1
|
Ricciardiello R, Forleo G, Cipolla L, van Winckel G, Marconi C, Nouspikel T, Halazonetis TD, Zgheib O, Sabbioneda S. Homozygous substitution of threonine 191 by proline in polymerase η causes Xeroderma pigmentosum variant. Sci Rep 2024; 14:1117. [PMID: 38212351 PMCID: PMC10784498 DOI: 10.1038/s41598-023-51120-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 12/31/2023] [Indexed: 01/13/2024] Open
Abstract
DNA polymerase eta (Polη) is the only translesion synthesis polymerase capable of error-free bypass of UV-induced cyclobutane pyrimidine dimers. A deficiency in Polη function is associated with the human disease Xeroderma pigmentosum variant (XPV). We hereby report the case of a 60-year-old woman known for XPV and carrying a Polη Thr191Pro variant in homozygosity. We further characterize the variant in vitro and in vivo, providing molecular evidence that the substitution abrogates polymerase activity and results in UV sensitivity through deficient damage bypass. This is the first functional molecular characterization of a missense variant of Polη, whose reported pathogenic variants have thus far been loss of function truncation or frameshift mutations. Our work allows the upgrading of Polη Thr191Pro from 'variant of uncertain significance' to 'likely pathogenic mutant', bearing direct impact on molecular diagnosis and genetic counseling. Furthermore, we have established a robust experimental approach that will allow a precise molecular analysis of further missense mutations possibly linked to XPV. Finally, it provides insight into critical Polη residues that may be targeted to develop small molecule inhibitors for cancer therapeutics.
Collapse
Affiliation(s)
- Roberto Ricciardiello
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, Italy
- Dipartimento di Biologia e Biotecnologie 'Lazzaro Spallanzani', Università degli Studi di Pavia, Pavia, Italy
| | - Giulia Forleo
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, Italy
| | - Lina Cipolla
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, Italy
| | - Geraldine van Winckel
- Division of Medical Genetics, Diagnostics Department, Geneva University Hospitals, Geneva, Switzerland
| | - Caterina Marconi
- Division of Medical Genetics, Diagnostics Department, Geneva University Hospitals, Geneva, Switzerland
| | - Thierry Nouspikel
- Division of Medical Genetics, Diagnostics Department, Geneva University Hospitals, Geneva, Switzerland
| | - Thanos D Halazonetis
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Omar Zgheib
- Division of Medical Genetics, Diagnostics Department, Geneva University Hospitals, Geneva, Switzerland.
| | - Simone Sabbioneda
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, Italy.
| |
Collapse
|
2
|
Gilea AI, Magistrati M, Notaroberto I, Tiso N, Dallabona C, Baruffini E. The Saccharomyces cerevisiae mitochondrial DNA polymerase and its contribution to the knowledge about human POLG-related disorders. IUBMB Life 2023; 75:983-1002. [PMID: 37470284 DOI: 10.1002/iub.2770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/05/2023] [Indexed: 07/21/2023]
Abstract
Most eukaryotes possess a mitochondrial genome, called mtDNA. In animals and fungi, the replication of mtDNA is entrusted by the DNA polymerase γ, or Pol γ. The yeast Pol γ is composed only of a catalytic subunit encoded by MIP1. In humans, Pol γ is a heterotrimer composed of a catalytic subunit homolog to Mip1, encoded by POLG, and two accessory subunits. In the last 25 years, more than 300 pathological mutations in POLG have been identified as the cause of several mitochondrial diseases, called POLG-related disorders, which are characterized by multiple mtDNA deletions and/or depletion in affected tissues. In this review, at first, we summarize the biochemical properties of yeast Mip1, and how mutations, especially those introduced recently in the N-terminal and C-terminal regions of the enzyme, affect the in vitro activity of the enzyme and the in vivo phenotype connected to the mtDNA stability and to the mtDNA extended and point mutability. Then, we focus on the use of yeast harboring Mip1 mutations equivalent to the human ones to confirm their pathogenicity, identify the phenotypic defects caused by these mutations, and find both mechanisms and molecular compounds able to rescue the detrimental phenotype. A closing chapter will be dedicated to other polymerases found in yeast mitochondria, namely Pol ζ, Rev1 and Pol η, and to their genetic interactions with Mip1 necessary to maintain mtDNA stability and to avoid the accumulation of spontaneous or induced point mutations.
Collapse
Affiliation(s)
- Alexandru Ionut Gilea
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Martina Magistrati
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Ilenia Notaroberto
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Natascia Tiso
- Department of Biology, University of Padova, Padova, Italy
| | - Cristina Dallabona
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Enrico Baruffini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| |
Collapse
|
3
|
Garcia-Moreno H, Langbehn DR, Abiona A, Garrood I, Fleszar Z, Manes MA, Morley AMS, Craythorne E, Mohammed S, Henshaw T, Turner S, Naik H, Bodi I, Sarkany RPE, Fassihi H, Lehmann AR, Giunti P. Neurological disease in xeroderma pigmentosum: prospective cohort study of its features and progression. Brain 2023; 146:5044-5059. [PMID: 38040034 PMCID: PMC10690019 DOI: 10.1093/brain/awad266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/22/2023] [Accepted: 07/16/2023] [Indexed: 12/03/2023] Open
Abstract
Xeroderma pigmentosum (XP) results from biallelic mutations in any of eight genes involved in DNA repair systems, thus defining eight different genotypes (XPA, XPB, XPC, XPD, XPE, XPF, XPG and XP variant or XPV). In addition to cutaneous and ophthalmological features, some patients present with XP neurological disease. It is unknown whether the different neurological signs and their progression differ among groups. Therefore, we aim to characterize the XP neurological disease and its evolution in the heterogeneous UK XP cohort. Patients with XP were followed in the UK National XP Service, from 2009 to 2021. Age of onset for different events was recorded. Cerebellar ataxia and additional neurological signs and symptoms were rated with the Scale for the Assessment and Rating of Ataxia (SARA), the Inventory of Non-Ataxia Signs (INAS) and the Activities of Daily Living questionnaire (ADL). Patients' mutations received scores based on their predicted effects. Data from available ancillary tests were collected. Ninety-three XP patients were recruited. Thirty-six (38.7%) reported neurological symptoms, especially in the XPA, XPD and XPG groups, with early-onset and late-onset forms, and typically appearing after cutaneous and ophthalmological symptoms. XPA, XPD and XPG patients showed higher SARA scores compared to XPC, XPE and XPV. SARA total scores significantly increased over time in XPD (0.91 points/year, 95% confidence interval: 0.61, 1.21) and XPA (0.63 points/year, 95% confidence interval: 0.38, 0.89). Hyporeflexia, hypopallesthaesia, upper motor neuron signs, chorea, dystonia, oculomotor signs and cognitive impairment were frequent findings in XPA, XPD and XPG. Cerebellar and global brain atrophy, axonal sensory and sensorimotor neuropathies, and sensorineural hearing loss were common findings in patients. Some XPC, XPE and XPV cases presented with abnormalities on examination and/or ancillary tests, suggesting underlying neurological involvement. More severe mutations were associated with a faster progression in SARA total score in XPA (0.40 points/year per 1-unit increase in severity score) and XPD (0.60 points/year per 1-unit increase), and in ADL total score in XPA (0.35 points/year per 1-unit increase). Symptomatic and asymptomatic forms of neurological disease are frequent in XP patients, and neurological symptoms can be an important cause of disability. Typically, the neurological disease will be preceded by cutaneous and ophthalmological features, and these should be actively searched in patients with idiopathic late-onset neurological syndromes. Scales assessing cerebellar function, especially walking and speech, and disability can show progression in some of the groups. Mutation severity can be used as a prognostic biomarker for stratification purposes in clinical trials.
Collapse
Affiliation(s)
- Hector Garcia-Moreno
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Douglas R Langbehn
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Adesoji Abiona
- UK National Xeroderma Pigmentosum Service, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 7EH, UK
| | - Isabel Garrood
- UK National Xeroderma Pigmentosum Service, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 7EH, UK
| | - Zofia Fleszar
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Marta Antonia Manes
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Ana M Susana Morley
- UK National Xeroderma Pigmentosum Service, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 7EH, UK
- Department of Ophthalmology, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 7EH, UK
| | - Emma Craythorne
- UK National Xeroderma Pigmentosum Service, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 7EH, UK
| | - Shehla Mohammed
- UK National Xeroderma Pigmentosum Service, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 7EH, UK
| | - Tanya Henshaw
- UK National Xeroderma Pigmentosum Service, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 7EH, UK
| | - Sally Turner
- UK National Xeroderma Pigmentosum Service, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 7EH, UK
| | - Harsha Naik
- UK National Xeroderma Pigmentosum Service, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 7EH, UK
| | - Istvan Bodi
- Clinical Neuropathology, Academic Neuroscience Building, King’s College Hospital, London SE5 9RS, UK
| | - Robert P E Sarkany
- UK National Xeroderma Pigmentosum Service, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 7EH, UK
| | - Hiva Fassihi
- UK National Xeroderma Pigmentosum Service, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 7EH, UK
| | - Alan R Lehmann
- UK National Xeroderma Pigmentosum Service, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 7EH, UK
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Paola Giunti
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- UK National Xeroderma Pigmentosum Service, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 7EH, UK
| |
Collapse
|
4
|
Yeom M, Hong JK, Shin JH, Lee Y, Guengerich FP, Choi JY. Identification of Three Human POLH Germline Variants Defective in Complementing the UV- and Cisplatin-Sensitivity of POLH-Deficient Cells. Int J Mol Sci 2023; 24:5198. [PMID: 36982269 PMCID: PMC10048814 DOI: 10.3390/ijms24065198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/04/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023] Open
Abstract
DNA polymerase (pol) η is responsible for error-free translesion DNA synthesis (TLS) opposite ultraviolet light (UV)-induced cis-syn cyclobutane thymine dimers (CTDs) and cisplatin-induced intrastrand guanine crosslinks. POLH deficiency causes one form of the skin cancer-prone disease xeroderma pigmentosum variant (XPV) and cisplatin sensitivity, but the functional impacts of its germline variants remain unclear. We evaluated the functional properties of eight human POLH germline in silico-predicted deleterious missense variants, using biochemical and cell-based assays. In enzymatic assays, utilizing recombinant pol η (residues 1-432) proteins, the C34W, I147N, and R167Q variants showed 4- to 14-fold and 3- to 5-fold decreases in specificity constants (kcat/Km) for dATP insertion opposite the 3'-T and 5'-T of a CTD, respectively, compared to the wild-type, while the other variants displayed 2- to 4-fold increases. A CRISPR/Cas9-mediated POLH knockout increased the sensitivity of human embryonic kidney 293 cells to UV and cisplatin, which was fully reversed by ectopic expression of wild-type pol η, but not by that of an inactive (D115A/E116A) or either of two XPV-pathogenic (R93P and G263V) mutants. Ectopic expression of the C34W, I147N, and R167Q variants, unlike the other variants, did not rescue the UV- and cisplatin-sensitivity in POLH-knockout cells. Our results indicate that the C34W, I147N, and R167Q variants-substantially reduced in TLS activity-failed to rescue the UV- and cisplatin-sensitive phenotype of POLH-deficient cells, which also raises the possibility that such hypoactive germline POLH variants may increase the individual susceptibility to UV irradiation and cisplatin chemotherapy.
Collapse
Affiliation(s)
- Mina Yeom
- Department of Pharmacology, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Jin-Kyung Hong
- Department of Pharmacology, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Joo-Ho Shin
- Department of Pharmacology, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Yunjong Lee
- Department of Pharmacology, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | | | - Jeong-Yun Choi
- Department of Pharmacology, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| |
Collapse
|
5
|
Feltes BC, Menck CFM. Current state of knowledge of human DNA polymerase eta protein structure and disease-causing mutations. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108436. [PMID: 35952573 DOI: 10.1016/j.mrrev.2022.108436] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 06/29/2022] [Accepted: 07/31/2022] [Indexed: 01/01/2023]
Abstract
POLη, encoded by the POLH gene, is a crucial protein for replicating damaged DNA and the most studied specialized translesion synthesis polymerases. Mutations in POLη are associated with cancer and the human syndrome xeroderma pigmentosum variant, which is characterized by extreme photosensitivity and an increased likelihood of developing skin cancers. The myriad of structural information about POLη is vast, covering dozens of different mutants, numerous crucial residues, domains, and posttranslational modifications that are essential for protein function within cells. Since POLη is key vital enzyme for cell survival, and mutations in this protein are related to aggressive diseases, understanding its structure is crucial for biomedical sciences, primarily due to its similarities with other Y-family polymerases and its potential as a targeted therapy-drug for tumors. This work provides an up-to-date review on structural aspects of the human POLη: from basic knowledge about critical residues and protein domains to its mutant variants, posttranslational modifications, and our current understanding of therapeutic molecules that target POLη. Thus, this review provides lessons about POLη's structure and gathers critical discussions and hypotheses that may contribute to understanding this protein's vital roles within the cells.
