1
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Le J, Min JH. Structural modeling and analyses of genetic variations in the human XPC nucleotide excision repair protein. J Biomol Struct Dyn 2023; 41:13535-13562. [PMID: 36890638 PMCID: PMC10485178 DOI: 10.1080/07391102.2023.2177349] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 01/27/2023] [Indexed: 03/10/2023]
Abstract
Xeroderma pigmentosum C (XPC) is a key initiator in the global genome nucleotide excision repair pathway in mammalian cells. Inherited mutations in the XPC gene can cause xeroderma pigmentosum (XP) cancer predisposition syndrome that dramatically increases the susceptibility to sunlight-induced cancers. Various genetic variants and mutations of the protein have been reported in cancer databases and literature. The current lack of a high-resolution 3-D structure of human XPC makes it difficult to assess the structural impact of the mutations/genetic variations. Using the available high-resolution crystal structure of its yeast ortholog, Rad4, we built a homology model of human XPC protein and compared it with a model generated by AlphaFold. The two models are largely consistent with each other in the structured domains. We have also assessed the degree of conservation for each residue using 966 sequences of XPC orthologs. Our structure- and sequence conservation-based assessments largely agree with the variant's impact on the protein's structural stability, computed by FoldX and SDM. Known XP missense mutations such as Y585C, W690S, and C771Y are consistently predicted to destabilize the protein's structure. Our analyses also reveal several highly conserved hydrophobic regions that are surface-exposed, which may indicate novel intermolecular interfaces that are yet to be characterized.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jennifer Le
- Department of Chemistry & Biochemistry, Baylor University, Waco, TX 76798, USA
| | - Jung-Hyun Min
- Department of Chemistry & Biochemistry, Baylor University, Waco, TX 76798, USA
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2
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Rahmouni M, Laville V, Spadoni JL, Jdid R, Eckhart L, Gruber F, Labib T, Coulonges C, Carpentier W, Latreille J, Morizot F, Tschachler E, Ezzedine K, Le Clerc S, Zagury JF. Identification of New Biological Pathways Involved in Skin Aging From the Analysis of French Women Genome-Wide Data. Front Genet 2022; 13:836581. [PMID: 35401686 PMCID: PMC8987498 DOI: 10.3389/fgene.2022.836581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/01/2022] [Indexed: 11/30/2022] Open
Abstract
Skin aging is an ineluctable process leading to the progressive loss of tissue integrity and is characterized by various outcomes such as wrinkling and sagging. Researchers have identified impacting environmental factors (sun exposure, smoking, etc.) and several molecular mechanisms leading to skin aging. We have previously performed genome-wide association studies (GWAS) in 502 very-well characterized French women, looking for associations with four major outcomes of skin aging, namely, photoaging, solar lentigines, wrinkling, and sagging, and this has led to new insights into the molecular mechanisms of skin aging. Since individual SNP associations in GWAS explain only a small fraction of the genetic impact in complex polygenic phenotypes, we have made the integration of these genotypes into the reference Kegg biological pathways and looked for associations by the gene set enrichment analysis (GSEA) approach. 106 pathways were tested for association with the four outcomes of skin aging. This biological pathway analysis revealed new relevant pathways and genes, some likely specific of skin aging such as the WNT7B and PRKCA genes in the “melanogenesis” pathway and some likely involved in global aging such as the DDB1 gene in the “nucleotide excision repair” pathway, not picked up in the previously published GWAS. Overall, our results suggest that the four outcomes of skin aging possess specific molecular mechanisms such as the “proteasome” and “mTOR signaling pathway” but may also share common molecular mechanisms such as “nucleotide excision repair.”
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Affiliation(s)
- Myriam Rahmouni
- Équipe Génomique, Bioinformatique et Chimie Moléculaire (EA 7528), Conservatoire National des Arts et Métiers, HESAM Université, Paris, France
| | - Vincent Laville
- Équipe Génomique, Bioinformatique et Chimie Moléculaire (EA 7528), Conservatoire National des Arts et Métiers, HESAM Université, Paris, France
| | - Jean-Louis Spadoni
- Équipe Génomique, Bioinformatique et Chimie Moléculaire (EA 7528), Conservatoire National des Arts et Métiers, HESAM Université, Paris, France
| | - Randa Jdid
- Chanel R&T, Department of Skin Knowledge and Women Beauty, Pantin, France
| | - Leopold Eckhart
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Florian Gruber
- Department of Dermatology, Medical University of Vienna, Vienna, Austria.,Christian Doppler Laboratory for Skin Multimodal Analytical Imaging of Aging and Senescence (SKINMAGINE), Medical University of Vienna, Vienna, Austria
| | - Taoufik Labib
- Équipe Génomique, Bioinformatique et Chimie Moléculaire (EA 7528), Conservatoire National des Arts et Métiers, HESAM Université, Paris, France
| | - Cedric Coulonges
- Équipe Génomique, Bioinformatique et Chimie Moléculaire (EA 7528), Conservatoire National des Arts et Métiers, HESAM Université, Paris, France
| | - Wassila Carpentier
- Plate-Forme Post-Génomique P3S, Hôpital Pitié-Salpêtrière, Paris, France
| | - Julie Latreille
- Chanel R&T, Department of Skin Knowledge and Women Beauty, Pantin, France
| | - Frederique Morizot
- Chanel R&T, Department of Skin Knowledge and Women Beauty, Pantin, France
| | - Erwin Tschachler
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Khaled Ezzedine
- Department of Dermatology, Hôpital Henri Mondor and EA 7379 EPIDERM, Créteil, France
| | - Sigrid Le Clerc
- Équipe Génomique, Bioinformatique et Chimie Moléculaire (EA 7528), Conservatoire National des Arts et Métiers, HESAM Université, Paris, France
| | - Jean-François Zagury
- Équipe Génomique, Bioinformatique et Chimie Moléculaire (EA 7528), Conservatoire National des Arts et Métiers, HESAM Université, Paris, France
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3
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Zebian A, El-Dor M, Shaito A, Mazurier F, Rezvani HR, Zibara K. XPC multifaceted roles beyond DNA damage repair: p53-dependent and p53-independent functions of XPC in cell fate decisions. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 789:108400. [PMID: 35690409 DOI: 10.1016/j.mrrev.2021.108400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 11/19/2021] [Accepted: 11/19/2021] [Indexed: 06/15/2023]
Abstract
Xeroderma pigmentosum group C protein (XPC) acts as a DNA damage recognition factor for bulky adducts and as an initiator of global genome nucleotide excision repair (GG-NER). Novel insights have shown that the role of XPC is not limited to NER, but is also implicated in DNA damage response (DDR), as well as in cell fate decisions upon stress. Moreover, XPC has a proteolytic role through its interaction with p53 and casp-2S. XPC is also able to determine cellular outcomes through its interaction with downstream proteins, such as p21, ARF, and p16. XPC interactions with effector proteins may drive cells to various fates such as apoptosis, senescence, or tumorigenesis. In this review, we explore XPC's involvement in different molecular pathways in the cell and suggest that XPC can be considered not only as a genomic caretaker and gatekeeper but also as a tumor suppressor and cellular-fate decision maker. These findings envisage that resistance to cell death, induced by DNA-damaging therapeutics, in highly prevalent P53-deficent tumors might be overcome through new therapeutic approaches that aim to activate XPC in these tumors. Moreover, this review encourages care providers to consider XPC status in cancer patients before chemotherapy in order to improve the chances of successful treatment and enhance patients' survival.
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Affiliation(s)
- Abir Zebian
- University of Bordeaux, INSERM U1035, BMGIC, Bordeaux, France; PRASE, Lebanese University, Beirut, Lebanon
| | | | - Abdullah Shaito
- Biomedical Research Center, Qatar University, P.O. Box 2713, Doha, Qatar
| | | | | | - Kazem Zibara
- PRASE, Lebanese University, Beirut, Lebanon; Biology Department, Faculty of Sciences - I, Lebanese University, Beirut, Lebanon.
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4
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Feltes BC. Revisiting the structural features of the xeroderma pigmentosum proteins: Focus on mutations and knowledge gaps. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 789:108416. [PMID: 35690419 DOI: 10.1016/j.mrrev.2022.108416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 06/15/2023]
Abstract
The nucleotide excision repair pathway is a broadly studied DNA repair mechanism because impairments of its key players, the xeroderma pigmentosum proteins (XPA to XPG), are associated with multiple hereditary diseases. Due to the massive number of novel mutations reported for these proteins and new structural data published every year, proper categorization and discussion of relevant observations is needed to organize this extensive inflow of knowledge. This review aims to revisit the structural data of all XP proteins while updating it with the information developed in of the past six years. Discussions and interpretations of mutation outcomes, mechanisms of action, and knowledge gaps regarding their structures are provided, as well as new perspectives based on recent research.
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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.
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5
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Quintero-Ruiz N, Corradi C, Moreno NC, de Souza TA, Pereira Castro L, Rocha CRR, Menck CFM. Mutagenicity Profile Induced by UVB Light in Human Xeroderma Pigmentosum Group C Cells †. Photochem Photobiol 2021; 98:713-731. [PMID: 34516658 DOI: 10.1111/php.13516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 09/07/2021] [Indexed: 11/29/2022]
Abstract
Nucleotide excision repair (NER) is one of the main pathways for genome protection against structural DNA damage caused by sunlight, which in turn is extensively related to skin cancer development. The mutation spectra induced by UVB were investigated by whole-exome sequencing of randomly selected clones of NER-proficient and XP-C-deficient human skin fibroblasts. As a model, a cell line unable to recognize and remove lesions (XP-C) was used and compared to the complemented isogenic control (COMP). As expected, a significant increase of mutagenesis was observed in irradiated XP-C cells, mainly C>T transitions, but also CC>TT and C>A base substitutions. Remarkably, the C>T mutations occur mainly at the second base of dipyrimidine sites in pyrimidine-rich sequence contexts, with 5'TC sequence the most mutated. Although T>N mutations were also significantly increased, they were not directly related to pyrimidine dimers. Moreover, the large-scale study of a single UVB irradiation on XP-C cells allowed recovering the typical mutation spectrum found in human skin cancer tumors. Eventually, the data may be used for comparison with the mutational profiles of skin tumors obtained from XP-C patients and may help to understand the mutational process in nonaffected individuals.
