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Frye CC, Tennant L, Yeager A, Azimzadeh P, Bhardwaj P, Xu Y, Liu J, Othoum G, Maher CA, Chernock R, Goedegebuure SP, Gillanders W, Olson JA, Brown TC. Overexpression of human DNA polymerase theta is a biomarker of aggressive and DNA repair-deficient papillary thyroid cancers. Surgery 2024; 176:1380-1387. [PMID: 38897886 DOI: 10.1016/j.surg.2024.05.006] [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: 08/07/2023] [Revised: 04/19/2024] [Accepted: 05/05/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND DNA polymerase theta (POLQ) is an enzyme that repairs double-strand DNA breaks. POLQ is overexpressed in several cancer types, and increased expression is associated with a poor prognosis. Ablating POLQ function in vitro increases drug sensitivity to agents that cause double-strand DNA breaks, including chemotherapies and ionizing radiation. POLQ's role in thyroid cancer remains poorly understood. METHODS Expression of POLQ and other genes of interest were analyzed in 513 papillary thyroid cancers (505 primary tumors and 8 metastatic lesions) and 59 normal thyroid samples available in the Cancer Genome Atlas. The Cancer Genome Atlas RNA and DNA sequencing data were queried with the Xena platform. The Recombination Proficiency Score was calculated to assess DNA repair efficiency. Other signaling events associated with thyroid tumorigenesis and clinical outcomes were analyzed. Univariate and multivariate analyses were performed. Treatment with the POLQ inhibitors ART558 and Novobiocin tested the effect of POLQ inhibition on in vitro thyroid cancer growth. RESULTS POLQ expression was increased in papillary thyroid cancers compared to normal thyroid tissue (P < .05). POLQ expression levels were inversely correlated with Recombination Proficiency Score levels (P < .05). POLQ expression was highest in tall cell papillary thyroid cancers and in metastases. Higher POLQ expression was also associated with dedifferentiation, BRAF signaling, and shorter progression-free intervals (P < .05). Treatment with POLQ inhibitors decreased in vitro thyroid cancer growth (P < .05). CONCLUSION These findings suggest that increased POLQ expression could serve as a valuable clinical marker and a potential therapeutic target in the treatment of thyroid cancer.
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Affiliation(s)
- C Corbin Frye
- Department of Surgery, Section of Surgical Oncology, Washington University School of Medicine, Saint Louis, MO.
| | - Lena Tennant
- Department of Surgery, Section of Surgical Oncology, Washington University School of Medicine, Saint Louis, MO
| | - Ashley Yeager
- Department of Surgery, Section of Surgical Oncology, Washington University School of Medicine, Saint Louis, MO
| | - Pedram Azimzadeh
- Department of Surgery, Section of Surgical Oncology, Washington University School of Medicine, Saint Louis, MO
| | - Priya Bhardwaj
- Department of Surgery, Section of Surgical Oncology, Washington University School of Medicine, Saint Louis, MO
| | - Yifei Xu
- Department of Surgery, Division of Public Health Sciences, Washington University School of Medicine, St. Louis, MO
| | - Jingxia Liu
- Department of Surgery, Division of Public Health Sciences, Washington University School of Medicine, St. Louis, MO
| | - Ghofran Othoum
- Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, MO
| | - Christopher A Maher
- Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, MO
| | - Rebecca Chernock
- Department of Pathology and Immunology, Division of Anatomic and Molecular Pathology, Washington University School of Medicine, Saint Louis, MO
| | - S Peter Goedegebuure
- Department of Surgery, Section of Surgical Oncology, Washington University School of Medicine, Saint Louis, MO
| | - William Gillanders
- Department of Surgery, Section of Surgical Oncology, Washington University School of Medicine, Saint Louis, MO
| | - John A Olson
- Department of Surgery, Section of Surgical Oncology, Washington University School of Medicine, Saint Louis, MO
| | - Taylor C Brown
- Department of Surgery, Section of Surgical Oncology, Washington University School of Medicine, Saint Louis, MO
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Thomas C, Green S, Kimball L, Schmidtke IR, Rothwell L, Griffin M, Par I, Schobel S, Palacio Y, Towle-Weicksel JB, Weicksel SE. Zebrafish Pol-Theta and Human Pol-Theta, Orthologues with Homologous Function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.27.615541. [PMID: 39386538 PMCID: PMC11463350 DOI: 10.1101/2024.09.27.615541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
DNA polymerase theta (Pol θ)is a conserved an A-family polymerase that plays an essential role in repairing double strand breaks, through micro-homology end joining, and bypassing DNA lesions, through translesion synthesis, to protect genome integrity. Despite its essential role in DNA repair, Pol θ is inherently error prone. Recently, Pol θ has been identified in various cancer types, suggesting Pol θ's promiscuous nature aids in cancer progression. Here we present a study comparing the structure and function of the polymerase domain of zebrafish and human Pol θ to determine the potential of zebrafish as a model for Pol θ function. We show that these two proteins share a large amount of sequence and structural homology, but differ in key loop areas thought to drive defining functions of the enzyme. Despite these differences zebrafish Pol θ still displays characteristics identify in human Pol θ, including DNA template extension, microhomology-mediated end joining, and translesion synthesis. Additionally, we found several important residues within loops of the polymerase domain that support function unique to Pol θ. These results will support future studies with zebrafish as a model to investigate Pol θ function.