Collapse
Affiliation(s)
- Bruno César Feltes
- Department of Theoretical Informatics, Institute of Informatics, Department of Theoretical Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS Brazil; Department of Genetics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Department of Biophysics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | |
Collapse
|
6
|
Sarkany R, Norton S, Canfield M, Morgan M, Foster L, Sainsbury K, Araujo-Soares V, Wulf HC, Weinman J, Walburn J. Identifying the psychosocial predictors of ultraviolet exposure to the face in patients with xeroderma pigmentosum: a study of the behavioural factors affecting clinical outcomes in this genetic disease. J Med Genet 2022; 59:1095-1103. [PMID: 35393336 PMCID: PMC9613853 DOI: 10.1136/jmedgenet-2021-108323] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 02/14/2022] [Indexed: 01/24/2023]
Abstract
Background For patients with xeroderma pigmentosum (XP), the main means of preventing skin and eye cancers is extreme protection against ultraviolet radiation (UVR), particularly for the face. We have recently developed a methodology for objectively measuring photoprotection behaviour (‘UVR dose to facial skin’) and have found that the degree of photoprotection varies greatly between patients with XP. We have previously identified factors affecting photoprotection behaviour in XP using a subjective measure of photoprotection. Here, we have used this objective methodology to identify the factors which determine photoprotection behaviour in XP. Methods We studied 29 psychological, social, demographic and clinical variables in 36 patients with XP. We have previously objectively measured UVR protection (by measuring the dose of UVR reaching the skin of the face over a 3-week period) in these patients. Here, we use linear mixed-effects model analysis to identify the factors which lead to the differences in degree of photoprotection observed in these patients. Results Psychosocial factors accounted for as much of the interindividual variation in photoprotection behaviour (29%) as demographic and clinical factors (24%). Psychosocial factors significantly associated with worse UVR protection included: automaticity of the behaviours, and a group of beliefs and perceptions about XP and photoprotection known to associate with poor treatment adherence in other diseases. Conclusions We have identified factors contributing to poor photoprotection in XP. Identifying these potentially reversible psychosocial features has enabled us to design an intervention to improve photoprotection in patients with XP, aiming to prevent skin and eye cancers in these patients.
Collapse
Affiliation(s)
- Robert Sarkany
- Xeroderma Pigmentosum Unit, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Sam Norton
- Health Psychology Section, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Martha Canfield
- Health Psychology Section, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Myfanwy Morgan
- School of Cancer and Pharmaceutical Sciences, King's College London, London, UK
| | - Lesley Foster
- Xeroderma Pigmentosum Unit, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Kirby Sainsbury
- Population Health Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Vera Araujo-Soares
- Population Health Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,Health Technology and Services Research, Technical Medical Centre, University of Twente, Enschede, The Netherlands
| | | | - John Weinman
- School of Cancer and Pharmaceutical Sciences, King's College London, London, UK
| | - Jessica Walburn
- School of Cancer and Pharmaceutical Sciences, King's College London, London, UK
| |
Collapse
|
7
|
Sarkany RPE, Canfield M, Morgan M, Foster L, Johnstone K, Sainsbury K, Araujo-Soares V, Wulf HC, Weinman J, Walburn J, Norton S. Ultraviolet exposure to the face in patients with xeroderma pigmentosum and healthy controls: applying a novel methodology to define photoprotection behaviour. Br J Dermatol 2021; 186:713-720. [PMID: 34783007 PMCID: PMC9306996 DOI: 10.1111/bjd.20899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND In Xeroderma Pigmentosum (XP), the main means of preventing skin and eye cancers is extreme protection against ultraviolet radiation (UVR). Protection is most important for the face. OBJECTIVES We aimed to assess how well patients with XP adhere to medical advice to protect against UVR by objectively estimating the mean daily dose of UVR to the face. METHODS We objectively estimated the UVR dose to the face in 36 XP patients and 25 healthy individuals over 3 weeks in the summer. We used a new methodology which combined UVR dose measurements from a wrist-worn dosimeter with an activity diary record of face photoprotection behaviour for each 15 minute period spent outside. A protection factor was associated with each behaviour, and the data analysed using a negative binomial mixed-effects model. RESULTS The mean daily UVR dose (weighted for DNA damage capacity) to the face in the XP patients was 0.13 Standard Erythemal Doses (SED) (mean in healthy individuals = 0.51 SED). There was wide variation between patients (range <0.01 - 0.48 SED/day). Self-caring adult patients had a very similar UV dose to the face to cared-for patients (0.13 vs 0.12 SED/day) despite photoprotecting much more poorly when outside, because the self-caring adults were outside in daylight much less. CONCLUSIONS Photoprotection behaviour varies widely within the XP group indicating that non-adherence to photoprotection advice is a significant issue. Timing and duration of going outside are as important as photoprotective measures taken when outside, to determine the UVR exposure to the face. This new methodology will be of value in identifying the sources of UVR exposure in other conditions where facial UV exposure is a key outcome, particularly in patients with multiple non-melanoma skin cancers.
Collapse
Affiliation(s)
- R P E Sarkany
- Xeroderma Pigmentosum Unit, Guys and St Thomas' NHS Foundation Trust, UK
| | - M Canfield
- Health Psychology Section, Institute of Psychiatry, King's College London, Psychology & Neuroscience, UK
| | - M Morgan
- School of Cancer and Pharmaceutical Sciences, King's College London, UK
| | - L Foster
- Xeroderma Pigmentosum Unit, Guys and St Thomas' NHS Foundation Trust, UK
| | - K Johnstone
- School of Cancer and Pharmaceutical Sciences, King's College London, UK
| | - K Sainsbury
- Population Health Institute, Faculty of Medical Sciences, Newcastle University, UK
| | - V Araujo-Soares
- Population Health Institute, Faculty of Medical Sciences, Newcastle University, UK.,Health Technology and Services Research, Technical Medical Centre, University of Twente, The Netherlands
| | - H C Wulf
- Department of Dermatology, Bispebjerg University Hospital, Copenhagen, Denmark
| | - J Weinman
- School of Cancer and Pharmaceutical Sciences, King's College London, UK
| | - J Walburn
- School of Cancer and Pharmaceutical Sciences, King's College London, UK
| | - S Norton
- Health Psychology Section, Institute of Psychiatry, King's College London, Psychology & Neuroscience, UK
| |
Collapse
|
8
|
Xue Y, Braslavsky I, Quake SR. Temperature effect on polymerase fidelity. J Biol Chem 2021; 297:101270. [PMID: 34695416 PMCID: PMC8592868 DOI: 10.1016/j.jbc.2021.101270] [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: 07/13/2021] [Revised: 09/24/2021] [Accepted: 09/29/2021] [Indexed: 11/21/2022] Open
Abstract
The discovery of extremophiles helped enable the development of groundbreaking technology such as PCR. Temperature variation is often an essential step of these technology platforms, but the effect of temperature on the error rate of polymerases from different origins is underexplored. Here, we applied high-throughput sequencing to profile the error rates of DNA polymerases from psychrophilic, mesophilic, and thermophilic origins with single-molecule resolution. We found that the reaction temperature substantially increases substitution and deletion error rates of psychrophilic and mesophilic DNA polymerases. Our motif analysis shows that the substitution error profiles cluster according to phylogenetic similarity of polymerases, not the reaction temperature, thus suggesting that the reaction temperature increases the global error rate of polymerases independent of the sequence context. Intriguingly, we also found that the DNA polymerase I of psychrophilic bacteria exhibits higher polymerization activity than its mesophilic ortholog across all temperature ranges, including down to -19 °C, which is well below the freezing temperature of water. Our results provide a useful reference for how the reaction temperature, a crucial parameter of biochemistry, can affect DNA polymerase fidelity in organisms adapted to a wide range of thermal environments.
Collapse
Affiliation(s)
- Yuan Xue
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Ido Braslavsky
- The Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, California, USA; Department of Applied Physics, Stanford University, Stanford, California, USA; Chan Zuckerberg Biohub, Mission Bay, California, USA.
| |
Collapse
|
9
|
Pereira TDSF, Castro LP, Menck CFM, Maia MHT, Souza LLD, Fonseca FP, Pontes HAR, Pontes FSC, Gomez RS. Xeroderma pigmentosum variant: squamous cell carcinoma of the lower lip harboring exon 11 mutation of POLH. Oral Surg Oral Med Oral Pathol Oral Radiol 2021; 132:e97-e105. [PMID: 34030998 DOI: 10.1016/j.oooo.2021.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/09/2021] [Accepted: 03/21/2021] [Indexed: 10/21/2022]
Abstract
Xeroderma pigmentosum (XP) is a rare inherited disease caused by deficiencies in DNA damage repair, which mainly results from the failure of nucleotide excision repair or defects in translesion DNA synthesis. The development of multiple malignancies is one of the most prominent features of this condition, which is clinically characterized by the occurrence of hyperpigmentation and lesions associated with sunlight exposure. Lip squamous cell carcinoma in patients with XP has rarely been reported, and information regarding the genetic analysis of these patients is limited. In this report, a case of a 20-year-old patient who developed squamous cell carcinoma in the lower lip is described. Although the tumor was surgically excised, the patient presented with recurrence a few months later. Targeted sequencing using a customized panel of DNA repair genes revealed a mutation in POLH, the gene encoding DNA polymerase eta. Therefore, molecular characterization is important to further improve the understanding of possible phenotype-genotype correlations and mechanisms involved in the pathogenesis of XP.
Collapse
Affiliation(s)
| | - Ligia Pereira Castro
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Maria Helena Thomaz Maia
- Human and Medical Genetics, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Lucas Lacerda de Souza
- Department of Oral Pathology, University Hospital João de Barros Barreto, Federal University of Pará, Belém, Pará, Brazil
| | - Felipe Paiva Fonseca
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Helder Antônio Rebelo Pontes
- Department of Oral Pathology, University Hospital João de Barros Barreto, Federal University of Pará, Belém, Pará, Brazil
| | - Flavia Sirotheau Correa Pontes
- Department of Oral Pathology, University Hospital João de Barros Barreto, Federal University of Pará, Belém, Pará, Brazil
| | - Ricardo Santiago Gomez
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| |
Collapse
|
10
|
Zhang N, Fu X, Chen X, Chen L, Wang M. Variant subtype of xeroderma pigmentosum with multiple basal cell carcinomas diagnosed in a Chinese woman. PHOTODERMATOLOGY PHOTOIMMUNOLOGY & PHOTOMEDICINE 2020; 37:161-164. [PMID: 33095961 PMCID: PMC8048588 DOI: 10.1111/phpp.12621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 09/21/2020] [Accepted: 10/19/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Na Zhang
- Department of Dermatology, Jinhua Municipal Central Hospital (Affiliated Jinhua Hospital, Zhejiang University School of Medicine), JinHua, China
| | - Xuefeng Fu
- Department of Dermatology, Jinhua Municipal Central Hospital (Affiliated Jinhua Hospital, Zhejiang University School of Medicine), JinHua, China
| | - Xiaoxiao Chen
- Department of Dermatology, Jinhua Municipal Central Hospital (Affiliated Jinhua Hospital, Zhejiang University School of Medicine), JinHua, China
| | - Lin Chen
- Department of Intensive Care Unit, Jinhua Municipal Central Hospital (Affiliated Jinhua Hospital, Zhejiang University School of Medicine), JinHua, China
| | - Meiyan Wang
- Department of Dermatology, Jinhua Municipal Central Hospital (Affiliated Jinhua Hospital, Zhejiang University School of Medicine), JinHua, China
| |
Collapse
|
11
|
Soares IFZ, Christofolini DM, Silva LG, Feder D, de Siqueira Carvalho AA. Novel variants in POLH and TREM2 genes associated with a complex phenotype of xeroderma pigmentosum variant type and early-onset dementia. Mol Genet Genomic Med 2020; 8:e1491. [PMID: 32935933 PMCID: PMC7667349 DOI: 10.1002/mgg3.1491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/10/2020] [Accepted: 07/31/2020] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Xeroderma pigmentosum (XP) is a rare, genetically heterogeneous, autosomal recessive disorder caused by defects in the genes involved in repairing DNA damaged by ultraviolet radiation. These defects lead to a propensity to develop skin cancer at early ages as a hallmark, and progressive neurological degeneration can be observed in around 25% of patients. Eight clinically heterogeneous groups have been identified so far (XPA to XPG and XPV). Xeroderma pigmentosum variant type (XPV) is associated with pathogenic variants in POLH on chromosome 6, and no neurological dysfunction has been seen in these cases. However, on the same chromosome, it has been shown that TREM2 is associated with some types of dementia, particularly in patients with a behavioral variant frontotemporal phenotype. METHODS Gene mutational analysis was performed by whole-exome sequencing. RESULTS We report a case of a Caucasian woman with XP that developed behavioral and cognitive impairment at age 37. Whole-exome sequencing identified novel homozygous variants in POLH c.638C>G (p.Ser213*) and TREM2 c.154C>T (p.Arg52Cys), classifying the patient as XPV and suggesting that her frontotemporal dementia phenotype could be related to the variant in TREM2. CONCLUSION This paper describes a rare case of a patient with two novel variants in the same chromosome associated with XPV and early-onset dementia.