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Affiliation(s)
- Nathalia Quintero-Ruiz
- Laboratorio de reparo de DNA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Camila Corradi
- Laboratorio de reparo de DNA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Natália Cestari Moreno
- Laboratorio de reparo de DNA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Tiago Antonio de Souza
- Laboratorio de reparo de DNA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil.,Tau GC Bioinformatics, São Paulo, Brazil
| | - Ligia Pereira Castro
- Laboratorio de reparo de DNA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Clarissa Ribeiro Reily Rocha
- Laboratorio de reparo de DNA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil.,Drug resistance and mutagenesis Laboratory, Departmento de Oncologia Clínica e Experimental, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Carlos Frederico Martins Menck
- Laboratorio de reparo de DNA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
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6
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de Semir D, Bezrookove V, Nosrati M, Dar AA, Miller JR, Leong SP, Kim KB, Liao W, Soroceanu L, McAllister S, Debs RJ, Schadendorf D, Leachman SA, Cleaver JE, Kashani-Sabet M. Nuclear Receptor Coactivator NCOA3 Regulates UV Radiation-Induced DNA Damage and Melanoma Susceptibility. Cancer Res 2021; 81:2956-2969. [PMID: 33766890 DOI: 10.1158/0008-5472.can-20-3450] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 02/10/2021] [Accepted: 03/15/2021] [Indexed: 11/16/2022]
Abstract
Melanoma occurs as a consequence of inherited susceptibility to the disease and exposure to UV radiation (UVR) and is characterized by uncontrolled cellular proliferation and a high mutational load. The precise mechanisms by which UVR contributes to the development of melanoma remain poorly understood. Here we show that activation of nuclear receptor coactivator 3 (NCOA3) promotes melanomagenesis through regulation of UVR sensitivity, cell-cycle progression, and circumvention of the DNA damage response (DDR). Downregulation of NCOA3 expression, either by genetic silencing or small-molecule inhibition, significantly suppressed melanoma proliferation in melanoma cell lines and patient-derived xenografts. NCOA3 silencing suppressed expression of xeroderma pigmentosum C and increased melanoma cell sensitivity to UVR. Suppression of NCOA3 expression led to activation of DDR effectors and reduced expression of cyclin B1, resulting in G2-M arrest and mitotic catastrophe. A SNP in NCOA3 (T960T) reduced NCOA3 protein expression and was associated with decreased melanoma risk, given a significantly lower prevalence in a familial melanoma cohort than in a control cohort without cancer. Overexpression of wild-type NCOA3 promoted melanocyte survival following UVR and was accompanied by increased levels of UVR-induced DNA damage, both of which were attenuated by overexpression of NCOA3 (T960T). These results describe NCOA3-regulated pathways by which melanoma can develop, with germline NCOA3 polymorphisms enabling enhanced melanocyte survival in the setting of UVR exposure, despite an increased mutational burden. They also identify NCOA3 as a novel therapeutic target for melanoma. SIGNIFICANCE: This study explores NCOA3 as a regulator of the DDR and a therapeutic target in melanoma, where activation of NCOA3 contributes to melanoma development following exposure to ultraviolet light.
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Affiliation(s)
- David de Semir
- Center for Melanoma Research and Treatment, California Pacific Medical Center Research Institute, San Francisco, California.,California Pacific Medical Center Research Institute, San Francisco, California
| | - Vladimir Bezrookove
- Center for Melanoma Research and Treatment, California Pacific Medical Center Research Institute, San Francisco, California.,California Pacific Medical Center Research Institute, San Francisco, California
| | - Mehdi Nosrati
- Center for Melanoma Research and Treatment, California Pacific Medical Center Research Institute, San Francisco, California.,California Pacific Medical Center Research Institute, San Francisco, California
| | - Altaf A Dar
- Center for Melanoma Research and Treatment, California Pacific Medical Center Research Institute, San Francisco, California.,California Pacific Medical Center Research Institute, San Francisco, California
| | - James R Miller
- Center for Melanoma Research and Treatment, California Pacific Medical Center Research Institute, San Francisco, California.,California Pacific Medical Center Research Institute, San Francisco, California
| | - Stanley P Leong
- Center for Melanoma Research and Treatment, California Pacific Medical Center Research Institute, San Francisco, California.,California Pacific Medical Center Research Institute, San Francisco, California
| | - Kevin B Kim
- Center for Melanoma Research and Treatment, California Pacific Medical Center Research Institute, San Francisco, California.,California Pacific Medical Center Research Institute, San Francisco, California
| | - Wilson Liao
- Department of Dermatology, University of California San Francisco, San Francisco, California
| | - Liliana Soroceanu
- California Pacific Medical Center Research Institute, San Francisco, California
| | - Sean McAllister
- California Pacific Medical Center Research Institute, San Francisco, California
| | - Robert J Debs
- California Pacific Medical Center Research Institute, San Francisco, California
| | - Dirk Schadendorf
- Department of Dermatology, University Duisburg-Essen, Essen, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Sancy A Leachman
- Department of Dermatology and Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - James E Cleaver
- Department of Dermatology, University of California San Francisco, San Francisco, California
| | - Mohammed Kashani-Sabet
- Center for Melanoma Research and Treatment, California Pacific Medical Center Research Institute, San Francisco, California. .,California Pacific Medical Center Research Institute, San Francisco, California
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7
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Clinical and Mutational Spectrum of Xeroderma Pigmentosum in Egypt: Identification of Six Novel Mutations and Implications for Ancestral Origins. Genes (Basel) 2021; 12:genes12020295. [PMID: 33672602 PMCID: PMC7924063 DOI: 10.3390/genes12020295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 12/11/2022] Open
Abstract
Xeroderma pigmentosum is a rare autosomal recessive skin disorder characterized by freckle-like dry pigmented skin, photosensitivity, and photophobia. Skin and ocular symptoms are confined to sun exposed areas of the body. Patients have markedly increased risk for UV-induced skin, ocular, and oral cancers. Some patients develop neurodegenerative symptoms, including diminished tendon reflexes and microcephaly. In this study, we describe clinical and genetic findings of 36 XP patients from Egypt, a highly consanguineous population from North Africa. Thorough clinical evaluation followed by Sanger sequencing of XPA and XPC genes were done. Six novel and seven previously reported mutations were identified. Phenotype-genotype correlation was investigated. We report clinical and molecular findings consistent with previous reports of countries sharing common population structure, and geographical and historical backgrounds with implications on common ancestral origins and historical migration flows. Clinical and genetic profiling improves diagnosis, management, counselling, and implementation of future targeted therapies.
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8
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Macke EL, Morales-Rosado JA, Gupta A, Schmitz CT, Kruisselbrink T, Lanpher B, Klee EW. A novel missense variant and multiexon deletion causing a delayed presentation of xeroderma pigmentosum, group C. Cold Spring Harb Mol Case Stud 2020; 6:a005165. [PMID: 32843428 PMCID: PMC7476405 DOI: 10.1101/mcs.a005165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/23/2020] [Indexed: 12/02/2022] Open
Abstract
Pathogenic variants in the XPC complex subunit, DNA damage recognition, and repair factor (XPC) are the cause of xeroderma pigmentosum, group C (MIM: 278720). Xeroderma pigmentosum is an inherited condition characterized by hypersensitivity to ultraviolet (UV) irradiation and increased risk of skin cancer due to a defect in nucleotide excision repair (NER). Here we describe an individual with a novel missense variant and deletion of exons 14-15 in XPC presenting with a history of recurrent melanomas. The proband is a 39-yr-old female evaluated through the Mayo Clinic Department of Clinical Genomics. Prior to age 36, she had more than 60 skin biopsies that showed dysplastic nevi, many of which had atypia. At age 36 she presented with her first melanoma in situ, and since then has had more than 10 melanomas. The proband underwent research whole-exome sequencing (WES) through the Mayo Clinic's Center for Individualized Medicine and a novel heterozygous variant of uncertain significance (VUS) in XPC (c.1709T > G, p.Val570Gly) was identified. Clinical confirmation pursued via XPC gene sequencing and deletion/duplication analysis of XPC revealed a pathogenic heterozygous deletion of ∼1 kb within XPC, including exons 14 and 15. Research studies determined the alterations to be in trans Although variants in XPC generally result in early-onset skin cancer in childhood, the proband is atypical in that she did not present with her first melanoma until age 36. Review of the patient's clinical, pathological, and genetic findings points to a diagnosis of delayed presentation of xeroderma pigmentosum.
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Affiliation(s)
- Erica L Macke
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Joel A Morales-Rosado
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Aditi Gupta
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | | | | | - Brendan Lanpher
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
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9
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Yi GZ, Huang G, Guo M, Zhang X, Wang H, Deng S, Li Y, Xiang W, Chen Z, Pan J, Li Z, Yu L, Lei B, Liu Y, Qi S. Acquired temozolomide resistance in MGMT-deficient glioblastoma cells is associated with regulation of DNA repair by DHC2. Brain 2020; 142:2352-2366. [PMID: 31347685 PMCID: PMC6658867 DOI: 10.1093/brain/awz202] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 04/05/2019] [Accepted: 04/12/2019] [Indexed: 01/05/2023] Open
Abstract
The acquisition of temozolomide resistance is a major clinical challenge for glioblastoma treatment. Chemoresistance in glioblastoma is largely attributed to repair of temozolomide-induced DNA lesions by O6-methylguanine-DNA methyltransferase (MGMT). However, some MGMT-deficient glioblastomas are still resistant to temozolomide, and the underlying molecular mechanisms remain unclear. We found that DYNC2H1 (DHC2) was expressed more in MGMT-deficient recurrent glioblastoma specimens and its expression strongly correlated to poor progression-free survival in MGMT promotor methylated glioblastoma patients. Furthermore, silencing DHC2, both in vitro and in vivo, enhanced temozolomide-induced DNA damage and significantly improved the efficiency of temozolomide treatment in MGMT-deficient glioblastoma. Using a combination of subcellular proteomics and in vitro analyses, we showed that DHC2 was involved in nuclear localization of the DNA repair proteins, namely XPC and CBX5, and knockdown of either XPC or CBX5 resulted in increased temozolomide-induced DNA damage. In summary, we identified the nuclear transportation of DNA repair proteins by DHC2 as a critical regulator of acquired temozolomide resistance in MGMT-deficient glioblastoma. Our study offers novel insights for improving therapeutic management of MGMT-deficient glioblastoma.
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Affiliation(s)
- Guo-Zhong Yi
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, People's Republic of China.,The Laboratory for Precision Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, People's Republic of China
| | - Guanglong Huang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, People's Republic of China.,Department of Neurosurgery, Longgang Central Hospital of Shenzhen, Shenzhen 518116, Guangdong, People's Republic of China
| | - Manlan Guo
- The Laboratory for Precision Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, People's Republic of China
| | - Xi'an Zhang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, People's Republic of China
| | - Hai Wang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, People's Republic of China
| | - Shengze Deng
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, People's Republic of China
| | - Yaomin Li
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, People's Republic of China
| | - Wei Xiang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, People's Republic of China.,Department of Neurosurgery, The First Affliated Hospital, Southwest Medical University, Luzhou 646000, Sichuan, People's Republic of China
| | - Ziyang Chen
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, People's Republic of China
| | - Jun Pan
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, People's Republic of China
| | - Zhiyong Li
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, People's Republic of China
| | - Lei Yu
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, People's Republic of China
| | - Bingxi Lei
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, People's Republic of China
| | - Yawei Liu
- The Laboratory for Precision Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, People's Republic of China
| | - Songtao Qi
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, People's Republic of China.,Nanfang Glioma Center, Guangzhou 510515, Guangdong, People's Republic of China
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10
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Ali MZ, Blatterer J, Khan MA, Schaflinger E, Petek E, Ahmad S, Khan E, Windpassinger C. Identification of a novel protein truncating mutation p.Asp98* in XPC associated with xeroderma pigmentosum in a consanguineous Pakistani family. Mol Genet Genomic Med 2020; 8:e1060. [PMID: 31923348 PMCID: PMC7005610 DOI: 10.1002/mgg3.1060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/12/2019] [Accepted: 10/23/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Xeroderma pigmentosum (XP) is a rare genetic disorder, which is characterized by hyper-sensitivity to solar ultraviolet (UV) radiation. Clinical consequences of sun exposure are skin lesions and an increased risk of developing skin cancer. Genetic studies have identified eight genes associated with xeroderma pigmentosum. The proteins encoded by these genes are mainly involved in DNA repair mechanisms. METHODS Molecular genetic characterization of patients with xeroderma pigmentosum involved positional cloning methods such as homozygosity mapping and subsequent candidate gene analysis. Mutation screening was performed through Sanger DNA sequencing. RESULTS AND DISCUSSION In this case study, we report a novel protein truncating mutation in XPC associated with autosomal recessive xeroderma pigmentosum in a consanguineous Pakistani family. Genetic mapping revealed a novel single base insertion of a thymine nucleotide NM_004628.4: c.291dupT (c.291_292insT) in the second exon of XPC. The identified mutation leads to a premature stop codon (TGA) at amino acid position 98 (p.Asp98*) and thus presumably results in a truncated protein. The Xeroderma pigmentosum, complementation group C (XPC) is located on 3p25.1 and encodes a protein involved in nucleotide excision repair. The identified mutation presumably truncates all functional domains of the XPC protein, which likely results in the loss of protein function. CONCLUSION The study expands the knowledge of the mutational spectrum of XPC and is valuable for genetic counseling of affected individuals and their families.
