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Sharma AK, Giri AK. Engineering CRISPR/Cas9 therapeutics for cancer precision medicine. Front Genet 2024; 15:1309175. [PMID: 38725484 PMCID: PMC11079134 DOI: 10.3389/fgene.2024.1309175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 04/09/2024] [Indexed: 05/12/2024] Open
Abstract
The discovery of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) technology has revolutionized field of cancer treatment. This review explores usage of CRISPR/Cas9 for editing and investigating genes involved in human carcinogenesis. It provides insights into the development of CRISPR as a genetic tool. Also, it explores recent developments and tools available in designing CRISPR/Cas9 systems for targeting oncogenic genes for cancer treatment. Further, we delve into an overview of cancer biology, highlighting key genetic alterations and signaling pathways whose deletion prevents malignancies. This fundamental knowledge enables a deeper understanding of how CRISPR/Cas9 can be tailored to address specific genetic aberrations and offer personalized therapeutic approaches. In this review, we showcase studies and preclinical trials that show the utility of CRISPR/Cas9 in disrupting oncogenic targets, modulating tumor microenvironment and increasing the efficiency of available anti treatments. It also provides insight into the use of CRISPR high throughput screens for cancer biomarker identifications and CRISPR based screening for drug discovery. In conclusion, this review offers an overview of exciting developments in engineering CRISPR/Cas9 therapeutics for cancer treatment and highlights the transformative potential of CRISPR for innovation and effective cancer treatments.
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Affiliation(s)
- Aditya Kumar Sharma
- Department of Pathology, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Anil K. Giri
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Foundation for the Finnish Cancer Institute, Helsinki, Finland
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2
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Yang Z, Wilkinson E, Cui YH, Li H, He YY. NAT10 regulates the repair of UVB-induced DNA damage and tumorigenicity. Toxicol Appl Pharmacol 2023; 477:116688. [PMID: 37716414 PMCID: PMC10591715 DOI: 10.1016/j.taap.2023.116688] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/18/2023]
Abstract
Chemical modifications in messenger RNA (mRNA) regulate gene expression and play critical roles in stress responses and diseases. Recently we have shown that N6-methyladenosine (m6A), the most abundant mRNA modification, promotes the repair of UVB-induced DNA damage by regulating global genome nucleotide excision repair (GG-NER). However, the roles of other mRNA modifications in the UVB-induced damage response remain understudied. N4-acetylcytidine (ac4C) is deposited in mRNA by the RNA-binding acetyltransferase NAT10. This NAT10-mediated ac4C in mRNA has been reported to increase both mRNA stability and translation. However, the role of ac4C and NAT10 in the UVB-induced DNA damage response remains poorly understood. Here we show that NAT10 plays a critical role in the repair of UVB-induced DNA damage lesions through regulating the expression of the key GG-NER gene DDB2. We found that knockdown of NAT10 enhanced the repair of UVB-induced DNA damage lesions by promoting the mRNA stability of DDB2. Our findings are in contrast to the previously reported role of NAT10-mediated ac4C deposition in promoting mRNA stability and may represent a novel mechanism for ac4C in the UVB damage response. Furthermore, NAT10 knockdown in skin cancer cells decreased skin cancer cell proliferation in vitro and tumorigenicity in vivo. Chronic UVB irradiation increases NAT10 protein levels in mouse skin. Taken together, our findings demonstrate a novel role for NAT10 in the repair of UVB-induced DNA damage products by decreasing the mRNA stability of DDB2 and suggest that NAT10 is a potential novel target for preventing and treating skin cancer.
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Affiliation(s)
- Zizhao Yang
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA
| | - Emma Wilkinson
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA; Committee on Cancer Biology, University of Chicago, Chicago, IL, USA
| | - Yan-Hong Cui
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA
| | - Haixia Li
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA
| | - Yu-Ying He
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA.
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3
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Popov AA, Orishchenko KE, Naumenko KN, Evdokimov AN, Petruseva IO, Lavrik OI. A Method for Assessing the Efficiency of the Nucleotide Excision Repair System Ex Vivo. Acta Naturae 2021; 13:122-125. [PMID: 34707905 PMCID: PMC8526188 DOI: 10.32607/actanaturae.11430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 04/23/2021] [Indexed: 11/20/2022] Open
Abstract
The nucleotide excision repair (NER) is one of the main repair systems present in the cells of living organisms. It is responsible for the removal of a wide range of bulky DNA lesions. We succeeded in developing a method for assessing the efficiency of NER in the cell (ex vivo), which is a method based on the recovery of TagRFP fluorescent protein production through repair of the damage that blocks the expression of the appropriate gene. Our constructed plasmids containing bulky nFlu or nAnt lesions near the tagrfp gene promoter were shown to undergo repair in eukaryotic cells (HEK 293T) and that they can be used to analyze the efficiency of NER ex vivo. A comparative analysis of the time dependence of fluorescent cells accumulation after transfection with nFlu- and nAnt-DNA revealed that there are differences in how efficient their repair by the NER system of HEK 293T cells can be. The method can be used to assess the cell repair status and the repair efficiency of different structural damages.
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Affiliation(s)
- A. A. Popov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090 Russia
| | - K. E. Orishchenko
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090 Russia
- Novosibirsk National Research State University, Novosibirsk, 630090 Russia
| | - K. N. Naumenko
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090 Russia
| | - A. N. Evdokimov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090 Russia
| | - I. O. Petruseva
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090 Russia
| | - O. I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090 Russia
- Novosibirsk National Research State University, Novosibirsk, 630090 Russia
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4
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Schweer D, McCorkle JR, Rohr J, Tsodikov OV, Ueland F, Kolesar J. Mithramycin and Analogs for Overcoming Cisplatin Resistance in Ovarian Cancer. Biomedicines 2021; 9:70. [PMID: 33445667 PMCID: PMC7828137 DOI: 10.3390/biomedicines9010070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 12/12/2022] Open
Abstract
Ovarian cancer is a highly deadly malignancy in which recurrence is considered incurable. Resistance to platinum-based chemotherapy bodes a particularly abysmal prognosis, underscoring the need for novel therapeutic agents and strategies. The use of mithramycin, an antineoplastic antibiotic, has been previously limited by its narrow therapeutic window. Recent advances in semisynthetic methods have led to mithramycin analogs with improved pharmacological profiles. Mithramycin inhibits the activity of the transcription factor Sp1, which is closely linked with ovarian tumorigenesis and platinum-resistance. This article summarizes recent clinical developments related to mithramycin and postulates a role for the use of mithramycin, or its analog, in the treatment of platinum-resistant ovarian cancer.
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Affiliation(s)
- David Schweer
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology Lexington, University of Kentucky Markey Cancer Center, Lexington, KY 40536, USA; (D.S.); (F.U.)
| | - J. Robert McCorkle
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA; (J.R.M.); (J.R.); (O.V.T.)
| | - Jurgen Rohr
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA; (J.R.M.); (J.R.); (O.V.T.)
| | - Oleg V. Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA; (J.R.M.); (J.R.); (O.V.T.)
| | - Frederick Ueland
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology Lexington, University of Kentucky Markey Cancer Center, Lexington, KY 40536, USA; (D.S.); (F.U.)
| | - Jill Kolesar
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology Lexington, University of Kentucky Markey Cancer Center, Lexington, KY 40536, USA; (D.S.); (F.U.)
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5
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Gul S, Khan A, Raza A, Khan I, Ehtisham S. Association of XPD Lys751Gln gene polymorphism with susceptibility and clinical outcome of colorectal cancer in Pakistani population: a case-control pharmacogenetic study. Genes Genomics 2020; 42:1389-1398. [PMID: 33025549 DOI: 10.1007/s13258-020-01004-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 09/19/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND XPD Lys751Gln polymorphism may modulate inter-individual variation in repair capacity of DNA, which may enhance a person's susceptibility to develop colorectal cancer (CRC). The analysis of XPD Lys751Gln polymorphism may provide important information for identifying high-risk individuals and for selecting the most appropriate treatment for poor prognostic CRC patients. OBJECTIVE The overall objective was to find out the association of XPD Lys751Gln gene polymorphism with the risk of having a colorectal cancer and the ultimate clinical outcomes. In this study a total of 300 subjects (CRC and Controls), were genotyped for XPD Lys751Gln. METHODS Using PCR-RFLP methods, the association of XPD Lys751Gln gene polymorphism with the risk of having a colorectal cancer was studied. In addition to overall risk assessment, genotyping results were also investigated with respect to the lifestyle risk factors, patients treated with oxaliplatin-based chemotherapy and clinicopathological characteristics. RESULTS The overall correlation between the XPD Lys751Gln genetic variation and the CRC risk was observed to be significant with both the homozygous variant genotype Gln/Gln as well as heterozygous genotype Lys/Gln being associated with the increased risk of CRC. Additional stratified analyses revealed that XPD Lys751Gln variants remarkably increased risk of CRC in males and younger individuals (≤ 50 years), Naswar users (8.09-fold) and high intake of red meat. CONCLUSIONS Our findings suggest that the relationship between the XPD Lys751Gln variants and lifestyle factors modulates the risk for CRC in Pakistani population.
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Affiliation(s)
- Sumera Gul
- Department of Pharmacy, University of Swabi, Swabi, 23340, Pakistan
| | - Abad Khan
- Department of Pharmacy, University of Swabi, Swabi, 23340, Pakistan.
| | - Abida Raza
- National Institute of Laser and Optronics, Pakistan Atomic Energy Commission, Islamabad, 44000, Pakistan
| | - Ismail Khan
- Department of Pharmacy, University of Swabi, Swabi, 23340, Pakistan
| | - Shumaila Ehtisham
- Department of Statistics, Islamia College Peshawar, Peshawar, 25120, Pakistan
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6
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Protection from Ultraviolet Damage and Photocarcinogenesis by Vitamin D Compounds. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1268:227-253. [PMID: 32918222 DOI: 10.1007/978-3-030-46227-7_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Exposure of skin cells to UV radiation results in DNA damage, which if inadequately repaired, may cause mutations. UV-induced DNA damage and reactive oxygen and nitrogen species also cause local and systemic suppression of the adaptive immune system. Together, these changes underpin the development of skin tumours. The hormone derived from vitamin D, calcitriol (1,25-dihydroxyvitamin D3) and other related compounds, working via the vitamin D receptor and at least in part through endoplasmic reticulum protein 57 (ERp57), reduce cyclobutane pyrimidine dimers and oxidative DNA damage in keratinocytes and other skin cell types after UV. Calcitriol and related compounds enhance DNA repair in keratinocytes, in part through decreased reactive oxygen species, increased p53 expression and/or activation, increased repair proteins and increased energy availability in the cell when calcitriol is present after UV exposure. There is mitochondrial damage in keratinocytes after UV. In the presence of calcitriol, but not vehicle, glycolysis is increased after UV, along with increased energy-conserving autophagy and changes consistent with enhanced mitophagy. Reduced DNA damage and reduced ROS/RNS should help reduce UV-induced immune suppression. Reduced UV immune suppression is observed after topical treatment with calcitriol and related compounds in hairless mice. These protective effects of calcitriol and related compounds presumably contribute to the observed reduction in skin tumour formation in mice after chronic exposure to UV followed by topical post-irradiation treatment with calcitriol and some, though not all, related compounds.
