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Ricciardiello R, Forleo G, Cipolla L, van Winckel G, Marconi C, Nouspikel T, Halazonetis TD, Zgheib O, Sabbioneda S. Homozygous substitution of threonine 191 by proline in polymerase η causes Xeroderma pigmentosum variant. Sci Rep 2024; 14:1117. [PMID: 38212351 PMCID: PMC10784498 DOI: 10.1038/s41598-023-51120-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 12/31/2023] [Indexed: 01/13/2024] Open
Abstract
DNA polymerase eta (Polη) is the only translesion synthesis polymerase capable of error-free bypass of UV-induced cyclobutane pyrimidine dimers. A deficiency in Polη function is associated with the human disease Xeroderma pigmentosum variant (XPV). We hereby report the case of a 60-year-old woman known for XPV and carrying a Polη Thr191Pro variant in homozygosity. We further characterize the variant in vitro and in vivo, providing molecular evidence that the substitution abrogates polymerase activity and results in UV sensitivity through deficient damage bypass. This is the first functional molecular characterization of a missense variant of Polη, whose reported pathogenic variants have thus far been loss of function truncation or frameshift mutations. Our work allows the upgrading of Polη Thr191Pro from 'variant of uncertain significance' to 'likely pathogenic mutant', bearing direct impact on molecular diagnosis and genetic counseling. Furthermore, we have established a robust experimental approach that will allow a precise molecular analysis of further missense mutations possibly linked to XPV. Finally, it provides insight into critical Polη residues that may be targeted to develop small molecule inhibitors for cancer therapeutics.
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Affiliation(s)
- Roberto Ricciardiello
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, Italy
- Dipartimento di Biologia e Biotecnologie 'Lazzaro Spallanzani', Università degli Studi di Pavia, Pavia, Italy
| | - Giulia Forleo
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, Italy
| | - Lina Cipolla
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, Italy
| | - Geraldine van Winckel
- Division of Medical Genetics, Diagnostics Department, Geneva University Hospitals, Geneva, Switzerland
| | - Caterina Marconi
- Division of Medical Genetics, Diagnostics Department, Geneva University Hospitals, Geneva, Switzerland
| | - Thierry Nouspikel
- Division of Medical Genetics, Diagnostics Department, Geneva University Hospitals, Geneva, Switzerland
| | - Thanos D Halazonetis
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Omar Zgheib
- Division of Medical Genetics, Diagnostics Department, Geneva University Hospitals, Geneva, Switzerland.
| | - Simone Sabbioneda
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, Italy.
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2
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Hodáková Z, Grishkovskaya I, Brunner HL, Bolhuis DL, Belačić K, Schleiffer A, Kotisch H, Brown NG, Haselbach D. Cryo-EM structure of the chain-elongating E3 ubiquitin ligase UBR5. EMBO J 2023; 42:e113348. [PMID: 37409633 PMCID: PMC10425842 DOI: 10.15252/embj.2022113348] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/30/2023] [Accepted: 06/14/2023] [Indexed: 07/07/2023] Open
Abstract
UBR5 is a nuclear E3 ligase that ubiquitinates a vast range of substrates for proteasomal degradation. This HECT domain-containing ubiquitin ligase has recently been identified as an important regulator of oncogenes, e.g., MYC, but little is known about its structure or mechanisms of substrate engagement and ubiquitination. Here, we present the cryo-EM structure of human UBR5, revealing an α-solenoid scaffold with numerous protein-protein interacting motifs, assembled into an antiparallel dimer that adopts further oligomeric states. Using cryo-EM processing tools, we observe the dynamic nature of the UBR5 catalytic domain, which we postulate is important for its enzymatic activity. We characterise the proteasomal nuclear import factor AKIRIN2 as an interacting protein and propose UBR5 as an efficient ubiquitin chain elongator. This preference for ubiquitinated substrates and several distinct domains for protein-protein interactions may explain how UBR5 is linked to several different signalling pathways and cancers. Together, our data expand on the limited knowledge of the structure and function of HECT E3 ligases.