Collapse
Affiliation(s)
| | | | - Lis Gomes Silva
- Department of Neurosciences, Centro Universitário Saúde ABC, Santo Andre, São Paulo, Brazil
| | - David Feder
- Department of Neurosciences, Centro Universitário Saúde ABC, Santo Andre, São Paulo, Brazil
| | | |
Collapse
|
12
|
Borroni RG, Diegoli M, Grasso M, Concardi M, Agozzino M, Vignini M, Arbustini E. Rare exon 10 deletion in POLH gene in a family with xeroderma pigmentosum variant correlating with protein expression by immunohistochemistry. GIORN ITAL DERMAT V 2020; 155:349-354. [PMID: 32635709 DOI: 10.23736/s0392-0488.16.05158-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Xeroderma pigmentosum (XP) is a rare autosomal recessive disease characterized by severe cutaneous and ocular sensitivity to sunlight, leading to skin cancer. Most XP patients belong to the XP complementation groups (XP-A to XP-G), due to mutations in genes involved in nucleotide excision repair (NER). On the other hand, the XP Variant type (XP-V, OMIM#278750), which accounts for about 20% of all XP patients, is associated with normal NER function. The disease gene is POLH, which encodes polymerase η (pol η) allowing translesion synthesis in regions of DNA damage. We observed an Italian family presenting with photosensitivity, freckling since childhood and multiple skin cancers. Complete sequence analysis of XPA, XPC, XPD/ERCC2 genes and exons 1-9 and 11 of POLH gene did not reveal pathological mutations. No PCR product was observed for exon 10 in POLH gene. By RT-PCR analysis followed by POLH exon 10 sequencing, all affected members were found to harbor a homozygous 170-nucleotide deletion. The same deletion was previously described in 3 XP-V families, one of southern Italian descent and two from Algeria, suggesting a possible founder mutation. The deletion determines a severe protein truncation and defective pol η activity. Immunohistochemical study showed markedly reduced pol η expression in skin lesions of the affected siblings compared to the normal control skin.
Collapse
Affiliation(s)
- Riccardo G Borroni
- Laboratories of Experimental Research in Transplantation, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy -
| | - Marta Diegoli
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Maurizia Grasso
- Laboratories of Experimental Research in Transplantation, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Monica Concardi
- Laboratories of Experimental Research in Transplantation, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Manuela Agozzino
- Laboratories of Experimental Research in Transplantation, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Mariadelaide Vignini
- Division of Dermatology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.,Division of Dermatology, Department of Surgical, Diagnostics, and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Eloisa Arbustini
- Laboratories of Experimental Research in Transplantation, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| |
Collapse
|
13
|
Santiago KM, Castro LP, Neto JPD, de Nóbrega AF, Pinto CAL, Ashton-Prolla P, Pinto E Vairo F, de Medeiros PFV, Ribeiro EM, Ribeiro BFR, do Valle FF, Doriqui MJR, Leite CHB, Rocha RM, Moura LMS, Munford V, Galante PAF, Menck CFM, Rogatto SR, Achatz MI. Comprehensive germline mutation analysis and clinical profile in a large cohort of Brazilian xeroderma pigmentosum patients. J Eur Acad Dermatol Venereol 2020; 34:2392-2401. [PMID: 32239545 DOI: 10.1111/jdv.16405] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 03/05/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND Xeroderma pigmentosum (XP) patients present a high risk of developing skin cancer and other complications at an early age. This disease is characterized by mutations in the genes related to the DNA repair system. OBJECTIVES To describe the clinical and molecular findings in a cohort of 32 Brazilian individuals who received a clinical diagnosis of XP. METHODS Twenty-seven families were screened for germline variants in eight XP-related genes. RESULTS All patients (N = 32) were diagnosed with bi-allelic germline pathogenic or potentially pathogenic variants, including nine variants previously undescribed. The c.2251-1G>C XPC pathogenic variant, reported as the founder mutation in Comorian and Pakistani patients, was observed in 15 cases in homozygous or compound heterozygous. Seven homozygous patients for POLH/XPV variants developed their symptoms by an average age of 7.7 years. ERCC2/XPD, DDB2/XPE and ERCC5/XPG variants were found in a few patients. Aside from melanoma and non-melanoma skin tumours, a set of patients developed skin sebaceous carcinoma, leiomyosarcoma, angiosarcoma, mucoepidermoid carcinoma, gastric adenocarcinoma and serous ovarian carcinoma. CONCLUSIONS We reported a high frequency of XPC variants in 32 XP Brazilian patients. Nine new variants in XP-related genes, unexpected non-skin cancer lesions and an anticipation of the clinical manifestation in POLH/XPV cases were also described.
Collapse
Affiliation(s)
- K M Santiago
- Department of Oncogenetics, A.C.Camargo Cancer Center, São Paulo, São Paulo, Brazil.,International Research Center (CIPE), A.C.Camargo Cancer Center, São Paulo, São Paulo, Brazil
| | - L P Castro
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, São Paulo, São Paulo, Brazil
| | - J P D Neto
- Department of Skin Cancer, A.C.Camargo Cancer Center, São Paulo, São Paulo, Brazil
| | - A F de Nóbrega
- Department of Oncogenetics, A.C.Camargo Cancer Center, São Paulo, São Paulo, Brazil.,International Research Center (CIPE), A.C.Camargo Cancer Center, São Paulo, São Paulo, Brazil
| | - C A L Pinto
- Department of Pathology, A.C.Camargo Cancer Center, São Paulo, São Paulo, Brazil
| | - P Ashton-Prolla
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil.,Department of Genetics, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - F Pinto E Vairo
- Center for Individualized Medicine and Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - P F V de Medeiros
- University Hospital Alcides Carneiro, Federal University of Campina Grande, Campina Grande, Paraíba, Brazil
| | - E M Ribeiro
- Associação Cearense de Doenças Genéticas, Fortaleza, Ceará, Brazil
| | - B F R Ribeiro
- Children's Hospital, Secretaria de Estado de Saúde do Acre, Rio Branco, Acre, Brazil
| | - F F do Valle
- Amazonas Federal University, Manaus, Amazonas, Brazil
| | - M J R Doriqui
- Hospital Infantil Dr Juvêncio Mattos, São Luís, Maranhão, Brazil
| | - C H B Leite
- Department of Radiation Oncology, Instituto do Câncer do Ceará, Fortaleza, Ceará, Brazil
| | - R M Rocha
- Gynecology Department, Paulista Medicine School, Federal University of São Paulo (UNIFESP), São Paulo, São Paulo, Brazil
| | - L M S Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, São Paulo, São Paulo, Brazil
| | - V Munford
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, São Paulo, São Paulo, Brazil
| | - P A F Galante
- Molecular Oncology Center, Hospital Sírio-Libanês, São Paulo, São Paulo, Brazil
| | - C F M Menck
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, São Paulo, São Paulo, Brazil
| | - S R Rogatto
- Department of Clinical Genetics, University Hospital, Institute of Regional Health Research, University of Southern Denmark, Vejle, Denmark
| | - M I Achatz
- Centro de Oncologia, Hospital Sírio-Libanês, São Paulo, São Paulo, Brazil
| |
Collapse
|
14
|
Fang X, Sun Y. Whole-Exome Sequencing Enables the Diagnosis of Variant-Type Xeroderma Pigmentosum. Front Genet 2019; 10:495. [PMID: 31178899 PMCID: PMC6543889 DOI: 10.3389/fgene.2019.00495] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 05/06/2019] [Indexed: 12/22/2022] Open
Abstract
Background Xeroderma pigmentosum (XP) is a rare autosomal, recessive, inherited disease. XP patients exhibit high sensitivity to sunlight and increased incidence of skin cancer. The different XP subtypes, which are caused by mutations of eight distinct genes, show some specific clinical manifestations. XP variant (XPV) is caused by mutations in the gene encoding DNA polymerase eta (POLH). Case Presentation We report a family that included two XP patients whose parents were first cousins. The proband is a 36-year-old male who developed a large number of pigmented freckle-like lesions starting at 4 years of age; later, he displayed typical psoriasis manifestation, abnormal renal function and hyperglycaemia. He was suspected as suffering from dyschromatosis symmetrica hereditaria (DSH), but negative results were obtained in candidate gene analyses. Whole-exome sequencing was performed in four subjects, including the two patients and two controls, and a new pathogenic homozygous nonsense mutation (c.353dupA, p. Y118_V119delinsX) of the POLH gene, which was identified in all nine family members by Sanger sequencing, was detected in the patients. Conclusion A novel XPV pathogenic homozygous nonsense mutation in the POLH gene was identified. Our case proves that next-generation sequencing is an effective method for the rapid diagnosis and determination of XP genetic etiology.
Collapse
Affiliation(s)
- Xiaokai Fang
- Shandong Provincial Hospital of Dermatology, Shandong University, Jinan, China
| | - Yonghu Sun
- Shandong Provincial Hospital of Dermatology, Shandong University, Jinan, China
| |
Collapse
|
15
|
Gallo D, Brown GW. Post-replication repair: Rad5/HLTF regulation, activity on undamaged templates, and relationship to cancer. Crit Rev Biochem Mol Biol 2019; 54:301-332. [PMID: 31429594 DOI: 10.1080/10409238.2019.1651817] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/12/2019] [Accepted: 07/31/2019] [Indexed: 12/18/2022]
Abstract
The eukaryotic post-replication repair (PRR) pathway allows completion of DNA replication when replication forks encounter lesions on the DNA template and are mediated by post-translational ubiquitination of the DNA sliding clamp proliferating cell nuclear antigen (PCNA). Monoubiquitinated PCNA recruits translesion synthesis (TLS) polymerases to replicate past DNA lesions in an error-prone manner while addition of K63-linked polyubiquitin chains signals for error-free template switching to the sister chromatid. Central to both branches is the E3 ubiquitin ligase and DNA helicase Rad5/helicase-like transcription factor (HLTF). Mutations in PRR pathway components lead to genomic rearrangements, cancer predisposition, and cancer progression. Recent studies have challenged the notion that the PRR pathway is involved only in DNA lesion tolerance and have shed new light on its roles in cancer progression. Molecular details of Rad5/HLTF recruitment and function at replication forks have emerged. Mounting evidence indicates that PRR is required during lesion-less replication stress, leading to TLS polymerase activity on undamaged templates. Analysis of PRR mutation status in human cancers and PRR function in cancer models indicates that down regulation of PRR activity is a viable strategy to inhibit cancer cell growth and reduce chemoresistance. Here, we review these findings, discuss how they change our views of current PRR models, and look forward to targeting the PRR pathway in the clinic.