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7
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Shah P, Zhao B, Qiang L, He YY. Phosphorylation of xeroderma pigmentosum group C regulates ultraviolet-induced DNA damage repair. Nucleic Acids Res 2019; 46:5050-5060. [PMID: 29660033 PMCID: PMC6007576 DOI: 10.1093/nar/gky239] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 03/21/2018] [Indexed: 12/18/2022] Open
Abstract
Nucleotide excision repair (NER) is the most versatile DNA repair system that removes bulky DNA damage induced by various endogenous and exogenous factors, including UV radiation. Defects in NER can lead to the xeroderma pigmentosum (XP) syndrome, mainly characterized by increased carcinogenesis in the skin. The function of NER factors, including xeroderma pigmentosum group C (XPC), can be regulated by post-translational modifications such as ubiquitination. However, the role of phosphorylation in XPC function remains unknown. Here, we show that phosphorylation of XPC acts as a novel post-translational regulatory mechanism of the NER pathway. We show that XPC is phosphorylated at serine 94. Moreover, after UVB irradiation, XPC phosphorylation regulates recruitment of ubiquitinated XPC and its downstream NER factors to the chromatin. In addition, upon evaluating the predicted kinases for XPC phosphorylation, we found that casein kinase II (CK2) promotes NER. Furthermore, CK2 kinase mediates XPC phosphorylation at serine 94, and also promotes recruitment of ubiquitinated XPC to the chromatin after UVB irradiation. Our findings have identified XPC phosphorylation as a new mechanism for regulating NER following UV-induced DNA damage.
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Affiliation(s)
- Palak Shah
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL 60637, USA.,Committee on Molecular Pathogenesis and Molecular Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Baozhong Zhao
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL 60637, USA
| | - Lei Qiang
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL 60637, USA.,School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210008, China
| | - Yu-Ying He
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL 60637, USA.,Committee on Molecular Pathogenesis and Molecular Medicine, University of Chicago, Chicago, IL 60637, USA
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8
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YwqL (EndoV), ExoA and PolA act in a novel alternative excision pathway to repair deaminated DNA bases in Bacillus subtilis. PLoS One 2019; 14:e0211653. [PMID: 30726292 PMCID: PMC6364969 DOI: 10.1371/journal.pone.0211653] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/17/2019] [Indexed: 11/19/2022] Open
Abstract
DNA deamination generates base transitions and apurinic/apyrimidinic (AP)-sites which are potentially genotoxic and cytotoxic. In Bacillus subtilis uracil can be removed from DNA by the uracil DNA-glycosylase through the base excision repair pathway. Genetic evidence suggests that B. subtilis YwqL, a homolog of Endonuclease-V (EndoV), acts on a wider spectrum of deaminated bases but the factors that complete this pathway have remained elusive. Here, we report that a purified His6-YwqL (hereafter BsEndoV) protein had in vitro endonuclease activity against double-stranded DNAs containing a single uracil (U), hypoxanthine (Hx), xanthine (X) or an AP site. Interestingly, while BsEndoV catalyzed a single strand break at the second phosphodiester bond towards the 3'-end of the U and AP lesions, there was an additional cleavage of the phosphodiester bond preceding the Hx and X lesions. Remarkably, the repair event initiated by BsEndoV on Hx and X, was completed by a recombinant B. subtilis His6-DNA polymerase A (BsPolA), but not on BsEndoV-processed U and AP lesions. For the latter lesions a second excision event performed by a recombinant B. subtilis His6-ExoA (BsExoA) was necessary before completion of their repair by BsPolA. These results suggest the existence of a novel alternative excision repair pathway in B. subtilis that counteracts the genotoxic effects of base deamination. The presence of this novel pathway in vivo in B. subtilis was also supported by analysis of effects of single or multiple deletions of exoA, endoV and polA on spontaneous mutations in growing cells, and the sensitivity of growing wild-type and mutant cells to a DNA deaminating agent.
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9
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Bommi PV, Ravindran S, Raychaudhuri P, Bagchi S. DDB2 regulates Epithelial-to-Mesenchymal Transition (EMT) in Oral/Head and Neck Squamous Cell Carcinoma. Oncotarget 2018; 9:34708-34718. [PMID: 30410671 PMCID: PMC6205178 DOI: 10.18632/oncotarget.26168] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 09/08/2018] [Indexed: 01/21/2023] Open
Abstract
DDB2 is a sensor of DNA damage and it plays an important role in Global Genomic Repair (GG-NER). Our previous studies show that DDB2 is involved in the regulation of metastasis in colon adenocarcinoma. Squamous Cell Carcinomas in the Oral/Head & Neck region (HNSCC) are particularly aggressive due to high incidence of recurrence and distant metastasis. In this study, we show that DDB2 expression is downregulated in advanced HNSCCs and loss of DDB2 expression coincides with reduced survival. Recent meta-analysis of gene expression data characterized the mesenchymal-type (EMT-type) as one most aggressive cancer cluster in HNSCC. Here, we report that DDB2 constitutively represses mRNA expression of the EMT- regulatory transcription factors SNAIL, ZEB1, and angiogenic factor VEGF in HNSCC cells. As a result, re-expression of DDB2 in metastatic cells reversed EMT with transcriptional upregulation of epithelial marker E-cadherin, and downregulation of mesenchymal markers N-cadherin, Vimentin, and Fibronectin. Interestingly, in a reverse assay, depletion of DDB2 in non-metastatic cells induced expression of the same EMT-regulatory transcription factors. TGFβs are major regulators of Snail and Zeb1, and we observed that DDB2 transcriptionally regulates expression of TGFB2 in HNSCC cells. Re-expression of DDB2 in mouse embryonic fibroblasts (MEFs) isolated from Ddb2 (-/-) knockout-mice resulted in repression of EMT-regulatory factors Zeb1, Snail and Tgfb2. Taken together, these results support the active role of DDB2 as a candidate suppressor of the EMT-process in HNSCC. Early detection leads to significantly higher survival in HNSCC and DDB2 expression in tumors can be a predictor of EMT progression.
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Affiliation(s)
- Prashant V Bommi
- Department of Oral Biology, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois, USA.,Current Address: Department of Clinical Cancer Prevention, Biological Sciences Research Building (BSRB), University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sriram Ravindran
- Department of Oral Biology, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Pradip Raychaudhuri
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Srilata Bagchi
- Department of Oral Biology, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois, USA
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10
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Pitta K, Krishnan M. Molecular Mechanism, Dynamics, and Energetics of Protein-Mediated Dinucleotide Flipping in a Mismatched DNA: A Computational Study of the RAD4-DNA Complex. J Chem Inf Model 2018; 58:647-660. [PMID: 29474070 DOI: 10.1021/acs.jcim.7b00636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
DNA damage alters genetic information and adversely affects gene expression pathways leading to various complex genetic disorders and cancers. DNA repair proteins recognize and rectify DNA damage and mismatches with high fidelity. A critical molecular event that occurs during most protein-mediated DNA repair processes is the extrusion of orphaned bases at the damaged site facilitated by specific repairing enzymes. The molecular-level understanding of the mechanism, dynamics, and energetics of base extrusion is necessary to elucidate the molecular basis of protein-mediated DNA damage repair. The present article investigates the molecular mechanism of dinucleotide extrusion in a mismatched DNA (containing a stretch of three contiguous thymidine-thymidine base pairs) facilitated by Radiation sensitive 4 (RAD4), a key DNA repair protein, on an atom-by-atom basis using molecular dynamics (MD) and umbrella-sampling (US) simulations. Using atomistic models of RAD4-free and RAD4-bound mismatched DNA, the free energy profiles associated with extrusion of mismatched partner bases are determined for both systems. The mismatched bases adopted the most stable intrahelical conformation, and their extrusion was unfavorable in RAD4-free mismatched DNA due to the presence of prohibitively high barriers (>12.0 kcal/mol) along the extrusion pathways. Upon binding of RAD4 to the DNA, the global free energy minimum is shifted to the extrahelical state indicating the key role of RAD4-DNA interactions in catalyzing the dinucleotide base extrusion in the DNA-RAD4 complex. The critical residues of RAD4 contributing to the conformational stability of the mismatched bases are identified, and the energetics of insertion of a β-hairpin of RAD4 into the DNA duplex is examined. The conformational energy landscape-based mechanistic insight into RAD4-mediated base extrusion provided here may serve as a useful baseline to understand the molecular basis of xeroderma pigmentosum C (XPC)-mediated DNA damage repair in humans.
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Affiliation(s)
- Kartheek Pitta
- Center for Computational Natural Sciences and Bioinformatics , International Institute of Information Technology , Gachibowli 500032 , Hyderabad , Telangana , India
| | - Marimuthu Krishnan
- Center for Computational Natural Sciences and Bioinformatics , International Institute of Information Technology , Gachibowli 500032 , Hyderabad , Telangana , India
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11
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Abstract
Peptide nucleic acids (PNAs) can bind duplex DNA in a sequence-targeted manner, forming a triplex structure capable of inducing DNA repair and producing specific genome modifications. Since the first description of PNA-mediated gene editing in cell free extracts, PNAs have been used to successfully correct human disease-causing mutations in cell culture and in vivo in preclinical mouse models. Gene correction via PNAs has resulted in clinically-relevant functional protein restoration and disease improvement, with low off-target genome effects, indicating a strong therapeutic potential for PNAs in the treatment or cure of genetic disorders. This review discusses the progress that has been made in developing PNAs as an effective, targeted agent for gene editing, with an emphasis on recent in vivo, nanoparticle-based strategies.
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12
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Lawania S, Singh N, Behera D, Sharma S. Association of XPA Polymorphisms Towards Lung Cancer Susceptibility and its Predictive Role in Overall Survival of North Indians. Biochem Genet 2018. [PMID: 29516319 DOI: 10.1007/s10528-018-9850-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The present study investigated the role of Xeroderma pigmentosum group A (XPA) polymorphism (A23G and G709A) with lung cancer risk and its association with overall survival in North Indians. 370 cases and 370 controls were investigated to evaluate association between XPA polymorphism (A23G and G709A) with lung cancer risk using logistic regression analysis. A follow-up study was also conducted for 291 lung cancer cases illustrating correlation between overall survival in lung cancer patients and XPA variants. GG genotype showed an increased lung cancer risk (p = 0.0007) for A23G polymorphism whereas G709A polymorphism was associated with significant protective effect in heterozygous (AG) subjects (p = 0.001). When stratified according to smoking status an increased risk for lung cancer was observed for GG genotype in A23G polymorphism (p = 0.0002). A poor survival in females carrying variant genotype (GG) was observed (p = 0.001; MST = 4.16 months) for A23G polymorphism. Adenocarcinoma patients with heterozygous genotype showed an increased hazard ratio (p = 0.02) for A23G polymorphism. G709A was associated with a reduced hazard ratio marking a better survival among mutant females (HR 0.17; p = 0.05; MST = 18.63 months). It can be concluded that A23G polymorphism might contribute to increased lung cancer risk in North Indian population emphasizing on poor survival among females. G709A polymorphism might result in protective effect in lung cancer subjects. The present study had a low sample size but it could act as reference for the large sample studies in future.
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Affiliation(s)
- Shweta Lawania
- Department of Biotechnology, Thapar University, Patiala, Punjab, 147002, India
| | - Navneet Singh
- Department of Pulmonary Medicine, Post Graduate Institute of Medical Education & Research (PGIMER), Sector 14, Chandigarh, India
| | - Digambar Behera
- Department of Pulmonary Medicine, Post Graduate Institute of Medical Education & Research (PGIMER), Sector 14, Chandigarh, India
| | - Siddharth Sharma
- Department of Biotechnology, Thapar University, Patiala, Punjab, 147002, India.
