1
|
Zhu Z, Li S, Yin X, Sun K, Song J, Ren W, Gao L, Zhi K. Review: Protein O-GlcNAcylation regulates DNA damage response: A novel target for cancer therapy. Int J Biol Macromol 2024; 264:130351. [PMID: 38403231 DOI: 10.1016/j.ijbiomac.2024.130351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 02/02/2024] [Accepted: 02/19/2024] [Indexed: 02/27/2024]
Abstract
The DNA damage response (DDR) safeguards the stable genetic information inheritance by orchestrating a complex protein network in response to DNA damage. However, this mechanism can often hamper the effectiveness of radiotherapy and DNA-damaging chemotherapy in destroying tumor cells, causing cancer resistance. Inhibiting DDR can significantly improve tumor cell sensitivity to radiotherapy and DNA-damaging chemotherapy. Thus, DDR can be a potential target for cancer treatment. Post-translational modifications (PTMs) of DDR-associated proteins profoundly affect their activity and function by covalently attaching new functional groups. O-GlcNAcylation (O-linked-N-acetylglucosaminylation) is an emerging PTM associated with adding and removing O-linked N-acetylglucosamine to serine and threonine residues of proteins. It acts as a dual sensor for nutrients and stress in the cell and is sensitive to DNA damage. However, the explanation behind the specific role of O-GlcNAcylation in the DDR remains remains to be elucidated. To illustrate the complex relationship between O-GlcNAcylation and DDR, this review systematically describes the role of O-GlcNAcylation in DNA repair, cell cycle, and chromatin. We also discuss the defects of current strategies for targeting O-GlcNAcylation-regulated DDR in cancer therapy and suggest potential directions to address them.
Collapse
Affiliation(s)
- Zhuang Zhu
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Shaoming Li
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Xiaopeng Yin
- Department of Oral and Maxillofacial Surgery, Central Laboratory of Jinan Stamotological Hospital, Jinan Key Laboratory of Oral Tissue Regeneration, Jinan 250001, Shandong Province, China
| | - Kai Sun
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Jianzhong Song
- Department of Oral and Maxilloafacial Surgery, People's Hospital of Rizhao, Rizhao, Shandong, China
| | - Wenhao Ren
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
| | - Ling Gao
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Key Lab of Oral Clinical Medicine, the Affiliated Hospital of Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
| | - Keqian Zhi
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Key Lab of Oral Clinical Medicine, the Affiliated Hospital of Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
| |
Collapse
|
2
|
Sharma A, Das A, Bal A, Srinivasan R, Malhotra P, Prakash G, Kumar R. Prognostic Value of Differential Expression of Polymerase Eta Gene in Nonresponding Patients With Diffuse Large B-cell Lymphoma. Appl Immunohistochem Mol Morphol 2024; 32:32-36. [PMID: 37867373 DOI: 10.1097/pai.0000000000001168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/19/2023] [Indexed: 10/24/2023]
Abstract
Diffuse large B-cell lymphoma (DLBCL) represents the most common subtype of non-Hodgkins lymphoma. After the introduction of rituximab therapy like rituximab, cyclophosphamide, doxorubicin vincristine, prednisolone, there has been considerable improvement in the 5-year overall survival in this group of patients, but the nonresponding patients are a challenge to the clinician. The translesion polymerases are unique polymerases that make cells tolerant to DNA damage. Many point mutations are introduced owing to their inherent property of bypassing the points of lesions, preventing the cell from stalling replication. However, the impaired activity of these polymerases can lead to the development of tumors with aggressive clinical course. In this study, the gene expression levels of polymerase eta ( POLE ) were compared in 2 cohorts of patients with DLBCL: the first cohort, patients who had achieved complete response, and the second cohort, patients who were refractory to the treatment or had relapse within 2 years of treatment. There was a significantly upregulated expression in the refractory/relapse cohort compared with the complete remission cohort ( P = 0.0001). The high POLE expression levels correlated significantly with advanced disease stages (III and IV) and poor disease-free survival in the Kaplan-Meier curve. The high POLE expression levels were correlated with poor disease-free survival in nonresponder patients with DLBCL. The results concluded that patients with DLBCL with a high polymerase gene expression may show nonresponsiveness to chemotherapy; hence the functional impact of upregulated expression of POLE in DLBCL requires an in-depth assessment.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Rajendar Kumar