Collapse
Affiliation(s)
- David Gallo
- Department of Biochemistry and Donnelly Centre, University of Toronto , Toronto , Canada
| | - Grant W Brown
- Department of Biochemistry and Donnelly Centre, University of Toronto , Toronto , Canada
| |
Collapse
|
16
|
Moreno NC, Garcia CCM, Munford V, Rocha CRR, Pelegrini AL, Corradi C, Sarasin A, Menck CFM. The key role of UVA-light induced oxidative stress in human Xeroderma Pigmentosum Variant cells. Free Radic Biol Med 2019; 131:432-442. [PMID: 30553972 DOI: 10.1016/j.freeradbiomed.2018.12.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 12/08/2018] [Accepted: 12/12/2018] [Indexed: 01/11/2023]
Abstract
The UVA component of sunlight induces DNA damage, which are basically responsible for skin cancer formation. Xeroderma Pigmentosum Variant (XP-V) patients are defective in the DNA polymerase pol eta that promotes translesion synthesis after sunlight-induced DNA damage, implying in a clinical phenotype of increased frequency of skin cancer. However, the role of UVA-light in the carcinogenesis of these patients is not completely understood. The goal of this work was to characterize UVA-induced DNA damage and the consequences to XP-V cells, compared to complemented cells. DNA damage were induced in both cells by UVA, but lesion removal was particularly affected in XP-V cells, possibly due to the oxidation of DNA repair proteins, as indicated by the increase of carbonylated proteins. Moreover, UVA irradiation promoted replication fork stalling and cell cycle arrest in the S-phase for XP-V cells. Interestingly, when cells were treated with the antioxidant N-acetylcysteine, all these deleterious effects were consistently reverted, revealing the role of oxidative stress in these processes. Together, these results strongly indicate the crucial role of oxidative stress in UVA-induced cytotoxicity and are of interest for the protection of XP-V patients.
Collapse
Affiliation(s)
- Natália Cestari Moreno
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, SP, Brazil
| | | | - Veridiana Munford
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, SP, Brazil
| | | | - Alessandra Luiza Pelegrini
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Camila Corradi
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Alain Sarasin
- Laboratory of Genetic Instability and Oncogenesis, UMR8200 CNRS, University Paris-Sud, Institut Gustave Roussy, Villejuif, France
| | | |
Collapse
|
17
|
Leung W, Baxley RM, Moldovan GL, Bielinsky AK. Mechanisms of DNA Damage Tolerance: Post-Translational Regulation of PCNA. Genes (Basel) 2018; 10:genes10010010. [PMID: 30586904 PMCID: PMC6356670 DOI: 10.3390/genes10010010] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/18/2018] [Accepted: 12/19/2018] [Indexed: 12/12/2022] Open
Abstract
DNA damage is a constant source of stress challenging genomic integrity. To ensure faithful duplication of our genomes, mechanisms have evolved to deal with damage encountered during replication. One such mechanism is referred to as DNA damage tolerance (DDT). DDT allows for replication to continue in the presence of a DNA lesion by promoting damage bypass. Two major DDT pathways exist: error-prone translesion synthesis (TLS) and error-free template switching (TS). TLS recruits low-fidelity DNA polymerases to directly replicate across the damaged template, whereas TS uses the nascent sister chromatid as a template for bypass. Both pathways must be tightly controlled to prevent the accumulation of mutations that can occur from the dysregulation of DDT proteins. A key regulator of error-prone versus error-free DDT is the replication clamp, proliferating cell nuclear antigen (PCNA). Post-translational modifications (PTMs) of PCNA, mainly by ubiquitin and SUMO (small ubiquitin-like modifier), play a critical role in DDT. In this review, we will discuss the different types of PTMs of PCNA and how they regulate DDT in response to replication stress. We will also cover the roles of PCNA PTMs in lagging strand synthesis, meiotic recombination, as well as somatic hypermutation and class switch recombination.
Collapse
Affiliation(s)
- Wendy Leung
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Ryan M Baxley
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| |
Collapse
|
18
|
Armenta AM, Massey PR, Khan SG, Tamura D, Levy ML, DiGiovanna JJ, Kraemer KH, Fox MC. Variant subtype of xeroderma pigmentosum diagnosed in a 77-year-old woman. JAAD Case Rep 2018; 4:1074-1076. [PMID: 30511002 PMCID: PMC6250902 DOI: 10.1016/j.jdcr.2018.08.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Andrew M Armenta
- University of Texas Medical Branch School of Medicine, Galveston, Texas
| | - Paul R Massey
- Division of Dermatology, Dell Medical School, University of Texas at Austin, Austin, Texas
| | - Sikandar G Khan
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Deborah Tamura
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Moise L Levy
- Division of Dermatology, Dell Medical School, University of Texas at Austin, Austin, Texas.,Department of Pediatrics, Dell Medical School, University of Texas at Austin, Austin, Texas.,Dell Children's Medical Center, Austin, Texas
| | - John J DiGiovanna
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Kenneth H Kraemer
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Matthew C Fox
- Division of Dermatology, Dell Medical School, University of Texas at Austin, Austin, Texas
| |
Collapse
|
19
|
Tsao WC, Eckert KA. Detours to Replication: Functions of Specialized DNA Polymerases during Oncogene-induced Replication Stress. Int J Mol Sci 2018; 19:ijms19103255. [PMID: 30347795 PMCID: PMC6214091 DOI: 10.3390/ijms19103255] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 10/15/2018] [Accepted: 10/15/2018] [Indexed: 01/10/2023] Open
Abstract
Incomplete and low-fidelity genome duplication contribute to genomic instability and cancer development. Difficult-to-Replicate Sequences, or DiToRS, are natural impediments in the genome that require specialized DNA polymerases and repair pathways to complete and maintain faithful DNA synthesis. DiToRS include non B-DNA secondary structures formed by repetitive sequences, for example within chromosomal fragile sites and telomeres, which inhibit DNA replication under endogenous stress conditions. Oncogene activation alters DNA replication dynamics and creates oncogenic replication stress, resulting in persistent activation of the DNA damage and replication stress responses, cell cycle arrest, and cell death. The response to oncogenic replication stress is highly complex and must be tightly regulated to prevent mutations and tumorigenesis. In this review, we summarize types of known DiToRS and the experimental evidence supporting replication inhibition, with a focus on the specialized DNA polymerases utilized to cope with these obstacles. In addition, we discuss different causes of oncogenic replication stress and its impact on DiToRS stability. We highlight recent findings regarding the regulation of DNA polymerases during oncogenic replication stress and the implications for cancer development.
Collapse
Affiliation(s)
- Wei-Chung Tsao
- Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Hershey, PA 17033, USA.
| | - Kristin A Eckert
- Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Hershey, PA 17033, USA.
| |
Collapse
|
20
|
Barnes RP, Tsao WC, Moldovan GL, Eckert KA. DNA Polymerase Eta Prevents Tumor Cell-Cycle Arrest and Cell Death during Recovery from Replication Stress. Cancer Res 2018; 78:6549-6560. [DOI: 10.1158/0008-5472.can-17-3931] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 06/19/2018] [Accepted: 09/26/2018] [Indexed: 11/16/2022]
|
21
|
Abstract
Xeroderma pigmentosum is a rare autosomal recessive disorder which is caused by germinal mutations responsible for the repair of ultraviolet (UV) radiation-induced DNA lesions. It is characterized by hypersensitivity to UV radiation, poikiloderma, ocular surface disease, and in some patients pronounced sunburn and neurological disease. Patients have a very high risk of developing ocular and skin cancer on exposed body sites. No cure is available for these patients except complete protection from all types of UV radiation.
Collapse
Affiliation(s)
- M Ettinger
- Universitätsklinik für Dermatologie, Franz-Josef-Strauß Allee 11, 93053, Regensburg, Deutschland
| | - M Berneburg
- Universitätsklinik für Dermatologie, Franz-Josef-Strauß Allee 11, 93053, Regensburg, Deutschland.
| |
Collapse
|
22
|
Waraky A, Lin Y, Warsito D, Haglund F, Aleem E, Larsson O. Nuclear insulin-like growth factor 1 receptor phosphorylates proliferating cell nuclear antigen and rescues stalled replication forks after DNA damage. J Biol Chem 2017; 292:18227-18239. [PMID: 28924044 DOI: 10.1074/jbc.m117.781492] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/15/2017] [Indexed: 12/20/2022] Open
Abstract
We have previously shown that the insulin-like growth factor 1 receptor (IGF-1R) translocates to the cell nucleus, where it binds to enhancer-like regions and increases gene transcription. Further studies have demonstrated that nuclear IGF-1R (nIGF-1R) physically and functionally interacts with some nuclear proteins, i.e. the lymphoid enhancer-binding factor 1 (Lef1), histone H3, and Brahma-related gene-1 proteins. In this study, we identified the proliferating cell nuclear antigen (PCNA) as a nIGF-1R-binding partner. PCNA is a pivotal component of the replication fork machinery and a main regulator of the DNA damage tolerance (DDT) pathway. We found that IGF-1R interacts with and phosphorylates PCNA in human embryonic stem cells and other cell lines. In vitro MS analysis of PCNA co-incubated with the IGF-1R kinase indicated tyrosine residues 60, 133, and 250 in PCNA as IGF-1R targets, and PCNA phosphorylation was followed by mono- and polyubiquitination. Co-immunoprecipitation experiments suggested that these ubiquitination events may be mediated by DDT-dependent E2/E3 ligases (e.g. RAD18 and SHPRH/HLTF). Absence of IGF-1R or mutation of Tyr-60, Tyr-133, or Tyr-250 in PCNA abrogated its ubiquitination. Unlike in cells expressing IGF-1R, externally induced DNA damage in IGF-1R-negative cells caused G1 cell cycle arrest and S phase fork stalling. Taken together, our results suggest a role of IGF-1R in DDT.
Collapse
Affiliation(s)
- Ahmed Waraky
- From the Department of Oncology-Pathology, Cancer Center Karolinska, Karolinska Institutet, Stockholm SE-171 76, Sweden
| | - Yingbo Lin
- From the Department of Oncology-Pathology, Cancer Center Karolinska, Karolinska Institutet, Stockholm SE-171 76, Sweden
| | - Dudi Warsito
- From the Department of Oncology-Pathology, Cancer Center Karolinska, Karolinska Institutet, Stockholm SE-171 76, Sweden
| | - Felix Haglund
- From the Department of Oncology-Pathology, Cancer Center Karolinska, Karolinska Institutet, Stockholm SE-171 76, Sweden
| | - Eiman Aleem
- From the Department of Oncology-Pathology, Cancer Center Karolinska, Karolinska Institutet, Stockholm SE-171 76, Sweden
| | - Olle Larsson
- From the Department of Oncology-Pathology, Cancer Center Karolinska, Karolinska Institutet, Stockholm SE-171 76, Sweden
| |
Collapse
|
23
|
De Palma A, Morren MA, Ged C, Pouvelle C, Taïeb A, Aoufouchi S, Sarasin A. Diagnosis of Xeroderma pigmentosum variant in a young patient with two novel mutations in the POLH gene. Am J Med Genet A 2017; 173:2511-2516. [PMID: 28688171 DOI: 10.1002/ajmg.a.38340] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 06/01/2017] [Accepted: 06/06/2017] [Indexed: 12/13/2022]
Abstract
We describe the characterization of Xeroderma Pigmentosum variant (XPV) in a young Caucasian patient with phototype I, who exhibited a high sensitivity to sunburn and multiple cutaneous tumors at the age of 15 years. Two novel mutations in the POLH gene, which encodes the translesion DNA polymerase η, with loss of function due to two independent exon skippings, are reported to be associated as a compound heterozygous state in the patient. Western blot analysis performed on proteins from dermal fibroblasts derived from the patient and analysis of the mutation spectrum on immunoglobulin genes produced during the somatic hypermutation process in his memory B cells, show the total absence of translesion polymerase η activity in the patient. The total lack of Polη activity, necessary to bypass in an error-free manner UVR-induced pyrimidine dimers following sun exposure, explains the early unusual clinical appearance of this patient.