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13
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Wada T, Fukuda T, Shimomura M, Inoue Y, Kawanishi M, Tasaka R, Yasui T, Ikeda K, Sumi T. XPA expression is a predictive marker of the effectiveness of neoadjuvant chemotherapy for locally advanced uterine cervical cancer. Oncol Lett 2018; 15:3766-3771. [PMID: 29556276 DOI: 10.3892/ol.2018.7810] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 12/11/2017] [Indexed: 12/12/2022] Open
Abstract
The standard treatment for locally advanced uterine cervical cancer is concurrent chemoradiotherapy. Successful neoadjuvant chemotherapy (NAC) may reduce tumor size and facilitate a hysterectomy, thereby improving the prognosis for patients with locally advanced cervical cancer. In contrast, unsuccessful NAC may worsen the prognosis because if a hysterectomy is not possible, the change in treatment plan may delay the initiation of core treatment. Therefore, there is a need to identify biomarkers that predict the efficacy of NAC in patients with uterine cervical cancer. The xeroderma pigmentosum complementation group A (XPA) protein serves a major role in nucleotide excision repair, which is a key DNA damage response pathway involved in cisplatin resistance. In the present study, the association between XPA expression in tumor tissue and the efficacy of NAC for locally advanced uterine cervical cancer was investigated. Data from 56 patients aged <70 years with locally advanced uterine cervical cancer (FIGO stages IIIA or IIIB) who were classified into two groups based on effective (n=31) and ineffective (n=25) responses to NAC treatment was evaluated. Tumor tissue samples were obtained by punch biopsy prior to NAC and XPA expression was examined immunohistochemically and scored using a weighted scoring system. In addition, the effects of RNA interference-mediated downregulation of XPA on the cisplatin sensitivity of uterine cervical cancer cells was investigated in vitro. It was revealed that the NAC effective group had significantly lower weighted XPA scores than the NAC ineffective group (P=0.001). Similarly, low tumor expression of XPA was significantly associated with higher sensitivity to NAC (P=0.001). Additionally, the downregulation of XPA expression in cervical cancer cells significantly increased their sensitivity to cisplatin in vitro. The results of the present study suggest that low XPA expression may be a predictive biomarker of NAC efficacy for patients with locally advanced uterine cervical cancer, which may be helpful for improving their prognosis.
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Affiliation(s)
- Takuma Wada
- Department of Obstetrics and Gynecology, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan.,Department of Anatomy and Regenerative Biology, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan
| | - Takeshi Fukuda
- Department of Obstetrics and Gynecology, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan
| | - Masahiro Shimomura
- Department of Obstetrics and Gynecology, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan
| | - Yuta Inoue
- Department of Obstetrics and Gynecology, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan
| | - Masaru Kawanishi
- Department of Obstetrics and Gynecology, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan
| | - Reiko Tasaka
- Department of Obstetrics and Gynecology, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan
| | - Tomoyo Yasui
- Department of Obstetrics and Gynecology, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan
| | - Kazuo Ikeda
- Department of Anatomy and Regenerative Biology, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan
| | - Toshiyuki Sumi
- Department of Obstetrics and Gynecology, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan
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14
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Shah P, Qiang L, Yang S, Soltani K, He YY. Regulation of XPC deubiquitination by USP11 in repair of UV-induced DNA damage. Oncotarget 2017; 8:96522-96535. [PMID: 29228550 PMCID: PMC5722502 DOI: 10.18632/oncotarget.22105] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/13/2017] [Indexed: 12/31/2022] Open
Abstract
Nucleotide excision repair (NER) is the most versatile DNA repair pathway for removing DNA damage caused by UV radiation and many environmental carcinogens. NER is essential for suppressing tumorigenesis in the skin, lungs and brain. Although the core NER proteins have been identified and characterized, molecular regulation of NER remains poorly understood. Here we show that ubiquitin-specific peptidase 11 (USP11) positively regulates NER by deubiquitinating xeroderma pigmentosum complementation group C (XPC) and promoting its retention at the DNA damage sites. In addition, UV irradiation induces both USP11 recruitment to the chromatin and USP11 interaction with XPC in an XPC-ubiquitination-dependent manner. Furthermore, we found that USP11 is down-regulated in chronically UV-exposed mouse skin and in skin tumors from mice and humans. Our findings indicate that USP11 plays an important role in maintaining NER capacity, and suggest that USP11 acts as a tumor suppressor via its role in DNA repair.
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Affiliation(s)
- Palak Shah
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA
- Committee on Molecular Pathogenesis and Molecular Medicine, University of Chicago, Chicago, IL, USA
| | - Lei Qiang
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA
| | - Seungwon Yang
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA
| | - Keyoumars Soltani
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA
| | - Yu-Ying He
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA
- Committee on Molecular Pathogenesis and Molecular Medicine, University of Chicago, Chicago, IL, USA
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15
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Feki-Tounsi M, Khlifi R, Louati I, Fourati M, Mhiri MN, Hamza-Chaffai A, Rebai A. Polymorphisms in XRCC1, ERCC2, and ERCC3 DNA repair genes, CYP1A1 xenobiotic metabolism gene, and tobacco are associated with bladder cancer susceptibility in Tunisian population. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:22476-22484. [PMID: 28803404 DOI: 10.1007/s11356-017-9767-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 07/12/2017] [Indexed: 06/07/2023]
Abstract
Other than the established environmental risk factors associated with bladder cancer (BC), little is known about the genetic variations determining the individual susceptibility of this complex disease. This study aimed to investigate the relationship of BC with environmental agents and polymorphisms in XRCC1, ERCC2, and ERCC3 DNA repair genes and CYP1A1, CYP2D6, NAT1, and NAT2 xenobiotic metabolism genes through a hospital-based case-control study in Tunisia. The selection of the single nucleotide polymorphisms (SNPs) (rs25487, rs 13181, rs415407, rs446421, rs1058172, rs4921880, and rs1208) was performed using the dbSNP database. DNA genotyping was determined by PCR-RFLP after DNA extraction from whole blood. The risks of BC associated with every polymorphism as well as the studied environmental factors were estimated by multivariate-adjusted logistic regression using R software. In addition, gene-gene interactions were analyzed using generalized multifactor dimensionality reduction (GMDR) methods. Results showed that tobacco smoking and chewing parameters were significantly associated with BC risk. Single-gene variant analysis showed significant associations of the TT genotype of CYP1A1 and the rare GG genotype of ERCC2 with bladder cancer susceptibility (OR = 1.34, 95% CI 1.22-1.40, P < 0.0001). According to GMDR analysis, our findings indicated a significant association between BC and gene-gene interaction among the CYP1A1, ERCC3, and XRCC1. The present results suggest a potential role of XRCC1, ERCC2, ERCC3, and CYP1A1 besides tobacco intake in susceptibility to BC.
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Affiliation(s)
- Molka Feki-Tounsi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, Po Box 1177, 3018, Sfax, Tunisia.
- Unit of Marine and Environmental Toxicology, UR 09-03, Sfax University, IPEIS, BP 1172, 3018, Sfax, Tunisia.
| | - Rim Khlifi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, Po Box 1177, 3018, Sfax, Tunisia
- Unit of Marine and Environmental Toxicology, UR 09-03, Sfax University, IPEIS, BP 1172, 3018, Sfax, Tunisia
| | - Ibtihel Louati
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, Po Box 1177, 3018, Sfax, Tunisia
| | - Mohamed Fourati
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, Po Box 1177, 3018, Sfax, Tunisia
- Unit of Marine and Environmental Toxicology, UR 09-03, Sfax University, IPEIS, BP 1172, 3018, Sfax, Tunisia
- Department of Urology, Habib Bourguiba Hospital, Sfax, Tunisia
| | | | - Amel Hamza-Chaffai
- Unit of Marine and Environmental Toxicology, UR 09-03, Sfax University, IPEIS, BP 1172, 3018, Sfax, Tunisia
| | - Ahmed Rebai
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, Po Box 1177, 3018, Sfax, Tunisia
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16
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Murata Y, Osakabe M. Photo-enzymatic repair of UVB-induced DNA damage in the two-spotted spider mite Tetranychus urticae. EXPERIMENTAL & APPLIED ACAROLOGY 2017; 71:15-34. [PMID: 27873138 DOI: 10.1007/s10493-016-0100-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 11/10/2016] [Indexed: 06/06/2023]
Abstract
Ambient ultraviolet-B (UVB) radiation induces lethal effects in the two-spotted spider mite Tetranychus urticae, whereas photoreactivation by irradiation with ultraviolet-A and visible light (VIS) plays an important role to increase survival of mites irradiated by UVB. The physiological mechanisms and ecological significance of photoreactivation in terrestrial arthropods have not been shown clearly. We verified the biological impact and accumulation of DNA lesions by UVB irradiation and the repair of them by photoreactivation in T. urticae larvae. Survival of UVB-irradiated larvae decreased with increasing UVB dose, but recovered remarkably with VIS exposure after UVB irradiation (photoreactivation). The DNA lesions, cyclobutane pyrimidine dimers (CPDs) and 6-4 pyrimidine-pyrimidine photoproducts (6-4PPs) linearly increased with the UVB dose. The CPDs were repaired after exposure to VIS, whereas the frequency of 6-4PPs was unaffected by VIS; CPD photolyase genes, but not (6-4) photolyase genes, have been found in the T. urticae genome. Therefore, DNA damage and CPD photo enzymatic repair (PER) is significant for survival in this mite under ambient UVB radiation. Unexpectedly, gene expression of CPD photolyase was unaffected by irradiation with UVB and VIS. Instead, expression of xeroderma pigmentosum A (XPA) was increased by irradiation. XPA is a core factor in nucleotide excision repair (NER), which is a repair system unrelated to photo energy. The relationship between gene expression and enzymatic repair remains unclear. To elucidate the PER process in T. urticae, further study will be necessary on the gene expression patterns and molecular functions of CPD photolyase in PER and of XPA in NER.
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Affiliation(s)
- Yasumasa Murata
- Laboratory of Ecological Information, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
| | - Masahiro Osakabe
- Laboratory of Ecological Information, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
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17
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Roy S. Impact of UV Radiation on Genome Stability and Human Health. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 996:207-219. [DOI: 10.1007/978-3-319-56017-5_17] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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18
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Khlifi R, Olmedo P, Gil F, Hammami B, Hamza-Chaffai A, Rebai A. Gene-environment interactions between ERCC2, ERCC3, XRCC1 and cadmium exposure in nasal polyposis disease. J Appl Genet 2016; 58:221-229. [PMID: 27838878 DOI: 10.1007/s13353-016-0375-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 11/01/2016] [Accepted: 11/03/2016] [Indexed: 11/27/2022]
Abstract
Gene-environment interactions have long been known to play an important role in complex disease aetiology, such as nasal polyposis (NP). The present study supports the concept that DNA repair gene polymorphisms play critical roles in modifying individual susceptibility to environmental diseases. In fact, we investigated the role of polymorphisms in DNA repair genes and cadmium as risk factors for Tunisian patients with NP. To the best of our knowledge, this is the first report on the impact of combined effects of cadmium and ERCC3 7122 A>G (rs4150407), ERCC2 Lys751Gln (rs13181) and XRCC1 Arg399Gln (rs25487) genes in the susceptibility to NP disease. Significant associations between the risk of developing NP disease and ERCC2 [odds ratio (OR) = 2.0, 95 % confidence interval (CI) = 1.1-3.7, p = 0.023] and ERCC3 (OR = 2.2, 95 % CI = 1.2-4.1, p = 0.013) genotypes polymorphisms were observed. Blood concentrations of Cd in NP patients (2.2 μg/L) were significantly higher than those of controls (0.5 μg/L). A significant interaction between ERCC3 (7122 A>G) polymorphism and blood-Cd levels (for the median of blood-Cd levels: OR = 3.8, 95 % CI = 1.3-10.8, p = 0.014 and for the 75th percentiles of blood-Cd levels: OR = 2.7, 95 % CI = 1.1-7.2, p = 0.041) was found in association with the risk of NP disease. In addition, when we stratified ERCC2, ERCC3 and XRCC1 polymorphism genotypes by the median and 75th percentiles of blood-Cd levels, we found also significant interactions between ERCC2 (Lys751Gln) and ERCC3 (7122 A>G) genotypes polymorphism and this metal in association with NP disease. However, no interaction was found between XRCC1 (Arg399Gln) polymorphism genotypes and Cd in association with NP disease.