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Affiliation(s)
- Zuzana Hodáková
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Irina Grishkovskaya
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Hanna L Brunner
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD ProgramDoctoral School of the University of Vienna and Medical University of ViennaViennaAustria
| | - Derek L Bolhuis
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer CenterUniversity of North Carolina School of MedicineChapel HillNCUSA
| | - Katarina Belačić
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Harald Kotisch
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Nicholas G Brown
- Department of Pharmacology and Lineberger Comprehensive Cancer CenterUniversity of North Carolina School of MedicineChapel HillNCUSA
| | - David Haselbach
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
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3
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Anand J, Chiou L, Sciandra C, Zhang X, Hong J, Wu D, Zhou P, Vaziri C. Roles of trans-lesion synthesis (TLS) DNA polymerases in tumorigenesis and cancer therapy. NAR Cancer 2023; 5:zcad005. [PMID: 36755961 PMCID: PMC9900426 DOI: 10.1093/narcan/zcad005] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/10/2022] [Accepted: 01/30/2023] [Indexed: 02/08/2023] Open
Abstract
DNA damage tolerance and mutagenesis are hallmarks and enabling characteristics of neoplastic cells that drive tumorigenesis and allow cancer cells to resist therapy. The 'Y-family' trans-lesion synthesis (TLS) DNA polymerases enable cells to replicate damaged genomes, thereby conferring DNA damage tolerance. Moreover, Y-family DNA polymerases are inherently error-prone and cause mutations. Therefore, TLS DNA polymerases are potential mediators of important tumorigenic phenotypes. The skin cancer-propensity syndrome xeroderma pigmentosum-variant (XPV) results from defects in the Y-family DNA Polymerase Pol eta (Polη) and compensatory deployment of alternative inappropriate DNA polymerases. However, the extent to which dysregulated TLS contributes to the underlying etiology of other human cancers is unclear. Here we consider the broad impact of TLS polymerases on tumorigenesis and cancer therapy. We survey the ways in which TLS DNA polymerases are pathologically altered in cancer. We summarize evidence that TLS polymerases shape cancer genomes, and review studies implicating dysregulated TLS as a driver of carcinogenesis. Because many cancer treatment regimens comprise DNA-damaging agents, pharmacological inhibition of TLS is an attractive strategy for sensitizing tumors to genotoxic therapies. Therefore, we discuss the pharmacological tractability of the TLS pathway and summarize recent progress on development of TLS inhibitors for therapeutic purposes.
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Affiliation(s)
- Jay Anand
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
| | - Lilly Chiou
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Carly Sciandra
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xingyuan Zhang
- Department of Biostatistics, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3101 McGavran-Greenberg Hall, Chapel Hill, NC 27599, USA
| | - Jiyong Hong
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Di Wu
- Department of Biostatistics, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3101 McGavran-Greenberg Hall, Chapel Hill, NC 27599, USA
| | - Pei Zhou
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
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4
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Eckert KA. Nontraditional Roles of DNA Polymerase Eta Support Genome Duplication and Stability. Genes (Basel) 2023; 14:genes14010175. [PMID: 36672916 PMCID: PMC9858799 DOI: 10.3390/genes14010175] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
DNA polymerase eta (Pol η) is a Y-family polymerase and the product of the POLH gene. Autosomal recessive inheritance of POLH mutations is the cause of the xeroderma pigmentosum variant, a cancer predisposition syndrome. This review summarizes mounting evidence for expanded Pol η cellular functions in addition to DNA lesion bypass that are critical for maintaining genome stability. In vitro, Pol η displays efficient DNA synthesis through difficult-to-replicate sequences, catalyzes D-loop extensions, and utilizes RNA-DNA hybrid templates. Human Pol η is constitutively present at the replication fork. In response to replication stress, Pol η is upregulated at the transcriptional and protein levels, and post-translational modifications regulate its localization to chromatin. Numerous studies show that Pol η is required for efficient common fragile site replication and stability. Additionally, Pol η can be recruited to stalled replication forks through protein-protein interactions, suggesting a broader role in replication fork recovery. During somatic hypermutations, Pol η is recruited by mismatch repair proteins and is essential for VH gene A:T basepair mutagenesis. Within the global context of repeat-dense genomes, the recruitment of Pol η to perform specialized functions during replication could promote genome stability by interrupting pure repeat arrays with base substitutions. Alternatively, not engaging Pol η in genome duplication is costly, as the absence of Pol η leads to incomplete replication and increased chromosomal instability.