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3
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Ouyang Y, Al-Amodi A, Tehseen M, Alhudhali L, Shirbini A, Takahashi M, Raducanu VS, Yi G, Danazumi A, De Biasio A, Hamdan S. Single-molecule characterization of SV40 replisome and novel factors: human FPC and Mcm10. Nucleic Acids Res 2024; 52:8880-8896. [PMID: 38967018 PMCID: PMC11347169 DOI: 10.1093/nar/gkae565] [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: 08/27/2023] [Revised: 06/06/2024] [Accepted: 06/18/2024] [Indexed: 07/06/2024] Open
Abstract
The simian virus 40 (SV40) replisome only encodes for its helicase; large T-antigen (L-Tag), while relying on the host for the remaining proteins, making it an intriguing model system. Despite being one of the earliest reconstituted eukaryotic systems, the interactions coordinating its activities and the identification of new factors remain largely unexplored. Herein, we in vitro reconstituted the SV40 replisome activities at the single-molecule level, including DNA unwinding by L-Tag and the single-stranded DNA-binding protein Replication Protein A (RPA), primer extension by DNA polymerase δ, and their concerted leading-strand synthesis. We show that RPA stimulates the processivity of L-Tag without altering its rate and that DNA polymerase δ forms a stable complex with L-Tag during leading-strand synthesis. Furthermore, similar to human and budding yeast Cdc45-MCM-GINS helicase, L-Tag uses the fork protection complex (FPC) and the mini-chromosome maintenance protein 10 (Mcm10) during synthesis. Hereby, we demonstrate that FPC increases this rate, and both FPC and Mcm10 increase the processivity by stabilizing stalled replisomes and increasing their chances of restarting synthesis. The detailed kinetics and novel factors of the SV40 replisome establish it as a closer mimic of the host replisome and expand its application as a model replication system.
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Affiliation(s)
- Yujing Ouyang
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Amani Al-Amodi
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Muhammad Tehseen
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Lubna Alhudhali
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Afnan Shirbini
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Masateru Takahashi
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Vlad-Stefan Raducanu
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Gang Yi
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Ammar Usman Danazumi
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Alfredo De Biasio
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Samir M Hamdan
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
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4
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Blanch JR, Krishnamurthy M, McVey M. A non-tethering role for the Drosophila Pol θ linker domain in promoting damage resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.27.609911. [PMID: 39253446 PMCID: PMC11383001 DOI: 10.1101/2024.08.27.609911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
DNA polymerase theta ( Pol θ ) is an error-prone translesion polymerase that becomes crucial for DNA double-strand break repair when cells are deficient in homologous recombination or non-homologous end joining. In some organisms, Pol θ also promotes tolerance of DNA interstrand crosslinks. Due to its importance in DNA damage tolerance, Pol θ is an emerging target for treatment of cancer and disease. Prior work has characterized the functions of the Pol θ helicase-like and polymerase domains, but the roles of the linker domain are largely unknown. Here, we show that the Drosophila melanogaster Pol θ linker domain promotes egg development and is required for tolerance of DNA double-strand breaks and interstrand crosslinks. While a linker domain with scrambled amino acid residues is sufficient for DNA repair, replacement of the linker with part of the Homo sapiens Pol θ linker or a disordered region from the FUS RNA-binding protein does not restore function. These results demonstrate that the linker domain is not simply a random tether between the helicase-like and polymerase domains. Furthermore, they suggest that intrinsic amino acid residue properties, rather than protein interaction motifs, are more critical for Pol θ linker functions in DNA repair.
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Affiliation(s)
- Justin R Blanch
- Department of Biology, Tufts University, Medford, Massachusetts, 02155, United States of America
| | - Manan Krishnamurthy
- Department of Biology, Tufts University, Medford, Massachusetts, 02155, United States of America
- Icahn School of Medicine at Mount Sinai, New York City, New York, 10029, United States of America
| | - Mitch McVey
- Department of Biology, Tufts University, Medford, Massachusetts, 02155, United States of America
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5
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Bazan Russo TD, Mujacic C, Di Giovanni E, Vitale MC, Ferrante Bannera C, Randazzo U, Contino S, Bono M, Gristina V, Galvano A, Perez A, Badalamenti G, Russo A, Bazan V, Incorvaia L. Polθ: emerging synthetic lethal partner in homologous recombination-deficient tumors. Cancer Gene Ther 2024:10.1038/s41417-024-00815-2. [PMID: 39122831 DOI: 10.1038/s41417-024-00815-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024]
Abstract
The most remarkable finding in synthetic lethality (SL) is the hypersensitivity to PARP inhibitors (PARPis) of the tumors harboring defects in genes involved in homologous repair (HR) such as BRCA1/2. Despite initial responsiveness to PARPi, the penetrance of the synthetic lethal interactions between BRCA1/2 genes and PARPi is incomplete. Thus, a significant proportion of HR-defective tumors experience intrinsic or acquired resistance, representing a key challenge of clinical research. An expanded concept of SL is opening new ways and includes novel forms of genetic interactions, investigating not only traditional SL of pairs genes but also SL between biological pathways that regulate the same essential survival cell function. In this context, recent research showed that HR and theta-mediated end-joining (TMEJ) pathways exhibit SL. DNA polymerase theta (Polθ) is encoded by the POLQ gene and is a key component of the TMEJ, an essential backup pathway, intrinsically mutagenic, to repair resected double-strand breaks (DSBs) when the non-homologous end joining (NHEJ) and HR are impaired. Polθ is broadly expressed in normal tissues, overexpressed in several cancers, and typically associated with poor outcomes and shorter relapse-free survival. Notably, HR-deficient tumor cells present the characteristic mutational signatures of the error-prone TMEJ pathway. According to this observation, the loss of HR proteins, such as BRCA1 or BRCA2, contributes to increasing the TMEJ-specific genomic profile, suggesting synthetic lethal interactions between loss of the POLQ and HR genes, and resulting in the emerging interest for Polθ as a potential therapeutic target in BRCA1/2-associated tumors.This review summarizes the converging roles of the POLQ and HR genes in DNA DSB repair, the early-stage clinical trials using Polθ inhibitor to treat HR-defective tumors and to overcome BRCA-reversion mutations responsible for therapeutic resistance, and the novel pleiotropic effects of Polθ, paving the way for the development of unexplored synthetic lethality strategies.