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Affiliation(s)
- Rim Khlifi
- Unit of Marine and Environmental Toxicology, UR 09-03, Institut Préparatoire aux Etudes d'Ingénieur de Sfax (IPEIS), Sfax, Tunisia.
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, Sfax, Tunisia.
| | - Pablo Olmedo
- Department of Legal Medicine and Toxicology, University of Granada, Granada, Spain
| | - Fernando Gil
- Department of Legal Medicine and Toxicology, University of Granada, Granada, Spain
| | - Boutheina Hammami
- Department of Otorhinolaryngology, Habib Bourguiba Hospital, Sfax, Tunisia
| | - Amel Hamza-Chaffai
- Unit of Marine and Environmental Toxicology, UR 09-03, Institut Préparatoire aux Etudes d'Ingénieur de Sfax (IPEIS), Sfax, Tunisia
| | - Ahmed Rebai
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, Sfax, Tunisia
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19
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Transcriptional and Posttranslational Regulation of Nucleotide Excision Repair: The Guardian of the Genome against Ultraviolet Radiation. Int J Mol Sci 2016; 17:ijms17111840. [PMID: 27827925 PMCID: PMC5133840 DOI: 10.3390/ijms17111840] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 10/31/2016] [Accepted: 11/01/2016] [Indexed: 11/24/2022] Open
Abstract
Ultraviolet (UV) radiation from sunlight represents a constant threat to genome stability by generating modified DNA bases such as cyclobutane pyrimidine dimers (CPD) and pyrimidine-pyrimidone (6-4) photoproducts (6-4PP). If unrepaired, these lesions can have deleterious effects, including skin cancer. Mammalian cells are able to neutralize UV-induced photolesions through nucleotide excision repair (NER). The NER pathway has multiple components including seven xeroderma pigmentosum (XP) proteins (XPA to XPG) and numerous auxiliary factors, including ataxia telangiectasia and Rad3-related (ATR) protein kinase and RCC1 like domain (RLD) and homologous to the E6-AP carboxyl terminus (HECT) domain containing E3 ubiquitin protein ligase 2 (HERC2). In this review we highlight recent data on the transcriptional and posttranslational regulation of NER activity.
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20
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Kamarthapu V, Epshtein V, Benjamin B, Proshkin S, Mironov A, Cashel M, Nudler E. ppGpp couples transcription to DNA repair in E. coli. Science 2016; 352:993-6. [PMID: 27199428 DOI: 10.1126/science.aad6945] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 04/07/2016] [Indexed: 12/29/2022]
Abstract
The small molecule alarmone (p)ppGpp mediates bacterial adaptation to nutrient deprivation by altering the initiation properties of RNA polymerase (RNAP). ppGpp is generated in Escherichia coli by two related enzymes, RelA and SpoT. We show that ppGpp is robustly, but transiently, induced in response to DNA damage and is required for efficient nucleotide excision DNA repair (NER). This explains why relA-spoT-deficient cells are sensitive to diverse genotoxic agents and ultraviolet radiation, whereas ppGpp induction renders them more resistant to such challenges. The mechanism of DNA protection by ppGpp involves promotion of UvrD-mediated RNAP backtracking. By rendering RNAP backtracking-prone, ppGpp couples transcription to DNA repair and prompts transitions between repair and recovery states.
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Affiliation(s)
- Venu Kamarthapu
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA. Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Vitaly Epshtein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Bradley Benjamin
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Sergey Proshkin
- Engelhardt Institute of Molecular Biology, Russian Academy of Science, Moscow 119991, Russia
| | - Alexander Mironov
- Engelhardt Institute of Molecular Biology, Russian Academy of Science, Moscow 119991, Russia
| | - Michael Cashel
- Division of Developmental Biology, Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA. Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA.
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21
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Wirth N, Gross J, Roth HM, Buechner CN, Kisker C, Tessmer I. Conservation and Divergence in Nucleotide Excision Repair Lesion Recognition. J Biol Chem 2016; 291:18932-46. [PMID: 27405761 DOI: 10.1074/jbc.m116.739425] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Indexed: 11/06/2022] Open
Abstract
Nucleotide excision repair is an important and highly conserved DNA repair mechanism with an exceptionally large range of chemically and structurally unrelated targets. Lesion verification is believed to be achieved by the helicases UvrB and XPD in the prokaryotic and eukaryotic processes, respectively. Using single molecule atomic force microscopy analyses, we demonstrate that UvrB and XPD are able to load onto DNA and pursue lesion verification in the absence of the initial lesion detection proteins. Interestingly, our studies show different lesion recognition strategies for the two functionally homologous helicases, as apparent from their distinct DNA strand preferences, which can be rationalized from the different structural features and interactions with other nucleotide excision repair protein factors of the two enzymes.
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Affiliation(s)
- Nicolas Wirth
- From the Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080 Würzburg, Germany
| | - Jonas Gross
- From the Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080 Würzburg, Germany
| | - Heide M Roth
- From the Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080 Würzburg, Germany
| | - Claudia N Buechner
- From the Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080 Würzburg, Germany
| | - Caroline Kisker
- From the Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080 Würzburg, Germany
| | - Ingrid Tessmer
- From the Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080 Würzburg, Germany
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22
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Single nucleotide polymorphisms in DNA repair genes and putative cancer risk. Arch Toxicol 2016; 90:2369-88. [PMID: 27334373 DOI: 10.1007/s00204-016-1771-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 06/15/2016] [Indexed: 02/07/2023]
Abstract
Single nucleotide polymorphisms (SNPs) are the most frequent type of genetic alterations between individuals. An SNP located within the coding sequence of a gene may lead to an amino acid substitution and in turn might alter protein function. Such a change in protein sequence could be functionally relevant and therefore might be associated with susceptibility to human diseases, such as cancer. DNA repair mechanisms are known to play an important role in cancer development, as shown in various human cancer syndromes, which arise due to mutations in DNA repair genes. This leads to the question whether subtle genetic changes such as SNPs in DNA repair genes may contribute to cancer susceptibility. In numerous epidemiological studies, efforts have been made to associate specific SNPs in DNA repair genes with altered DNA repair and cancer. The present review describes some of the common and most extensively studied SNPs in DNA repair genes and discusses whether they are functionally relevant and subsequently increase the likelihood that cancer will develop.
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23
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Knips A, Zacharias M. Influence of a cis,syn-cyclobutane pyrimidine dimer damage on DNA conformation studied by molecular dynamics simulations. Biopolymers 2016; 103:215-22. [PMID: 25382106 DOI: 10.1002/bip.22586] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 11/03/2014] [Indexed: 02/01/2023]
Abstract
The photo-induced formation of cis-syn-cyclobutane pyrimidine dimers (CPD) is a highly mutagenic and cancerogenic DNA lesion. In bacteria photolyases can efficiently reverse the dimer formation employing a light-driven reaction after looping out the CPD damaged bases into the enzyme active site. The exact mechanism how the repair enzyme identifies a damaged site within a large surplus of undamaged DNA is not fully understood. The CPD damage may alter the DNA structure and dynamics already in the absence of the repair enzyme which can facilitate the initial binding of a photolyase repair enzyme. To characterize the effect of a CPD damage, extensive comparative molecular dynamics (MD) simulations on duplex DNA with central regular or CPD damaged nucleotides were performed supplemented with simulations of the DNA-photolyase complex. Although no spontaneous flipping out transitions of the damaged bases were observed, the simulations showed significant differences in the conformational states of regular and CPD damage DNA. The isolated damaged DNA adopted transient conformations which resembled the global shape of the repair enzyme bound conformation more closely compared to regular B-DNA. In particular, these conformational changes were observed in most of helical and structural parameters where the protein bound DNA differs drastically from regular B-DNA. It is likely that the transient overlap of isolated DNA with the enzyme bound DNA conformation plays a decisive role for the specific and rapid initial recognition by the repair enzyme prior to the looping out process of the damaged DNA.
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Affiliation(s)
- Alexander Knips
- Physik-Department T38, Technische Universität München, James-Franck-Str. 1, D-85748, Garching, Germany
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24
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Murray HC, Maltby VE, Smith DW, Bowden NA. Nucleotide excision repair deficiency in melanoma in response to UVA. Exp Hematol Oncol 2016; 5:6. [PMID: 26913219 PMCID: PMC4765239 DOI: 10.1186/s40164-016-0035-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/13/2016] [Indexed: 11/29/2022] Open
Abstract
Background The causative link between UV exposure and melanoma development is well known, however the mechanistic relationship remains incompletely characterised. UVA and UVB components of sunlight are implicated in melanomagenesis; however the majority of studies have focused on the effects of UVB and UVC light. Interestingly, melanoma tumour sequencing has revealed an overrepresentation of mutations signature of unrepaired UV-induced DNA damage. Repair of UVA-induced DNA damage is thought to occur primarily through the Nucleotide Excision Repair (NER) pathway, which recognises and repairs damage either coupled to transcription (Transcription Coupled Repair; TCR), or through global genome scanning (Global Genome Repair; GGR). Current literature suggests NER is deficient in melanoma, however the cause of this remains unknown; and whether reduced NER activity in response to UVA may be involved in melanoma development remains uncharacterised. In this study we aimed to determine if melanoma cells exhibit reduced levels of NER activity in response to UVA. Methods Melanocyte and melanoma cell lines were UVA-irradiated, and DNA damage levels assessed by immunodetection of Cyclobutane Pyrimidine Dimer (CPD) and (6-4) Photoproduct [(6-4)PP] lesions. Expression of NER pathway components and p53 following UVA treatment was quantified by qPCR and western blot. Results UVA did not induce detectable induction of (6-4)PP lesions, consistent with previous studies. Repair of CPDs induced by UVA was initiated at 4 h and complete within 48 h in normal melanocytes, whereas repair initiation was delayed to 24 h and >40 % of lesions remained in melanoma cell lines at 48 h. This was coupled with a delayed and reduced induction of GGR component XPC in melanoma cells, independent of p53. Conclusion These findings support that NER activity is reduced in melanoma cells due to deficient GGR. Further investigation into the role of NER in UVA-induced melanomagenesis is warranted and may have implications for melanoma treatment.