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Affiliation(s)
- Muhammad Z Ali
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Jasmin Blatterer
- Diagnostic & Research Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Muzammil A Khan
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Erich Schaflinger
- Diagnostic & Research Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Erwin Petek
- Diagnostic & Research Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Safeer Ahmad
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Ejazullah Khan
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Christian Windpassinger
- Diagnostic & Research Institute of Human Genetics, Medical University of Graz, Graz, Austria
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Pugh J, Khan SG, Tamura D, Goldstein AM, Landi MT, DiGiovanna JJ, Kraemer KH. Use of Big Data to Estimate Prevalence of Defective DNA Repair Variants in the US Population. JAMA Dermatol 2019; 155:72-78. [PMID: 30516811 DOI: 10.1001/jamadermatol.2018.4473] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Importance Wide use of genomic sequencing to diagnose disease has raised concern about the extent of genotype-phenotype correlations. Objective To correlate disease-associated allele frequencies with expected and reported prevalence of clinical disease. Design, Setting, and Participants Xeroderma pigmentosum (XP), a recessive, cancer-prone, neurocutaneous disorder, was used as a model for this study. From January 1, 2017, to May 4, 2018, the Human Gene Mutation Database and a cohort of patients at the National Institutes of Health were searched and screened to identify reported mutations associated with XP. The clinical phenotype of these patients was confirmed from reports in the literature and National Institutes of Health medical records. The genetically predicted prevalence of disease based on frequency of known pathogenic mutations was compared with the prevalence of patients clinically diagnosed with phenotypic XP. Exome sequencing of more than 200 000 alleles from the Genome Aggregation Database, the National Cancer Institute Division of Cancer Epidemiology and Genetics database of healthy controls, and an Inova Hospital Study database was used to investigate the frequencies of these mutations in the general population. Main Outcomes and Measures Listing of all reported mutations associated with XP, their frequencies in 3 large exome sequence databases, determination of the number of patients in the United States with XP using modeling equations, and comparison of the observed and reported numbers of patients with XP with specific mutations. Results A total of 156 pathogenic missense and nonsense mutations associated with XP were identified in the National Institutes of Health cohort and the Human Gene Mutation Database. The Genome Aggregation Database provided frequency data for 65 of these mutations, with a total allele frequency of 1.13%. The XPF (ERCC4) mutation, p.P379S, had an allele frequency of 0.4%, and the XPC mutation, p.P334H, had an allele frequency of 0.3%. With the Hardy-Weinberg equation, it was determined that there should be more than 8000 patients who are homozygous for these mutations in the United States. In contrast, only 3 patients with XP were reported as having the XPF mutation, and 1 patient was reported as having the XPC mutation. Conclusions and Relevance The findings from this study suggest that clinicians should approach large genomic databases with caution when trying to correlate the clinical implications of genetic variants with the prevalence of disease risk. Unsuspected mutations in known genes with a predisposition for skin cancer may be responsible for some of the high frequency of skin cancers in the general population.
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Affiliation(s)
- Jennifer Pugh
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland.,Academy Enrichment Program Scholar, Office of Intramural Training & Education, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - Sikandar G Khan
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Deborah Tamura
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Alisa M Goldstein
- Human Genetics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Maria Teresa Landi
- Human Genetics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - John J DiGiovanna
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Kenneth H Kraemer
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
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12
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Sugasawa K. Mechanism and regulation of DNA damage recognition in mammalian nucleotide excision repair. DNA Repair (Amst) 2019; 45:99-138. [DOI: 10.1016/bs.enz.2019.06.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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13
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Stepien KM, Heaton R, Rankin S, Murphy A, Bentley J, Sexton D, Hargreaves IP. Evidence of Oxidative Stress and Secondary Mitochondrial Dysfunction in Metabolic and Non-Metabolic Disorders. J Clin Med 2017; 6:E71. [PMID: 28753922 PMCID: PMC5532579 DOI: 10.3390/jcm6070071] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 07/07/2017] [Accepted: 07/14/2017] [Indexed: 01/07/2023] Open
Abstract
Mitochondrial dysfunction and oxidative stress have been implicated in the pathogenesis of a number of diseases and conditions. Oxidative stress occurs once the antioxidant defenses of the body become overwhelmed and are no longer able to detoxify reactive oxygen species (ROS). The ROS can then go unchallenged and are able to cause oxidative damage to cellular lipids, DNA and proteins, which will eventually result in cellular and organ dysfunction. Although not always the primary cause of disease, mitochondrial dysfunction as a secondary consequence disease of pathophysiology can result in increased ROS generation together with an impairment in cellular energy status. Mitochondrial dysfunction may result from either free radical-induced oxidative damage or direct impairment by the toxic metabolites which accumulate in certain metabolic diseases. In view of the importance of cellular antioxidant status, a number of therapeutic strategies have been employed in disorders associated with oxidative stress with a view to neutralising the ROS and reactive nitrogen species implicated in disease pathophysiology. Although successful in some cases, these adjunct therapies have yet to be incorporated into the clinical management of patients. The purpose of this review is to highlight the emerging evidence of oxidative stress, secondary mitochondrial dysfunction and antioxidant treatment efficacy in metabolic and non-metabolic diseases in which there is a current interest in these parameters.
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Affiliation(s)
- Karolina M Stepien
- The Mark Holland Metabolic Unit Salford Royal NHS Foundation Trust Stott Lane, Salford M6 8HD, UK.
| | - Robert Heaton
- School of Pharmacy, Liverpool John Moore University, Byrom Street, Liverpool L3 3AF, UK.
| | - Scott Rankin
- School of Pharmacy, Liverpool John Moore University, Byrom Street, Liverpool L3 3AF, UK.
| | - Alex Murphy
- School of Pharmacy, Liverpool John Moore University, Byrom Street, Liverpool L3 3AF, UK.
| | - James Bentley
- School of Pharmacy, Liverpool John Moore University, Byrom Street, Liverpool L3 3AF, UK.
| | - Darren Sexton
- School of Pharmacy, Liverpool John Moore University, Byrom Street, Liverpool L3 3AF, UK.
| | - Iain P Hargreaves
- School of Pharmacy, Liverpool John Moore University, Byrom Street, Liverpool L3 3AF, UK.
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Xeroderma Pigmentosum with Severe Neurological Manifestations/De Sanctis-Cacchione Syndrome and a Novel XPC Mutation. Case Rep Med 2017; 2017:7162737. [PMID: 28255305 PMCID: PMC5309409 DOI: 10.1155/2017/7162737] [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: 07/21/2016] [Revised: 12/20/2016] [Accepted: 01/11/2017] [Indexed: 11/21/2022] Open
Abstract
Several genetic disorders caused by defective nucleotide excision repair that affect the skin and the nervous system have been described, including Xeroderma Pigmentosum (XP), De Sanctis–Cacchione syndrome (DSC), Cockayne syndrome, and Trichothiodystrophy. Cutaneous photosensitivity with an increased risk of skin malignancy is a common feature of these disorders, but clinical manifestations commonly overlap these syndromes. Several genes have been found to be altered in these pathologies, but we lack more genotype-phenotype correlations in order to make an accurate diagnosis. Very few cases of DSC syndrome have been reported in the literature. We present a case of a 12-year-old Colombian male, with multiple skin lesions in sun-exposed areas from the age of 3 months and a history of 15 skin cancers. He also displayed severe neurologic abnormalities (intellectual disability, ataxia, altered speech, and hyperreflexia), short stature, and microcephaly, which are features associated with DSC. Genetic testing revealed a novel germline mutation in the XP-C gene (c.547A>T). This is the first case of an XP-C mutation causing De Sanctis–Cacchione syndrome. Multigene panel testing is becoming more widely available and accessible in the clinical setting and will help rapidly unveil the molecular etiology of these rare genetic disorders.
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The Nucleotide Excision Repair Pathway Limits L1 Retrotransposition. Genetics 2016; 205:139-153. [PMID: 28049704 PMCID: PMC5223499 DOI: 10.1534/genetics.116.188680] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 10/30/2016] [Indexed: 12/25/2022] Open
Abstract
Long interspersed elements 1 (L1) are active mobile elements that constitute almost 17% of the human genome. They amplify through a “copy-and-paste” mechanism termed retrotransposition, and de novo insertions related to these elements have been reported to cause 0.2% of genetic diseases. Our previous data demonstrated that the endonuclease complex ERCC1-XPF, which cleaves a 3′ DNA flap structure, limits L1 retrotransposition. Although the ERCC1-XPF endonuclease participates in several different DNA repair pathways, such as single-strand annealing, or in telomere maintenance, its recruitment to DNA lesions is best characterized in the nucleotide excision repair (NER) pathway. To determine if the NER pathway prevents the insertion of retroelements in the genome, we monitored the retrotransposition efficiencies of engineered L1 elements in NER-deficient cells and in their complemented versions. Core proteins of the NER pathway, XPD and XPA, and the lesion binding protein, XPC, are involved in limiting L1 retrotransposition. In addition, sequence analysis of recovered de novo L1 inserts and their genomic locations in NER-deficient cells demonstrated the presence of abnormally large duplications at the site of insertion, suggesting that NER proteins may also play a role in the normal L1 insertion process. Here, we propose new functions for the NER pathway in the maintenance of genome integrity: limitation of insertional mutations caused by retrotransposons and the prevention of potentially mutagenic large genomic duplications at the site of retrotransposon insertion events.