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Affiliation(s)
- Tancredi Didier Bazan Russo
- Department of Precision Medicine in Medical, Surgical and Critical Care (Me.Pre.C.C.), Section of Medical Oncology, University of Palermo, 90127, Palermo, Italy
| | - Clarissa Mujacic
- Department of Precision Medicine in Medical, Surgical and Critical Care (Me.Pre.C.C.), Section of Medical Oncology, University of Palermo, 90127, Palermo, Italy
| | - Emilia Di Giovanni
- Department of Precision Medicine in Medical, Surgical and Critical Care (Me.Pre.C.C.), Section of Medical Oncology, University of Palermo, 90127, Palermo, Italy
| | - Maria Concetta Vitale
- Department of Precision Medicine in Medical, Surgical and Critical Care (Me.Pre.C.C.), Section of Medical Oncology, University of Palermo, 90127, Palermo, Italy
| | - Carla Ferrante Bannera
- Department of Precision Medicine in Medical, Surgical and Critical Care (Me.Pre.C.C.), Section of Medical Oncology, University of Palermo, 90127, Palermo, Italy
| | - Ugo Randazzo
- Department of Precision Medicine in Medical, Surgical and Critical Care (Me.Pre.C.C.), Section of Medical Oncology, University of Palermo, 90127, Palermo, Italy
| | - Silvia Contino
- Department of Precision Medicine in Medical, Surgical and Critical Care (Me.Pre.C.C.), Section of Medical Oncology, University of Palermo, 90127, Palermo, Italy
| | - Marco Bono
- Department of Precision Medicine in Medical, Surgical and Critical Care (Me.Pre.C.C.), Section of Medical Oncology, University of Palermo, 90127, Palermo, Italy
| | - Valerio Gristina
- Department of Precision Medicine in Medical, Surgical and Critical Care (Me.Pre.C.C.), Section of Medical Oncology, University of Palermo, 90127, Palermo, Italy
| | - Antonio Galvano
- Department of Precision Medicine in Medical, Surgical and Critical Care (Me.Pre.C.C.), Section of Medical Oncology, University of Palermo, 90127, Palermo, Italy
| | - Alessandro Perez
- Department of Precision Medicine in Medical, Surgical and Critical Care (Me.Pre.C.C.), Section of Medical Oncology, University of Palermo, 90127, Palermo, Italy
| | - Giuseppe Badalamenti
- Department of Precision Medicine in Medical, Surgical and Critical Care (Me.Pre.C.C.), Section of Medical Oncology, University of Palermo, 90127, Palermo, Italy.
| | - Antonio Russo
- Department of Precision Medicine in Medical, Surgical and Critical Care (Me.Pre.C.C.), Section of Medical Oncology, University of Palermo, 90127, Palermo, Italy.
| | - Viviana Bazan
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), Section of Medical Oncology, University of Palermo, 90127, Palermo, Italy
| | - Lorena Incorvaia
- Department of Precision Medicine in Medical, Surgical and Critical Care (Me.Pre.C.C.), Section of Medical Oncology, University of Palermo, 90127, Palermo, Italy
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6
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Liang P, Peng M, Tao J, Wang B, Wei J, Lin L, Cheng B, Xiong S, Li J, Li C, Yu Z, Li C, Wang J, Li H, Chen Z, Fan J, Liang W, He J. Development of a genome atlas for discriminating benign, preinvasive, and invasive lung nodules. MedComm (Beijing) 2024; 5:e644. [PMID: 39036344 PMCID: PMC11258453 DOI: 10.1002/mco2.644] [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: 12/26/2023] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 07/23/2024] Open
Abstract
To tackle misdiagnosis in lung cancer screening with low-dose computed tomography (LDCT), we aimed to compile a genome atlas for differentiating benign, preinvasive, and invasive lung nodules and characterize their molecular pathogenesis. We collected 432 lung nodule tissue samples from Chinese patients, spanning benign, atypical adenomatous hyperplasia (AAH), adenocarcinoma in situ (AIS), minimally invasive adenocarcinoma (MIA), and invasive adenocarcinoma (IA). We performed comprehensive sequencing, examining somatic variants, gene expressions, and methylation levels. Our findings uncovered EGFR and TP53 mutations as key drivers in - early lung cancer development, with EGFR mutation frequency increasing with disease progression. Both EGFR mutations and EGF/EGFR hypo-methylation activated the EGFR pathway, fueling cancer growth. Transcriptome analysis identified four lung nodule subtypes (G1-4) with distinct molecular features and immune cell infiltrations: EGFR-driven G1, EGFR/TP53 co-mutation G2, inflamed G3, stem-like G4. Estrogen/androgen response was associated with the EGFR pathway, proposing a new therapy combining tyrosine kinase inhibitors with antiestrogens. Preinvasive nodules exhibited stem cell pathway enrichment, potentially hindering invasion. Epigenetic regulation of various genes was essential for lung cancer initiation and development. This study provides insights into the molecular mechanism of neoplastic progression and identifies potential diagnostic biomarkers and therapeutic targets for lung cancer.