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Affiliation(s)
- Heather C Murray
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Hunter Medical Research Institute, University Dr, Callaghan, NSW 2308 Australia
| | - Vicki E Maltby
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Hunter Medical Research Institute, University Dr, Callaghan, NSW 2308 Australia
| | - Doug W Smith
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Hunter Medical Research Institute, University Dr, Callaghan, NSW 2308 Australia
| | - Nikola A Bowden
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Hunter Medical Research Institute, University Dr, Callaghan, NSW 2308 Australia
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25
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Abstract
Nucleotide excision repair (NER) is a highly versatile and efficient DNA repair process, which is responsible for the removal of a large number of structurally diverse DNA lesions. Its extreme broad substrate specificity ranges from DNA damages formed upon exposure to ultraviolet radiation to numerous bulky DNA adducts induced by mutagenic environmental chemicals and cytotoxic drugs used in chemotherapy. Defective NER leads to serious diseases, such as xeroderma pigmentosum (XP). Eight XP complementation groups are known of which seven (XPA-XPG) are caused by mutations in genes involved in the NER process. The eighth gene, XPV, codes for the DNA polymerase ɳ, which replicates through DNA lesions in a process called translesion synthesis (TLS). Over the past decade, detailed structural information of these DNA repair proteins involved in eukaryotic NER and TLS have emerged. These structures allow us now to understand the molecular mechanism of the NER and TLS processes in quite some detail and we have begun to understand the broad substrate specificity of NER. In this review, we aim to highlight recent advances in the process of damage recognition and repair as well as damage tolerance by the XP proteins.
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26
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Kumar A, Beloglazova N, Bundalovic-Torma C, Phanse S, Deineko V, Gagarinova A, Musso G, Vlasblom J, Lemak S, Hooshyar M, Minic Z, Wagih O, Mosca R, Aloy P, Golshani A, Parkinson J, Emili A, Yakunin AF, Babu M. Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli. Cell Rep 2016; 14:648-661. [PMID: 26774489 DOI: 10.1016/j.celrep.2015.12.060] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 11/08/2015] [Accepted: 12/10/2015] [Indexed: 11/27/2022] Open
Abstract
As antibiotic resistance is increasingly becoming a public health concern, an improved understanding of the bacterial DNA damage response (DDR), which is commonly targeted by antibiotics, could be of tremendous therapeutic value. Although the genetic components of the bacterial DDR have been studied extensively in isolation, how the underlying biological pathways interact functionally remains unclear. Here, we address this by performing systematic, unbiased, quantitative synthetic genetic interaction (GI) screens and uncover widespread changes in the GI network of the entire genomic integrity apparatus of Escherichia coli under standard and DNA-damaging growth conditions. The GI patterns of untreated cultures implicated two previously uncharacterized proteins (YhbQ and YqgF) as nucleases, whereas reorganization of the GI network after DNA damage revealed DDR roles for both annotated and uncharacterized genes. Analyses of pan-bacterial conservation patterns suggest that DDR mechanisms and functional relationships are near universal, highlighting a modular and highly adaptive genomic stress response.
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Affiliation(s)
- Ashwani Kumar
- Department of Computer Science, University of Regina, Regina, SK S4S 0A2, Canada
| | - Natalia Beloglazova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - Cedoljub Bundalovic-Torma
- Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G OX4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Sadhna Phanse
- Terrence Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Viktor Deineko
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Alla Gagarinova
- Terrence Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Biochemistry, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Gabriel Musso
- Department of Medicine, Harvard Medical School and Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - James Vlasblom
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Sofia Lemak
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - Mohsen Hooshyar
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Zoran Minic
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Omar Wagih
- Terrence Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Roberto Mosca
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, c/Baldiri i Reixac 10-12, Barcelona, 08028, Catalonia, Spain
| | - Patrick Aloy
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, c/Baldiri i Reixac 10-12, Barcelona, 08028, Catalonia, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, Barcelona, 08010, Catalonia, Spain
| | - Ashkan Golshani
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - John Parkinson
- Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G OX4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Andrew Emili
- Terrence Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada.
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Nadkarni A, Burns JA, Gandolfi A, Chowdhury MA, Cartularo L, Berens C, Geacintov NE, Scicchitano DA. Nucleotide Excision Repair and Transcription-coupled DNA Repair Abrogate the Impact of DNA Damage on Transcription. J Biol Chem 2016; 291:848-61. [PMID: 26559971 PMCID: PMC4705403 DOI: 10.1074/jbc.m115.685271] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/23/2015] [Indexed: 11/06/2022] Open
Abstract
DNA adducts derived from carcinogenic polycyclic aromatic hydrocarbons like benzo[a]pyrene (B[a]P) and benzo[c]phenanthrene (B[c]Ph) impede replication and transcription, resulting in aberrant cell division and gene expression. Global nucleotide excision repair (NER) and transcription-coupled DNA repair (TCR) are among the DNA repair pathways that evolved to maintain genome integrity by removing DNA damage. The interplay between global NER and TCR in repairing the polycyclic aromatic hydrocarbon-derived DNA adducts (+)-trans-anti-B[a]P-N(6)-dA, which is subject to NER and blocks transcription in vitro, and (+)-trans-anti-B[c]Ph-N(6)-dA, which is a poor substrate for NER but also blocks transcription in vitro, was tested. The results show that both adducts inhibit transcription in human cells that lack both NER and TCR. The (+)-trans-anti-B[a]P-N(6)-dA lesion exhibited no detectable effect on transcription in cells proficient in NER but lacking TCR, indicating that NER can remove the lesion in the absence of TCR, which is consistent with in vitro data. In primary human cells lacking NER, (+)-trans-anti-B[a]P-N(6)-dA exhibited a deleterious effect on transcription that was less severe than in cells lacking both pathways, suggesting that TCR can repair the adduct but not as effectively as global NER. In contrast, (+)-trans-anti-B[c]Ph-N(6)-dA dramatically reduces transcript production in cells proficient in global NER but lacking TCR, indicating that TCR is necessary for the removal of this adduct, which is consistent with in vitro data showing that it is a poor substrate for NER. Hence, both global NER and TCR enhance the recovery of gene expression following DNA damage, and TCR plays an important role in removing DNA damage that is refractory to NER.
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Affiliation(s)
- Aditi Nadkarni
- From the Departments of Biology and Chemistry, New York University, New York, New York 10003
| | - John A Burns
- From the Departments of Biology and Chemistry, New York University, New York, New York 10003
| | - Alberto Gandolfi
- the Dipartimento di Matematica e Informatica "Ulisse Dini," Università di Firenze, 50134 Firenze, Italy, the Division of Science, New York University Abu Dhabi, Post Office Box 129188, Abu Dhabi, United Arab Emirates
| | - Moinuddin A Chowdhury
- From the Departments of Biology and Chemistry, New York University, New York, New York 10003
| | - Laura Cartularo
- From the Departments of Biology and Chemistry, New York University, New York, New York 10003
| | - Christian Berens
- the Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Jena, Germany, 07743, and
| | - Nicholas E Geacintov
- From the Departments of Biology and Chemistry, New York University, New York, New York 10003
| | - David A Scicchitano
- From the Departments of Biology and Chemistry, New York University, New York, New York 10003, the Division of Science, New York University Abu Dhabi, Post Office Box 129188, Abu Dhabi, United Arab Emirates
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Jiao F, Qian P, Qin Y, Xia Y, Deng C, Nie Z. A novel and label-free biosensors for uracil-DNA glycosylase activity based on the electrochemical oxidation of guanine bases at the graphene modified electrode. Talanta 2015; 147:98-102. [PMID: 26592582 DOI: 10.1016/j.talanta.2015.09.045] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 09/13/2015] [Accepted: 09/18/2015] [Indexed: 01/30/2023]
Abstract
Uracil-DNA glycosylase (UDG) as an important base excision repair enzymes is widely distributed in organism, and it plays a crucial role in sustaining the genome integrity. Therefore, it is significant to carry out the analysis of UDG activity. In this present work, a novel and label-free electrochemical sensing platform for the sensitive detection of uracil DNA glycosylase (UDG) activity has been developed. Herein, the graphene modified glassy carbon (GC) electrode was prepared. And two complementary DNA strands were hybridized to form dsDNA (P1P2). In the presence of UDG, the uracil bases in P1P2 were specifically hydrolyzed, inducing the unwinding of the DNA duplex, and accompanied by the release of P1. Thus, the released P1 was adsorbed onto the graphene/GC electrode surface via π-π stacking. By investigating the electrochemical behavior of P1 at the graphene/GC electrode, the electrochemical oxidation of guanine bases in P1 was obviously observed. Therefore, using the current responses of guanine base in P1 as a signal indicator, UDG activity can be simply determined with high sensitivity, and the detectable lowest concentration is 0.01U/mL. This present design does not need covalent attachment of redox indicator to DNA, preventing participation of redox labels in the background. Meanwhile, the proposed strategy for the assay of UDG activity also has a remarkable sensitivity due to the excellent properties of graphene, which could increase both the immobilization amount of released ssDNA and the conductivity of the sensing system. All these elucidate that this developed protocol may lay a potential foundation for the sensitive detection of UDG activity in clinical diagnosis.
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Affiliation(s)
- Feipeng Jiao
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, PR China
| | - Pin Qian
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, PR China
| | - Yun Qin
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, PR China
| | - Yalin Xia
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Chunyan Deng
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, PR China.
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China.
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Abstract
XPC has long been considered instrumental in DNA damage recognition during global genome nucleotide excision repair (GG-NER). While this recognition is crucial for organismal health and survival, as XPC's recognition of lesions stimulates global genomic repair, more recent lines of research have uncovered many new non-canonical pathways in which XPC plays a role, such as base excision repair (BER), chromatin remodeling, cell signaling, proteolytic degradation, and cellular viability. Since the first discovery of its yeast homolog, Rad4, the involvement of XPC in cellular regulation has expanded considerably. Indeed, our understanding appears to barely scratch the surface of the incredible potential influence of XPC on maintaining proper cellular function. Here, we first review the canonical role of XPC in lesion recognition and then explore the new world of XPC function.
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Temiz NA, Donohue DE, Bacolla A, Vasquez KM, Cooper DN, Mudunuri U, Ivanic J, Cer RZ, Yi M, Stephens RM, Collins JR, Luke BT. The somatic autosomal mutation matrix in cancer genomes. Hum Genet 2015; 134:851-64. [PMID: 26001532 PMCID: PMC4495249 DOI: 10.1007/s00439-015-1566-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 05/12/2015] [Indexed: 01/26/2023]
Abstract
DNA damage in somatic cells originates from both environmental and endogenous sources, giving rise to mutations through multiple mechanisms. When these mutations affect the function of critical genes, cancer may ensue. Although identifying genomic subsets of mutated genes may inform therapeutic options, a systematic survey of tumor mutational spectra is required to improve our understanding of the underlying mechanisms of mutagenesis involved in cancer etiology. Recent studies have presented genome-wide sets of somatic mutations as a 96-element vector, a procedure that only captures the immediate neighbors of the mutated nucleotide. Herein, we present a 32 × 12 mutation matrix that captures the nucleotide pattern two nucleotides upstream and downstream of the mutation. A somatic autosomal mutation matrix (SAMM) was constructed from tumor-specific mutations derived from each of 909 individual cancer genomes harboring a total of 10,681,843 single-base substitutions. In addition, mechanistic template mutation matrices (MTMMs) representing oxidative DNA damage, ultraviolet-induced DNA damage, (5m)CpG deamination, and APOBEC-mediated cytosine mutation, are presented. MTMMs were mapped to the individual tumor SAMMs to determine the maximum contribution of each mutational mechanism to the overall mutation pattern. A Manhattan distance across all SAMM elements between any two tumor genomes was used to determine their relative distance. Employing this metric, 89.5% of all tumor genomes were found to have a nearest neighbor from the same tissue of origin. When a distance-dependent 6-nearest neighbor classifier was used, 10.4% of the SAMMs had an Undetermined tissue of origin, and 92.2% of the remaining SAMMs were assigned to the correct tissue of origin. [corrected]. Thus, although tumors from different tissues may have similar mutation patterns, their SAMMs often display signatures that are characteristic of specific tissues.