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Schubert S, Rieper P, Ohlenbusch A, Seebode C, Lehmann J, Gratchev A, Emmert S. A unique chromosomal in-frame deletion identified among seven XP-C patients. PHOTODERMATOLOGY PHOTOIMMUNOLOGY & PHOTOMEDICINE 2016; 32:276-283. [DOI: 10.1111/phpp.12251] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/05/2016] [Indexed: 12/01/2022]
Affiliation(s)
- Steffen Schubert
- Department of Dermatology, Venereology and Allergology; University Medical Center Göttingen; Göttingen Germany
| | - Petra Rieper
- Department of Dermatology, Venereology and Allergology; University Medical Center Göttingen; Göttingen Germany
| | - Andreas Ohlenbusch
- Department of Pediatrics and Adolescent Medicine; Division of Pediatric Neurology; University Medical Center Göttingen; Göttingen Germany
| | - Christina Seebode
- Clinic for Dermatology and Venereology; University Medical Center Rostock; Rostock Germany
| | - Janin Lehmann
- Clinic for Dermatology and Venereology; University Medical Center Rostock; Rostock Germany
| | - Alexei Gratchev
- Department of Dermatology, Venereology and Allergology; University Medical Center Heidelberg; Heidelberg Germany
- Institute of Carcinogenesis, NN Blokhin Cancer Research Center, Russian Academy of Medical Sciences; Moscow Russia
| | - Steffen Emmert
- Clinic for Dermatology and Venereology; University Medical Center Rostock; Rostock Germany
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17
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Lin TY. Simple sequence repeat variations expedite phage divergence: Mechanisms of indels and gene mutations. Mutat Res 2016; 789:48-56. [PMID: 27133219 DOI: 10.1016/j.mrfmmm.2016.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 03/26/2016] [Accepted: 04/11/2016] [Indexed: 12/27/2022]
Abstract
Phages are the most abundant biological entities and influence prokaryotic communities on Earth. Comparing closely related genomes sheds light on molecular events shaping phage evolution. Simple sequence repeat (SSR) variations impart over half of the genomic changes between T7M and T3, indicating an important role of SSRs in accelerating phage genetic divergence. Differences in coding and noncoding regions of phages infecting different hosts, coliphages T7M and T3, Yersinia phage ϕYeO3-12, and Salmonella phage ϕSG-JL2, frequently arise from SSR variations. Such variations modify noncoding and coding regions; the latter efficiently changes multiple amino acids, thereby hastening protein evolution. Four classes of events are found to drive SSR variations: insertion/deletion of SSR units, expansion/contraction of SSRs without alteration of genome length, changes of repeat motifs, and generation/loss of repeats. The categorization demonstrates the ways SSRs mutate in genomes during phage evolution. Indels are common constituents of genome variations and human diseases, yet, how they occur without preexisting repeat sequence is less understood. Non-repeat-unit-based misalignment-elongation (NRUBME) is proposed to be one mechanism for indels without adjacent repeats. NRUBME or consecutive NRUBME may also change repeat motifs or generate new repeats. NRUBME invoking a non-Watson-Crick base pair explains insertions that initiate mononucleotide repeats. Furthermore, NRUBME successfully interprets many inexplicable human di- to tetranucleotide repeat generations. This study provides the first evidence of SSR variations expediting phage divergence, and enables insights into the events and mechanisms of genome evolution. NRUBME allows us to emulate natural evolution to design indels for various applications.
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Affiliation(s)
- Tiao-Yin Lin
- Department of Biological Science and Technology, Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsin Chu, Taiwan.
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18
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Meneses M, Chavez-Bourgeois M, Badenas C, Villablanca S, Aguilera P, Bennàssar A, Alos L, Puig S, Malvehy J, Carrera C. Atypical Clinical Presentation of Xeroderma Pigmentosum in a Patient Harboring a Novel Missense Mutation in the XPC Gene: The Importance of Clinical Suspicion. Dermatology 2015; 231:217-21. [PMID: 26278556 DOI: 10.1159/000433527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 05/20/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Xeroderma pigmentosum (XP) is a genodermatosis caused by abnormal DNA repair. XP complementation group C (XPC) is the most frequent type in Mediterranean countries. We describe a case with a novel mutation in the XPC gene. CASE A healthy Caucasian male patient was diagnosed with multiple primary melanomas. Digital follow-up and molecular studies were carried out. RESULTS During digital follow-up 8 more additional melanomas were diagnosed. Molecular studies did not identify mutations in CDKN2A, CDK4 or MITF genes. Two heterozygous mutations in the XPC gene were detected: c.2287delC (p.Leu763Cysfs*4) frameshift and c.2212A>G (p.Thr738Ala) missense mutations. CONCLUSION The p.Thr738Ala missense mutation has not been previously described. Missense mutations in the XPC gene may allow partial functionality that could explain this unusual late onset XP. Atypical clinical presentation of XPC could be misdiagnosed when genetic aberrations allow partial DNA repair capacity.
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Affiliation(s)
- Marina Meneses
- Melanoma Unit, Dermatology Department, Hospital Clinic of Barcelona, Barcelona, Spain
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Okamura K, Toyoda M, Hata K, Nakabayashi K, Umezawa A. Whole-exome sequencing of fibroblast and its iPS cell lines derived from a patient diagnosed with xeroderma pigmentosum. GENOMICS DATA 2015; 6:4-6. [PMID: 26697316 PMCID: PMC4664661 DOI: 10.1016/j.gdata.2015.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 07/12/2015] [Indexed: 11/30/2022]
Abstract
Cells from a patient with a DNA repair-deficiency disorder are anticipated to bear a large number of somatic mutations. Because such mutations occur independently in each cell, there is a high degree of mosaicism in patients' tissues. While major mutations that have been expanded in many cognate cells are readily detected by sequencing, minor ones are overlaid with a large depth of non-mutated alleles and are not detected. However, cell cloning enables us to observe such cryptic mutations as well as major mutations. In the present study, we focused on a fibroblastic cell line that is derived from a patient diagnosed with xeroderma pigmentosum (XP), which is an autosomal recessive disorder caused by a deficiency in nucleotide excision repair. By making a list of somatic mutations, we can expect to see a characteristic pattern of mutations caused by the hereditary disorder. We cloned a cell by generating an iPS cell line and performed a whole-exome sequencing analysis of the progenitor and its iPS cell lines. Unexpectedly, we failed to find causal mutations in the XP-related genes, but we identified many other mutations including homozygous deletion of GSTM1 and GSTT1. In addition, we found that the long arm of chromosome 9 formed uniparental disomy in the iPS cell line, which was also confirmed by a structural mutation analysis using a SNP array. Type and number of somatic mutations were different from those observed in XP patients. Taken together, we conclude that the patient might be affected by a different type of the disorder and that some of the mutations that we identified here may be responsible for exhibiting the phenotype. Sequencing and SNP-array data have been submitted to SRA and GEO under accession numbers SRP059858 and GSE55520, respectively.
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Affiliation(s)
- Kohji Okamura
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Masashi Toyoda
- Department of Research Team for Geriatric Medicine, Tokyo Metropolitan Institute of Gerontology, Tokyo 173-0015, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Akihiro Umezawa
- Department of Reproductive Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
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Rocco ML, Balzamino BO, Petrocchi Passeri P, Micera A, Aloe L. Effect of purified murine NGF on isolated photoreceptors of a rodent developing retinitis pigmentosa. PLoS One 2015; 10:e0124810. [PMID: 25897972 PMCID: PMC4405340 DOI: 10.1371/journal.pone.0124810] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 03/18/2015] [Indexed: 01/27/2023] Open
Abstract
A number of different studies have shown that neurotrophins, including nerve growth factor (NGF) support the survival of retinal ganglion neurons during a variety if insults. Recently, we have reported that that eye NGF administration can protect also photoreceptor degeneration in a mice and rat with inherited retinitis pigmentosa. However, the evidence that NGF acts directly on photoreceptors and that other retinal cells mediate the NGF effect could not be excluded. In the present study we have isolated retinal cells from rats with inherited retinitis pigmentosa (RP) during the post-natal stage of photoreceptor degenerative. In presence of NGF, these cells are characterized by enhanced expression of NGF-receptors and rhodopsin, the specific marker of photoreceptor and better cell survival, as well as neuritis outgrowth. Together these observations support the hypothesis that NGF that NGF acts directly on photoreceptors survival and prevents photoreceptor degeneration as previously suggested by in vivo studies.
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Affiliation(s)
| | | | - Pamela Petrocchi Passeri
- Institute of Cell Biology and Neurobiology, CNR, Rome, Italy
- Dept. Medicine of Systems, University of Rome Tor Vergata, Rome, Italy
| | | | - Luigi Aloe
- Institute of Cell Biology and Neurobiology, CNR, Rome, Italy
- * E-mail:
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21
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Zhilova MB, Kubanov AA. Molecular markers of the risk of development of skin cancer in psoriasis patients receiving a phototherapy. VESTNIK DERMATOLOGII I VENEROLOGII 2014. [DOI: 10.25208/0042-4609-2014-90-6-62-68] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
State Research Center of Dermatovenereology and Cosmetology, Ministry of Healthcare of the Russian Federation Korolenko str., 3, bldg 6, Moscow, 107076, Russia Goal. To study potential molecular and genetic markers of an increased risk of development of malignant skin melanomas on the basis of the assessment of nucleotide replacements of genes in the excision system of DNA repair in psoriasis patients receiving a phototherapy. Materials and methods. Biological blood samples taken from 47 psoriasis patients, 24 patients with malignant skin melanomas and 20 healthy subjects. The following methods were used in the study: clinical, molecular and biological (DNA extraction, amplification, PcR, sequencing). Results. The study revealed molecular markers of an increased risk of development of malignant skin melanomas in psoriasis patients: CC genotype of the XPD gene at the 35931 locus (p = 0.00001); TC genotype of the XPF gene at the 27945 locus (p = 0.0067). It also revealed a molecular marker of an increased risk of development of malignant skin melanomas in healthy people: CC genotype of the XPD gene at the 35931 locus (p = 0.0042).
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Feltes BC, Bonatto D. Overview of xeroderma pigmentosum proteins architecture, mutations and post-translational modifications. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2014; 763:306-20. [PMID: 25795128 DOI: 10.1016/j.mrrev.2014.12.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 12/08/2014] [Accepted: 12/09/2014] [Indexed: 12/15/2022]
Abstract
The xeroderma pigmentosum complementation group proteins (XPs), which include XPA through XPG, play a critical role in coordinating and promoting global genome and transcription-coupled nucleotide excision repair (GG-NER and TC-NER, respectively) pathways in eukaryotic cells. GG-NER and TC-NER are both required for the repair of bulky DNA lesions, such as those induced by UV radiation. Mutations in genes that encode XPs lead to the clinical condition xeroderma pigmentosum (XP). Although the roles of XPs in the GG-NER/TC-NER subpathways have been extensively studied, complete knowledge of their three-dimensional structure is only beginning to emerge. Hence, this review aims to summarize the current knowledge of mapped mutations and other structural information on XP proteins that influence their function and protein-protein interactions. We also review the possible post-translational modifications for each protein and the impact of these modifications on XP protein functions.
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Affiliation(s)
- Bruno César Feltes
- Biotechnology Center of the Federal University of Rio Grande do Sul, Department of Molecular Biology and Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Diego Bonatto
- Biotechnology Center of the Federal University of Rio Grande do Sul, Department of Molecular Biology and Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil.