- Department of Nuclear Medicine, PGIMER, Chandigarh, India
| |
Collapse
|
3
|
Lin A, Mou W, Zhu L, Yang T, Zhou C, Zhang J, Luo P. Mutations in the DNA polymerase binding pathway affect the immune microenvironment of patients with small-cell lung cancer and enhance the efficacy of platinum-based chemotherapy. CANCER INNOVATION 2023; 2:500-512. [PMID: 38125769 PMCID: PMC10730006 DOI: 10.1002/cai2.84] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 12/23/2023]
Abstract
Background Small-cell lung cancer (SCLC) is characterized by its high malignancy and is associated with a poor prognosis. In the early stages of the disease, platinum-based chemotherapy is the recommended first-line treatment and has demonstrated efficacy. However, SCLC is prone to recurrence and is generally resistant to chemotherapy in its later stages. Methods Here, we collected samples from SCLC patients who received platinum-based chemotherapy, performed genomic and transcriptomic analyses, and validated our results with publicly available data. Results SCLC patients with DNA polymerase binding pathway mutations had an improved prognosis after platinum chemotherapy compared with patients without such mutations. Patients in the mutant (MT) group had higher infiltration of T cells, B cells, and M1 macrophages compared with patients without DNA polymerase binding pathway mutations. Conclusions DNA polymerase binding pathway mutations can be used as prognostic markers for platinum-based chemotherapy in SCLC.
Collapse
Affiliation(s)
- Anqi Lin
- Department of Oncology, Zhujiang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
| | - Weiming Mou
- Department of Oncology, Zhujiang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
- The First Clinical Medical SchoolSouthern Medical UniversityGuangzhouGuangdongChina
- Department of Urology, Shanghai General HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Lingxuan Zhu
- The First Clinical Medical SchoolSouthern Medical UniversityGuangzhouGuangdongChina
- Department of Etiology and CarcinogenesisNational Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Tao Yang
- The First Clinical Medical SchoolSouthern Medical UniversityGuangzhouGuangdongChina
- Department of Medical OncologyNational Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Chaozheng Zhou
- The First Clinical Medical SchoolSouthern Medical UniversityGuangzhouGuangdongChina
| | - Jian Zhang
- Department of Oncology, Zhujiang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
| | - Peng Luo
- Department of Oncology, Zhujiang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
| |
Collapse
|
4
|
Daks A, Fedorova O, Parfenyev S, Nevzorov I, Shuvalov O, Barlev NA. The Role of E3 Ligase Pirh2 in Disease. Cells 2022; 11:1515. [PMID: 35563824 PMCID: PMC9101203 DOI: 10.3390/cells11091515] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 02/04/2023] Open
Abstract
The p53-dependent ubiquitin ligase Pirh2 regulates a number of proteins involved in different cancer-associated processes. Targeting the p53 family proteins, Chk2, p27Kip1, Twist1 and others, Pirh2 participates in such cellular processes as proliferation, cell cycle regulation, apoptosis and cellular migration. Thus, it is not surprising that Pirh2 takes part in the initiation and progression of different diseases and pathologies including but not limited to cancer. In this review, we aimed to summarize the available data on Pirh2 regulation, its protein targets and its role in various diseases and pathological processes, thus making the Pirh2 protein a promising therapeutic target.
Collapse
Affiliation(s)
- Alexandra Daks
- Institute of Cytology RAS, 194064 St. Petersburg, Russia; (O.F.); (S.P.); (I.N.); (O.S.)
| | | | | | | | | | - Nickolai A. Barlev
- Institute of Cytology RAS, 194064 St. Petersburg, Russia; (O.F.); (S.P.); (I.N.); (O.S.)