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Affiliation(s)
- Nuri A. Temiz
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
- />Masonic Cancer Center, University of Minnesota, 2-120 CCRB, 2231 6th St SE, Minneapolis, MN 55455 USA
| | - Duncan E. Donohue
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
- />US Army Medical Research and Material Command, 568 Doughten Dr., Fort Detrick, Frederick, MD 21702 USA
| | - Albino Bacolla
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
- />Division of Pharmacology and Toxicology, The University of Texas at Austin, Austin, TX 78723 USA
| | - Karen M. Vasquez
- />Division of Pharmacology and Toxicology, The University of Texas at Austin, Austin, TX 78723 USA
| | - David N. Cooper
- />Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN UK
| | - Uma Mudunuri
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
| | - Joseph Ivanic
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
| | - Regina Z. Cer
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
- />Naval Medical Research Center-Frederick, 8400 Research Plaza, Fort Detrick, Frederick, MD 21702 USA
| | - Ming Yi
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
| | - Robert M. Stephens
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
| | - Jack R. Collins
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
| | - Brian T. Luke
- />In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., P.O. Box B, Frederick, MD 21702 USA
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Ohnishi H, Kawasaki T, Deguchi T, Yuba S. Generation of Xeroderma Pigmentosum-A Patient-Derived Induced Pluripotent Stem Cell Line for Use As Future Disease Model. Cell Reprogram 2015; 17:268-74. [PMID: 26090552 DOI: 10.1089/cell.2014.0104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Xeroderma pigmentosum group A (XP-A) is a genetic disorder in which there is an abnormality in nucleotide excision repair that causes hypersensitivity to sunlight and multiple skin cancers. The development of central and peripheral neurological disorders not correlated to ultraviolet light exposure is associated with XP-A. The genes responsible for XP-A have been identified and a XPA knockout mouse has been generated. These knockout mice exhibit cutaneous symptoms, but they do not show neurological disorders. The mechanism of pathogenesis of neurological disorders is still unclear and therapeutic methods have not been established. Therefore, we generated XP-A patient-derived human induced pluripotent stem cells (XPA-iPSCs) to produce in vitro models of neurological disorders. We obtained iPSC lines from fibroblasts of two patients carrying different mutations. Drugs screened using XPA-iPSC lines can be helpful for treating XP-A patients in Japan. Additionally, we revealed that these iPSCs have the potential to differentiate into neural lineage cells, including dopaminergic neurons, which decrease in XP-A patients. Our results indicate that expression of the normal XPA gene without mutations is not required for generation of iPSCs and differentiation of iPSCs into neural lineage cells. XPA-iPSCs may become useful models that clarify our understanding of neurological pathogenesis and help to establish therapeutic methods.
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Affiliation(s)
- Hiroe Ohnishi
- 1 Tissue Engineering Research Group, Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) , Amagasaki, Hyogo 661-0974, Japan .,4 Present address: Department of Otolaryngology, Graduate School of Medicine, Kyoto University , Kyoto 606-8507, Japan
| | - Takashi Kawasaki
- 2 Functional Biomolecular Research Group, Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) , Amagasaki, Hyogo 661-0974, Japan
| | - Tomonori Deguchi
- 3 Stress Signal Research Group, Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) , Ikeda, Osaka 563-8577, Japan
| | - Shunsuke Yuba
- 1 Tissue Engineering Research Group, Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) , Amagasaki, Hyogo 661-0974, Japan
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32
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He L, Deng T, Luo H. XPA A23G polymorphism and risk of digestive system cancers: a meta-analysis. Onco Targets Ther 2015; 8:385-94. [PMID: 25709470 PMCID: PMC4332261 DOI: 10.2147/ott.s75767] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Several studies have reported an association between the A23G polymorphism (rs 1800975) in the xeroderma pigmentosum group A (XPA) gene and risk of digestive system cancers. However, the results are inconsistent. In this study, we performed a meta-analysis to assess the association between XPA A23G polymorphism and the risk of digestive system cancers. Methods Relevant studies were identified using the PubMed, Web of Science, China National Knowledge Infrastructure, WanFang, and VIP databases up to August 30, 2014. The pooled odds ratio (OR) with a 95% confidence interval (CI) was calculated using the fixed or random effects model. Results A total of 18 case-control studies from 16 publications with 4,170 patients and 6,929 controls were included. Overall, no significant association was found between XPA A23G polymorphism and the risk of digestive system cancers (dominant model: GA + AA versus GG, OR 0.89, 95% CI 0.74–1.08; recessive model: AA versus GA + GG, OR 0.94, 95% CI 0.74–1.20; GA versus GG, OR 0.89, 95% CI 0.77–1.03; and AA versus GG, OR 0.87, 95% CI 0.64–1.19). When the analysis was stratified by ethnicity, similar results were observed among Asians and Caucasians in all genetic models. In stratified analysis based on tumor type, we also failed to detect any association between XPA A23G polymorphism and the risk of esophageal, gastric, or colorectal cancers. Conclusion This meta-analysis indicates that the XPA A23G polymorphism is not associated with a risk of digestive system cancers.
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Affiliation(s)
- Lei He
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Tao Deng
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Hesheng Luo
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, People's Republic of China
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DNA damage and repair in plants under ultraviolet and ionizing radiations. ScientificWorldJournal 2015; 2015:250158. [PMID: 25729769 PMCID: PMC4333283 DOI: 10.1155/2015/250158] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 10/27/2014] [Accepted: 11/04/2014] [Indexed: 11/17/2022] Open
Abstract
Being sessile, plants are continuously exposed to DNA-damaging agents present in the environment such as ultraviolet (UV) and ionizing radiations (IR). Sunlight acts as an energy source for photosynthetic plants; hence, avoidance of UV radiations (namely, UV-A, 315–400 nm; UV-B, 280–315 nm; and UV-C, <280 nm) is unpreventable. DNA in particular strongly absorbs UV-B; therefore, it is the most important target for UV-B induced damage. On the other hand, IR causes water radiolysis, which generates highly reactive hydroxyl radicals (OH•) and causes radiogenic damage to important cellular components. However, to maintain genomic integrity under UV/IR exposure, plants make use of several DNA repair mechanisms. In the light of recent breakthrough, the current minireview (a) introduces UV/IR and overviews UV/IR-mediated DNA damage products and (b) critically discusses the biochemistry and genetics of major pathways responsible for the repair of UV/IR-accrued DNA damage. The outcome of the discussion may be helpful in devising future research in the current context.
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34
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Abstract
XPA (xeroderma pigmentosum group A) protein is an essential factor for NER (nucleotide excision repair) which is believed to be involved in DNA damage recognition/verification, NER factor recruiting and stabilization of repair intermediates. Past studies on the structure of XPA have focused primarily on XPA interaction with damaged DNA. However, how XPA interacts with other DNA structures remains unknown though recent evidence suggest that these structures could be important for its roles in both NER and non-NER activities. Previously, we reported that XPA recognizes undamaged DNA ds/ssDNA (double-strand/single-strandDNA) junctions with a binding affinity much higher than its ability to bind bulky DNA damage. To understand how this interaction occurs biochemically we implemented a structural determination of the interaction using a MS-based protein footprinting method and limited proteolysis. By monitoring surface accessibility of XPA lysines to NHS-biotin modification in the free protein and the DNA junction-bound complex we show that XPA physically interacts with the DNA junctions via two lysines, K168 and K179, located in the previously known XPA(98–219) DBD (DNA-binding domain). Importantly, we also uncovered new lysine residues, outside of the known DBD, involved in the binding. We found that residues K221, K222, K224 and K236 in the C-terminal domain are involved in DNA binding. Limited proteolysis analysis of XPA–DNA interactions further confirmed this observation. Structural modelling with these data suggests a clamp-like DBD for the XPA binding to ds/ssDNA junctions. Our results provide a novel structure-function view of XPA–DNA junction interactions.
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35
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Latimer JJ, Majekwana VJ, Pabón-Padín YR, Pimpley MR, Grant SG. Regulation and disregulation of mammalian nucleotide excision repair: a pathway to nongermline breast carcinogenesis. Photochem Photobiol 2014; 91:493-500. [PMID: 25393451 DOI: 10.1111/php.12387] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 10/27/2014] [Indexed: 12/13/2022]
Abstract
Nucleotide excision repair (NER) is an important modulator of disease, especially in constitutive deficiencies such as the cancer predisposition syndrome Xeroderma pigmentosum. We have found profound variation in NER capacity among normal individuals, between cell-types and during carcinogenesis. NER is a repair system for many types of DNA damage, and therefore many types of genotoxic carcinogenic exposures, including ultraviolet light, products of organic combustion, metals and oxidative stress. Because NER is intimately related to cellular metabolism, requiring components of both the DNA replicative and transcription machinery, it has a narrow range of functional viability. Thus, genes in the NER pathway are expressed at the low levels manifested by, for example, nuclear transcription factors. As NER activity and gene expression vary by cell-type, it is inherently epigenetically regulated. Furthermore, this epigenetic modulation is disregulated during sporadic breast carcinogenesis. Loss of NER is one basis of genomic instability, a required element in cellular transformation, and one that potentially influences response to therapy. In this study, we demonstrate differences in NER capacity in eight adult mouse tissues, and place this result into the context of our previous work on mouse extraembryonic tissues, normal human tissues and sporadic early stage human breast cancer.
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Affiliation(s)
- Jean J Latimer
- Department of Pharmaceutical Sciences, College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL
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36
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O'Grady S, Finn SP, Cuffe S, Richard DJ, O'Byrne KJ, Barr MP. The role of DNA repair pathways in cisplatin resistant lung cancer. Cancer Treat Rev 2014; 40:1161-70. [PMID: 25458603 DOI: 10.1016/j.ctrv.2014.10.003] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 10/11/2014] [Indexed: 11/19/2022]
Abstract
Platinum chemotherapeutic agents such as cisplatin are currently used in the treatment of various malignancies such as lung cancer. However, their efficacy is significantly hindered by the development of resistance during treatment. While a number of factors have been reported that contribute to the onset of this resistance phenotype, alterations in the DNA repair capacity of damaged cells is now recognised as an important factor in mediating this phenomenon. The mode of action of cisplatin has been linked to its ability to crosslink purine bases on the DNA, thereby interfering with DNA repair mechanisms and inducing DNA damage. Following DNA damage, cells respond by activating a DNA-damage response that either leads to repair of the lesion by the cell thereby promoting resistance to the drug, or cell death via activation of the apoptotic response. Therefore, DNA repair is a vital target to improving cancer therapy and reduce the resistance of tumour cells to DNA damaging agents currently used in the treatment of cancer patients. To date, despite the numerous findings that differential expression of components of the various DNA repair pathways correlate with response to cisplatin, translation of such findings in the clinical setting are still warranted. The identification of alterations in specific proteins and pathways that contribute to these unique DNA repair pathways in cisplatin resistant cancer cells may potentially lead to a renewed interest in the development of rational novel therapies for cisplatin resistant cancers, in particular, lung cancer.