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Affiliation(s)
- Kristin A Eckert
- Gittlen Cancer Research Laboratories, Department of Pathology, Penn State University College of Medicine, 500 University Drive, Hershey, PA 17036, USA
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5
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Burgess EF, Sanders JA, Livasy C, Symanowski J, Gatalica Z, Steuerwald NM, Arguello D, Brouwer CR, Korn WM, Grigg CM, Zhu J, Matulay JT, Clark PE, Heath EI, Raghavan D. Identification of potential biomarkers and novel therapeutic targets through genomic analysis of small cell bladder carcinoma and associated clinical outcomes. Urol Oncol 2022; 40:383.e1-383.e10. [DOI: 10.1016/j.urolonc.2022.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/09/2022] [Accepted: 04/28/2022] [Indexed: 11/27/2022]
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6
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Liu MH, Wang CR, Liu WJ, Tian XR, Xu Q, Zhang CY. Construction of a dephosphorylation-mediated chemiluminescent biosensor for multiplexed detection of DNA glycosylases in cancer cells. J Mater Chem B 2022; 10:3277-3284. [PMID: 35362489 DOI: 10.1039/d2tb00491g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA glycosylases are engaged in the base excision repair process and play a vital role in maintaining genomic integrity. It remains a challenge for multiplexed detection of DNA glycosylases in cancer cells. Herein, we demonstrate the construction of a dephosphorylation-mediated chemiluminescent biosensor for multiplexed detection of human alkyladenine DNA glycosylase (hAAG) and uracil DNA glycosylase (UDG) in cancer cells. In this biosensor, the generation of chemiluminescence signals relies on the dephosphorylation of 3-(2'-spiroadamantyl)-4-methoxy-4-(3''-phosphoryloxyphenyl)-1,2-dioxetane (AMPPD) catalyzed by alkaline phosphatase (ALP). We design a bifunctional double-stranded DNA (dsDNA) substrate, a biotin-labelled poly-(T) probe, and two capture probes for the hAAG and UDG assay. This assay involves four steps including (1) the cleavage of the bifunctional dsDNA substrate induced by DNA glycosylases, (2) the recognition of the 3'-OH terminus of the primer by TdT and the subsequent TdT-mediated polymerization reaction, (3) the construction of the AuNPs-dsDNA-ALP nanostructures, and (4) the streptavidin-alkaline phosphatase (SA-ALP)-initiated dephosphorylation of AMPPD for the generation of an enhanced chemiluminescence signal. By taking advantage of the unique features of TdT-mediated polymerization and the intrinsic superiority of the ALP-AMPPD-based chemiluminescence system, this biosensor exhibits good specificity and high sensitivity with a detection limit of 1.53 × 10-6 U mL-1 for hAAG and 1.77 × 10-6 U mL-1 for UDG, and it can even quantify multiple DNA glycosylases at the single-cell level. Moreover, this biosensor can be applied for the measurement of kinetic parameters and the screening of DNA glycosylase inhibitors, holding great potential in DNA damage-related biomedical research and disease diagnostics.
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Affiliation(s)
- Ming-Hao Liu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
| | - Chuan-Rui Wang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
| | - Wen-Jing Liu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Xiao-Rui Tian
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
| | - Qinfeng Xu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
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7
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Pereira AC, De Pascale J, Resende R, Cardoso S, Ferreira I, Neves BM, Carrascal MA, Zuzarte M, Madeira N, Morais S, Macedo A, do Carmo A, Moreira PI, Cruz MT, Pereira CF. ER-mitochondria communication is involved in NLRP3 inflammasome activation under stress conditions in the innate immune system. Cell Mol Life Sci 2022; 79:213. [PMID: 35344105 PMCID: PMC11072401 DOI: 10.1007/s00018-022-04211-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 12/11/2022]
Abstract
Endoplasmic reticulum (ER) stress and mitochondrial dysfunction, which are key events in the initiation and/or progression of several diseases, are correlated with alterations at ER-mitochondria contact sites, the so-called "Mitochondria-Associated Membranes" (MAMs). These intracellular structures are also implicated in NLRP3 inflammasome activation which is an important driver of sterile inflammation, however, the underlying molecular basis remains unclear. This work aimed to investigate the role of ER-mitochondria communication during ER stress-induced NLRP3 inflammasome activation in both peripheral and central innate immune systems, by using THP-1 human monocytes and BV2 microglia cells, respectively, as in vitro models. Markers of ER stress, mitochondrial dynamics and mass, as well as NLRP3 inflammasome activation were evaluated by Western Blot, IL-1β secretion was measured by ELISA, and ER-mitochondria contacts were quantified by transmission electron microscopy. Mitochondrial Ca2+ uptake and polarization were analyzed with fluorescent probes, and measurement of aconitase and SOD2 activities monitored mitochondrial ROS accumulation. ER stress was demonstrated to activate the NLRP3 inflammasome in both peripheral and central immune cells. Studies in monocytes indicate that ER stress-induced NLRP3 inflammasome activation occurs by a Ca2+-dependent and ROS-independent mechanism, which is coupled with upregulation of MAMs-resident chaperones, closer ER-mitochondria contacts, as well as mitochondrial depolarization and impaired dynamics. Moreover, enhanced ER stress-induced NLRP3 inflammasome activation in the immune system was found associated with pathological conditions since it was observed in monocytes derived from bipolar disorder (BD) patients, supporting a pro-inflammatory status in BD. In conclusion, by demonstrating that ER-mitochondria communication plays a key role in the response of the innate immune cells to ER stress, this work contributes to elucidate the molecular mechanisms underlying NLRP3 inflammasome activation under stress conditions, and to disclose novel potential therapeutic targets for diseases associated with sterile inflammation.