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Affiliation(s)
- Peng Liang
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
| | - Minhua Peng
- AnchorDx Medical Co., LtdGuangzhouGuangdongChina
| | - Jinsheng Tao
- AnchorDx Medical Co., LtdGuangzhouGuangdongChina
| | - Bo Wang
- AnchorDx Medical Co., LtdGuangzhouGuangdongChina
| | - Jinwang Wei
- Department of Data ScienceGenomicare Biotechnology (Shanghai) Co., Ltd.ShanghaiChina
- Department of Data ScienceShanghai CreateCured Biotechnology Co., Ltd.ShanghaiChina
| | - Lixuan Lin
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
| | - Bo Cheng
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
| | - Shan Xiong
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
| | - Jianfu Li
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
| | - Caichen Li
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
| | - Ziwen Yu
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
| | - Chunyan Li
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
| | - Jun Wang
- AnchorDx Medical Co., LtdGuangzhouGuangdongChina
| | - Hui Li
- AnchorDx Medical Co., LtdGuangzhouGuangdongChina
| | - Zhiwei Chen
- AnchorDx Medical Co., LtdGuangzhouGuangdongChina
- AnchorDx Inc.FremontCaliforniaUSA
| | - Jian‐Bing Fan
- AnchorDx Medical Co., LtdGuangzhouGuangdongChina
- Department of PathologySouthern Medical UniversityGuangzhouGuangdongChina
| | - Wenhua Liang
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
| | - Jianxing He
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
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Previtali V, Bagnolini G, Ciamarone A, Ferrandi G, Rinaldi F, Myers SH, Roberti M, Cavalli A. New Horizons of Synthetic Lethality in Cancer: Current Development and Future Perspectives. J Med Chem 2024; 67:11488-11521. [PMID: 38955347 DOI: 10.1021/acs.jmedchem.4c00113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
In recent years, synthetic lethality has been recognized as a solid paradigm for anticancer therapies. The discovery of a growing number of synthetic lethal targets has led to a significant expansion in the use of synthetic lethality, far beyond poly(ADP-ribose) polymerase inhibitors used to treat BRCA1/2-defective tumors. In particular, molecular targets within DNA damage response have provided a source of inhibitors that have rapidly reached clinical trials. This Perspective focuses on the most recent progress in synthetic lethal targets and their inhibitors, within and beyond the DNA damage response, describing their design and associated therapeutic strategies. We will conclude by discussing the current challenges and new opportunities for this promising field of research, to stimulate discussion in the medicinal chemistry community, allowing the investigation of synthetic lethality to reach its full potential.
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Affiliation(s)
- Viola Previtali
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Greta Bagnolini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Andrea Ciamarone
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Giovanni Ferrandi
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Francesco Rinaldi
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Samuel Harry Myers
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Marinella Roberti
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Andrea Cavalli
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
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Thomas C, Avalos-Irving L, Victorino J, Green S, Andrews M, Rodrigues N, Ebirim S, Mudd A, Towle-Weicksel JB. Melanoma-Derived DNA Polymerase Theta Variants Exhibit Altered DNA Polymerase Activity. Biochemistry 2024; 63:1107-1117. [PMID: 38671548 PMCID: PMC11080051 DOI: 10.1021/acs.biochem.3c00670] [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: 11/29/2023] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024]
Abstract
DNA polymerase θ (Pol θ or POLQ) is primarily involved in repairing double-stranded breaks in DNA through an alternative pathway known as microhomology-mediated end joining (MMEJ) or theta-mediated end joining (TMEJ). Unlike other DNA repair polymerases, Pol θ is thought to be highly error-prone yet critical for cell survival. We have identified several POLQ gene variants from human melanoma tumors that experience altered DNA polymerase activity, including a propensity for incorrect nucleotide selection and reduced polymerization rates compared to WT Pol θ. Variants are 30-fold less efficient at incorporating a nucleotide during repair and up to 70-fold less accurate at selecting the correct nucleotide opposite a templating base. This suggests that aberrant Pol θ has reduced DNA repair capabilities and may also contribute to increased mutagenesis. Moreover, the variants were identified in established tumors, suggesting that cancer cells may use mutated polymerases to promote metastasis and drug resistance.