| |
Collapse
|
5
|
Saha P, Mandal T, Talukdar AD, Kumar D, Kumar S, Tripathi PP, Wang QE, Srivastava AK. DNA polymerase eta: A potential pharmacological target for cancer therapy. J Cell Physiol 2020; 236:4106-4120. [PMID: 33184862 DOI: 10.1002/jcp.30155] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/21/2020] [Accepted: 11/02/2020] [Indexed: 12/24/2022]
Abstract
In the last two decades, intensive research has been carried out to improve the survival rates of cancer patients. However, the development of chemoresistance that ultimately leads to tumor relapse poses a critical challenge for the successful treatment of cancer patients. Many cancer patients experience tumor relapse and ultimately die because of treatment failure associated with acquired drug resistance. Cancer cells utilize multiple lines of self-defense mechanisms to bypass chemotherapy and radiotherapy. One such mechanism employed by cancer cells is translesion DNA synthesis (TLS), in which specialized TLS polymerases bypass the DNA lesion with the help of monoubiquitinated proliferating cell nuclear antigen. Among all TLS polymerases (Pol η, Pol ι, Pol κ, REV1, Pol ζ, Pol μ, Pol λ, Pol ν, and Pol θ), DNA polymerase eta (Pol η) is well studied and majorly responsible for the bypass of cisplatin and UV-induced DNA damage. TLS polymerases contribute to chemotherapeutic drug-induced mutations as well as therapy resistance. Therefore, targeting these polymerases presents a novel therapeutic strategy to combat chemoresistance. Mounting evidence suggests that inhibition of Pol η may have multiple impacts on cancer therapy such as sensitizing cancer cells to chemotherapeutics, suppressing drug-induced mutagenesis, and inhibiting the development of secondary tumors. Herein, we provide a general introduction of Pol η and its clinical implications in blocking acquired drug resistance. In addition; this review addresses the existing gaps and challenges of Pol η mediated TLS mechanisms in human cells. A better understanding of the Pol η mediated TLS mechanism will not merely establish it as a potential pharmacological target but also open possibilities to identify novel drug targets for future therapy.
Collapse
Affiliation(s)
- Priyanka Saha
- Cancer Biology & Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, Kolkata, West Bengal, India
| | - Tanima Mandal
- Cancer Biology & Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, Kolkata, West Bengal, India
| | - Anupam D Talukdar
- Department of Life Science and Bioinformatics, Assam University, Silchar, Assam, India
| | - Deepak Kumar
- Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata, West Bengal, India
| | - Sanjay Kumar
- Division of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Andhra Pradesh, India
| | - Prem P Tripathi
- Cell Biology & Physiology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, West Bengal, India
| | - Qi-En Wang
- Department of Radiation Oncology, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Amit K Srivastava
- Cancer Biology & Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, Kolkata, West Bengal, India
| |
Collapse
|
6
|
Silvestri R, Landi S. DNA polymerases in the risk and prognosis of colorectal and pancreatic cancers. Mutagenesis 2020; 34:363-374. [PMID: 31647559 DOI: 10.1093/mutage/gez031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/17/2019] [Indexed: 12/30/2022] Open
Abstract
Human cancers arise from the alteration of genes involved in important pathways that mainly affect cell growth and proliferation. DNA replication and DNA damages recognition and repair are among these pathways and DNA polymerases that take part in these processes are frequently involved in cancer onset and progression. For example, damaging alterations within the proofreading domain of replicative polymerases, often reported in patients affected by colorectal cancer (CRC), are considered risk factors and drivers of carcinogenesis as they can lead to the accumulation of several mutations throughout the genome. Thus, replicative polymerases can be involved in cancer when losses of their physiological functions occur. On the contrary, reparative polymerases are often involved in cancer precisely because of their physiological role. In fact, their ability to repair and bypass DNA damages, which confers genome stability, can also counteract the effect of most anticancer drugs. In addition, the altered expression can characterise some type of cancers, which exacerbates this aspect. For example, all of the DNA polymerases involved a damage bypass mechanism, known as translesion synthesis, with the only exception of polymerase theta, are downregulated in CRC. Conversely, in pancreatic ductal adenocarcinoma (PDAC), most of these polymerase result upregulated. This suggests that different types of cancer can rely on different reparative polymerases to acquire drug resistance. Here we will examine all of the aspects that link DNA polymerases with CRC and PDAC.