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Kraemer KH, DiGiovanna JJ. Global contributions to the understanding of DNA repair and skin cancer. J Invest Dermatol 2014; 134:E8-17. [PMID: 25302472 PMCID: PMC6334767 DOI: 10.1038/skinbio.2014.3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Kenneth H Kraemer
- Dermatology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - John J DiGiovanna
- Dermatology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
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Repair of UV photolesions in xeroderma pigmentosum group C cells induced by translational readthrough of premature termination codons. Proc Natl Acad Sci U S A 2013; 110:19483-8. [PMID: 24218596 DOI: 10.1073/pnas.1312088110] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
About 12% of human genetic disorders involve premature termination codons (PTCs). Aminoglycoside antibiotics have been proposed for restoring full-length proteins by readthrough of PTC. To assess the efficiency of readthrough, we selected homozygous and compound heterozygous skin fibroblasts from xeroderma pigmentosum (XP) patients with different PTCs in the XPC DNA repair gene. XP patients have a nucleotide excision repair defect and a 10,000-fold increased risk of UV-induced skin cancer. In six of eight PTC-containing XP-C cells, treatment with Geneticin and gentamicin resulted in (i) stabilized XPC-mRNA, which would have been degraded by nonsense-mediated decay; (ii) increased expression of XPC protein that localized to UV-damaged sites; (iii) recruitment of XPB and XPD proteins to UV DNA damage sites; and (iv) increased repair of 6-4 photoproducts and cyclobutane pyrimidine dimers. Expression of PTC in a transfected vector revealed that readthrough depends on the PTC sequence and its location within the gene. This sensitive DNA repair assay system demonstrates the complexity of response to PTC readthrough inducers. The efficiency of aminoglycoside-mediated readthrough depends on the type and copy number of PTC, the downstream 4+ nucleotide, and the location within the exon. Treatment with small-molecule nonaminoglycoside compounds (PTC124, BZ16, or RTC14) resulted in similarly increased XPC mRNA expression and photoproduct removal with less toxicity than with the aminoglycosides. Characterizing PTC structure and parameters governing effective PTC readthrough may provide a unique prophylactic therapy for skin cancer prevention in XP-C patients.
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Lai JP, Liu YC, Alimchandani M, Liu Q, Aung PP, Matsuda K, Lee CCR, Tsokos M, Hewitt S, Rushing EJ, Tamura D, Levens DL, DiGiovanna JJ, Fine HA, Patronas N, Khan SG, Kleiner DE, Oberholtzer JC, Quezado MM, Kraemer KH. The influence of DNA repair on neurological degeneration, cachexia, skin cancer and internal neoplasms: autopsy report of four xeroderma pigmentosum patients (XP-A, XP-C and XP-D). Acta Neuropathol Commun 2013; 1:4. [PMID: 24252196 PMCID: PMC3776212 DOI: 10.1186/2051-5960-1-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 02/27/2013] [Indexed: 02/08/2023] Open
Abstract
Background To investigate the association of DNA nucleotide excision repair (NER) defects with neurological degeneration, cachexia and cancer, we performed autopsies on 4 adult xeroderma pigmentosum (XP) patients with different clinical features and defects in NER complementation groups XP-A, XP-C or XP-D. Results The XP-A (XP12BE) and XP-D (XP18BE) patients exhibited progressive neurological deterioration with sensorineural hearing loss. The clinical spectrum encompassed severe cachexia in the XP-A (XP12BE) patient, numerous skin cancers in the XP-A and two XP-C (XP24BE and XP1BE) patients and only few skin cancers in the XP-D patient. Two XP-C patients developed internal neoplasms including glioblastoma in XP24BE and uterine adenocarcinoma in XP1BE. At autopsy, the brains of the 44 yr XP-A and the 45 yr XP-D patients were profoundly atrophic and characterized microscopically by diffuse neuronal loss, myelin pallor and gliosis. Unlike the XP-A patient, the XP-D patient had a thickened calvarium, and the brain showed vacuolization of the neuropil in the cerebrum, cerebellum and brainstem, and patchy Purkinje cell loss. Axonal neuropathy and chronic denervation atrophy of the skeletal muscles were observed in the XP-A patient, but not in the XP-D patient. Conclusions These clinical manifestations and autopsy findings indicate advanced involvement of the central and peripheral nervous system. Despite similar defects in DNA repair, different clinicopathological phenotypes are seen in the four cases, and therefore distinct patterns of neurodegeneration characterize XP-D, XP-A and XP-C patients.
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Petkova R, Chelenkova P, Yemendzhiev H, Tsekov I, Chakarov S, Kalvatchev Z. HPV Has Left the Building—the Absence of Detectable HPV DNA and the Presence of R Allele/S for the P72R Polymorphism in the TP53Gene May Call for More Aggressive Therapeutic Approach in HPV-Associated Tumours. BIOTECHNOL BIOTEC EQ 2013. [DOI: 10.5504/bbeq.2013.0104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Abstract
The progress of molecular genetics helps clinicians to prove or exclude a suspected diagnosis for a vast and yet increasing number of genodermatoses. This leads to precise genetic counselling, prenatal diagnosis and preimplantation genetic haplotyping for many inherited skin conditions. It is also helpful in such occasions as phenocopy, late onset and incomplete penetrance, uniparental disomy, mitochondrial inheritance and pigmentary mosaicism. Molecular methods of two genodermatoses are explained in detail, i.e. genodermatoses with skin fragility and neurofibromatosis type 1.
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Affiliation(s)
- Vesarat Wessagowit
- Molecular Genetics Laboratory, The Institute of Dermatology, Bangkok, Thailand.
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Schäfer A, Hofmann L, Gratchev A, Laspe P, Schubert S, Schürer A, Ohlenbusch A, Tzvetkov M, Hallermann C, Reichrath J, Schön MP, Emmert S. Molecular genetic analysis of 16 XP-C patients from Germany: environmental factors predominately contribute to phenotype variations. Exp Dermatol 2012; 22:24-9. [DOI: 10.1111/exd.12052] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2012] [Indexed: 12/24/2022]
Affiliation(s)
- Annika Schäfer
- Department of Dermatology, Venerology and Allergology; University Medical Center Göttingen; Göttingen; Germany
| | - Lars Hofmann
- Department of Dermatology, Venerology and Allergology; University Medical Center Göttingen; Göttingen; Germany
| | - Alexei Gratchev
- Department of Dermatology, Venerology, and Allergology; University Medical Center Mannheim; Mannheim; Germany
| | - Petra Laspe
- Department of Dermatology, Venerology and Allergology; University Medical Center Göttingen; Göttingen; Germany
| | - Steffen Schubert
- Department of Dermatology, Venerology and Allergology; University Medical Center Göttingen; Göttingen; Germany
| | - Anke Schürer
- Department of Dermatology, Venerology and Allergology; University Medical Center Göttingen; Göttingen; Germany
| | - Andreas Ohlenbusch
- Department of Pediatrics; University Medical Center Göttingen; Göttingen; Germany
| | - Mladen Tzvetkov
- Department of Clinical Pharmacology; University Medical Center Göttingen; Göttingen; Germany
| | | | - Jörg Reichrath
- Department of Dermatology, Venereology, and Allergology; University Clinic Saarland; Homburg; Germany
| | - Michael P. Schön
- Department of Dermatology, Venerology and Allergology; University Medical Center Göttingen; Göttingen; Germany
| | - Steffen Emmert
- Department of Dermatology, Venerology and Allergology; University Medical Center Göttingen; Göttingen; Germany
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Senhaji MA, Abidi O, Nadifi S, Benchikhi H, Khadir K, Ben Rekaya M, Eloualid A, Messaoud O, Abdelhak S, Barakat A. c.1643_1644delTG XPC mutation is more frequent in Moroccan patients with xeroderma pigmentosum. Arch Dermatol Res 2012; 305:53-57. [PMID: 23143338 DOI: 10.1007/s00403-012-1299-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Revised: 10/29/2012] [Accepted: 11/01/2012] [Indexed: 11/28/2022]
Abstract
Xeroderma pigmentosum is a rare autosomal recessive disease characterized by hypersensitivity to UV light which is due to alterations of the nucleotide excision repair pathway. Eight genes (XPA to XPG and XPV) are responsible for the disease. Among them, the XPC gene is known to be the most mutated in Mediterranean patients. The aim of this study was to determine the frequency of the most common XPC mutation and describe the clinical features of Moroccan patients with xeroderma pigmentosum. Twenty four patients belonging to 21 unrelated Moroccan families and 58 healthy subjects were investigated. After clinical examination, the screening for the c.1643_1644delTG (p.Val548AlafsX25) mutation in the XPC gene was performed by PCR and automated sequencing of exon 9 in all patients and controls. The molecular analysis showed that among the 24 patients, 17 were homozygous for the c.1643_1644delTG mutation and all their tested parents were heterozygous, whereas the others (7 patients) did not carry the mutation. The frequency of this mutation was estimated to be 76.19 % (16/21 families). None of the 58 healthy individuals carried this mutation. In addition, clinical investigation showed that the majority of the patients bearing this mutation have the same clinical features. Our results revealed that the p.Val548AlafsX25 mutation is the major cause (76.19 %) of xeroderma pigmentosum in Moroccan families. This would have an important impact on improving management of patients and their relatives.
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Affiliation(s)
- Mohamed Amine Senhaji
- Laboratoire de Génétique Moléculaire Humaine, Département de la Recherche Scientifique, Institut Pasteur du Maroc, 1 Place Louis Pasteur, 20360, Casablanca, Morocco
| | - Omar Abidi
- Laboratoire de Génétique Moléculaire Humaine, Département de la Recherche Scientifique, Institut Pasteur du Maroc, 1 Place Louis Pasteur, 20360, Casablanca, Morocco
| | - Sellama Nadifi
- Laboratory of Human Genetics and Molecular Pathology, Faculty of medicine, Hassan II University, Casablanca, Morocco
| | - Hakima Benchikhi
- Department of Dermatology, Hospital University Ibn Rochd, Casablanca, Morocco
| | - Khadija Khadir
- Department of Dermatology, Hospital University Ibn Rochd, Casablanca, Morocco
| | - Mariem Ben Rekaya
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Abdelmajid Eloualid
- Laboratoire de Génétique Moléculaire Humaine, Département de la Recherche Scientifique, Institut Pasteur du Maroc, 1 Place Louis Pasteur, 20360, Casablanca, Morocco
| | - Olfa Messaoud
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Abdelhamid Barakat
- Laboratoire de Génétique Moléculaire Humaine, Département de la Recherche Scientifique, Institut Pasteur du Maroc, 1 Place Louis Pasteur, 20360, Casablanca, Morocco.