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Affiliation(s)
- Ana Catarina Pereira
- CNC-Center for Neuroscience and Cell Biology, CIBB-Center for Innovative Biomedicine and Biotechnology, University Coimbra, Coimbra, Portugal
- Faculty of Medicine, University Coimbra, Coimbra, Portugal
- CACC-Clinical Academic Center of Coimbra, Coimbra, Portugal
| | - Jessica De Pascale
- CNC-Center for Neuroscience and Cell Biology, CIBB-Center for Innovative Biomedicine and Biotechnology, University Coimbra, Coimbra, Portugal
| | - Rosa Resende
- CNC-Center for Neuroscience and Cell Biology, CIBB-Center for Innovative Biomedicine and Biotechnology, University Coimbra, Coimbra, Portugal
- CACC-Clinical Academic Center of Coimbra, Coimbra, Portugal
| | - Susana Cardoso
- CNC-Center for Neuroscience and Cell Biology, CIBB-Center for Innovative Biomedicine and Biotechnology, University Coimbra, Coimbra, Portugal
- CACC-Clinical Academic Center of Coimbra, Coimbra, Portugal
| | - Isabel Ferreira
- CNC-Center for Neuroscience and Cell Biology, CIBB-Center for Innovative Biomedicine and Biotechnology, University Coimbra, Coimbra, Portugal
- CACC-Clinical Academic Center of Coimbra, Coimbra, Portugal
- Faculty of Pharmacy, University Coimbra, Coimbra, Portugal
| | - Bruno Miguel Neves
- iBiMED-Department of Medical Sciences and Institute for Biomedicine, University Aveiro, Aveiro, Portugal
| | - Mylène A Carrascal
- CACC-Clinical Academic Center of Coimbra, Coimbra, Portugal
- Tecnimede Group, Sintra, Portugal
| | - Mónica Zuzarte
- Faculty of Medicine, University Coimbra, Coimbra, Portugal
- CACC-Clinical Academic Center of Coimbra, Coimbra, Portugal
- iCBR-Institute for Clinical and Biomedical Research, University Coimbra, Coimbra, Portugal
| | - Nuno Madeira
- Faculty of Medicine, University Coimbra, Coimbra, Portugal
- CACC-Clinical Academic Center of Coimbra, Coimbra, Portugal
- CIBIT-Coimbra Institute for Biomedical Imaging and Translational Research, University Coimbra, Coimbra, Portugal
- Department of Psychiatry, CHUC-UC-Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Sofia Morais
- Faculty of Medicine, University Coimbra, Coimbra, Portugal
- CACC-Clinical Academic Center of Coimbra, Coimbra, Portugal
- Department of Psychiatry, CHUC-UC-Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - António Macedo
- Faculty of Medicine, University Coimbra, Coimbra, Portugal
- CACC-Clinical Academic Center of Coimbra, Coimbra, Portugal
- Department of Psychiatry, CHUC-UC-Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Anália do Carmo
- CACC-Clinical Academic Center of Coimbra, Coimbra, Portugal
- Department of Clinical Pathology, CHUC-UC-Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Paula I Moreira
- CNC-Center for Neuroscience and Cell Biology, CIBB-Center for Innovative Biomedicine and Biotechnology, University Coimbra, Coimbra, Portugal
- Faculty of Medicine, University Coimbra, Coimbra, Portugal
- CACC-Clinical Academic Center of Coimbra, Coimbra, Portugal
| | - Maria Teresa Cruz
- CNC-Center for Neuroscience and Cell Biology, CIBB-Center for Innovative Biomedicine and Biotechnology, University Coimbra, Coimbra, Portugal
- CACC-Clinical Academic Center of Coimbra, Coimbra, Portugal
- Faculty of Pharmacy, University Coimbra, Coimbra, Portugal
| | - Cláudia F Pereira
- CNC-Center for Neuroscience and Cell Biology, CIBB-Center for Innovative Biomedicine and Biotechnology, University Coimbra, Coimbra, Portugal.