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Affiliation(s)
- Corey Thomas
- Department of Physical Sciences, Rhode Island College, 600 Mount Pleasant Avenue, Providence, Rhode Island 02908, United States
| | - Lisbeth Avalos-Irving
- Department of Physical Sciences, Rhode Island College, 600 Mount Pleasant Avenue, Providence, Rhode Island 02908, United States
| | - Jorge Victorino
- Department of Physical Sciences, Rhode Island College, 600 Mount Pleasant Avenue, Providence, Rhode Island 02908, United States
| | - Sydney Green
- Department of Physical Sciences, Rhode Island College, 600 Mount Pleasant Avenue, Providence, Rhode Island 02908, United States
| | - Morgan Andrews
- Department of Physical Sciences, Rhode Island College, 600 Mount Pleasant Avenue, Providence, Rhode Island 02908, United States
| | - Naisha Rodrigues
- Department of Physical Sciences, Rhode Island College, 600 Mount Pleasant Avenue, Providence, Rhode Island 02908, United States
| | - Sarah Ebirim
- Department of Physical Sciences, Rhode Island College, 600 Mount Pleasant Avenue, Providence, Rhode Island 02908, United States
| | - Ayden Mudd
- Department of Physical Sciences, Rhode Island College, 600 Mount Pleasant Avenue, Providence, Rhode Island 02908, United States
| | - Jamie B. Towle-Weicksel
- Department of Physical Sciences, Rhode Island College, 600 Mount Pleasant Avenue, Providence, Rhode Island 02908, United States
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Yue W, Wang J, Lin B, Fu Y. Identifying lncRNAs and mRNAs related to survival of NSCLC based on bioinformatic analysis and machine learning. Aging (Albany NY) 2024; 16:7799-7817. [PMID: 38696317 PMCID: PMC11131976 DOI: 10.18632/aging.205783] [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: 02/03/2023] [Accepted: 12/06/2023] [Indexed: 05/04/2024]
Abstract
Non-small cell lung cancer (NSCLC) is the most common histopathological type, and it is purposeful for screening potential prognostic biomarkers for NSCLC. This study aims to identify the lncRNAs and mRNAs related to survival of non-small cell lung cancer (NSCLC). The expression profile data of lung adenocarcinoma and lung squamous cell carcinoma were downloaded in The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) dataset. A total of eight survival related long non-coding RNAs (lncRNAs) and 262 survival related mRNAs were filtered. By gene set enrichment analysis, 17 significantly correlated Gene Ontology signal pathways and 14 Kyoto Encyclopedia of Genes and Genomes signal pathways were screened. Based on the clinical survival and prognosis information of the samples, we screened eight lncRNAs and 193 mRNAs by single factor Cox regression analysis. Further single and multifactor Cox regression analysis were performed, 30 independent prognostication-related mRNAs were obtained. The PPI network was further constructed. We then performed the machine learning algorithms (Least absolute shrinkage and selection operator, Recursive feature elimination, and Random forest) to screen the optimized DEGs combination, and a total of 17 overlapping mRNAs were obtained. Based on the 17 characteristic mRNAs obtained, we firstly built a Nomogram prediction model, and the ROC values of training set and testing set were 0.835 and 0.767, respectively. By overlapping the 17 characteristic mRNAs and PPI network hub genes, three genes were obtained: CDC6, CEP55, TYMS, which were considered as key factors associated with survival of NSCLC. The in vitro experiments were performed to examine the effect of CDC6, CEP55, and TYMS on NSCLC cells. Finally, the lncRNAs-mRNAs networks were constructed.
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Affiliation(s)
- Wei Yue
- Innovation Centre for Information, Binjiang Institute of Zhejiang University, Hangzhou 310053, China
| | - Jing Wang
- Innovation Centre for Information, Binjiang Institute of Zhejiang University, Hangzhou 310053, China
| | - Bo Lin
- Innovation Centre for Information, Binjiang Institute of Zhejiang University, Hangzhou 310053, China
- College of Computer Science and Technology, Zhejiang University, Hangzhou 310027, China
| | - Yongping Fu
- Department of Cardiovascular Medicine, Affiliated Hospital of Shaoxing University, Shaoxing 312099, China
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10
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Yuan B, Bi C, Tian Y, Wang J, Jin Y, Alsayegh K, Tehseen M, Yi G, Zhou X, Shao Y, Romero FV, Fischle W, Izpisua Belmonte JC, Hamdan S, Huang Y, Li M. Modulation of the microhomology-mediated end joining pathway suppresses large deletions and enhances homology-directed repair following CRISPR-Cas9-induced DNA breaks. BMC Biol 2024; 22:101. [PMID: 38685010 PMCID: PMC11059712 DOI: 10.1186/s12915-024-01896-z] [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: 06/12/2023] [Accepted: 04/18/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND CRISPR-Cas9 genome editing often induces unintended, large genomic rearrangements, posing potential safety risks. However, there are no methods for mitigating these risks. RESULTS Using long-read individual-molecule sequencing (IDMseq), we found the microhomology-mediated end joining (MMEJ) DNA repair pathway plays a predominant role in Cas9-induced large deletions (LDs). We targeted MMEJ-associated genes genetically and/or pharmacologically and analyzed Cas9-induced LDs at multiple gene loci using flow cytometry and long-read sequencing. Reducing POLQ levels or activity significantly decreases LDs, while depleting or overexpressing RPA increases or reduces LD frequency, respectively. Interestingly, small-molecule inhibition of POLQ and delivery of recombinant RPA proteins also dramatically promote homology-directed repair (HDR) at multiple disease-relevant gene loci in human pluripotent stem cells and hematopoietic progenitor cells. CONCLUSIONS Our findings reveal the contrasting roles of RPA and POLQ in Cas9-induced LD and HDR, suggesting new strategies for safer and more precise genome editing.
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Affiliation(s)
- Baolei Yuan
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Chongwei Bi
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Yeteng Tian
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Jincheng Wang
- Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, College of Chemistry, College of Engineering, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yiqing Jin
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Khaled Alsayegh
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Present address: King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNG-HA), Jeddah, Saudi Arabia
| | - Muhammad Tehseen
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Gang Yi
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Xuan Zhou
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | | | - Fernanda Vargas Romero
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Wolfgang Fischle
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Juan Carlos Izpisua Belmonte
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Altos Labs, Inc, San Diego, CA, 92121, USA
| | - Samir Hamdan
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Yanyi Huang
- Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, College of Chemistry, College of Engineering, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen, China
| | - Mo Li
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
- Bioengineering Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
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11
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He Y, Chen Y, Li Z, Wu C. The m 6A demethylase FTO targets POLQ to promote ccRCC cell proliferation and genome stability maintenance. J Cancer Res Clin Oncol 2024; 150:30. [PMID: 38270643 PMCID: PMC10810938 DOI: 10.1007/s00432-023-05541-0] [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: 10/01/2023] [Accepted: 12/04/2023] [Indexed: 01/26/2024]
Abstract
BACKGROUND AND AIM As the first identified m6A demethylase, FTO has been implicated in the progression of various cancers. However, the specific mechanism of FTO in clear cell renal cell carcinoma (ccRCC) remains incompletely understood. In this study, we aimed to explore the potential molecular mechanisms influencing the progression of ccRCC. METHODS We initially assessed the expression of FTO in tumor and adjacent tissues using TCGA database, RT-qPCR, and Western blot. We then conducted CCK-8, cell cycle analysis, and colony formation assay to investigate the impact of FTO on ccRCC cell proliferation. MeRIP-seq and RNA-seq were employed to identify potential downstream targets of FTO in ccRCC, and these findings were further validated through dual-luciferase reporter assays and MeRIP-qPCR. Then, DNA damage and cell death were assessed separately through gammaH2AX immunofluorescence detection and the LIVE/DEAD Fixable Dead Cell Stain assay, respectively. Subsequently, we identified downstream pathways influenced by FTO's regulation of POLQ through TCGA database analysis and GSEA enrichment analysis. Validation was carried out through Western blot. RESULTS FTO is highly expressed in ccRCC tissues and cell lines. Furthermore, ROC curve demonstrates that FTO contributes to the diagnosis of ccRCC. FTO modulates m6A modification, consequently influencing the expression of POLQ, thus facilitating cell proliferation and maintaining genome stability in ccRCC. CONCLUSION FTO could potentially serve as a diagnostic marker for ccRCC. FTO promotes the progression of ccRCC by regulating m6A modification, making the inhibition of FTO a potential novel therapeutic strategy in ccRCC.