Collapse
Affiliation(s)
| | - Stefano Landi
- Department of Biology, University of Pisa, Pisa, Italy
| |
Collapse
|
7
|
Affiliation(s)
- Vito Genna
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Elisa Donati
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| |
Collapse
|
8
|
Choi JS, Kim S, Motea E, Berdis A. Inhibiting translesion DNA synthesis as an approach to combat drug resistance to DNA damaging agents. Oncotarget 2018; 8:40804-40816. [PMID: 28489578 PMCID: PMC5522278 DOI: 10.18632/oncotarget.17254] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/11/2017] [Indexed: 01/03/2023] Open
Abstract
Anti-cancer agents exert therapeutic effects by damaging DNA. Unfortunately, DNA polymerases can effectively replicate the formed DNA lesions to cause drug resistance and create more aggressive cancers. To understand this process at the cellular level, we developed an artificial nucleoside that visualizes the replication of damaged DNA to identify cells that acquire drug resistance through this mechanism. Visualization is achieved using "click" chemistry to covalently attach azide-containing fluorophores to the ethynyl group present on the nucleoside analog after its incorporation opposite damaged DNA. Flow cytometry and microscopy techniques demonstrate that the extent of nucleotide incorporation into genomic DNA is enhanced by treatment with DNA damaging agents. In addition, this nucleoside analog inhibits translesion DNA synthesis and synergizes the therapeutic activity of certain anti-cancer agents such as temozolomide. The combined diagnostic and therapeutic activities of this synthetic nucleoside analog represent a new paradigm in personalized medicine.
Collapse
Affiliation(s)
- Jung-Suk Choi
- Department of Chemistry, Cleveland State University, Cleveland, OH 44115, USA
| | - Seol Kim
- Department of Biological, Geological, and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA
| | - Edward Motea
- Departments of Radiation Oncology and Pharmacology, Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Anthony Berdis
- Department of Chemistry, Cleveland State University, Cleveland, OH 44115, USA.,Department of Biological, Geological, and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA.,Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH 44115, USA.,Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| |
Collapse
|
9
|
Lerner LK, Francisco G, Soltys DT, Rocha CRR, Quinet A, Vessoni AT, Castro LP, David TIP, Bustos SO, Strauss BE, Gottifredi V, Stary A, Sarasin A, Chammas R, Menck CFM. Predominant role of DNA polymerase eta and p53-dependent translesion synthesis in the survival of ultraviolet-irradiated human cells. Nucleic Acids Res 2017; 45:1270-1280. [PMID: 28180309 PMCID: PMC5388406 DOI: 10.1093/nar/gkw1196] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/15/2016] [Accepted: 11/17/2016] [Indexed: 01/19/2023] Open
Abstract
Genome lesions trigger biological responses that help cells manage damaged DNA, improving cell survival. Pol eta is a translesion synthesis (TLS) polymerase that bypasses lesions that block replicative polymerases, avoiding continued stalling of replication forks, which could lead to cell death. p53 also plays an important role in preventing cell death after ultraviolet (UV) light exposure. Intriguingly, we show that p53 does so by favoring translesion DNA synthesis by pol eta. In fact, the p53-dependent induction of pol eta in normal and DNA repair-deficient XP-C human cells after UV exposure has a protective effect on cell survival after challenging UV exposures, which was absent in p53- and Pol H-silenced cells. Viability increase was associated with improved elongation of nascent DNA, indicating the protective effect was due to more efficient lesion bypass by pol eta. This protection was observed in cells proficient or deficient in nucleotide excision repair, suggesting that, from a cell survival perspective, proper bypass of DNA damage can be as relevant as removal. These results indicate p53 controls the induction of pol eta in DNA damaged human cells, resulting in improved TLS and enhancing cell tolerance to DNA damage, which parallels SOS responses in bacteria.