- Faculty of Medicine, University Coimbra, Coimbra, Portugal.
- CACC-Clinical Academic Center of Coimbra, Coimbra, Portugal.
- , Coimbra, Portugal.
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Tian X, Wang X, Cui Z, Liu J, Huang X, Shi C, Zhang M, Liu T, Du X, Li R, Huang L, Gong D, Tian R, Cao C, Jin P, Zeng Z, Pan G, Xia M, Zhang H, Luo B, Xie Y, Li X, Li T, Wu J, Zhang Q, Chen G, Hu Z. A Fifteen-Gene Classifier to Predict Neoadjuvant Chemotherapy Responses in Patients with Stage IB to IIB Squamous Cervical Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2001978. [PMID: 34026427 PMCID: PMC8132153 DOI: 10.1002/advs.202001978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 02/01/2021] [Indexed: 05/09/2023]
Abstract
Neoadjuvant chemotherapy (NACT) remains an attractive alternative for controlling locally advanced cervical cancer. However, approximately 15-34% of women do not respond to induction therapy. To develop a risk stratification tool, 56 patients with stage IB-IIB cervical cancer are included in 2 research centers from the discovery cohort. Patient-specific somatic mutations led to NACT non-responsiveness are identified by whole-exome sequencing. Next, CRISPR/Cas9-based library screenings are performed based on these genes to confirm their biological contribution to drug resistance. A 15-gene classifier is developed by generalized linear regression analysis combined with the logistic regression model. In an independent validation cohort of 102 patients, the classifier showed good predictive ability with an area under the curve of 0.80 (95% confidence interval (CI), 0.69-0.91). Furthermore, the 15-gene classifier is significantly associated with patient responsiveness to NACT in both univariate (odds ratio, 10.8; 95% CI, 3.55-32.86; p = 2.8 × 10-5) and multivariate analysis (odds ratio, 17.34; 95% CI, 4.04-74.40; p = 1.23 × 10-4) in the validation set. In conclusion, the 15-gene classifier can accurately predict the clinical response to NACT before treatment, representing a promising approach for guiding the selection of appropriate treatment strategies for locally advanced cervical cancer.
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Affiliation(s)
- Xun Tian
- Department of Obstetrics and GynecologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
- Department of Obstetrics and GynecologyAcademician expert workstation, The Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Xin Wang
- Department of Obstetrics and GynecologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Zifeng Cui
- Department of Gynecological and OncologyThe First Affiliated Hospital of Sun Yat‐sen UniversityZhongshan 2nd Road, YuexiuGuangzhouGuangdong510080China
| | - Jia Liu
- Department of Obstetrics and GynecologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Xiaoyuan Huang
- Department of Obstetrics and GynecologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Caixia Shi
- Department of Gynecological and OncologyHunan Cancer HospitalThe Affiliated Cancer Hospital of Xiangya School of MedicineCentral South UniversityJiefang Avenue 1095#WuhanHubei430030China
| | - Min Zhang
- NGS Research CenterNovogene Co, LtdBuilding 301, Zone A10 JiuxianqiaoBeijing100015China
| | - Ting Liu
- Department of Obstetrics and GynecologyAcademician expert workstation, The Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Xiaofang Du
- Department of Obstetrics and GynecologyAcademician expert workstation, The Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Rui Li
- Department of Obstetrics and GynecologyAcademician expert workstation, The Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Lei Huang
- Department of Obstetrics and GynecologyAcademician expert workstation, The Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Danni Gong
- Department of Obstetrics and GynecologyAcademician expert workstation, The Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Rui Tian
- Department of Gynecological and OncologyThe First Affiliated Hospital of Sun Yat‐sen UniversityZhongshan 2nd Road, YuexiuGuangzhouGuangdong510080China