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Affiliation(s)
- Yichen He
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, China
- Institute of Cell Therapy, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, China
- Department of Urology, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, China
| | - Yimeng Chen
- Department of Urology, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, China
| | - Zhengsheng Li
- Department of Urology, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, China
| | - Changping Wu
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, China.
- Institute of Cell Therapy, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, China.
- Department of Oncology, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, China.
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12
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Hsieh MJ, Lo YS, Ho HY, Lin CC, Chuang YC, Chen MK. The Interaction between CLSPN Gene Polymorphisms and Alcohol Consumption Contributes to Oral Cancer Progression. Int J Mol Sci 2024; 25:1098. [PMID: 38256171 PMCID: PMC10816373 DOI: 10.3390/ijms25021098] [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: 11/03/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
Most disease single nucleotide polymorphisms (SNPs) are regulatory and approximately half of heritability is occupied by the top 1% of genes, with the gene-level structure varying with the number of variants associated with the most common alleles. Cancer occurrence and progression are significantly affected by Claspin (CLSPN) gene polymorphism present in the population, which alters the expression, function, and regulation of the gene. CLSPN genotypes are associated with oral cancer, but the literature on this association is limited. As a result, the goal of this study is to investigate the correlation between CLSPN genotypes and oral cancers' development. This study will explore the presence of four CLSPN SNPs including rs12058760, rs16822339, rs535638 and rs7520495 gene polymorphisms, and analyze the expression of these genes in 304 cancer-free controls and 402 oral squamous cell carcinoma (OSCC) cases. Attempts have been made to obtain insight into the role of CLSPN gene polymorphisms in oral cancer through the analysis of this study. We demonstrated that the OSCC risk of individuals with four CLSPN SNPs relative to the wild type did not differ significantly from that of the wild type when the polymorphisms are analyzed according to individual habits. We further studied the mechanism by which CLSPN polymorphisms affect the progression of clinicopathological features in OSCC patients. The results of the degree of cell differentiation showed that compared with patients of rs7520495 SNP carrying the CC genotype, the incidence of poor cell differentiation in patients carrying the CC + GG genotype was higher (AOR: 1.998-fold; 95% CI, 1.127-3.545; p = 0.018). In particular, patients with the G genotype of rs7520495 had increased poor cell differentiation compared with patients with the C genotype (AOR: 4.736-fold; 95% CI, 1.306-17.178; p = 0.018), especially in the drinking group. On the basis of our analysis of the Cancer Genome Atlas dataset, we found that higher CLSPN levels were associated with poorer cell differentiation in oral cancers. In this study, we provide the first evidence showing that CLSPN SNPs contribute to oral cancer. Whether or not rs7520495 can be used as a confirmatory factor in the future is uncertain, but it seems likely that it can be used as an important factor in predicting recurrence, response to treatment and medication toxicity to patients with oral cancer.
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Affiliation(s)
- Ming-Ju Hsieh
- Oral Cancer Research Center, Changhua Christian Hospital, Changhua 500, Taiwan
- Doctoral Program in Tissue Engineering and Regenerative Medicine, College of Medicine, National Chung Hsing University, Taichung 402, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404, Taiwan
| | - Yu-Sheng Lo
- Oral Cancer Research Center, Changhua Christian Hospital, Changhua 500, Taiwan
| | - Hsin-Yu Ho
- Oral Cancer Research Center, Changhua Christian Hospital, Changhua 500, Taiwan
| | - Chia-Chieh Lin
- Oral Cancer Research Center, Changhua Christian Hospital, Changhua 500, Taiwan
| | - Yi-Ching Chuang
- Oral Cancer Research Center, Changhua Christian Hospital, Changhua 500, Taiwan
| | - Mu-Kuan Chen
- Department of Otorhinolaryngology, Head and Neck Surgery, Changhua Christian Hospital, Changhua 500, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung 402, Taiwan
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13
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Thomas C, Avalos-Irving L, Victorino J, Green S, Andrews M, Rodrigues N, Ebirim S, Mudd A, Towle-Weicksel JB. Melanoma-derived DNA polymerase theta variants exhibit altered DNA polymerase activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.566933. [PMID: 38014040 PMCID: PMC10680777 DOI: 10.1101/2023.11.14.566933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
DNA Polymerase θ (Pol θ or POLQ) is primarily involved in repairing double-stranded breaks in DNA through the alternative pathway known as microhomology-mediated end joining (MMEJ) or theta-mediated end joining (TMEJ). Unlike other DNA repair polymerases, Pol θ is thought to be highly error prone, yet critical for cell survival. We have identified several mutations in the POLQ gene from human melanoma tumors. Through biochemical analysis, we have demonstrated that all three cancer-associated variants experienced altered DNA polymerase activity including a propensity for incorrect nucleotide selection and reduced polymerization rates compared to WT Pol θ. Moreover, the variants are 30 fold less efficient at incorporating a nucleotide during repair and up to 70 fold less accurate at selecting the correct nucleotide opposite a templating base. Taken together, this suggests that aberrant Pol θ has reduced DNA repair capabilities and may also contribute to increased mutagenesis. While this may be beneficial to normal cell survival, the variants were identified in established tumors suggesting that cancer cells may use this promiscuous polymerase to its advantage to promote metastasis and drug resistance.