Collapse
Affiliation(s)
- Armando De Palma
- Department of Dermatology, University hospitals Leuven, Leuven, Belgium
| | - Marie-Anne Morren
- Department of Dermatology, University hospitals Leuven, Leuven, Belgium
| | - Cécile Ged
- Unité INSERM U1035 and Center de Référence pour les Maladies Rares de la Peau, CHU de Bordeaux, Bordeaux, France
| | - Caroline Pouvelle
- Laboratory of Genetic Instability and Oncogenesis, UMR8200 CNRS, Gustave Roussy, Université Paris-Sud, Villejuif, France
| | - Alain Taïeb
- Unité INSERM U1035 and Center de Référence pour les Maladies Rares de la Peau, CHU de Bordeaux, Bordeaux, France
| | - Said Aoufouchi
- Laboratory of Genetic Instability and Oncogenesis, UMR8200 CNRS, Gustave Roussy, Université Paris-Sud, Villejuif, France.,Université Pierre et Marie Curie, Paris, France
| | - Alain Sarasin
- Laboratory of Genetic Instability and Oncogenesis, UMR8200 CNRS, Gustave Roussy, Université Paris-Sud, Villejuif, France
| |
Collapse
|
24
|
Munford V, Castro LP, Souto R, Lerner LK, Vilar JB, Quayle C, Asif H, Schuch AP, de Souza TA, Ienne S, Alves FIA, Moura LMS, Galante PAF, Camargo AA, Liboredo R, Pena SDJ, Sarasin A, Chaibub SC, Menck CFM. A genetic cluster of patients with variant xeroderma pigmentosum with two different founder mutations. Br J Dermatol 2017; 176:1270-1278. [PMID: 27664908 DOI: 10.1111/bjd.15084] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2016] [Indexed: 01/04/2023]
Abstract
BACKGROUND Xeroderma pigmentosum (XP) is a rare human syndrome associated with hypersensitivity to sunlight and a high frequency of skin tumours at an early age. We identified a community in the state of Goias (central Brazil), a sunny and tropical region, with a high incidence of XP (17 patients among approximately 1000 inhabitants). OBJECTIVES To identify gene mutations in the affected community and map the distribution of the affected alleles, correlating the mutations with clinical phenotypes. METHODS Functional analyses of DNA repair capacity and cell-cycle responses after ultraviolet exposure were investigated in cells from local patients with XP, allowing the identification of the mutated gene, which was then sequenced to locate the mutations. A specific assay was designed for mapping the distribution of these mutations in the community. RESULTS Skin primary fibroblasts showed normal DNA damage removal but abnormal DNA synthesis after ultraviolet irradiation and deficient expression of the Polη protein, which is encoded by POLH. We detected two different POLH mutations: one at the splice donor site of intron 6 (c.764 +1 G>A), and the other in exon 8 (c.907 C>T, p.Arg303X). The mutation at intron 6 is novel, whereas the mutation at exon 8 has been previously described in Europe. Thus, these mutations were likely brought to the community long ago, suggesting two founder effects for this rare disease. CONCLUSIONS This work describes a genetic cluster involving POLH, and, particularly unexpected, with two independent founder mutations, including one that likely originated in Europe.
Collapse
Affiliation(s)
- V Munford
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - L P Castro
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - R Souto
- Secretariat of Health, Goiania, GO, Brazil
| | - L K Lerner
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - J B Vilar
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - C Quayle
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - H Asif
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - A P Schuch
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.,Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - T A de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - S Ienne
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - F I A Alves
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - L M S Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - P A F Galante
- Molecular Oncology Center, Hospital Sírio-Libanês, São Paulo, SP, Brazil
| | - A A Camargo
- Molecular Oncology Center, Hospital Sírio-Libanês, São Paulo, SP, Brazil
| | - R Liboredo
- Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - S D J Pena
- Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - A Sarasin
- UMR 8200 CNRS, Institut Gustave Roussy and University Paris-Saclay, Villejuif, France
| | - S C Chaibub
- General Hospital of Goiania, Goiania, GO, Brazil
| | - C F M Menck
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| |
Collapse
|
25
|
Comparative molecular dynamics studies of heterozygous open reading frames of DNA polymerase eta (η) in pathogenic yeast Candida albicans. Sci Rep 2017; 7:41087. [PMID: 28120914 PMCID: PMC5264235 DOI: 10.1038/srep41087] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 12/15/2016] [Indexed: 01/20/2023] Open
Abstract
Genomic instability in Candida albicans is believed to play a crucial role in fungal pathogenesis. DNA polymerases contribute significantly to stability of any genome. Although Candida Genome database predicts presence of S. cerevisiae DNA polymerase orthologs; functional and structural characterizations of Candida DNA polymerases are still unexplored. DNA polymerase eta (Polη) is unique as it promotes efficient bypass of cyclobutane pyrimidine dimers. Interestingly, C. albicans is heterozygous in carrying two Polη genes and the nucleotide substitutions were found only in the ORFs. As allelic differences often result in functional differences of the encoded proteins, comparative analyses of structural models and molecular dynamic simulations were performed to characterize these orthologs of DNA Polη. Overall structures of both the ORFs remain conserved except subtle differences in the palm and PAD domains. The complementation analysis showed that both the ORFs equally suppressed UV sensitivity of yeast rad30 deletion strain. Our study has predicted two novel molecular interactions, a highly conserved molecular tetrad of salt bridges and a series of π-π interactions spanning from thumb to PAD. This study suggests these ORFs as the homologues of yeast Polη, and due to its heterogeneity in C. albicans they may play a significant role in pathogenicity.
Collapse
|
26
|
Cipolla L, Maffia A, Bertoletti F, Sabbioneda S. The Regulation of DNA Damage Tolerance by Ubiquitin and Ubiquitin-Like Modifiers. Front Genet 2016; 7:105. [PMID: 27379156 PMCID: PMC4904029 DOI: 10.3389/fgene.2016.00105] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 05/25/2016] [Indexed: 11/13/2022] Open
Abstract
DNA replication is an extremely complex process that needs to be executed in a highly accurate manner in order to propagate the genome. This task requires the coordination of a number of enzymatic activities and it is fragile and prone to arrest after DNA damage. DNA damage tolerance provides a last line of defense that allows completion of DNA replication in the presence of an unrepaired template. One of such mechanisms is called post-replication repair (PRR) and it is used by the cells to bypass highly distorted templates caused by damaged bases. PRR is extremely important for the cellular life and performs the bypass of the damage both in an error-free and in an error-prone manner. In light of these two possible outcomes, PRR needs to be tightly controlled in order to prevent the accumulation of mutations leading ultimately to genome instability. Post-translational modifications of PRR proteins provide the framework for this regulation with ubiquitylation and SUMOylation playing a pivotal role in choosing which pathway to activate, thus controlling the different outcomes of damage bypass. The proliferating cell nuclear antigen (PCNA), the DNA clamp for replicative polymerases, plays a central role in the regulation of damage tolerance and its modification by ubiquitin, and SUMO controls both the error-free and error-prone branches of PRR. Furthermore, a significant number of polymerases are involved in the bypass of DNA damage possess domains that can bind post-translational modifications and they are themselves target for ubiquitylation. In this review, we will focus on how ubiquitin and ubiquitin-like modifications can regulate the DNA damage tolerance systems and how they control the recruitment of different proteins to the replication fork.
Collapse
Affiliation(s)
- Lina Cipolla
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia Italia
| | - Antonio Maffia
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia Italia
| | - Federica Bertoletti
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia Italia
| | - Simone Sabbioneda
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia Italia
| |
Collapse
|
27
|
Guo J, Jiang Z, Li X, Wang XI, Xiao Y. miR-20b downregulates polymerases κ and θ in XP-V tumor cells. Oncol Lett 2016; 11:3790-3794. [PMID: 27313696 DOI: 10.3892/ol.2016.4447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 03/18/2016] [Indexed: 11/06/2022] Open
Abstract
XP-V is a subtype of Xeroderma pigmentosum diseases with typical pigmentation and cancers in sun-exposed regions. The present study investigated the role of microRNA-20b (miR-20b) in the imbalance of polymerase expression levels in XP-V tumor cells. Following software prediction results, certain miRNAs were chosen as candidate regulators for the observed imbalance in polymerases in XP-V tumor cells. Reverse transcription-quantitative polymerase chain reaction and western blot were used to test candidate miRNAs for their ability to reduce the expression of these polymerases. A luciferase reporter assay was used to further verify the western blot results. Polymerases κ and θ were expressed at lower levels in XP-V tumor cells compared to normal control cells. A positive correlation was demonstrated between miR-20b and polymerases κ and θ. It was also demonstrated that a proportion of miRNAs had no effect on polymerases κ and θ, despite the software predicting that these miRNAs would target these two polymerases. Therefore, miR-20b may be responsible for the low expression levels of polymerase κ and θ in XP-V tumor cells, which accelerated mismatch in DNA replication repairing.
Collapse
Affiliation(s)
- Jia Guo
- Department of Endodontics, Oral Medical Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Zheng Jiang
- Department of Endodontics, Xiamen Stomatological Hospital, Xiamen, Fujian 361004, P.R. China
| | - Xiangru Li
- Department of Endodontics, Oral Medical Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - X I Wang
- Department of Endodontics, Oral Medical Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Yan Xiao
- Department of Endodontics, Oral Medical Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| |
Collapse
|
28
|
Abstract
Xeroderma pigmentosum (XP) is a rare disorder of defective UV-radiation induced damage repair that is characterized by photosensitivity with easy skin burning following minimal sun exposure, early freckling and development of lentiginous pigmentation along with other features of poikiloderma and a propensity for developing skin cancer at an early age. In this short review, the clinical, pathological, genetic and molecular aspects of XP are reviewed in the current literature. XP encompasses a spectrum of disease that overlaps with other diseases of DNA repair systems. In addition to cutaneous complications, patients are susceptible to eye conditions, neurodegenerative processes, central nervous system tumors and other tumors as a result of UV radiation exposure and its byproducts. Patients with XP frequently experience a shorter life span due to skin cancer and neurodegenerative sequelae, but aggressive preventative measures to minimize UV radiation exposure and damage can improve the course of disease and prolong life. The disease has served as a model for photoaging and UV radiation-induced cancer and has led to a better understanding of cell processes that prevent development of these disease features in normal individuals.
Collapse
Affiliation(s)
- Jennifer O. Black
- Division of Pediatric Pathology, Department of Pathology and Laboratory Medicine, Children’s Hospital Colorado, University of Colorado Anschutz Medical Campus, 13123 East 16th Avenue, Box 120, Aurora, CO 80045 USA
| |
Collapse
|
29
|
Genna V, Gaspari R, Dal Peraro M, De Vivo M. Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η. Nucleic Acids Res 2016; 44:2827-36. [PMID: 26935581 PMCID: PMC4824119 DOI: 10.1093/nar/gkw128] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/19/2016] [Indexed: 12/18/2022] Open
Abstract
Trans-lesion synthesis polymerases, like DNA Polymerase-η (Pol-η), are essential for cell survival. Pol-η bypasses ultraviolet-induced DNA damages via a two-metal-ion mechanism that assures DNA strand elongation, with formation of the leaving group pyrophosphate (PPi). Recent structural and kinetics studies have shown that Pol-η function depends on the highly flexible and conserved Arg61 and, intriguingly, on a transient third ion resolved at the catalytic site, as lately observed in other nucleic acid-processing metalloenzymes. How these conserved structural features facilitate DNA replication, however, is still poorly understood. Through extended molecular dynamics and free energy simulations, we unravel a highly cooperative and dynamic mechanism for DNA elongation and repair, which is here described by an equilibrium ensemble of structures that connect the reactants to the products in Pol-η catalysis. We reveal that specific conformations of Arg61 help facilitate the recruitment of the incoming base and favor the proper formation of a pre-reactive complex in Pol-η for efficient DNA editing. Also, we show that a third transient metal ion, which acts concertedly with Arg61, serves as an exit shuttle for the leaving PPi. Finally, we discuss how this effective and cooperative mechanism for DNA repair may be shared by other DNA-repairing polymerases.
