polyposis and the occurrence of desmoid tumors in families with mutations before codon 1444 (6/8 families with desmoid). Conclusions This first comprehensive investigation of the APC and MUTYH mutation spectrum in Brazilian polyposis patients showed a high detection rate and identified novel pathogenic mutations. Notably, a significant number of APC-positive families were not consistent with the predicted genotype-phenotype correlations from other populations.
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Turco E, Ventura I, Minoprio A, Russo MT, Torreri P, Degan P, Molatore S, Ranzani GN, Bignami M, Mazzei F. Understanding the role of the Q338H MUTYH variant in oxidative damage repair. Nucleic Acids Res 2013; 41:4093-103. [PMID: 23460202 PMCID: PMC3627602 DOI: 10.1093/nar/gkt130] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The MUTYH DNA–glycosylase is indirectly engaged in the repair of the miscoding 7,8-dihydro-8-oxo-2′-deoxyguanine (8-oxodG) lesion by removing adenine erroneously incorporated opposite the oxidized purine. Inherited biallelic mutations in the MUTYH gene are responsible for a recessive syndrome, the MUTYH-associated polyposis (MAP), which confers an increased risk of colorectal cancer. In this study, we functionally characterized the Q338H variant using recombinant proteins, as well as cell-based assays. This is a common variant among human colorectal cancer genes, which is generally considered, unrelated to the MAP phenotype but recently indicated as a low-penetrance allele. We demonstrate that the Q338H variant retains a wild-type DNA–glycosylase activity in vitro, but it shows a reduced ability to interact with the replication sensor RAD9:RAD1:HUS1 (9–1–1) complex. In comparison with Mutyh−/− mouse embryo fibroblasts expressing a wild-type MUTYH cDNA, the expression of Q338H variant was associated with increased levels of DNA 8-oxodG, hypersensitivity to oxidant and accumulation of the population in the S phase of the cell cycle. Thus, an inefficient interaction of MUTYH with the 9–1–1 complex leads to a repair-defective phenotype, indicating that a proper communication between MUTYH enzymatic function and the S phase checkpoint is needed for effective repair of oxidative damage.
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Affiliation(s)
- Eleonora Turco
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, 00161 Roma, Italy
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Mazzei F, Viel A, Bignami M. Role of MUTYH in human cancer. Mutat Res 2013; 743-744:33-43. [PMID: 23507534 DOI: 10.1016/j.mrfmmm.2013.03.003] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 03/06/2013] [Accepted: 03/09/2013] [Indexed: 06/01/2023]
Abstract
MUTYH, a human ortholog of MutY, is a post-replicative DNA glycosylase, highly conserved throughout evolution, involved in the correction of mismatches resulting from a faulty replication of the oxidized base 8-hydroxyguanine (8-oxodG). In particular removal of adenine from A:8-oxodG mispairs by MUTYH activity is followed by error-free base excision repair (BER) events, leading to the formation of C:8-oxodG base pairs. These are the substrate of another BER enzyme, the OGG1 DNA glycosylase, which then removes 8-oxodG from DNA. Thus the combined action of OGG1 and MUTYH prevents oxidative damage-induced mutations, i.e. GC->TA transversions. Germline mutations in MUTYH are associated with a recessively heritable colorectal polyposis, now referred to as MUTYH-associated polyposis (MAP). Here we will review the phenotype(s) associated with MUTYH inactivation from bacteria to mammals, the structure of the MUTYH protein, the molecular mechanisms of its enzymatic activity and the functional characterization of MUTYH variants. The relevance of these results will be discussed to define the role of specific human mutations in colorectal cancer risk together with the possible role of MUTYH inactivation in sporadic cancer.
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Affiliation(s)
- Filomena Mazzei
- Department of Environment, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
| | - Alessandra Viel
- Experimental Oncology 1, Centro di Riferimento Oncologico, IRCCS, Via F.Gallini 2, 33081 Aviano, PN, Italy
| | - Margherita Bignami
- Department of Environment, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy.
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