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14
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Abbasi SF, Mahjabeen I, Parveen N, Qamar I, Haq MFU, Shafique R, Saeed N, Ashraf NS, Kayani MA. Exploring homologous recombination repair and base excision repair pathway genes for possible diagnostic markers in hematologic malignancies. Mol Genet Genomics 2023; 298:1527-1543. [PMID: 37861816 DOI: 10.1007/s00438-023-02078-2] [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: 03/20/2023] [Accepted: 10/04/2023] [Indexed: 10/21/2023]
Abstract
Hematologic malignancies (HMs) are a collection of malignant transformations, originating from the cells in the bone marrow and lymphoid organs. HMs comprise three main types; leukemia, lymphoma, and multiple myeloma. Globally, HMS accounts for approximately 10% of newly diagnosed cancer. DNA repair pathways defend the cells from recurrent DNA damage. Defective DNA repair mechanisms such as homologous recombination repair (HRR), nucleotide excision repair (NER), and base excision repair (BER) pathways may lead to genomic instability, which initiates HM progression and carcinogenesis. Expression deregulation of HRR, NER, and BER has been investigated in various malignancies. However, no studies have been reported to assess the differential expression of selected DNA repair genes combinedly in HMs. The present study was designed to assess the differential expression of HRR and BER pathway genes including RAD51, XRCC2, XRCC3, APEX1, FEN1, PARP1, and XRCC1 in blood cancer patients to highlight their significance as diagnostic/ prognostic marker in hematological malignancies. The study cohort comprised of 210 blood cancer patients along with an equal number of controls. For expression analysis, q-RT PCR was performed. DNA damage was measured in blood cancer patients and controls using the comet assay and LORD Q-assay. Data analysis showed significant downregulation of selected genes in blood cancer patients compared to healthy controls. To check the diagnostic value of selected genes, the Area under curve (AUC) was calculated and 0.879 AUC was observed for RAD51 (p < 0.0001) and 0.830 (p < 0.0001) for APEX1. Kaplan-Meier analysis showed that downregulation of RAD51 (p < 0.0001), XRCC3 (p < 0.02), and APEX1 (p < 0.0001) was found to be associated with a significant decrease in survival of blood cancer patients. Cox regression analysis showed that deregulation of RAD51 (p < 0.0001), XRCC2 (p < 0.02), XRCC3 (p < 0.003), and APEX1 (p < 0.00001) was found to be associated with the poor prognosis of blood cancer patients. Comet assay showed an increased number of comets in blood cancer patients compared to controls. These results are confirmed by performing the LORD q-assay and an increased frequency of lesions/Kb was observed in selected genes in cancer patients compared to controls. Our results showed significant downregulation of RAD51, XRCC2, XRCC3, APEX1, FEN1, PARP1, and XRCC1 genes with increased DNA damage in blood cancer patients. The findings of the current research suggested that deregulated expression of HRR and BER pathway genes can act as a diagnostic/prognostic marker in hematologic malignancies.
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Affiliation(s)
- Sumaira Fida Abbasi
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
| | - Ishrat Mahjabeen
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan.
| | - Neelam Parveen
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
| | - Imama Qamar
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
| | - Maria Fazal Ul Haq
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
| | - Rabia Shafique
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
| | - Nadia Saeed
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
| | - Nida Sarosh Ashraf
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
| | - Mahmood Akhtar Kayani
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
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15
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Shi S, Wen G, Lei C, Chang J, Yin X, Liu X, Huang S. A DNA Replication Stress-Based Prognostic Model for Lung Adenocarcinoma. Acta Naturae 2023; 15:100-110. [PMID: 37908773 PMCID: PMC10615186 DOI: 10.32607/actanaturae.25112] [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: 07/08/2023] [Accepted: 09/25/2023] [Indexed: 11/02/2023] Open
Abstract
Tumor cells endure continuous DNA replication stress, which opens the way to cancer development. Despite previous research, the prognostic implications of DNA replication stress on lung adenocarcinoma (LUAD) have yet to be investigated. Here, we aimed to investigate the potential of DNA replication stress-related genes (DNARSs) in predicting the prognosis of individuals with LUAD. Differentially expressed genes (DEGs) originated from the TCGA-LUAD dataset, and we constructed a 10-gene LUAD prognostic model based on DNARSs-related DEGs (DRSDs) using Cox regression analysis. The receiver operating characteristic (ROC) curve demonstrated excellent predictive capability for the LUAD prognostic model, while the Kaplan-Meier survival curve indicated a poorer prognosis in a high-risk (HR) group. Combined with clinical data, the Riskscore was found to be an independent predictor of LUAD prognosis. By incorporating Riskscore and clinical data, we developed a nomogram that demonstrated a capacity to predict overall survival and exhibited clinical utility, which was validated through the calibration curve, ROC curve, and decision curve analysis curve tests, confirming its effectiveness in prognostic evaluation. Immune analysis revealed that individuals belonging to the low-risk (LR) group exhibited a greater abundance of immune cell infiltration and higher levels of immune function. We calculated the immunopheno score and TIDE scores and tested them on the IMvigor210 and GSE78220 cohorts and found that individuals categorized in the LR group exhibited a higher likelihood of deriving therapeutic benefits from immunotherapy intervention. Additionally, we predicted that patients classified in the HR group would demonstrate enhanced sensitivity to Docetaxel using anti-tumor drugs. To summarize, we successfully developed and validated a prognostic model for LUAD by incorporating DNA replication stress as a key factor.