Collapse
Affiliation(s)
- Vito Genna
- Laboratory of Molecular Modeling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Roberto Gaspari
- CONCEPT Lab., Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland Swiss Institute of Bioinformatics (SIB), CH-1015, Lausanne, Switzerland
| | - Marco De Vivo
- Laboratory of Molecular Modeling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy IAS-5 / INM-9 Computational Biomedicine Forschungszentrum Jülich, Wilhelm-Johnen-Straße 52428 Jülich, Germany
| |
Collapse
|
30
|
Deep phenotyping of 89 xeroderma pigmentosum patients reveals unexpected heterogeneity dependent on the precise molecular defect. Proc Natl Acad Sci U S A 2016; 113:E1236-45. [PMID: 26884178 DOI: 10.1073/pnas.1519444113] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Xeroderma pigmentosum (XP) is a rare DNA repair disorder characterized by increased susceptibility to UV radiation (UVR)-induced skin pigmentation, skin cancers, ocular surface disease, and, in some patients, sunburn and neurological degeneration. Genetically, it is assigned to eight complementation groups (XP-A to -G and variant). For the last 5 y, the UK national multidisciplinary XP service has provided follow-up for 89 XP patients, representing most of the XP patients in the United Kingdom. Causative mutations, DNA repair levels, and more than 60 clinical variables relating to dermatology, ophthalmology, and neurology have been measured, using scoring systems to categorize disease severity. This deep phenotyping has revealed unanticipated heterogeneity of clinical features, between and within complementation groups. Skin cancer is most common in XP-C, XP-E, and XP-V patients, previously considered to be the milder groups based on cellular analyses. These patients have normal sunburn reactions and are therefore diagnosed later and are less likely to adhere to UVR protection. XP-C patients are specifically hypersensitive to ocular damage, and XP-F and XP-G patients appear to be much less susceptible to skin cancer than other XP groups. Within XP groups, different mutations confer susceptibility or resistance to neurological damage. Our findings on this large cohort of XP patients under long-term follow-up reveal that XP is more heterogeneous than has previously been appreciated. Our data now enable provision of personalized prognostic information and management advice for each XP patient, as well as providing new insights into the functions of the XP proteins.
Collapse
|
31
|
129-Derived Mouse Strains Express an Unstable but Catalytically Active DNA Polymerase Iota Variant. Mol Cell Biol 2015; 35:3059-70. [PMID: 26124279 DOI: 10.1128/mcb.00371-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 06/18/2015] [Indexed: 01/08/2023] Open
Abstract
Mice derived from the 129 strain have a nonsense codon mutation in exon 2 of the polymerase iota (Polι) gene and are therefore considered Polι deficient. When we amplified Polι mRNA from 129/SvJ or 129/Ola testes, only a small fraction of the full-length cDNA contained the nonsense mutation; the major fraction corresponded to a variant Polι isoform lacking exon 2. Polι mRNA lacking exon 2 contains an open reading frame, and the corresponding protein was detected using a polyclonal antibody raised against the C terminus of the murine Polι protein. The identity of the corresponding protein was further confirmed by mass spectrometry. Although the variant protein was expressed at only 5 to 10% of the level of wild-type Polι, it retained de novo DNA synthesis activity, the capacity to form replication foci following UV irradiation, and the ability to rescue UV light sensitivity in Polι(-/-) embryonic fibroblasts derived from a new, fully deficient Polι knockout (KO) mouse line. Furthermore, in vivo treatment of 129-derived male mice with Velcade, a drug that inhibits proteasome function, stabilized and restored a substantial amount of the variant Polι in these animals, indicating that its turnover is controlled by the proteasome. An analysis of two xeroderma pigmentosum-variant (XPV) cases corresponding to missense mutants of Polη, a related translesion synthesis (TLS) polymerase in the same family, similarly showed a destabilization of the catalytically active mutant protein by the proteasome. Collectively, these data challenge the prevailing hypothesis that 129-derived strains of mice are completely deficient in Polι activity. The data also document, both for 129-derived mouse strains and for some XPV patients, new cases of genetic defects corresponding to the destabilization of an otherwise functional protein, the phenotype of which is reversible by proteasome inhibition.
Collapse
|
32
|
Karass M, Naguib MM, Elawabdeh N, Cundiff CA, Thomason J, Steelman CK, Cone R, Schwenkter A, Jordan C, Shehata BM. Xeroderma pigmentosa: three new cases with an in depth review of the genetic and clinical characteristics of the disease. Fetal Pediatr Pathol 2015; 34:120-7. [PMID: 25454817 DOI: 10.3109/15513815.2014.982336] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Xeroderma pigmentosum (XP) is a rare autosomal recessive disorder characterized by hypersensitivity of the skin and eyes to UV-radiation as a result of a defect in one of eight genes. Seven genes (XPA-XPG) have a defect in Nucletoide Excision Repair (NER), while the eighth gene XPV has a defect in polymerase η, which is responsible for replication of UV-damaged DNA to produce corrected daughter strands. We present the varied clinical courses of three African-American female patients with XP. Additionally, we present a review of the literature that focuses on the various clinical manifestations as well as the genetic and molecular mechanisms underlying this disease.
Collapse
Affiliation(s)
- Michael Karass
- 1Children's Healthcare of Atlanta and Emory University School of Medicine , Pediatric Pathology, Atlanta, GA , USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Abstract
POLH (DNA polymerase η), a target of p53 tumour suppressor, plays a key role in TLS (translesion DNA synthesis). Loss of POLH is responsible for the human cancer-prone syndrome XPV (xeroderma pigmentosum variant). Owing to its critical role in DNA repair and genome stability, POLH expression and activity are regulated by multiple pathways. In the present study, we found that the levels of both POLH transcript and protein were decreased upon knockdown of the transcript encoding PCBP1 [poly(rC)-binding protein 1]. We also found that the half-life of POLH mRNA was markedly decreased upon knockdown of PCBP1. Moreover, we found that PCBP1 directly bound to the POLH 3'-UTR and the PCBP1-binding site in POLH mRNA is an atypical AU-rich element. Finally, we showed that the AU-rich element in POLH 3'-UTR was responsive to PCBP1 and sufficient for PCBP1 to regulate POLH expression. Taken together, we uncovered a novel mechanism by which POLH expression is controlled by PCBP1 via mRNA stability.
Collapse
|
34
|
Sethi M, Lehmann AR, Fawcett H, Stefanini M, Jaspers N, Mullard K, Turner S, Robson A, McGibbon D, Sarkany R, Fassihi H. Patients with xeroderma pigmentosum complementation groups C, E and V do not have abnormal sunburn reactions. Br J Dermatol 2014; 169:1279-87. [PMID: 23889214 DOI: 10.1111/bjd.12523] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2013] [Indexed: 01/08/2023]
Abstract
BACKGROUND Xeroderma pigmentosum (XP) is a rare autosomal recessive disorder of DNA repair. It is divided into eight complementation groups: XP-A to XP-G (classical XP) and XP variant (XP-V). Severe and prolonged sunburn reactions on minimal sun exposure have been considered a cardinal feature of classical XP. However, it has recently become clear that not all patients have abnormal sunburn reactions. OBJECTIVES To examine sunburn reactions in a cohort of patients with XP and correlate this to the complementation group. METHODS Sixty patients with XP attending the U.K. National XP Service from 2010 to 2012 were studied. Their history of burning after minimal sun exposure was assessed using a newly developed sunburn severity score. The age at which the first skin cancer was histologically diagnosed in each patient, and the presence of any neurological abnormality, was also recorded. RESULTS Sunburn severity scores were abnormally high in patients with XP-A, XP-D, XP-F and XP-G compared with non-XP controls. There was no significant difference in sunburn score of patients with XP-C, XP-E and XP-V compared with controls (P > 0·05). Patients with XP-C, XP-E and XP-V were more likely to have skin cancer diagnosed at an earlier age than those with severe sunburn on minimal sun exposure. In addition, patients with XP with severe sunburn had an increased frequency of neurological abnormalities. CONCLUSIONS Not all patients with XP have a history of severe and prolonged sunburn on minimal sun exposure. The normal sunburn response of patients with XP-C, XP-E and XP-V may relate to the preservation of transcription-coupled DNA repair in these groups. Those with a history of severe sunburn on minimal sun exposure developed their first skin cancer at an older age compared with patients with XP-C, XP-E and XP-V, but they had an increased frequency of neurological abnormalities. Physicians need to be aware that about half of all patients with XP will present without a history of abnormal sunburn.
Collapse
Affiliation(s)
- M Sethi
- UK National Xeroderma Pigmentosum Service, Department of Photodermatology, St John's Institute of Dermatology, Guy's and St Thomas' NHS Trust, London, U.K
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Opletalova K, Bourillon A, Yang W, Pouvelle C, Armier J, Despras E, Ludovic M, Mateus C, Robert C, Kannouche P, Soufir N, Sarasin A. Correlation of phenotype/genotype in a cohort of 23 xeroderma pigmentosum-variant patients reveals 12 new disease-causing POLH mutations. Hum Mutat 2014; 35:117-28. [PMID: 24130121 DOI: 10.1002/humu.22462] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 09/16/2013] [Accepted: 10/02/2013] [Indexed: 01/12/2023]
Abstract
Xeroderma pigmentosum variant (XP-V) is a rare genetic disease, characterized by some sunlight sensitivity and predisposition to cutaneous malignancies. We described clinical and genetic features of the largest collection ever published of 23 XPV patients (ages between 21 and 86) from 20 unrelated families. Primary fibroblasts from patients showed normal nucleotide excision repair but UV-hypersensitivity in the presence of caffeine, a signature of the XP-V syndrome. 87% of patients developed skin tumors with a median age of 21 for the first occurrence. The median numbers of basal-cell carcinoma was 13 per patient, six for squamous-cell carcinoma, and five for melanoma. XP-V is due to defects in the translesion-synthesis DNA polymerase Polη coded by the POLH gene. DNA sequencing of POLH revealed 29 mutations, where 12 have not been previously identified, leading to truncated polymerases in 69% of patients. Four missense mutations are correlated with the protein stability by structural modeling of the Polη polymerase domain. There is a clear relationship between the types of missense mutations and clinical severity. For truncating mutations, which lead to an absence of or to inactive proteins, the life-cumulated UV exposure is probably the best predictor of cancer incidence, reinforcing the necessity to protect XP-Vs from sun exposure.
Collapse
MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Caffeine
- Carcinoma, Basal Cell/epidemiology
- Carcinoma, Basal Cell/genetics
- Carcinoma, Basal Cell/pathology
- Carcinoma, Squamous Cell/epidemiology
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/pathology
- Cells, Cultured
- DNA Repair
- DNA-Directed DNA Polymerase/genetics
- DNA-Directed DNA Polymerase/metabolism
- Female
- Fibroblasts/metabolism
- Genetic Variation
- Genotype
- Humans
- Male
- Melanoma/epidemiology
- Melanoma/genetics
- Melanoma/pathology
- Middle Aged
- Models, Molecular
- Mutation, Missense
- Phenotype
- Protein Stability
- Retrospective Studies
- Skin Neoplasms/epidemiology
- Skin Neoplasms/genetics
- Skin Neoplasms/pathology
- Ultraviolet Rays
- Xeroderma Pigmentosum/complications
- Xeroderma Pigmentosum/genetics
- Xeroderma Pigmentosum/pathology
- Young Adult
Collapse
|
36
|
A founder large deletion mutation in Xeroderma pigmentosum-Variant form in Tunisia: implication for molecular diagnosis and therapy. BIOMED RESEARCH INTERNATIONAL 2014; 2014:256245. [PMID: 24877075 PMCID: PMC4024419 DOI: 10.1155/2014/256245] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 03/23/2014] [Indexed: 02/07/2023]
Abstract
Xeroderma pigmentosum Variant (XP-V) form is characterized by a late onset of skin symptoms. Our aim is the clinical and genetic investigations of XP-V Tunisian patients in order to develop a simple tool for early diagnosis. We investigated 16 suspected XP patients belonging to ten consanguineous families. Analysis of the POLH gene was performed by linkage analysis, long range PCR, and sequencing. Genetic analysis showed linkage to the POLH gene with a founder haplotype in all affected patients. Long range PCR of exon 9 to exon 11 showed a 3926 bp deletion compared to control individuals. Sequence analysis demonstrates that this deletion has occurred between two Alu-Sq2 repetitive sequences in the same orientation, respectively, in introns 9 and 10. We suggest that this mutation POLH NG_009252.1: g.36847_40771del3925 is caused by an equal crossover event that occurred between two homologous chromosomes at meiosis. These results allowed us to develop a simple test based on a simple PCR in order to screen suspected XP-V patients. In Tunisia, the prevalence of XP-V group seems to be underestimated and clinical diagnosis is usually later. Cascade screening of this founder mutation by PCR in regions with high frequency of XP provides a rapid and cost-effective tool for early diagnosis of XP-V in Tunisia and North Africa.