Collapse
Affiliation(s)
- Leticia K Lerner
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Guilherme Francisco
- Department of Center for Translational Oncology Cellular, Biology Group, Center for Translational Oncology, Cancer Institute of the State of São Paulo-ICESP, São Paulo, Brazil
| | - Daniela T Soltys
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Clarissa R R Rocha
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Annabel Quinet
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Alexandre T Vessoni
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Ligia P Castro
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Taynah I P David
- Viral Vector Laboratory, Heart Institute, University of São Paulo, São Paulo, Brazil
| | - Silvina O Bustos
- Department of Center for Translational Oncology Cellular, Biology Group, Center for Translational Oncology, Cancer Institute of the State of São Paulo-ICESP, São Paulo, Brazil
| | - Bryan E Strauss
- Viral Vector Laboratory, Heart Institute, University of São Paulo, São Paulo, Brazil
| | - Vanesa Gottifredi
- Cell Cycle and Genomic Stability Laboratory, Fundación Instituto Leloir-CONICET, Buenos Aires, Argentina
| | - Anne Stary
- CNRS-UMR8200, Université Paris-Sud, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Alain Sarasin
- CNRS-UMR8200, Université Paris-Sud, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Roger Chammas
- Department of Center for Translational Oncology Cellular, Biology Group, Center for Translational Oncology, Cancer Institute of the State of São Paulo-ICESP, São Paulo, Brazil
| | - Carlos F M Menck
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| |
Collapse
|
10
|
Genna V, Gaspari R, Dal Peraro M, De Vivo M. Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η. Nucleic Acids Res 2016; 44:2827-36. [PMID: 26935581 PMCID: PMC4824119 DOI: 10.1093/nar/gkw128] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/19/2016] [Indexed: 12/18/2022] Open
Abstract
Trans-lesion synthesis polymerases, like DNA Polymerase-η (Pol-η), are essential for cell survival. Pol-η bypasses ultraviolet-induced DNA damages via a two-metal-ion mechanism that assures DNA strand elongation, with formation of the leaving group pyrophosphate (PPi). Recent structural and kinetics studies have shown that Pol-η function depends on the highly flexible and conserved Arg61 and, intriguingly, on a transient third ion resolved at the catalytic site, as lately observed in other nucleic acid-processing metalloenzymes. How these conserved structural features facilitate DNA replication, however, is still poorly understood. Through extended molecular dynamics and free energy simulations, we unravel a highly cooperative and dynamic mechanism for DNA elongation and repair, which is here described by an equilibrium ensemble of structures that connect the reactants to the products in Pol-η catalysis. We reveal that specific conformations of Arg61 help facilitate the recruitment of the incoming base and favor the proper formation of a pre-reactive complex in Pol-η for efficient DNA editing. Also, we show that a third transient metal ion, which acts concertedly with Arg61, serves as an exit shuttle for the leaving PPi. Finally, we discuss how this effective and cooperative mechanism for DNA repair may be shared by other DNA-repairing polymerases.
Collapse
Affiliation(s)
- Vito Genna
- Laboratory of Molecular Modeling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Roberto Gaspari
- CONCEPT Lab., Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland Swiss Institute of Bioinformatics (SIB), CH-1015, Lausanne, Switzerland
| | - Marco De Vivo
- Laboratory of Molecular Modeling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy IAS-5 / INM-9 Computational Biomedicine Forschungszentrum Jülich, Wilhelm-Johnen-Straße 52428 Jülich, Germany
| |
Collapse
|
11
|
Fu L, Xu X, Ren R, Wu J, Zhang W, Yang J, Ren X, Wang S, Zhao Y, Sun L, Yu Y, Wang Z, Yang Z, Yuan Y, Qiao J, Izpisua Belmonte JC, Qu J, Liu GH. Modeling xeroderma pigmentosum associated neurological pathologies with patients-derived iPSCs. Protein Cell 2016; 7:210-21. [PMID: 26874523 PMCID: PMC4791426 DOI: 10.1007/s13238-016-0244-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 12/29/2015] [Indexed: 12/12/2022] Open
Abstract
Xeroderma pigmentosum (XP) is a group of genetic disorders caused by mutations of XP-associated genes, resulting in impairment of DNA repair. XP patients frequently exhibit neurological degeneration, but the underlying mechanism is unknown, in part due to lack of proper disease models. Here, we generated patient-specific induced pluripotent stem cells (iPSCs) harboring mutations in five different XP genes including XPA, XPB, XPC, XPG, and XPV. These iPSCs were further differentiated to neural cells, and their susceptibility to DNA damage stress was investigated. Mutation of XPA in either neural stem cells (NSCs) or neurons resulted in severe DNA damage repair defects, and these neural cells with mutant XPA were hyper-sensitive to DNA damage-induced apoptosis. Thus, XP-mutant neural cells represent valuable tools to clarify the molecular mechanisms of neurological abnormalities in the XP patients.