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Abbasi R, Efferth T, Kuhmann C, Opatz T, Hao X, Popanda O, Schmezer P. The endoperoxide ascaridol shows strong differential cytotoxicity in nucleotide excision repair-deficient cells. Toxicol Appl Pharmacol 2012; 259:302-10. [PMID: 22280988 DOI: 10.1016/j.taap.2012.01.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 12/19/2011] [Accepted: 01/09/2012] [Indexed: 12/17/2022]
Abstract
Targeting synthetic lethality in DNA repair pathways has become a promising anti-cancer strategy. However little is known about such interactions with regard to the nucleotide excision repair (NER) pathway. Therefore, cell lines with a defect in the NER genes ERCC6 or XPC and their normal counterparts were screened with 53 chemically defined phytochemicals isolated from plants used in traditional Chinese medicine for differential cytotoxic effects. The screening revealed 12 drugs that killed NER-deficient cells more efficiently than proficient cells. Five drugs were further analyzed for IC(50) values, effects on cell cycle distribution, and induction of DNA damage. Ascaridol was the most effective compound with a difference of >1000-fold in resistance between normal and NER-deficient cells (IC(50) values for cells with deficiency in ERCC6: 0.15μM, XPC: 0.18μM, and normal cells: >180μM). NER-deficiency combined with ascaridol treatment led to G2/M-phase arrest, an increased percentage of subG1 cells, and a substantially higher DNA damage induction. These results were confirmed in a second set of NER-deficient and -proficient cell lines with isogenic background. Finally, ascaridol was characterized for its ability to generate oxidative DNA damage. The drug led to a dose-dependent increase in intracellular levels of reactive oxygen species at cytotoxic concentrations, but only NER-deficient cells showed a strongly induced amount of 8-oxodG sites. In summary, ascaridol is a cytotoxic and DNA-damaging compound which generates intracellular reactive oxidative intermediates and which selectively affects NER-deficient cells. This could provide a new therapeutic option to treat cancer cells with mutations in NER genes.
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Affiliation(s)
- Rashda Abbasi
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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31
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Qiao B, Scott GB, Elliott F, Vaslin L, Bentley J, Hall J, Bishop DT, Knowles MA, Kiltie AE. Functional assays to determine the significance of two common XPC 3'UTR variants found in bladder cancer patients. BMC MEDICAL GENETICS 2011; 12:84. [PMID: 21689419 PMCID: PMC3142493 DOI: 10.1186/1471-2350-12-84] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Accepted: 06/20/2011] [Indexed: 12/02/2022]
Abstract
BACKGROUND XPC is involved in the nucleotide excision repair of DNA damaged by carcinogens known to cause bladder cancer. Individuals homozygous for the variant allele of XPC c.1496C > T (p.Ala499Val) were shown in a large pooled analysis to have an increased bladder cancer risk, and we found two 3'UTR variants, *611T > A and c.*618A > G, to be in strong linkage disequilibrium with c.1496T. Here we determined if these two 3'UTR variants can affect mRNA stability and assessed the impact of all three variants on mRNA and protein expression. METHODS In vitro mRNA stability assays were performed and mRNA and protein expression measured both in plasmid-based assays and in lymphocytes and lymphoblastoid cell lines from bladder and breast cancer patients. RESULTS The two 3'UTR variants were associated with reduced protein and mRNA expression in plasmid-based assays, suggesting an effect on mRNA stability and/or transcription/translation. A near-significant reduction in XPC protein expression (p = 0.058) was detected in lymphoblastoid cell lines homozygous for these alleles but no differences in mRNA stability in these lines was found or in mRNA or protein levels in lymphocytes heterozygous for these alleles. CONCLUSION The two 3'UTR variants may be the variants underlying the association of c.1496C > T and bladder cancer risk acting via a mechanism modulating protein expression.
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Affiliation(s)
- Boling Qiao
- Section of Experimental Oncology, Leeds Institute of Molecular Medicine, Leeds LS9 7TF, UK
| | - Gina B Scott
- Section of Experimental Oncology, Leeds Institute of Molecular Medicine, Leeds LS9 7TF, UK
| | - Faye Elliott
- Section of Epidemiology and Biostatistics, Leeds Institute of Molecular Medicine, Leeds LS9 7TF, UK
| | - Laurence Vaslin
- INSERM U612, Centre Universitaire, Orsay 91405, France and Institut Curie, Centre Universitaire, Orsay 91405, France
| | - Johanne Bentley
- Section of Experimental Oncology, Leeds Institute of Molecular Medicine, Leeds LS9 7TF, UK
| | - Janet Hall
- INSERM U612, Centre Universitaire, Orsay 91405, France and Institut Curie, Centre Universitaire, Orsay 91405, France
| | - D Timothy Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Molecular Medicine, Leeds LS9 7TF, UK
| | - Margaret A Knowles
- Section of Experimental Oncology, Leeds Institute of Molecular Medicine, Leeds LS9 7TF, UK
| | - Anne E Kiltie
- Section of Experimental Oncology, Leeds Institute of Molecular Medicine, Leeds LS9 7TF, United Kingdom and Gray Institute for Radiation Oncology and Biology, Department of Oncology, University of Oxford OX3 7DQ, UK
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32
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Zhilova MB, Kubanov AA, Lesnaya IN, Frigo NV, Volkov IA, Znamenskaya LF, Volnukhin VA. Clinical, molecular and genetic studies of efficacy and safety of using UV irradiation for psoriasis patients. VESTNIK DERMATOLOGII I VENEROLOGII 2010. [DOI: 10.25208/vdv902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
The authors give the results of clinical, molecular and genetic studies of efficacy and safety of treatment of 87 patients suffering
from extensive psoriasis with the use of UV irradiation of different spectral ranges. They showed that the administration of a course
of treatment with the use of the PUVA therapy or narrowband medium-wave UV therapy with the wavelength of 311 nm does not
result in the development of any clinically significant genetic mutations associated with the DNA excision repair system. They
revealed that the GC genotype of the XPC gene in the 32828 site and CC genotype of the XPF gene in the 27945 site may
be predictors of a pronounced therapeutic effect in treatment of patients with the use of phototherapy methods. The authors
obtained data confirming a possible protective role of T>C polymorphism in the 27945 site of the XPF gene in the development of
phototoxic reactions when psoriasis patients undergo an UV therapy.
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33
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Soufir N, Ged C, Bourillon A, Austerlitz F, Chemin C, Stary A, Armier J, Pham D, Khadir K, Roume J, Hadj-Rabia S, Bouadjar B, Taieb A, de Verneuil H, Benchiki H, Grandchamp B, Sarasin A. A Prevalent Mutation with Founder Effect in Xeroderma Pigmentosum Group C from North Africa. J Invest Dermatol 2010; 130:1537-42. [DOI: 10.1038/jid.2009.409] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Khan SG, Yamanegi K, Zheng ZM, Boyle J, Imoto K, Oh KS, Baker CC, Gozukara E, Metin A, Kraemer KH. XPC branch-point sequence mutations disrupt U2 snRNP binding, resulting in abnormal pre-mRNA splicing in xeroderma pigmentosum patients. Hum Mutat 2010; 31:167-75. [PMID: 19953607 DOI: 10.1002/humu.21166] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mutations in two branch-point sequences (BPS) in intron 3 of the XPC DNA repair gene affect pre-mRNA splicing in association with xeroderma pigmentosum (XP) with many skin cancers (XP101TMA) or no skin cancer (XP72TMA), respectively. To investigate the mechanism of these abnormalities we now report that transfection of minigenes with these mutations revealed abnormal XPC pre-mRNA splicing that mimicked pre-mRNA splicing in the patients' cells. DNA oligonucleotide-directed RNase H digestion demonstrated that mutations in these BPS disrupt U2 snRNP-BPS interaction. XP101TMA cells had no detectable XPC protein but XP72TMA had 29% of normal levels. A small amount of XPC protein was detected at sites of localized ultraviolet (UV)-damaged DNA in XP72TMA cells which then recruited other nucleotide excision repair (NER) proteins. In contrast, XP101TMA cells had no detectable recruitment of XPC or other NER proteins. Post-UV survival and photoproduct assays revealed greater reduction in DNA repair in XP101TMA cells than in XP72TMA. Thus mutations in XPC BPS resulted in disruption of U2 snRNP-BPS interaction leading to abnormal pre-mRNA splicing and reduced XPC protein. At the cellular level these changes were associated with features of reduced DNA repair including diminished NER protein recruitment, reduced post-UV survival and impaired photoproduct removal.
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Affiliation(s)
- Sikandar G Khan
- Dermatology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
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35
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Ben Rekaya M, Messaoud O, Talmoudi F, Nouira S, Ouragini H, Amouri A, Boussen H, Boubaker S, Mokni M, Mokthar I, Abdelhak S, Zghal M. High frequency of the V548A fs X572 XPC mutation in Tunisia: implication for molecular diagnosis. J Hum Genet 2009; 54:426-9. [PMID: 19478817 DOI: 10.1038/jhg.2009.50] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Xeroderma pigmentosum (XP, OMIM 278700-278780) is a group of autosomal recessive diseases characterized by hypersensitivity to UV rays. There are seven complementation groups of XP (XPA to XPG) and XPV. Among them, the XP group C (XP-C) is the most prevalent type in Western Europe and in the United States. We report here on the clinical and genetic investigation of XP-C patients in 14 Tunisian families. As the XPC V548A fs X572 mutation has been identified in Algerian and Moroccan populations, Tunisian patients were first screened for this mutation by a direct sequencing of exon 9 of the XPC gene. All patients with a severe clinical form had this mutation, thus showing the homogeneity of the mutational spectrum of XPC in Tunisia. A potential founder effect was searched and confirmed by haplotype analysis. Taking into account the similarity of the genetic background, we propose a direct screening of this mutation as a rapid and cost-effective tool for the diagnosis of XP-C in North Africa.
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Affiliation(s)
- M Ben Rekaya
- Molecular Investigation of Genetic Orphan Diseases' Research Unit, Pasteur Institute of Tunis, Tunis, Tunisia
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36
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Mahindra P, DiGiovanna JJ, Tamura D, Brahim JS, Hornyak TJ, Stern JB, Lee CCR, Khan SG, Brooks BP, Smith JA, Driscoll BP, Montemarano AD, Sugarman K, Kraemer KH. Skin cancers, blindness, and anterior tongue mass in African brothers. J Am Acad Dermatol 2009; 59:881-6. [PMID: 19119101 DOI: 10.1016/j.jaad.2008.06.030] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Revised: 05/14/2008] [Accepted: 06/22/2008] [Indexed: 11/13/2022]
Affiliation(s)
- Priya Mahindra
- Basic Research Laboratory, DNA Repair Section, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-4258, USA
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37
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Fotheringham S, Epping MT, Stimson L, Khan O, Wood V, Pezzella F, Bernards R, La Thangue NB. Genome-wide loss-of-function screen reveals an important role for the proteasome in HDAC inhibitor-induced apoptosis. Cancer Cell 2009; 15:57-66. [PMID: 19111881 DOI: 10.1016/j.ccr.2008.12.001] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Revised: 10/08/2008] [Accepted: 12/02/2008] [Indexed: 11/30/2022]
Abstract
Aberrant acetylation has been strongly linked to tumorigenesis, and the modulation of acetylation through targeting histone deacetylases (HDACs) is gathering increasing pace as a viable therapeutic strategy. A genome-wide loss-of-function screen identified HR23B, which shuttles ubiquitinated cargo proteins to the proteasome, as a sensitivity determinant for HDAC inhibitor-induced apoptosis. HR23B also governs tumor cell sensitivity to drugs that act directly on the proteasome. The level of HR23B influences the response of tumor cells to HDAC inhibitors, and HR23B is found at high levels in cutaneous T cell lymphoma in situ, a malignancy that responds favorably to HDAC inhibitor-based therapy. These results suggest that deregulated proteasome activity contributes to the anticancer activity of HDAC inhibitors.