Collapse
|
37
|
Yang W. An overview of Y-Family DNA polymerases and a case study of human DNA polymerase η. Biochemistry 2014; 53:2793-803. [PMID: 24716551 PMCID: PMC4018060 DOI: 10.1021/bi500019s] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
Y-Family
DNA polymerases specialize in translesion synthesis, bypassing
damaged bases that would otherwise block the normal progression of
replication forks. Y-Family polymerases have unique structural features
that allow them to bind damaged DNA and use a modified template base
to direct nucleotide incorporation. Each Y-Family polymerase is unique
and has different preferences for lesions to bypass and for dNTPs
to incorporate. Y-Family polymerases are also characterized by a low
catalytic efficiency, a low processivity, and a low fidelity on normal
DNA. Recruitment of these specialized polymerases to replication forks
is therefore regulated. The catalytic center of the Y-Family polymerases
is highly conserved and homologous to that of high-fidelity and high-processivity
DNA replicases. In this review, structural differences between Y-Family
and A- and B-Family polymerases are compared and correlated with their
functional differences. A time-resolved X-ray crystallographic study
of the DNA synthesis reaction catalyzed by the Y-Family DNA polymerase
human polymerase η revealed transient elements that led to the
nucleotidyl-transfer reaction.
Collapse
Affiliation(s)
- Wei Yang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| |
Collapse
|
38
|
Guo J, Zhou G, Zhang W, Song Y, Bian Z. A novel POLH mutation causes XP-V disease and XP-V tumor proneness may involve imbalance of numerous DNA polymerases. Oncol Lett 2013; 6:1583-1590. [PMID: 24260050 PMCID: PMC3834328 DOI: 10.3892/ol.2013.1604] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 09/30/2013] [Indexed: 11/09/2022] Open
Abstract
Xeroderma pigmentosum variant (XP-V) is a subtype of xeroderma pigmentosum (XP) disease with typical pigmentation and types of cancer in the oral maxillofacial and other sun-exposed regions. Few factors of tumor proneness in XP-V have been completely elucidated with the exception of the POLH [which encodes DNA polymerase η (pol η)] mutation. The aim of the present study was to identify the POLH mutation in an XP-V patient and to explore the roles of specific additional polymerases in XP-V tumor proneness. The POLH gene was sequenced in the patient and the expression of pol η, ι, κ, θ and ζ was tested in XP-V tumor cells and cell lines, as well as in HeLa cells with POLH knockdown. The results revealed a novel, large homozygous deletion of POLH (del exon 5–9) in the patient. Lower expression of pol κ, θ and ζ were observed in the XP-V cells and similar changes were observed in HeLa cells with POLH knockdown. Consistent with XP-V tumor cells, following UV irradiation, the expression of pol κ and θ presented was significantly increased in the XP-V cell lines compared with that in the normal control cells. The unusual expression of other polymerases, besides pol η, identified in the present study indicated that these polymerases may also be key in XP-V cells genetic instability, which accelerates tumor formation.
Collapse
Affiliation(s)
- Jia Guo
- State Key Laboratory Breeding Base of Basic Science of Stomatology and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, P.R. China
| | | | | | | | | |
Collapse
|
39
|
Beardslee RA, Suarez SC, Toffton SM, McCulloch SD. Mutation of the little finger domain in human DNA polymerase η alters fidelity when copying undamaged DNA. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2013; 54:638-651. [PMID: 23913529 PMCID: PMC4120640 DOI: 10.1002/em.21807] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 06/19/2013] [Accepted: 06/20/2013] [Indexed: 06/02/2023]
Abstract
DNA polymerase η (pol η) synthesizes past cyclobutane pyrimidine dimer and possibly 7,8-dihydro-8-oxoguanine (8-oxoG) lesions during DNA replication. Loss of pol η is associated with an increase in mutation rate, demonstrating its indispensable role in mutation suppression. It has been recently reported that β-strand 12 (amino acids 316-324) of the little finger region correctly positions the template strand with the catalytic core of the enzyme. The authors hypothesized that modification of β-strand 12 residues would disrupt correct enzyme-DNA alignment and alter pol η's activity and fidelity. To investigate this, the authors purified proteins containing the catalytic core of the polymerase, incorporated single amino acid changes to select β-strand 12 residues, and evaluated DNA synthesis activity for each pol η. Lesion bypass efficiencies and replication fidelities when copying DNA-containing cis-syn cyclobutane thymine-thymine dimer and 8-oxoG lesions were determined and compared with the corresponding values for the wild-type polymerase. The results confirm the importance of the β-strand in polymerase function and show that fidelity is most often altered when undamaged DNA is copied. Additionally, it is shown that DNA-protein contacts distal to the active site can significantly affect the fidelity of synthesis.
Collapse
Affiliation(s)
- Renee A. Beardslee
- Department of Environmental and Molecular Toxicology, North Carolina State University, Raleigh, North Carolina
| | - Samuel C. Suarez
- Department of Environmental and Molecular Toxicology, North Carolina State University, Raleigh, North Carolina
| | - Shannon M. Toffton
- Department of Environmental and Molecular Toxicology, North Carolina State University, Raleigh, North Carolina
| | - Scott D. McCulloch
- Department of Environmental and Molecular Toxicology, North Carolina State University, Raleigh, North Carolina
- Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina
| |
Collapse
|
40
|
Ortega-Recalde O, Vergara JI, Fonseca DJ, Ríos X, Mosquera H, Bermúdez OM, Medina CL, Vargas CI, Pallares AE, Restrepo CM, Laissue P. Whole-exome sequencing enables rapid determination of xeroderma pigmentosum molecular etiology. PLoS One 2013; 8:e64692. [PMID: 23755135 PMCID: PMC3670841 DOI: 10.1371/journal.pone.0064692] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 04/16/2013] [Indexed: 12/02/2022] Open
Abstract
Xeroderma pigmentosum (XP) is a rare autosomal recessive disorder characterized by extreme sensitivity to actinic pigmentation changes in the skin and increased incidence of skin cancer. In some cases, patients are affected by neurological alterations. XP is caused by mutations in 8 distinct genes (XPA through XPG and XPV). The XP-V (variant) subtype of the disease results from mutations in a gene (XPV, also named POLH) which encodes for Polη, a member of the Y-DNA polymerase family. Although the presence and severity of skin and neurological dysfunctions differ between XP subtypes, there are overlapping clinical features among subtypes such that the sub-type cannot be deduced from the clinical features. In this study, in order to overcome this drawback, we undertook whole-exome sequencing in two XP sibs and their father. We identified a novel homozygous nonsense mutation (c.897T>G, p.Y299X) in POLH which causes the disease. Our results demonstrate that next generation sequencing is a powerful approach to rapid determination of XP genetic etiology.
Collapse
Affiliation(s)
- Oscar Ortega-Recalde
- Unidad de Genética, Escuela de Medicina y Ciencias de la Salud, Universidad del Rosario, Bogotá, Colombia
| | - Jéssica Inés Vergara
- Departamento de Dermatología, Universidad Autónoma de Bucaramanga, Bucaramanga, Colombia
- Unidad de Dermatología, Clínica Carlos Ardila Lulle, Bucaramanga, Colombia
| | - Dora Janeth Fonseca
- Unidad de Genética, Escuela de Medicina y Ciencias de la Salud, Universidad del Rosario, Bogotá, Colombia
- Departamento de Biología Molecular, Genética Molecular de Colombia, Bogotá, Colombia
| | - Xiomara Ríos
- Departamento de Dermatología, Universidad Autónoma de Bucaramanga, Bucaramanga, Colombia
- Unidad de Dermatología, Clínica Carlos Ardila Lulle, Bucaramanga, Colombia
| | - Hernando Mosquera
- Departamento de Dermatología, Universidad Autónoma de Bucaramanga, Bucaramanga, Colombia
- Unidad de Dermatología, Clínica Carlos Ardila Lulle, Bucaramanga, Colombia
| | - Olga María Bermúdez
- Unidad de Genética, Escuela de Medicina y Ciencias de la Salud, Universidad del Rosario, Bogotá, Colombia
| | - Claudia Liliana Medina
- Departamento de Dermatología, Universidad Autónoma de Bucaramanga, Bucaramanga, Colombia
- Unidad de Dermatología, Clínica Carlos Ardila Lulle, Bucaramanga, Colombia
| | | | - Argemiro Enrique Pallares
- Departamento de Dermatología, Universidad Autónoma de Bucaramanga, Bucaramanga, Colombia
- Unidad de Dermatología, Clínica Carlos Ardila Lulle, Bucaramanga, Colombia
| | - Carlos Martín Restrepo
- Unidad de Genética, Escuela de Medicina y Ciencias de la Salud, Universidad del Rosario, Bogotá, Colombia
- Departamento de Biología Molecular, Genética Molecular de Colombia, Bogotá, Colombia
| | - Paul Laissue
- Unidad de Genética, Escuela de Medicina y Ciencias de la Salud, Universidad del Rosario, Bogotá, Colombia
- Departamento de Biología Molecular, Genética Molecular de Colombia, Bogotá, Colombia
- * E-mail:
| |
Collapse
|
41
|
Ono R, Masaki T, Takeuchi S, Shimizu A, Tanioka M, Kambe N, Matsue H, Kamide R, Nishigori C. Three school-age cases of xeroderma pigmentosum variant type. PHOTODERMATOLOGY PHOTOIMMUNOLOGY & PHOTOMEDICINE 2013; 29:132-9. [DOI: 10.1111/phpp.12038] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/24/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Ryusuke Ono
- Division of Dermatology, Department of Internal Related,; Kobe University Graduate School of Medicine; Kobe; Japan
| | - Taro Masaki
- Division of Dermatology, Department of Internal Related,; Kobe University Graduate School of Medicine; Kobe; Japan
| | - Seiji Takeuchi
- Division of Dermatology, Department of Internal Related,; Kobe University Graduate School of Medicine; Kobe; Japan
| | - Ayako Shimizu
- Dermatology, Chiba University Hospital Department of Dermatology; Chiba University Graduate School of Medicine; Chiba; Japan
| | | | - Naotomo Kambe
- Dermatology, Chiba University Hospital Department of Dermatology; Chiba University Graduate School of Medicine; Chiba; Japan
| | - Hiroyuki Matsue
- Dermatology, Chiba University Hospital Department of Dermatology; Chiba University Graduate School of Medicine; Chiba; Japan
| | - Ryoichi Kamide
- Department of Dermatology; Daisan Hospital, The Jikei University School of Medicine; Tokyo; Japan
| | - Chikako Nishigori
- Division of Dermatology, Department of Internal Related,; Kobe University Graduate School of Medicine; Kobe; Japan
| |
Collapse
|
42
|
Parsons JL, Nicolay NH, Sharma RA. Biological and therapeutic relevance of nonreplicative DNA polymerases to cancer. Antioxid Redox Signal 2013; 18:851-73. [PMID: 22794079 PMCID: PMC3557440 DOI: 10.1089/ars.2011.4203] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Apart from surgical approaches, the treatment of cancer remains largely underpinned by radiotherapy and pharmacological agents that cause damage to cellular DNA, which ultimately causes cancer cell death. DNA polymerases, which are involved in the repair of cellular DNA damage, are therefore potential targets for inhibitors for improving the efficacy of cancer therapy. They can be divided, according to their main function, into two groups, namely replicative and nonreplicative enzymes. At least 15 different DNA polymerases, including their homologs, have been discovered to date, which vary considerably in processivity and fidelity. Many of the nonreplicative (specialized) DNA polymerases replicate DNA in an error-prone fashion, and they have been shown to participate in multiple DNA damage repair and tolerance pathways, which are often aberrant in cancer cells. Alterations in DNA repair pathways involving DNA polymerases have been linked with cancer survival and with treatment response to radiotherapy or to classes of cytotoxic drugs routinely used for cancer treatment, particularly cisplatin, oxaliplatin, etoposide, and bleomycin. Indeed, there are extensive preclinical data to suggest that DNA polymerase inhibition may prove to be a useful approach for increasing the effectiveness of therapies in patients with cancer. Furthermore, specialized DNA polymerases warrant examination of their potential use as clinical biomarkers to select for particular cancer therapies, to individualize treatment for patients.