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Affiliation(s)
- Shane O'Grady
- Thoracic Oncology Research Group, Institute of Molecular Medicine, Trinity Centre for Health Sciences, St James's Hospital and Trinity College Dublin, Dublin 8, Ireland.
| | - Stephen P Finn
- Thoracic Oncology Research Group, Institute of Molecular Medicine, Trinity Centre for Health Sciences, St James's Hospital and Trinity College Dublin, Dublin 8, Ireland; Department of Histopathology, St James's Hospital and Trinity College Dublin, Ireland.
| | - Sinead Cuffe
- Thoracic Oncology Research Group, Institute of Molecular Medicine, Trinity Centre for Health Sciences, St James's Hospital and Trinity College Dublin, Dublin 8, Ireland.
| | - Derek J Richard
- Cancer and Ageing Research Program, Queensland University of Technology, Brisbane, Australia.
| | - Kenneth J O'Byrne
- Thoracic Oncology Research Group, Institute of Molecular Medicine, Trinity Centre for Health Sciences, St James's Hospital and Trinity College Dublin, Dublin 8, Ireland; Cancer and Ageing Research Program, Queensland University of Technology, Brisbane, Australia.
| | - Martin P Barr
- Thoracic Oncology Research Group, Institute of Molecular Medicine, Trinity Centre for Health Sciences, St James's Hospital and Trinity College Dublin, Dublin 8, Ireland.
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Yan S, Sorrell M, Berman Z. Functional interplay between ATM/ATR-mediated DNA damage response and DNA repair pathways in oxidative stress. Cell Mol Life Sci 2014; 71:3951-67. [PMID: 24947324 DOI: 10.1007/s00018-014-1666-4] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 06/03/2014] [Accepted: 06/05/2014] [Indexed: 02/07/2023]
Abstract
To maintain genome stability, cells have evolved various DNA repair pathways to deal with oxidative DNA damage. DNA damage response (DDR) pathways, including ATM-Chk2 and ATR-Chk1 checkpoints, are also activated in oxidative stress to coordinate DNA repair, cell cycle progression, transcription, apoptosis, and senescence. Several studies demonstrate that DDR pathways can regulate DNA repair pathways. On the other hand, accumulating evidence suggests that DNA repair pathways may modulate DDR pathway activation as well. In this review, we summarize our current understanding of how various DNA repair and DDR pathways are activated in response to oxidative DNA damage primarily from studies in eukaryotes. In particular, we analyze the functional interplay between DNA repair and DDR pathways in oxidative stress. A better understanding of cellular response to oxidative stress may provide novel avenues of treating human diseases, such as cancer and neurodegenerative disorders.
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Affiliation(s)
- Shan Yan
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC, 28223, USA,
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38
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UVC Mutagenicity Is Suppressed in Japanese Miso-Treated Human RSa Cells, PossiblyviaGRP78 Expression. Biosci Biotechnol Biochem 2014; 75:1685-91. [DOI: 10.1271/bbb.110175] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Sarangi P, Bartosova Z, Altmannova V, Holland C, Chavdarova M, Lee SE, Krejci L, Zhao X. Sumoylation of the Rad1 nuclease promotes DNA repair and regulates its DNA association. Nucleic Acids Res 2014; 42:6393-404. [PMID: 24753409 PMCID: PMC4041466 DOI: 10.1093/nar/gku300] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The Saccharomyces cerevisiae Rad1-Rad10 complex is a conserved, structure-specific endonuclease important for repairing multiple types of DNA lesions. Upon recruitment to lesion sites, Rad1-Rad10 removes damaged sequences, enabling subsequent gap filling and ligation. Acting at mid-steps of repair, the association and dissociation of Rad1-Rad10 with DNA can influence repair efficiency. We show that genotoxin-enhanced Rad1 sumoylation occurs after the nuclease is recruited to lesion sites. A single lysine outside Rad1's nuclease and Rad10-binding domains is sumoylated in vivo and in vitro. Mutation of this site to arginine abolishes Rad1 sumoylation and impairs Rad1-mediated repair at high doses of DNA damage, but sustains the repair of a single double-stranded break. The timing of Rad1 sumoylation and the phenotype bias toward high lesion loads point to a post-incision role for sumoylation, possibly affecting Rad1 dissociation from DNA. Indeed, biochemical examination shows that sumoylation of Rad1 decreases the complex's affinity for DNA without affecting other protein properties. These findings suggest a model whereby sumoylation of Rad1 promotes its disengagement from DNA after nuclease cleavage, allowing it to efficiently attend to large numbers of DNA lesions.
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Affiliation(s)
- Prabha Sarangi
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA Programs in Biochemistry, Cell, and Molecular Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Zdenka Bartosova
- Department of Biology, Masaryk University, Brno 62500, Czech Republic
| | | | - Cory Holland
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Melita Chavdarova
- National Centre for Biomolecular Research, Masaryk University, Brno 62500, Czech Republic
| | - Sang Eun Lee
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA Division of Radiation Biology, Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Lumir Krejci
- Department of Biology, Masaryk University, Brno 62500, Czech Republic National Centre for Biomolecular Research, Masaryk University, Brno 62500, Czech Republic International Clinical Research Center, St. Anne's University Hospital in Brno, Brno 60200, Czech Republic
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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Stavros KM, Hawkins EK, Rizzo CJ, Stone MP. Base-displaced intercalation of the 2-amino-3-methylimidazo[4,5-f]quinolone N2-dG adduct in the NarI DNA recognition sequence. Nucleic Acids Res 2014; 42:3450-63. [PMID: 24366876 PMCID: PMC3950664 DOI: 10.1093/nar/gkt1109] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 10/18/2013] [Accepted: 10/21/2013] [Indexed: 12/14/2022] Open
Abstract
2-Amino-3-methylimidazo[4,5-f]quinolone (IQ), a heterocyclic amine found in cooked meats, undergoes bioactivation to a nitrenium ion, which alkylates guanines at both the C8-dG and N2-dG positions. The conformation of a site-specific N2-dG-IQ adduct in an oligodeoxynucleotide duplex containing the iterated CG repeat restriction site of the NarI endonuclease has been determined. The IQ moiety intercalates, with the IQ H4a and CH3 protons facing the minor groove, and the IQ H7a, H8a and H9a protons facing the major groove. The adducted dG maintains the anti-conformation about the glycosyl bond. The complementary dC is extruded into the major groove. The duplex maintains its thermal stability, which is attributed to stacking between the IQ moiety and the 5'- and 3'-neighboring base pairs. This conformation is compared to that of the C8-dG-IQ adduct in the same sequence, which also formed a 'base-displaced intercalated' conformation. However, the C8-dG-IQ adopted the syn conformation placing the Watson-Crick edge of the modified dG into the major groove. In addition, the C8-dG-IQ adduct was oriented with the IQ CH3 group and H4a and H5a facing the major groove. These differences may lead to differential processing during DNA repair and replication.
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Affiliation(s)
| | | | | | - Michael P. Stone
- Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235-1822, USA
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41
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Epshtein V, Kamarthapu V, McGary K, Svetlov V, Ueberheide B, Proshkin S, Mironov A, Nudler E. UvrD facilitates DNA repair by pulling RNA polymerase backwards. Nature 2014; 505:372-7. [PMID: 24402227 DOI: 10.1038/nature12928] [Citation(s) in RCA: 170] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 12/02/2013] [Indexed: 11/09/2022]
Abstract
UvrD helicase is required for nucleotide excision repair, although its role in this process is not well defined. Here we show that Escherichia coli UvrD binds RNA polymerase during transcription elongation and, using its helicase/translocase activity, forces RNA polymerase to slide backward along DNA. By inducing backtracking, UvrD exposes DNA lesions shielded by blocked RNA polymerase, allowing nucleotide excision repair enzymes to gain access to sites of damage. Our results establish UvrD as a bona fide transcription elongation factor that contributes to genomic integrity by resolving conflicts between transcription and DNA repair complexes. Furthermore, we show that the elongation factor NusA cooperates with UvrD in coupling transcription to DNA repair by promoting backtracking and recruiting nucleotide excision repair enzymes to exposed lesions. Because backtracking is a shared feature of all cellular RNA polymerases, we propose that this mechanism enables RNA polymerases to function as global DNA damage scanners in bacteria and eukaryotes.
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Affiliation(s)
- Vitaly Epshtein
- 1] Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA [2]
| | - Venu Kamarthapu
- 1] Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA [2] Howard Hughes Medical Institute, New York University School of Medicine, New York, New York 10016, USA [3]
| | - Katelyn McGary
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
| | - Vladimir Svetlov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
| | - Sergey Proshkin
- State Research Institute of Genetics and Selection of Industrial Microorganisms, Moscow 117545, Russia
| | - Alexander Mironov
- 1] State Research Institute of Genetics and Selection of Industrial Microorganisms, Moscow 117545, Russia [2] Engelhardt Institute of Molecular Biology, Russian Academy of Science, Moscow 119991, Russia
| | - Evgeny Nudler
- 1] Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA [2] Howard Hughes Medical Institute, New York University School of Medicine, New York, New York 10016, USA
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42
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Buechner CN, Heil K, Michels G, Carell T, Kisker C, Tessmer I. Strand-specific recognition of DNA damages by XPD provides insights into nucleotide excision repair substrate versatility. J Biol Chem 2013; 289:3613-24. [PMID: 24338567 DOI: 10.1074/jbc.m113.523001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recognition and removal of DNA damages is essential for cellular and organismal viability. Nucleotide excision repair (NER) is the sole mechanism in humans for the repair of carcinogenic UV irradiation-induced photoproducts in the DNA, such as cyclobutane pyrimidine dimers. The broad substrate versatility of NER further includes, among others, various bulky DNA adducts. It has been proposed that the 5'-3' helicase XPD (xeroderma pigmentosum group D) protein plays a decisive role in damage verification. However, despite recent advances such as the identification of a DNA-binding channel and central pore in the protein, through which the DNA is threaded, as well as a dedicated lesion recognition pocket near the pore, the exact process of target site recognition and verification in eukaryotic NER still remained elusive. Our single molecule analysis by atomic force microscopy reveals for the first time that XPD utilizes different recognition strategies to verify structurally diverse lesions. Bulky fluorescein damage is preferentially detected on the translocated strand, whereas the opposite strand preference is observed for a cyclobutane pyrimidine dimer lesion. Both states, however, lead to similar conformational changes in the resulting specific complexes, indicating a merge to a "final" verification state, which may then trigger the recruitment of further NER proteins.
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Affiliation(s)
- Claudia N Buechner
- From the Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080 Würzburg, Germany and
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43
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Henry LG, Aruni W, Sandberg L, Fletcher HM. Protective role of the PG1036-PG1037-PG1038 operon in oxidative stress in Porphyromonas gingivalis W83. PLoS One 2013; 8:e69645. [PMID: 23990885 PMCID: PMC3747172 DOI: 10.1371/journal.pone.0069645] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 06/13/2013] [Indexed: 12/15/2022] Open
Abstract
As an anaerobe, Porphyromonas gingivalis is significantly affected by the harsh inflammatory environment of the periodontal pocket during initial colonization and active periodontal disease. We reported previously that the repair of oxidative stress-induced DNA damage involving 8-oxo-7,8-dihydroguanine (8-oxoG) may occur by an undescribed mechanism in P. gingivalis. DNA affinity fractionation identified PG1037, a conserved hypothetical protein, among other proteins, that were bound to the 8-oxoG lesion. PG1037 is part of the uvrA-PG1037-pcrA operon in P. gingivalis which is known to be upregulated under H2O2 induced stress. A PCR-based linear transformation method was used to inactivate the uvrA and pcrA genes by allelic exchange mutagenesis. Several attempts to inactivate PG1037 were unsuccessful. Similar to the wild-type when plated on Brucella blood agar, the uvrA and pcrA-defective mutants were black-pigmented and beta-hemolytic. These isogenic mutants also had reduced gingipain activities and were more sensitive to H2O2 and UV irradiation compared to the parent strain. Additionally, glycosylase assays revealed that 8-oxoG repair activities were similar in both wild-type and mutant P. gingivalis strains. Several proteins, some of which are known to have oxidoreducatse activity, were shown to interact with PG1037. The purified recombinant PG1037 protein could protect DNA from H2O2-induced damage. Collectively, these findings suggest that the uvrA-PG1037-pcrA operon may play an important role in hydrogen peroxide stress-induced resistance in P. gingivalis.