| | - Chen Cao
- Department of Obstetrics and GynecologyAcademician expert workstation, The Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Ping Jin
- Department of Obstetrics and GynecologyAcademician expert workstation, The Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Zhen Zeng
- Department of Obstetrics and GynecologyAcademician expert workstation, The Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Guangxin Pan
- Department of Obstetrics and GynecologyAcademician expert workstation, The Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Meng Xia
- Department of Obstetrics and GynecologyAcademician expert workstation, The Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Hongfeng Zhang
- Department of PathologyThe Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyShengli Street 26#, Jiang'an DistrictWuhanHubei430030China
| | - Bo Luo
- Department of PathologyThe Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyShengli Street 26#, Jiang'an DistrictWuhanHubei430030China
| | - Yonghui Xie
- Department of PathologyThe Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyShengli Street 26#, Jiang'an DistrictWuhanHubei430030China
| | - Xiaoming Li
- Department of Obstetrics and GynecologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Tianye Li
- Department of Obstetrics and GynecologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Jun Wu
- NGS Research CenterNovogene Co, LtdBuilding 301, Zone A10 JiuxianqiaoBeijing100015China
| | - Qinghua Zhang
- Department of Obstetrics and GynecologyAcademician expert workstation, The Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Gang Chen
- Department of Obstetrics and GynecologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
| | - Zheng Hu
- Department of Obstetrics and GynecologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
- Department of Obstetrics and GynecologyAcademician expert workstation, The Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyJiefang Avenue 1095#WuhanHubei430030China
- Department of Gynecological and OncologyThe First Affiliated Hospital of Sun Yat‐sen UniversityZhongshan 2nd Road, YuexiuGuangzhouGuangdong510080China
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Maiorano D, El Etri J, Franchet C, Hoffmann JS. Translesion Synthesis or Repair by Specialized DNA Polymerases Limits Excessive Genomic Instability upon Replication Stress. Int J Mol Sci 2021; 22:3924. [PMID: 33920223 PMCID: PMC8069355 DOI: 10.3390/ijms22083924] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/02/2021] [Accepted: 04/06/2021] [Indexed: 12/15/2022] Open
Abstract
DNA can experience "replication stress", an important source of genome instability, induced by various external or endogenous impediments that slow down or stall DNA synthesis. While genome instability is largely documented to favor both tumor formation and heterogeneity, as well as drug resistance, conversely, excessive instability appears to suppress tumorigenesis and is associated with improved prognosis. These findings support the view that karyotypic diversity, necessary to adapt to selective pressures, may be limited in tumors so as to reduce the risk of excessive instability. This review aims to highlight the contribution of specialized DNA polymerases in limiting extreme genetic instability by allowing DNA replication to occur even in the presence of DNA damage, to either avoid broken forks or favor their repair after collapse. These mechanisms and their key regulators Rad18 and Polθ not only offer diversity and evolutionary advantage by increasing mutagenic events, but also provide cancer cells with a way to escape anti-cancer therapies that target replication forks.
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Affiliation(s)
- Domenico Maiorano
- Institute of Human Genetics, UMR9002, CNRS-University of Montpellier, 34396 Montpellier, France; (D.M.); (J.E.E.)
| | - Jana El Etri
- Institute of Human Genetics, UMR9002, CNRS-University of Montpellier, 34396 Montpellier, France; (D.M.); (J.E.E.)