Collapse
Affiliation(s)
- Jason L Parsons
- Cancer Research UK-Medical Research Council, Oncology Department, Gray Institute for Radiation Oncology and Biology, University of Oxford, Oxford, United Kingdom
| | | | | |
Collapse
|
43
|
Durando M, Tateishi S, Vaziri C. A non-catalytic role of DNA polymerase η in recruiting Rad18 and promoting PCNA monoubiquitination at stalled replication forks. Nucleic Acids Res 2013; 41:3079-93. [PMID: 23345618 PMCID: PMC3597682 DOI: 10.1093/nar/gkt016] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Trans-lesion DNA synthesis (TLS) is a DNA damage-tolerance mechanism that uses low-fidelity DNA polymerases to replicate damaged DNA. The inherited cancer-propensity syndrome xeroderma pigmentosum variant (XPV) results from error-prone TLS of UV-damaged DNA. TLS is initiated when the Rad6/Rad18 complex monoubiquitinates proliferating cell nuclear antigen (PCNA), but the basis for recruitment of Rad18 to PCNA is not completely understood. Here, we show that Rad18 is targeted to PCNA by DNA polymerase eta (Polη), the XPV gene product that is mutated in XPV patients. The C-terminal domain of Polη binds to both Rad18 and PCNA and promotes PCNA monoubiquitination, a function unique to Polη among Y-family TLS polymerases and dissociable from its catalytic activity. Importantly, XPV cells expressing full-length catalytically-inactive Polη exhibit increased recruitment of other error-prone TLS polymerases (Polκ and Polι) after UV irradiation. These results define a novel non-catalytic role for Polη in promoting PCNA monoubiquitination and provide a new potential mechanism for mutagenesis and genome instability in XPV individuals.
Collapse
Affiliation(s)
- Michael Durando
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | | | | |
Collapse
|
44
|
Enervald E, Lindgren E, Katou Y, Shirahige K, Ström L. Importance of Polη for damage-induced cohesion reveals differential regulation of cohesion establishment at the break site and genome-wide. PLoS Genet 2013; 9:e1003158. [PMID: 23326240 PMCID: PMC3542068 DOI: 10.1371/journal.pgen.1003158] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 10/25/2012] [Indexed: 01/15/2023] Open
Abstract
Genome integrity depends on correct chromosome segregation, which in turn relies on cohesion between sister chromatids from S phase until anaphase. S phase cohesion, together with DNA double-strand break (DSB) recruitment of cohesin and formation of damage-induced (DI) cohesion, has previously been shown to be required also for efficient postreplicative DSB repair. The budding yeast acetyltransferase Eco1 (Ctf7) is a common essential factor for S phase and DI-cohesion. The fission yeast Eco1 ortholog, Eso1, is expressed as a fusion protein with the translesion synthesis (TLS) polymerase Polη. The involvement of Eso1 in S phase cohesion was attributed to the Eco1 homologous part of the protein and bypass of UV-induced DNA lesions to the Polη part. Here we describe an additional novel function for budding yeast Polη, i.e. formation of postreplicative DI genome-wide cohesion. This is a unique Polη function not shared with other TLS polymerases. However, Polη deficient cells are DSB repair competent, as Polη is not required for cohesion locally at the DSB. This reveals differential regulation of DSB–proximal cohesion and DI genome-wide cohesion, and challenges the importance of the latter for DSB repair. Intriguingly, we found that specific inactivation of DI genome-wide cohesion increases chromosomal mis-segregation at the entrance of the next cell cycle, suggesting that S phase cohesion is not sufficient for correct chromosome segregation in the presence of DNA damage. Correct chromosome segregation requires that sister chromatids are held together by the protein complex cohesin, from S phase until anaphase. This S phase established cohesion is, together with DSB recruitment of cohesin and formation of damage-induced (DI) cohesion, also important for repair of DSBs. Eco1 is a common essential factor for S phase and DI-cohesion. The fission yeast Eco1 ortholog, Eso1, is important both for S phase cohesion and for bypass of UV-induced lesions, and is expressed as a fusion protein with Polη. The cohesion function has been attributed solely to Eso1 and the lesion bypass function to the Polη part of the protein. As we found the interaction between the two proteins intriguing, we decided to look for a functional connection also in budding yeast. Indeed, despite being dispensable for S phase cohesion, budding yeast Polη is required for formation of DI genome-wide cohesion. However, Polη-deficient cells are DSB repair competent, revealing differential regulation of DI-cohesion at the break and genome-wide. This finding challenges the importance of DI genome-wide cohesion for DSB repair, and based on our findings we suggest that S phase cohesion is not sufficient for correct chromosome segregation in the presence of DNA damage.
Collapse
Affiliation(s)
- Elin Enervald
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Emma Lindgren
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Yuki Katou
- Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Katsuhiko Shirahige
- Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Lena Ström
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
- * E-mail:
| |
Collapse
|
45
|
|
46
|
Liu X, Zhang X, Qiao J, Fang H. Identification of a novel nonsense mutation in POLH in a Chinese pedigree with xeroderma pigmentosum, variant type. Int J Med Sci 2013; 10:766-70. [PMID: 23630442 PMCID: PMC3638301 DOI: 10.7150/ijms.6095] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 03/17/2013] [Indexed: 01/13/2023] Open
Abstract
Xeroderma pigmentosum-variant (XPV) is one type of XP, a rare autosomal recessive disorder, and caused by defects in the post replication repair machinery while nucleotide-excision repair (NER) is not impaired. In the present study, we reported a Chinese family with XPV phenotype, which was confirmed by histopathological results. Genetic variants were detected by polymerase chain reaction and exon sequencing. Furthermore, the reported molecular defects in XPV patients from previous literatures were reviewed. A homozygous c.67C>T mutation in the exon 2 of DNA polymerase eta (POLH), a novel non-sense mutation in POLH, was discovered.
Collapse
Affiliation(s)
- Xiaoyan Liu
- Department of Dermatology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | | | | | | |
Collapse
|
47
|
Walsh JM, Parasuram R, Rajput PR, Rozners E, Ondrechen MJ, Beuning PJ. Effects of non-catalytic, distal amino acid residues on activity of E. coli DinB (DNA polymerase IV). ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2012; 53:766-776. [PMID: 23034734 DOI: 10.1002/em.21730] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 08/08/2012] [Accepted: 08/06/2012] [Indexed: 06/01/2023]
Abstract
DinB is one of two Y family polymerases in E. coli and is involved in copying damaged DNA. DinB is specialized to bypass deoxyguanosine adducts that occur at the N(2) position, with its cognate lesion being the furfuryl adduct. Active site residues have been identified that make contact with the substrate and carry out deoxynucleotide triphosphate (dNTP) addition to the growing DNA strand. In DNA polymerases, these include negatively charged aspartate and glutamate residues (D8, D103, and E104 in E. coli DNA polymerase IV DinB). These residues position the essential magnesium ions correctly to facilitate nucleophilic attack by the primer hydroxyl group on the α-phosphate group of the incoming dNTP. To study the contribution of DinB residues to lesion bypass, the computational methods THEMATICS and POOL were employed. These methods correctly predict the known active site residues, as well as other residues known to be important for activity. In addition, these methods predict other residues involved in substrate binding as well as more remote residues. DinB variants with mutations at the predicted positions were constructed and assayed for bypass of the N(2) -furfuryl-dG lesion. We find a wide range of effects of predicted residues, including some mutations that abolish damage bypass. Moreover, most of the DinB variants constructed are unable to carry out the extension step of lesion bypass. The use of computational prediction methods represents another tool that will lead to a more complete understanding of translesion DNA synthesis.
Collapse
Affiliation(s)
- Jason M Walsh
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | | | | | | | | | | |
Collapse
|
48
|
Makridakis NM, Reichardt JKV. Translesion DNA polymerases and cancer. Front Genet 2012; 3:174. [PMID: 22973298 PMCID: PMC3434439 DOI: 10.3389/fgene.2012.00174] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 08/20/2012] [Indexed: 12/17/2022] Open
Abstract
DNA repair has been regarded as an important barrier to carcinogenesis. The newly discovered field of translesion synthesis (TLS) has made it apparent that mammalian cells need distinct polymerases to efficiently and accurately bypass DNA lesions. Perturbation of TLS polymerase activity by mutation, loss of expression, etc. is expected to result in the accumulation of mutations in cells exposed to specific carcinogens. Furthermore, several TLS polymerases can modulate cellular sensitivity to chemotherapeutic agents. TLS genes and TLS gene variations may thus be attractive pharmacologic and/or pharmacogenetic targets. We review herein current data with regards to the potential contribution of the primary TLS polymerase genes to cancer, their interaction with pharmacologic agents, and identify areas of interest for further research.
Collapse
Affiliation(s)
- Nick M Makridakis
- Tulane Cancer Center and Department of Epidemiology, Tulane University New Orleans, LA, USA
| | | |
Collapse
|
49
|
Nicolay NH, Carter R, Hatch SB, Schultz N, Prevo R, McKenna WG, Helleday T, Sharma RA. Homologous recombination mediates S-phase-dependent radioresistance in cells deficient in DNA polymerase eta. Carcinogenesis 2012; 33:2026-34. [PMID: 22822095 DOI: 10.1093/carcin/bgs239] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
DNA polymerase eta (pol η) is the only DNA polymerase causally linked to carcinogenesis in humans. Inherited deficiency of pol η in the variant form of xeroderma pigmentosum (XPV) predisposes to UV-light-induced skin cancer. Pol η-deficient cells demonstrate increased sensitivity to cisplatin and oxaliplatin chemotherapy. We have found that XP30R0 fibroblasts derived from a patient with XPV are more resistant to cell kill by ionising radiation (IR) than the same cells complemented with wild-type pol η. This phenomenon has been confirmed in Burkitt's lymphoma cells, which either expressed wild-type pol η or harboured a pol η deletion. Pol η deficiency was associated with accumulation of cells in S-phase, which persisted after IR. Cells deficient in pol η demonstrated increased homologous recombination (HR)-directed repair of double strand breaks created by IR. Depletion of the HR protein, X-ray repair cross-complementing protein 3 (XRCC3), abrogated the radioresistance observed in pol η-deficient cells as compared with pol η-complemented cells. These findings suggest that HR mediates S-phase-dependent radioresistance associated with pol η deficiency. We propose that pol η protein levels in tumours may potentially be used to identify patients who require treatment with chemo-radiotherapy rather than radiotherapy alone for adequate tumour control.
Collapse
Affiliation(s)
- Nils H Nicolay
- Cancer Research UK-Medical Research Council Gray Institute for Radiation Oncology and Biology, Oncology Department, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | | | | | | | | | | | | | | |
Collapse
|
50
|
Klarer AC, Stallons LJ, Burke TJ, Skaggs RL, McGregor WG. DNA polymerase eta participates in the mutagenic bypass of adducts induced by benzo[a]pyrene diol epoxide in mammalian cells. PLoS One 2012; 7:e39596. [PMID: 22745795 PMCID: PMC3380003 DOI: 10.1371/journal.pone.0039596] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Accepted: 05/28/2012] [Indexed: 11/18/2022] Open
Abstract
Y-family DNA-polymerases have larger active sites that can accommodate bulky DNA adducts allowing them to bypass these lesions during replication. One member, polymerase eta (pol eta), is specialized for the bypass of UV-induced thymidine-thymidine dimers, correctly inserting two adenines. Loss of pol eta function is the molecular basis for xeroderma pigmentosum (XP) variant where the accumulation of mutations results in a dramatic increase in UV-induced skin cancers. Less is known about the role of pol eta in the bypass of other DNA adducts. A commonly encountered DNA adduct is that caused by benzo[a]pyrene diol epoxide (BPDE), the ultimate carcinogenic metabolite of the environmental chemical benzo[a]pyrene. Here, treatment of pol eta-deficient fibroblasts from humans and mice with BPDE resulted in a significant decrease in Hprt gene mutations. These studies in mammalian cells support a number of in vitro reports that purified pol eta has error-prone activity on plasmids with site-directed BPDE adducts. Sequencing the Hprt gene from this work shows that the majority of mutations are G>T transversions. These data suggest that pol eta has error-prone activity when bypassing BPDE-adducts. Understanding the basis of environmental carcinogen-derived mutations may enable prevention strategies to reduce such mutations with the intent to reduce the number of environmentally relevant cancers.
Collapse
Affiliation(s)
- Alden C. Klarer
- Department of Biochemistry and Molecular Biology, University of Louisville, Louisville, Kentucky, United States of America
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - L. Jay Stallons
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky, United States of America
- * E-mail:
| | - Tom J. Burke
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Louisville, Louisville, Kentucky, United States of America
| | - Robert L. Skaggs
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky, United States of America
| | - W. Glenn McGregor
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky, United States of America
| |
Collapse
|