Collapse
Affiliation(s)
- Lina Fu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiuling Xu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ruotong Ren
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,FSU-CAS Innovation Institute, Foshan University, Foshan, 528000, China
| | - Jun Wu
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.,Universidad Católica San Antonio de Murcia (UCAM) Campus de los Jerónimos, Nº 135 Guadalupe 30107, Murcia, Spain
| | - Weiqi Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,FSU-CAS Innovation Institute, Foshan University, Foshan, 528000, China
| | - Jiping Yang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaoqing Ren
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Si Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yang Zhao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Liang Sun
- Beijing Hospital of the Ministry of Health, Beijing, 100730, China
| | - Yang Yu
- Department of Gynecology and Obstetrics, Peking University Third Hospital, Beijing, 100191, China
| | - Zhaoxia Wang
- Department of Neurology, Peking University First Hospital, Beijing, 100034, China
| | - Ze Yang
- Beijing Hospital of the Ministry of Health, Beijing, 100730, China
| | - Yun Yuan
- Department of Neurology, Peking University First Hospital, Beijing, 100034, China
| | - Jie Qiao
- Department of Gynecology and Obstetrics, Peking University Third Hospital, Beijing, 100191, China
| | - Juan Carlos Izpisua Belmonte
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Guang-Hui Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,FSU-CAS Innovation Institute, Foshan University, Foshan, 528000, China. .,Beijing Institute for Brain Disorders, Capital Medical University, Beijing, 100069, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
12
|
Malvezzi S, Sturla SJ, Tanasova M. Quantification of pyrophosphate as a universal approach to determine polymerase activity and assay polymerase inhibitors. Anal Biochem 2015; 478:1-7. [PMID: 25772306 DOI: 10.1016/j.ab.2015.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 02/24/2015] [Accepted: 03/03/2015] [Indexed: 11/17/2022]
Abstract
The importance of DNA polymerases in biology and biotechnology, and their recognition as potential therapeutic targets, drives development of methods for deriving kinetic characteristics of polymerases and their propensity to perform polynucleotide synthesis over modified DNA templates. Among various polymerases, translesion synthesis (TLS) polymerases enable cells to avoid the cytotoxic stalling of replicative DNA polymerases at chemotherapy-induced DNA lesions, thereby leading to drug resistance. Identification of TLS inhibitors to overcome drug-resistance necessitates the development of appropriate high-throughput assays. Since polymerase-mediated DNA synthesis involves the release of inorganic pyrophosphate (PPi), we established a universal and fast method for monitoring the progress of DNA polymerases based on the quantification of PPi with a fluorescence-based assay that we coupled to in vitro primer extension reactions. The established assay has a nanomolar detection limit in PPi and enables the evaluation of single nucleotide incorporation and DNA synthesis progression kinetics. The results demonstrated that the developed assay is a reliable method for monitoring TLS and identifying nucleoside and nucleotide-based TLS inhibitors.
Collapse
Affiliation(s)
- S Malvezzi
- Department of Health Sciences and Technology, ETH Zurich Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - S J Sturla
- Department of Health Sciences and Technology, ETH Zurich Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - M Tanasova
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA.
| |
Collapse
|
13
|
Site-directed Mutagenesis (Y52E) of POLH Affects Its Ability to Bypass Ultraviolet-induced DNA Lesions in HaCaT Cells. W INDIAN MED J 2014; 63:307-11. [PMID: 25429473 DOI: 10.7727/wimj.2014.063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 03/27/2014] [Indexed: 11/18/2022]
Abstract
DNA polymerase eta (Pol η) is one of several Y family trans-lesion synthesis (TLS) polymerases in humans and plays an important role in maintaining genome stability after ultraviolet (UV) irradiation, as it carries out error-free TLS at sites of UV-induced lesions. We performed site-directed mutagenesis of human polymerase η gene (Y52E), confirmed by sequencing, then cloned wild-type mutant and POLH genes into the eukaryotic vector pEGFP-N1. After transfecting wild-type and mutant plasmids into HaCaT keratinocytes, we tested for UV induced cis-syn cyclobutane pyrimidine dimer (CPDs) DNA lesions, and analysed cellular viability by MTT cell proliferation assay. The results showed that CPD levels decreased both with empty vector control (EVC), wild-type POLH, and Y52E-POLH over 48 hours post UV irradiation with 0.1 mW/cm2 UVB for 15 minutes (p = 0.025). The rate in CPD reduction of mutant POLH was less than in wild-type POLH. Cell viabilities of all three groups increased over 48 hours after UV irradiation, with the increased rate in the wild-type being higher than for mutant protein (p = 0.046). We conclude that Y52E POLH has reduced capacity to bypass UV induced DNA lesions in HaCaT cells.