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Affiliation(s)
- Susan Fotheringham
- Laboratory of Cancer Biology, Department of Clinical Pharmacology, Medical Sciences Division, University of Oxford, Old Road Campus Research Building, Oxford, UK
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Khan SG, Oh KS, Emmert S, Imoto K, Tamura D, DiGiovanna JJ, Shahlavi T, Armstrong N, Baker CC, Neuburg M, Zalewski C, Brewer C, Wiggs E, Schiffmann R, Kraemer KH. XPC initiation codon mutation in xeroderma pigmentosum patients with and without neurological symptoms. DNA Repair (Amst) 2009; 8:114-25. [PMID: 18955168 PMCID: PMC2684809 DOI: 10.1016/j.dnarep.2008.09.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Revised: 09/03/2008] [Accepted: 09/17/2008] [Indexed: 11/29/2022]
Abstract
Two unrelated xeroderma pigmentosum (XP) patients, with and without neurological abnormalities, respectively, had identical defects in the XPC DNA nucleotide excision repair (NER) gene. Patient XP21BE, a 27-year-old woman, had developmental delay and early onset of sensorineural hearing loss. In contrast, patient XP329BE, a 13-year-old boy, had a normal neurological examination. Both patients had marked lentiginous hyperpigmentation and multiple skin cancers at an early age. Their cultured fibroblasts showed similar hypersensitivity to killing by UV and reduced repair of DNA photoproducts. Cells from both patients had a homozygous c.2T>G mutation in the XPC gene which changed the ATG initiation codon to arginine (AGG). Both had low levels of XPC message and no detectable XPC protein on Western blotting. There was no functional XPC activity in both as revealed by the failure of localization of XPC and other NER proteins at the sites of UV-induced DNA damage in a sensitive in vivo immunofluorescence assay. XPC cDNA containing the initiation codon mutation was functionally inactive in a post-UV host cell reactivation (HCR) assay. Microsatellite markers flanking the XPC gene showed only a small region of identity ( approximately 30kBP), indicating that the patients were not closely related. Thus, the initiation codon mutation resulted in DNA repair deficiency in cells from both patients and greatly increased cancer susceptibility. The neurological abnormalities in patient XP21BE may be related to close consanguinity and simultaneous inheritance of other recessive genes or other gene modifying effects rather than the influence of XPC gene itself.
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Affiliation(s)
- Sikandar G. Khan
- Basic Research Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Kyu-Seon Oh
- Basic Research Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Steffen Emmert
- Basic Research Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Kyoko Imoto
- Basic Research Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Deborah Tamura
- Basic Research Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - John J. DiGiovanna
- Basic Research Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Division of Dermatopharmacology, Department of Dermatology, The Warren Alpert Medical School of Brown University, Providence, RI
| | - Tala Shahlavi
- Basic Research Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Najealicka Armstrong
- Basic Research Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Carl C. Baker
- Laboratory of Clinical Oncology, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Marcy Neuburg
- Department of Dermatology, Medical College of Wisconsin, Milwaukee, WI
| | - Chris Zalewski
- Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD
| | - Carmen Brewer
- Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD
| | - Edythe Wiggs
- Developmental and Metabolic Neurology Branch, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, MD
| | - Raphael Schiffmann
- Developmental and Metabolic Neurology Branch, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, MD
| | - Kenneth H. Kraemer
- Basic Research Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD
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Abstract
The XPC protein is a component of a heterotrimeric complex that is essential for damage recognition in a nucleotide excision repair subpathway that operates throughout the genome. Biochemical analyses have revealed that the broad substrate specificity of this repair system is based on the structure-specific DNA binding properties of the XPC complex. Other subunits of this complex, including human Rad23p orthologs and centrin 2, play individual roles in enhancing the damage recognition activity of XPC. Physical interaction with UV-damaged DNA-binding protein is also important for the efficient recruitment of XPC to sites containing DNA damage, particularly UV-induced photolesions. Furthermore, recent studies have suggested that XPC may also be involved in base excision repair and possibly in other cellular functions that may be mediated by posttranslational modifications.
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40
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Dissection of the molecular defects caused by pathogenic mutations in the DNA repair factor XPC. Mol Cell Biol 2008; 28:7225-35. [PMID: 18809580 DOI: 10.1128/mcb.00781-08] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
XPC is responsible for DNA damage sensing in nucleotide excision repair (NER). Mutations in XPC lead to a defect in NER and to xeroderma pigmentosum (XP-C). Here, we analyzed the biochemical properties behind mutations found within three patients: one amino acid substitution (P334H, XP1MI, and GM02096), one amino acid incorporation in a conserved domain (697insVal, XP8BE, and GM02249), and a stop mutation (R579St, XP67TMA, and GM14867). Using these mutants, we demonstrated that HR23B stabilizes XPC on DNA and protects it from degradation. XPC recruits the transcription/repair factor TFIIH and stimulates its XPB ATPase activity to initiate damaged DNA opening. In an effort to understand the severity of XP-C phenotypes, we also demonstrated that single mutations in XPC perturb other repair processes, such as base excision repair (e.g., the P334H mutation prevents the stimulation of Ogg1 glycosylase because it thwarts the interaction between XPC and Ogg1), thereby leading to a deeper understanding of the molecular repair defect of the XP-C patients.
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41
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Jacobelli S, Soufir N, Lacapere JJ, Regnier S, Bourillon A, Grandchamp B, Hétet G, Pham D, Palangie A, Avril MF, Dupin N, Sarasin A, Gorin I. Xeroderma pigmentosum group C in a French Caucasian patient with multiple melanoma and unusual long-term survival. Br J Dermatol 2008; 159:968-73. [PMID: 18717677 DOI: 10.1111/j.1365-2133.2008.08791.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
We report the case of an 83-year-old French woman with multiple melanomas showing a severe DNA repair deficiency, corrected after transfection by XPC cDNA. Two biallelic mutations in the XPC gene are reported: an inactivating frameshift mutation in exon 15 (c.2544delG, p.W848X) and a missense mutation in exon 11 (c.2108 C>T, P703L). We demonstrate that these new mutations are involved in the DNA repair deficiency and confirm the diagnosis of xeroderma pigmentosum from complementation group C (XP-C). We speculate that the coexistence of a MC1R variant may be involved in the phenotype of multiple melanomas and that the unusual long-term survival may be related to a lower ultraviolet radiation exposure and to a regular clinical follow-up. This patient appears to be the first French Caucasian XP-C case and one of the oldest living patients with XP reported worldwide.
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Affiliation(s)
- S Jacobelli
- Department of Dermatology, Tarnier-Cochin Hospital APHP, UPRES EA1833, Faculty of Medicine Paris 5, 89 rue d'Assas, 75006 Paris, France.
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Catalase overexpression reduces UVB-induced apoptosis in a human xeroderma pigmentosum reconstructed epidermis. Cancer Gene Ther 2008; 15:241-51. [PMID: 18202716 DOI: 10.1038/sj.cgt.7701102] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Xeroderma pigmentosum type C (XPC) is a rare autosomal recessive disorder that occurs due to inactivation of the XPC protein, an important DNA damage recognition protein involved in DNA nucleotide excision repair (NER). This defect, which prevents removal of a wide array of direct and indirect DNA lesions, is associated with a decrease in catalase activity. To test the hypothesis of a novel photoprotective approach, we irradiated epidermis reconstructed with XPC human keratinocytes sustainably overexpressing lentivirus-mediated catalase enzyme. Following UVB irradiation, there was a marked decrease in sunburn cell formation, caspase-3 activation and p53 accumulation in human XPC-reconstructed epidermis overexpressing catalase. Moreover, XPC-reconstructed epidermis was more resistant to UVB-induced apoptosis than normal reconstructed epidermis. While not correcting the gene defect, indirect gene therapy using antioxidant enzymes may be of help in limiting photosensitivity in XPC and probably in other monogenic/polygenic photosensitive disorders characterized by ROS accumulation.
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43
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In vivo destabilization and functional defects of the xeroderma pigmentosum C protein caused by a pathogenic missense mutation. Mol Cell Biol 2007. [PMID: 17682058 DOI: 10.1128/mcb/02166-06] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Xeroderma pigmentosum group C (XPC) protein plays an essential role in DNA damage recognition in mammalian global genome nucleotide excision repair (NER). Here, we analyze the functional basis of NER inactivation caused by a single amino acid substitution (Trp to Ser at position 690) in XPC, previously identified in the XPC patient XP13PV. The Trp690Ser change dramatically affects the in vivo stability of the XPC protein, thereby causing a significant reduction of its steady-state level in XP13PV fibroblasts. Despite normal heterotrimeric complex formation and physical interactions with other NER factors, the mutant XPC protein lacks binding affinity for both undamaged and damaged DNA. Thus, this single amino acid substitution is sufficient to compromise XPC function through both quantitative and qualitative alterations of the protein. Although the mutant XPC fails to recognize damaged DNA, it is still capable of accumulating in a UV-damaged DNA-binding protein (UV-DDB)-dependent manner to UV-damaged subnuclear domains. However, the NER factors transcription factor IIH and XPA failed to colocalize stably with the mutant XPC. As well as highlighting the importance of UV-DDB in recruiting XPC to UV-damaged sites, these findings demonstrate the role of DNA binding by XPC in the assembly of subsequent NER intermediate complexes.
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Yasuda G, Nishi R, Watanabe E, Mori T, Iwai S, Orioli D, Stefanini M, Hanaoka F, Sugasawa K. In vivo destabilization and functional defects of the xeroderma pigmentosum C protein caused by a pathogenic missense mutation. Mol Cell Biol 2007; 27:6606-14. [PMID: 17682058 PMCID: PMC2099227 DOI: 10.1128/mcb.02166-06] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Xeroderma pigmentosum group C (XPC) protein plays an essential role in DNA damage recognition in mammalian global genome nucleotide excision repair (NER). Here, we analyze the functional basis of NER inactivation caused by a single amino acid substitution (Trp to Ser at position 690) in XPC, previously identified in the XPC patient XP13PV. The Trp690Ser change dramatically affects the in vivo stability of the XPC protein, thereby causing a significant reduction of its steady-state level in XP13PV fibroblasts. Despite normal heterotrimeric complex formation and physical interactions with other NER factors, the mutant XPC protein lacks binding affinity for both undamaged and damaged DNA. Thus, this single amino acid substitution is sufficient to compromise XPC function through both quantitative and qualitative alterations of the protein. Although the mutant XPC fails to recognize damaged DNA, it is still capable of accumulating in a UV-damaged DNA-binding protein (UV-DDB)-dependent manner to UV-damaged subnuclear domains. However, the NER factors transcription factor IIH and XPA failed to colocalize stably with the mutant XPC. As well as highlighting the importance of UV-DDB in recruiting XPC to UV-damaged sites, these findings demonstrate the role of DNA binding by XPC in the assembly of subsequent NER intermediate complexes.