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Affiliation(s)
- Leroy G. Henry
- Division of Microbiology and Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California, United States of America
| | - Wilson Aruni
- Division of Microbiology and Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California, United States of America
| | - Lawrence Sandberg
- Division of Biochemistry, School of Medicine, Loma Linda University, Loma Linda, California, United States of America
| | - Hansel M. Fletcher
- Division of Microbiology and Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California, United States of America
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44
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Kaushik Tiwari M, Rogers FA. XPD-dependent activation of apoptosis in response to triplex-induced DNA damage. Nucleic Acids Res 2013; 41:8979-94. [PMID: 23913414 PMCID: PMC3799437 DOI: 10.1093/nar/gkt670] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
DNA sequences capable of forming triplexes are prevalent in the human genome and have been found to be intrinsically mutagenic. Consequently, a balance between DNA repair and apoptosis is critical to counteract their effect on genomic integrity. Using triplex-forming oligonucleotides to synthetically create altered helical distortions, we have determined that pro-apoptotic pathways are activated by the formation of triplex structures. Moreover, the TFIIH factor, XPD, occupies a central role in triggering apoptosis in response to triplex-induced DNA strand breaks. Here, we show that triplexes are capable of inducing XPD-independent double strand breaks, which result in the formation of γH2AX foci. XPD was subsequently recruited to the triplex-induced double strand breaks and co-localized with γH2AX at the damage site. Furthermore, phosphorylation of H2AX tyrosine 142 was found to stimulate the signaling pathway of XPD-dependent apoptosis. We suggest that this mechanism may play an active role in minimizing genomic instability induced by naturally occurring noncanonical structures, perhaps protecting against cancer initiation.
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Affiliation(s)
- Meetu Kaushik Tiwari
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
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45
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UV-induced nuclear import of XPA is mediated by importin-α4 in an ATR-dependent manner. PLoS One 2013; 8:e68297. [PMID: 23861882 PMCID: PMC3704644 DOI: 10.1371/journal.pone.0068297] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 05/28/2013] [Indexed: 12/29/2022] Open
Abstract
Xeroderma pigmentosum Group A (XPA) is a crucial factor in mammalian nucleotide excision repair (NER) and nuclear import of XPA from the cytoplasm for NER is regulated in cellular DNA damage responses in S-phase. In this study, experiments were carried out to determine the transport mechanisms that are responsible for the UV (ultraviolet)-induced nuclear import of XPA. We found that, in addition to the nuclear localization signal (NLS) of XPA, importin-α4 or/and importin-α7 are required for the XPA nuclear import. Further investigation indicated that, importin-α4 and importin-α7 directly interacted with XPA in cells. Interestingly, the binding of importin-α4 to XPA was dependent on UV-irradiation, while the binding of importin-α7 was not, suggesting a role for importin-α7 in nuclear translocation of XPA in the absence of DNA damage, perhaps with specificity to certain non-S-phases of the cell-cycle. Consistent with the previous report of a dependence of UV-induced XPA nuclear import on ataxia telangiectasia and Rad3-related protein (ATR) in S-phase, knockdown of ATR reduced the amount of XPA interacting with importin-α4. In contrast, the GTPase XPA binding protein 1 (XAB1), previously proposed to be required for XPA nuclear import, showed no effect on the nuclear import of XPA in our siRNA knockdown analysis. In conclusion, our results suggest that upon DNA damage transport adaptor importin-α4 imports XPA into the nucleus in an ATR-dependent manner, while XAB1 has no role in this process. In addition, these findings reveal a potential new therapeutic target for the sensitization of cancer cells to chemotherapy.
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46
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The influence of XPD, APE1, XRCC1, and NBS1 polymorphic variants on DNA repair in cells exposed to X-rays. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2013; 755:42-8. [DOI: 10.1016/j.mrgentox.2013.05.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 05/02/2013] [Accepted: 05/03/2013] [Indexed: 11/20/2022]
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47
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Santos AL, Moreirinha C, Lopes D, Esteves AC, Henriques I, Almeida A, Domingues MRM, Delgadillo I, Correia A, Cunha A. Effects of UV radiation on the lipids and proteins of bacteria studied by mid-infrared spectroscopy. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:6306-6315. [PMID: 23692317 DOI: 10.1021/es400660g] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Knowledge of the molecular effects of UV radiation (UVR) on bacteria can contribute to a better understanding of the environmental consequences of enhanced UV levels associated with global climate changes and will help to optimize UV-based disinfection strategies. In the present work, the effects of exposure to UVR in different spectral regions (UVC, 100-280 nm; UVB, 280-320 nm; and UVA, 320-400 nm) on the lipids and proteins of two bacterial strains ( Acinetobacter sp. strain PT5I1.2G and Pseudomonas sp. strain NT5I1.2B) with distinct UV sensitivities were studied by mid-infrared spectroscopy. Exposure to UVR caused an increase in methyl groups associated with lipids, lipid oxidation, and also led to alterations in lipid composition, which were confirmed by gas chromatography. Additionally, mid-infrared spectroscopy revealed the effects of UVR on protein conformation and protein composition, which were confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), oxidative damage to amino acids, and changes in the propionylation, glycosylation and/or phosphorylation status of cell proteins. Differences in the targets of UVR in the two strains tested were identified and may explain their discrepant UV sensitivities. The significance of the results is discussed from an ecological standpoint and with respect to potential improvements in UV-based disinfection technologies.
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Affiliation(s)
- Ana L Santos
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
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Zirkin S, Davidovich A, Don J. The PIM-2 kinase is an essential component of the ultraviolet damage response that acts upstream to E2F-1 and ATM. J Biol Chem 2013; 288:21770-83. [PMID: 23760264 DOI: 10.1074/jbc.m113.458851] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The oncogenic nature ascribed to the PIM-2 kinase relies mostly on phosphorylation of substrates that act as pro-survival/anti-apoptotic factors. Nevertheless, pro-survival effects can also result from activating DNA repair mechanisms following damage. In this study, we addressed the possibility that PIM-2 plays a role in the cellular response to UV damage, an issue that has never been addressed before. We found that in U2OS cells, PIM-2 expression and activity increased upon exposure to UVC radiation (2-50 mJ/cm(2)), and Pim-2-silenced cells were significantly more sensitive to UV radiation. Overexpression of PIM-2 accelerated removal of UV-induced DNA lesions over time, reduced γH2AX accumulation in damaged cells, and rendered these cells significantly more viable following UV radiation. The protective effect of PIM-2 was mediated by increased E2F-1 and activated ATM levels. Silencing E2F-1 reduced the protective effect of PIM-2, whereas inhibiting ATM activity abrogated this protective effect, irrespective of E2F-1 levels. The results obtained in this study place PIM-2 upstream to E2F-1 and ATM in the UV-induced DNA damage response.
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Affiliation(s)
- Shahar Zirkin
- Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
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49
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Nakao S, Zhang S, Vaara M, Syväoja JE, Lee MY, Tsurimoto T, Karran P, Oda S. Efficient long DNA gap-filling in a mammalian cell-free system: a potential new in vitro DNA replication assay. Biochimie 2013; 95:320-8. [PMID: 23063694 DOI: 10.1016/j.biochi.2012.09.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 09/27/2012] [Indexed: 11/22/2022]
Abstract
In vitro assay of mammalian DNA replication has been variously approached. Using gapped circular duplex substrates containing a 500-base single-stranded DNA region, we have constructed a mammalian cell-free system in which physiological DNA replication may be reproduced. Reaction of the gapped plasmid substrate with crude extracts of human HeLaS3 cells induces efficient DNA synthesis in vitro. The induced synthesis was strongly inhibited by aphidicolin and completely depended on dNTP added to the system. In cell extracts in which PCNA was depleted step-wise by immunoprecipitation, DNA synthesis was accordingly reduced. These data suggest that replicative DNA polymerases, particularly pol delta, may chiefly function in this system. Furthermore, DNA synthesis is made quantifiable in this system, which enables us to evaluate the efficiency of DNA replication induced. Our system sensitively and quantitatively detected the reduction of the DNA replication efficiency in the DNA substrates damaged by oxidation or UV cross-linking and in the presence of a potent chain terminator, ara-CTP. The quantitative assessment of mammalian DNA replication may provide various advantages not only in basic research but also in drug development.
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Affiliation(s)
- Seiki Nakao
- Cancer Genetics Laboratory, Clinical Research Institute, National Kyushu Cancer Center, Fukuoka 811-1395, Japan
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50
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Barakat KH, Jordheim LP, Perez-Pineiro R, Wishart D, Dumontet C, Tuszynski JA. Virtual screening and biological evaluation of inhibitors targeting the XPA-ERCC1 interaction. PLoS One 2012; 7:e51329. [PMID: 23272099 PMCID: PMC3522735 DOI: 10.1371/journal.pone.0051329] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2012] [Accepted: 10/10/2012] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Nucleotide excision repair (NER) removes many types of DNA lesions including those induced by UV radiation and platinum-based therapy. Resistance to platinum-based therapy correlates with high expression of ERCC1, a major element of the NER machinery. The interaction between ERCC1 and XPA is essential for a successful NER function. Therefore, one way to regulate NER is by inhibiting the activity of ERCC1 and XPA. METHODOLOGY/PRINCIPAL FINDINGS Here we continued our earlier efforts aimed at the identification and characterization of novel inhibitors of the ERCC1-XPA interaction. We used a refined virtual screening approach combined with a biochemical and biological evaluation of the compounds for their ability to interact with ERCC1 and to sensitize cells to UV radiation. Our findings reveal a new validated ERCC1-XPA inhibitor that significantly sensitized colon cancer cells to UV radiation indicating a strong inhibition of the ERCC1-XPA interaction. CONCLUSIONS NER is a major factor in acquiring resistance to platinum-based therapy. Regulating the NER pathway has the potential of improving the efficacy of platinum treatments. One approach that we followed is to inhibit the essential interaction between the two NER elements, ERCC1 and XPA. Here, we performed virtual screening against the ERCC1-XPA interaction and identified novel inhibitors that block the XPA-ERCC1 binding. The identified inhibitors significantly sensitized colon cancer cells to UV radiation indicating a strong inhibition of the ERCC1-XPA interaction.
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Affiliation(s)
- Khaled H. Barakat
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
- Department of Engineering Mathematics and Physics, Fayoum University, Fayoum, Egypt
| | - Lars P. Jordheim
- Université de Lyon, Lyon, France
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France
- CNRS UMR 5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | | | - David Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
| | - Charles Dumontet
- Université de Lyon, Lyon, France
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France
- CNRS UMR 5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Jack A. Tuszynski
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
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