| | - Camille Franchet
- Laboratoire D’Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 Avenue Irène-Joliot-Curie, 31059 Toulouse, France;
| | - Jean-Sébastien Hoffmann
- Laboratoire D’Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 Avenue Irène-Joliot-Curie, 31059 Toulouse, France;
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Gu YF, Ge XP. UBR5 inhibits the radiosensitivity of non-small cell lung cancer cells via the activation of the PI3K/AKT pathway. J Investig Med 2021; 69:970-975. [PMID: 33811132 DOI: 10.1136/jim-2020-001736] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2021] [Indexed: 12/25/2022]
Abstract
Ubiquitin protein ligase E3 component n-recognin 5 (UBR5) has been identified as an oncogene in diverse cancers; however, whether its expression was associated with radiosensitivities of non-small cell lung cancer (NSCLC) cells remains unclear. Expression levels of UBR5 in NSCLC tissues and cell lines were examined by immunohistochemical staining and western blotting. Colony formation assay, CCK-8 cell viability assay, flow cytometry, and caspase-3 activity assay were performed to evaluate the radiosensitization of UBR5 knockdown in NSCLC cells, and the underlying mechanism in vitro was also investigated. UBR5 was highly expressed in NSCLC tissues, and its high expression was associated with the poor prognosis in 50 patients with NSCLC. After X-ray irradiation, the protein expression levels of UBR5 were also increased in NSCLC cells. UBR5 inhibition enhanced the radiosensitivity of NSCLC cells by inhibiting the cell viability and inducing apoptosis. Further investigation indicated that UBR5 knockdown-mediated radiosensitization involved the phosphatidylinositol 3-kinase (PI3K)/AKT signaling pathway. Knockdown of UBR5 radiosensitizes NSCLC cells via the inactivation of the PI3K/AKT signal, which provided a novel therapeutic target for NSCLC radiosensitization.
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Affiliation(s)
- Yong-Fei Gu
- Radiotherapy Department, Second Ward, Yantai Yantai Shan Hospital, Yantai, Shandong, China
| | - Xing-Ping Ge
- Radiotherapy Department, Second Ward, Yantai Yantai Shan Hospital, Yantai, Shandong, China
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11
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Unravelling roles of error-prone DNA polymerases in shaping cancer genomes. Oncogene 2021; 40:6549-6565. [PMID: 34663880 PMCID: PMC8639439 DOI: 10.1038/s41388-021-02032-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/01/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022]
Abstract
Mutagenesis is a key hallmark and enabling characteristic of cancer cells, yet the diverse underlying mutagenic mechanisms that shape cancer genomes are not understood. This review will consider the emerging challenge of determining how DNA damage response pathways-both tolerance and repair-act upon specific forms of DNA damage to generate mutations characteristic of tumors. DNA polymerases are typically the ultimate mutagenic effectors of DNA repair pathways. Therefore, understanding the contributions of DNA polymerases is critical to develop a more comprehensive picture of mutagenic mechanisms in tumors. Selection of an appropriate DNA polymerase-whether error-free or error-prone-for a particular DNA template is critical to the maintenance of genome stability. We review different modes of DNA polymerase dysregulation including mutation, polymorphism, and over-expression of the polymerases themselves or their associated activators. Based upon recent findings connecting DNA polymerases with specific mechanisms of mutagenesis, we propose that compensation for DNA repair defects by error-prone polymerases may be a general paradigm molding the mutational landscape of cancer cells. Notably, we demonstrate that correlation of error-prone polymerase expression with mutation burden in a subset of patient tumors from The Cancer Genome Atlas can identify mechanistic hypotheses for further testing. We contrast experimental approaches from broad, genome-wide strategies to approaches with a narrower focus on a few hundred base pairs of DNA. In addition, we consider recent developments in computational annotation of patient tumor data to identify patterns of mutagenesis. Finally, we discuss the innovations and future experiments that will develop a more comprehensive portrait of mutagenic mechanisms in human tumors.
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12
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Wu PS, Enervald E, Joelsson A, Palmberg C, Rutishauser D, Hällberg BM, Ström L. Post-translational Regulation of DNA Polymerase η, a Connection to Damage-Induced Cohesion in Saccharomyces cerevisiae. Genetics 2020; 216:1009-1022. [PMID: 33033113 PMCID: PMC7768261 DOI: 10.1534/genetics.120.303494] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 10/06/2020] [Indexed: 12/11/2022] Open
Abstract
Double-strand breaks that are induced postreplication trigger establishment of damage-induced cohesion in Saccharomyces cerevisiae, locally at the break site and genome-wide on undamaged chromosomes. The translesion synthesis polymerase, polymerase η, is required for generation of damage-induced cohesion genome-wide. However, its precise role and regulation in this process is unclear. Here, we investigated the possibility that the cyclin-dependent kinase Cdc28 and the acetyltransferase Eco1 modulate polymerase η activity. Through in vitro phosphorylation and structure modeling, we showed that polymerase η is an attractive substrate for Cdc28 Mutation of the putative Cdc28-phosphorylation site Ser14 to Ala not only affected polymerase η protein level, but also prevented generation of damage-induced cohesion in vivo We also demonstrated that Eco1 acetylated polymerase η in vitro Certain nonacetylatable polymerase η mutants showed reduced protein level, deficient nuclear accumulation, and increased ultraviolet irradiation sensitivity. In addition, we found that both Eco1 and subunits of the cohesin network are required for cell survival after ultraviolet irradiation. Our findings support functionally important Cdc28-mediated phosphorylation, as well as post-translational modifications of multiple lysine residues that modulate polymerase η activity, and provide new insights into understanding the regulation of polymerase η for damage-induced cohesion.