Collapse
|
14
|
Mishra AK, Dormi SS, Turchi AM, Woods DS, Turchi JJ. Chemical inhibitor targeting the replication protein A-DNA interaction increases the efficacy of Pt-based chemotherapy in lung and ovarian cancer. Biochem Pharmacol 2014; 93:25-33. [PMID: 25449597 DOI: 10.1016/j.bcp.2014.10.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 10/22/2014] [Accepted: 10/23/2014] [Indexed: 01/28/2023]
Abstract
Platinum-based chemotherapeutics exert their therapeutic efficacy via the formation of DNA adducts which interfere with DNA replication, transcription and cell division and ultimately induce cell death. Repair and tolerance of these Pt-DNA lesions by nucleotide excision repair (NER) and homologous recombination (HR) can substantially reduce the effectiveness of therapy. Inhibition of these repair pathways, therefore, holds the potential to sensitize cancer cells to Pt treatment and increase clinical efficacy. Replication Protein A (RPA) plays essential roles in both NER and HR, along with its role in DNA replication and DNA damage checkpoint activation. Each of these functions is, in part, mediated by RPA binding to single-stranded DNA (ssDNA). Here we report the synthesis and characterization of novel derivatives of RPA small molecule inhibitors and their activity in models of epithelial ovarian cancer (EOC) and non-small cell lung cancer (NSCLC). We have synthesized analogs of our previously reported RPA inhibitor TDRL-505 and determined the structure-activity relationships. These data led us to the identification of TDRL-551, which exhibited a greater than 2-fold increase in in vitro activity. TDRL-551 showed synergy with Pt in tissue culture models of EOC and in vivo efficacy, as a single agent and in combination with platinum, in a NSCLC xenograft model. These data demonstrate the utility of RPA inhibition in EOC and NSCLC and the potential in developing novel anticancer therapeutics that target RPA-DNA interactions.
Collapse
Affiliation(s)
- Akaash K Mishra
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Silvana S Dormi
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Alaina M Turchi
- NERx Biosciences Inc. 351W. 10th Street, Suite 510, Indianapolis, IN 46202, USA
| | - Derek S Woods
- NERx Biosciences Inc. 351W. 10th Street, Suite 510, Indianapolis, IN 46202, USA
| | - John J Turchi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA; Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA; NERx Biosciences Inc. 351W. 10th Street, Suite 510, Indianapolis, IN 46202, USA.
| |
Collapse
|
15
|
Neher TM, Turchi JJ. Current advances in DNA repair: regulation of enzymes and pathways involved in maintaining genomic stability. Antioxid Redox Signal 2011; 14:2461-4. [PMID: 21235357 PMCID: PMC3096511 DOI: 10.1089/ars.2010.3748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Novel discoveries in the DNA repair field have lead to continuous and rapid advancement of our understanding of not only DNA repair but also DNA replication and recombination. Research in the field transcends numerous areas of biology, biochemistry, physiology, and medicine, making significant connections across these broad areas of study. From early studies conducted in bacterial systems to current analyses in eukaryotic systems and human disease, the innovative research into the mechanisms of repair machines and the consequences of ineffective DNA repair has impacted a wide scientific community. This Forum contains a select mix of primary research articles in addition to a number of timely reviews covering a subset of DNA repair pathways where recent advances and novel discoveries are improving our understanding of DNA repair, its regulation, and implications to human disease.
Collapse
Affiliation(s)
- Tracy M. Neher
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - John J. Turchi
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| |
Collapse
|