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Affiliation(s)
- Gentaro Yasuda
- Biosignal Research Center, Kobe University, 1-1 Rokkodai, Kobe, Hyogo, Japan
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45
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Bunick CG, Miller MR, Fuller BE, Fanning E, Chazin WJ. Biochemical and structural domain analysis of xeroderma pigmentosum complementation group C protein. Biochemistry 2007; 45:14965-79. [PMID: 17154534 PMCID: PMC2579963 DOI: 10.1021/bi061370o] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
XPC is a 940-residue multidomain protein critical for the sensing of aberrant DNA and initiation of global genome nucleotide excision repair. The C-terminal portion of XPC (residues 492-940; XPC-C) has critical interactions with DNA, RAD23B, CETN2, and TFIIH, whereas functional roles have not yet been assigned to the N-terminal portion (residues 1-491; XPC-N). In order to analyze the molecular basis for XPC function and mutational defects associated with xeroderma pigmentosum (XP) disease, a series of stable bacterially expressed N- and C-terminal fragments were designed on the basis of sequence analysis and produced for biochemical characterization. Limited proteolysis experiments combined with mass spectrometry revealed that the full XPC-C is stable but XPC-N is not. However, a previously unrecognized folded helical structural domain was found within XPC-N, XPC(156-325). Pull-down and protease protection assays demonstrated that XPC(156-325) physically interacts with the DNA repair factor XPA, establishing the first functional role for XPC-N. XPC-C exhibits binding characteristics of the full-length protein, including stimulation of DNA binding by physical interaction with RAD23B and CETN2. Analysis of an XPC missense mutation (Trp690Ser) found in certain patients with XP disease revealed that this mutation is associated with a diminished ability to bind DNA. Evidence of contributions to protein interactions from regions in both XPC-N and XPC-C along with recently recognized homologies to yeast PNGase prompted construction of a structural model of a folded XPC core. This model offers key insights into how domains from the two portions of the protein may cooperate in generating specific XPC functions.
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Affiliation(s)
- Christopher G. Bunick
- Departments of Biochemistry and Physics and Center for Structural Biology, 5140 BIOSCI/MRBIII, Vanderbilt University, Nashville, TN 37232-8725
| | - Michael R. Miller
- Departments of Biochemistry and Physics and Center for Structural Biology, 5140 BIOSCI/MRBIII, Vanderbilt University, Nashville, TN 37232-8725
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232-8725
| | - Brian E. Fuller
- Departments of Biochemistry and Physics and Center for Structural Biology, 5140 BIOSCI/MRBIII, Vanderbilt University, Nashville, TN 37232-8725
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232-8725
| | - Ellen Fanning
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232-8725
| | - Walter J. Chazin
- Departments of Biochemistry and Physics and Center for Structural Biology, 5140 BIOSCI/MRBIII, Vanderbilt University, Nashville, TN 37232-8725
- Address correspondence to: Walter J. Chazin, Center for Structural Biology, 465 21 Ave South, 5140 BIOSCI/MRBIII, Vanderbilt University, Nashville, TN 37232-8725, Tel. 615-936-2210; Fax. 615-936-2211; E-mail:
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46
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McDaniel LD, Rivera-Begeman A, Doughty AT, Schultz RA, Friedberg EC. Validation of XP-C pathogenic variations in archival material from a live XP patient. DNA Repair (Amst) 2006; 6:115-20. [PMID: 17084680 DOI: 10.1016/j.dnarep.2006.09.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2006] [Accepted: 09/25/2006] [Indexed: 11/19/2022]
Abstract
Xeroderma pigmentosum (XP) genetic complementation group C (XP-C) is the most common form of the disease worldwide. Thirty-four distinct genetic defects have been identified in 45 XP-C patients. Further identification of such defects and the frequency of their occurrence offers the potential of generating diagnostic and prognostic molecular screening panels. Archival material (such as formalin-fixed paraffin embedded skin) may be useful for the identification of novel genetic variations and for documenting the frequency of individual genetic defects in patients who are no longer available for study. However, the use of archival material precludes direct analysis of changes in the mRNA resulting from genomic changes. The serendipitous reacquisition of an XP individual in whom genetic defects were previously characterized in archival material allowed confirmation of the defects as well as a direct analysis of the consequences of these defects on mRNA, mRNA expression and on cellular phenotypes.
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Affiliation(s)
- Lisa D McDaniel
- Laboratory of Molecular Pathology, Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9072, USA
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47
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Rivera-Begeman A, McDaniel LD, Schultz RA, Friedberg EC. A novel XPC pathogenic variant detected in archival material from a patient diagnosed with Xeroderma Pigmentosum: a case report and review of the genetic variants reported in XPC. DNA Repair (Amst) 2006; 6:100-14. [PMID: 17079196 DOI: 10.1016/j.dnarep.2006.09.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2006] [Accepted: 09/25/2006] [Indexed: 10/24/2022]
Abstract
The disease Xeroderma Pigmentosum (XP) is genetically heterogeneous and defined by pathogenic variants (formerly termed mutations) in any of eight different genes. Pathogenic variants in the XPC gene are the most commonly observed in US patients. Moreover, pathogenic variants in just four of the genes, XPA, XPC, XPD/ERCC2 and XPV/POLH account for 91% of all XP cases worldwide. In the current study, we describe the clinical, histopathologic, molecular genetic, and pathophysiological features of a 19-year-old female patient clinically diagnosed with XP as an infant. Analysis of archival material reveals a novel variation of a 13 base pair deletion in XPC exon 14 and a previously reported A>C missense pathogenic variant in the proximal splice site for XPC exon 6. Both variations induce frameshifts most likely leading to a truncated XPC protein product. Quantitative RT-PCR also revealed reduced mRNA levels in the archived specimen. Analysis of the XPA, XPD/ERCC2 and XPV/POLH genes in the current specimen failed to reveal pathologic variants. All previously reported pathogenic variants, polymorphisms and known amino acid changes for the XPC gene are compiled and described in the current nomenclature. Given the relative ease of screening for genetic variation and the potential role for such variation in human disease, a proposal for screening appropriate archival materials for alterations in the four most prevalent XP genes is presented.
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Affiliation(s)
- Amanda Rivera-Begeman
- Laboratory of Molecular Pathology, Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9072, USA
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48
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Sugasawa K. UV-induced ubiquitylation of XPC complex, the UV-DDB-ubiquitin ligase complex, and DNA repair. J Mol Histol 2006; 37:189-202. [PMID: 16858626 DOI: 10.1007/s10735-006-9044-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Accepted: 06/21/2006] [Indexed: 12/31/2022]
Abstract
The DNA nucleotide excision repair (NER) system is our major defense against carcinogenesis. Defects in NER are associated with several human genetic disorders including xeroderma pigmentosum (XP), which is characterized by a marked predisposition to skin cancer. For initiation of the repair reaction at the genome-wide level, a complex containing one of the gene products involved in XP, the XPC protein, must bind to the damaged DNA site. The UV-damaged DNA-binding protein (UV-DDB), which is impaired in XP group E patients, has also been implicated in damage recognition in global genomic NER, but its precise functions and its relationship to the XPC complex have not been elucidated. However, the recent discovery of the association of UV-DDB with a cullin-based ubiquitin ligase has functionally linked the two damage recognition factors and shed light on novel mechanistic and regulatory aspects of global genomic NER. This article summarizes our current knowledge of the properties of the XPC complex and UV-DDB and discusses possible roles for ubiquitylation in the molecular mechanisms that underlie the efficient recognition and repair of DNA damage, particularly that induced by ultraviolet light irradiation, in preventing damage-induced mutagenesis as well as carcinogenesis.
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Affiliation(s)
- Kaoru Sugasawa
- Genome Damage Response Research Unit, Discovery Research Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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49
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Chen JM, Chuzhanova N, Stenson PD, Férec C, Cooper DN. Meta-analysis of gross insertions causing human genetic disease: novel mutational mechanisms and the role of replication slippage. Hum Mutat 2006; 25:207-21. [PMID: 15643617 DOI: 10.1002/humu.20133] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although gross insertions (>20 bp) comprise <1% of disease-causing mutations, they nevertheless represent an important category of pathological lesion. In an attempt to study these insertions in a systematic way, 158 gross insertions ranging in size between 21 bp and approximately 10 kb were identified using the Human Gene Mutation Database (www.hgmd.org). A careful meta-analytical study revealed extensive diversity in terms of the nature of the inserted DNA sequence and has provided new insights into the underlying mutational mechanisms. Some 70% of gross insertions were found to represent sequence duplications of different types (tandem, partial tandem, or complex). Although most of the tandem duplications were explicable by simple replication slippage, the three complex duplications appear to result from multiple slippage events. Some 11% of gross insertions were attributable to nonpolyglutamine repeat expansions (including octapeptide repeat expansions in the prion protein gene [PRNP] and polyalanine tract expansions) and evidence is presented to support the contention that these mutations are also caused by replication slippage rather than by unequal crossing over. Some 17% of gross insertions, all >or=276 bp in length, were found to be due to LINE-1 (L1) retrotransposition involving different types of element (L1 trans-driven Alu, L1 direct, and L1 trans-driven SVA). A second example of pathological mitochondrial-nuclear sequence transfer was identified in the USH1C gene but appears to arise via a novel mechanism, trans-replication slippage. Finally, evidence for another novel mechanism of human genetic disease, involving the possible capture of DNA oligonucleotides, is presented in the context of a 26-bp insertion into the ERCC6 gene.
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Affiliation(s)
- Jian-Min Chen
- INSERM (Institut National de la Santé et de la Recherche Médicale) U613-Génétique Moléculaire et Génétique Epidémiologique, Université de Bretagne Occidentale, Centre Hospitalier Universitaire, Brest, France.
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50
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Khan SG, Oh KS, Shahlavi T, Ueda T, Busch DB, Inui H, Emmert S, Imoto K, Muniz-Medina V, Baker CC, DiGiovanna JJ, Schmidt D, Khadavi A, Metin A, Gozukara E, Slor H, Sarasin A, Kraemer KH. Reduced XPC DNA repair gene mRNA levels in clinically normal parents of xeroderma pigmentosum patients. Carcinogenesis 2005; 27:84-94. [PMID: 16081512 DOI: 10.1093/carcin/bgi204] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Xeroderma pigmentosum group C (XP-C) is a rare autosomal recessive disorder. Patients with two mutant alleles of the XPC DNA repair gene have sun sensitivity and a 1000-fold increase in skin cancers. Clinically normal parents of XP-C patients have one mutant allele and one normal allele. As a step toward evaluating cancer risk in these XPC heterozygotes we characterized cells from 16 XP families. We identified 15 causative mutations (5 frameshift, 6 nonsense and 4 splicing) in the XPC gene in cells from 16 XP probands. All had premature termination codons (PTC) and absence of normal XPC protein on western blotting. The cell lines from 26 parents were heterozygous for the same mutations. We employed a real-time quantitative reverse transcriptase-PCR assay as a rapid and sensitive method to measure XPC mRNA levels. The mean XPC mRNA levels in the cell lines from the XP-C probands were 24% (P<10(-7)) of that in 10 normal controls. This reduced XPC mRNA level in cells from XP-C patients was caused by the PTC that induces nonsense-mediated mRNA decay. The mean XPC mRNA levels in cell lines from the heterozygous XP-C carriers were intermediate (59%, P=10(-4)) between the values for the XP patients and the normal controls. This study demonstrates reduced XPC mRNA levels in XP-C patients and heterozygotes. Thus, XPC mRNA levels may be evaluated as a marker of cancer susceptibility in carriers of mutations in the XPC gene.
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Affiliation(s)
- Sikandar G Khan
- Basic Research Laboratory and Laboratory of Cellular Oncology, CCR, NCI, Bethesda, MD, USA
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