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Affiliation(s)
- Pei-Shang Wu
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Elin Enervald
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Angelica Joelsson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Carina Palmberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Dorothea Rutishauser
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Lena Ström
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm SE-171 77, Sweden
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13
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Guo H, Xie J, Liao T, Tuo X. Exploring the binding mode of donepezil with calf thymus DNA using spectroscopic and molecular docking methods. LUMINESCENCE 2020; 36:35-44. [PMID: 32614132 DOI: 10.1002/bio.3911] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 06/18/2020] [Accepted: 06/30/2020] [Indexed: 01/21/2023]
Abstract
Donepezil (DNP) is one of approved drugs to treat Alzheimer's disease (AD). However, the potential effect of DNP on DNA is still unclear. Therefore, the interaction of DNP with calf thymus DNA (DNA) was studied in vitro using spectroscopic and molecular docking methods. Steady-state and transient fluorescence experiments showed that there was a clear binding interaction between DNP and DNA, resulting from DNP fluorescence being quenched using DNA. DNP and DNA have one binding site between them, and the binding constant (Kb ) was 0.78 × 104 L·mol-1 at 298 K. In this binding process, hydrophobic force was the main interaction force, because enthalpy change (ΔH) and entropy change (ΔS) of DNP-DNA were 67.92 kJ·mol-1 and 302.96 J·mol-1 ·K-1 , respectively. DNP bound to DNA in a groove-binding mode, which was verified using a competition displacement study and other typical spectroscopic methods. Fourier transform infrared (FTIR) spectrum results showed that DNP interacted with guanine (G) and cytosine (C) bases of DNA. The molecular docking results further supported the results of spectroscopic experiments, and suggested that both Pi-Sigma force and Pi-Alkyl force were the major hydrophobic force functioning between DNP and DNA.
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Affiliation(s)
- Hui Guo
- College of Chemistry, Nanchang University, Nanchang, Jiangxi, China
| | - Jiawen Xie
- College of Chemistry, Nanchang University, Nanchang, Jiangxi, China
| | - Tancong Liao
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Xun Tuo
- College of Chemistry, Nanchang University, Nanchang, Jiangxi, China
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Leboeuf D, Abakumova T, Prikazchikova T, Rhym L, Anderson DG, Zatsepin TS, Piatkov KI. Downregulation of the Arg/N-degron Pathway Sensitizes Cancer Cells to Chemotherapy In Vivo. Mol Ther 2020; 28:1092-1104. [PMID: 32087767 DOI: 10.1016/j.ymthe.2020.01.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/16/2020] [Indexed: 02/07/2023] Open
Abstract
The N-degron pathway is an emerging target for anti-tumor therapies, because of its capacity to positively regulate many hallmarks of cancer, including angiogenesis, cell proliferation, motility, and survival. Thus, inhibition of the N-degron pathway offers the potential to be a highly effective anti-cancer treatment. With the use of a small interfering RNA (siRNA)-mediated approach for selective downregulation of the four Arg/N-degron-dependent ubiquitin ligases, UBR1, UBR2, UBR4, and UBR5, we demonstrated decreased cell migration and proliferation and increased spontaneous apoptosis in cancer cells. Chronic treatment with lipid nanoparticles (LNPs) loaded with siRNA in mice efficiently downregulates the expression of UBR-ubiquitin ligases in the liver without any significant toxic effects but engages the immune system and causes inflammation. However, when used in a lower dose, in combination with a chemotherapeutic drug, downregulation of the Arg/N-degron pathway E3 ligases successfully reduced tumor load by decreasing proliferation and increasing apoptosis in a mouse model of hepatocellular carcinoma, while avoiding the inflammatory response. Our study demonstrates that UBR-ubiquitin ligases of the Arg/N-degron pathway are promising targets for the development of improved therapies for many cancer types.
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Affiliation(s)
| | | | | | - Luke Rhym
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Daniel G Anderson
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard and MIT Division of Health Science and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
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