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Affiliation(s)
- S. Shi
- Department of Cardiothoracic Surgery, The People’s Hospital of Dazu District, Chongqing, 402360 China
| | - G. Wen
- Department of Cardiothoracic Surgery, The People’s Hospital of Dazu District, Chongqing, 402360 China
| | - C. Lei
- Department of Cardiothoracic Surgery, The People’s Hospital of Dazu District, Chongqing, 402360 China
| | - J. Chang
- Department of Cardiothoracic Surgery, The People’s Hospital of Dazu District, Chongqing, 402360 China
| | - X. Yin
- Department of Cardiothoracic Surgery, The People’s Hospital of Dazu District, Chongqing, 402360 China
| | - X. Liu
- Department of Cardiothoracic Surgery, The People’s Hospital of Dazu District, Chongqing, 402360 China
| | - S. Huang
- Department of Orthopedics, The People’s Hospital of Dazu District, Chongqing, 402360 China
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16
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Oh G, Wang A, Wang L, Li J, Werba G, Weissinger D, Zhao E, Dhara S, Hernandez RE, Ackermann A, Porcella S, Kalfakakou D, Dolgalev I, Kawaler E, Golan T, Welling TH, Sfeir A, Simeone DM. POLQ inhibition elicits an immune response in homologous recombination-deficient pancreatic adenocarcinoma via cGAS/STING signaling. J Clin Invest 2023; 133:e165934. [PMID: 36976649 PMCID: PMC10232002 DOI: 10.1172/jci165934] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy that harbors mutations in homologous recombination-repair (HR-repair) proteins in 20%-25% of cases. Defects in HR impart a specific vulnerability to poly ADP ribose polymerase inhibitors and platinum-containing chemotherapy in tumor cells. However, not all patients who receive these therapies respond, and many who initially respond ultimately develop resistance. Inactivation of the HR pathway is associated with the overexpression of polymerase theta (Polθ, or POLQ). This key enzyme regulates the microhomology-mediated end-joining (MMEJ) pathway of double-strand break (DSB) repair. Using human and murine HR-deficient PDAC models, we found that POLQ knockdown is synthetically lethal in combination with mutations in HR genes such as BRCA1 and BRCA2 and the DNA damage repair gene ATM. Further, POLQ knockdown enhances cytosolic micronuclei formation and activates signaling of cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING), leading to enhanced infiltration of activated CD8+ T cells in BRCA2-deficient PDAC tumors in vivo. Overall, POLQ, a key mediator in the MMEJ pathway, is critical for DSB repair in BRCA2-deficient PDAC. Its inhibition represents a synthetic lethal approach to blocking tumor growth while concurrently activating the cGAS-STING signaling pathway to enhance tumor immune infiltration, highlighting what we believe to be a new role for POLQ in the tumor immune environment.
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Affiliation(s)
| | | | - Lidong Wang
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, USA
| | - Jiufeng Li
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, USA
| | - Gregor Werba
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, USA
| | - Daniel Weissinger
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, USA
| | - Ende Zhao
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, USA
| | - Surajit Dhara
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, USA
| | | | - Amanda Ackermann
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, USA
| | - Sarina Porcella
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Igor Dolgalev
- Department of Pathology, NYU Langone Health, New York, New York, USA
| | - Emily Kawaler
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, USA
| | | | | | - Agnel Sfeir
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Diane M. Simeone
- Department of Surgery and
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, USA
- Department of Pathology, NYU Langone Health, New York, New York, USA
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17
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Pismataro MC, Astolfi A, Barreca ML, Pacetti M, Schenone S, Bandiera T, Carbone A, Massari S. Small Molecules Targeting DNA Polymerase Theta (POLθ) as Promising Synthetic Lethal Agents for Precision Cancer Therapy. J Med Chem 2023; 66:6498-6522. [PMID: 37134182 DOI: 10.1021/acs.jmedchem.2c02101] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Synthetic lethality (SL) is an innovative strategy in targeted anticancer therapy that exploits tumor genetic vulnerabilities. This topic has come to the forefront in recent years, as witnessed by the increased number of publications since 2007. The first proof of concept for the effectiveness of SL was provided by the approval of poly(ADP-ribose)polymerase inhibitors, which exploit a SL interaction in BRCA-deficient cells, although their use is limited by resistance. Searching for additional SL interactions involving BRCA mutations, the DNA polymerase theta (POLθ) emerged as an exciting target. This review summarizes, for the first time, the POLθ polymerase and helicase inhibitors reported to date. Compounds are described focusing on chemical structure and biological activity. With the aim to enable further drug discovery efforts in interrogating POLθ as a target, we propose a plausible pharmacophore model for POLθ-pol inhibitors and provide a structural analysis of the known POLθ ligand binding sites.
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Affiliation(s)
- Maria Chiara Pismataro
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Andrea Astolfi
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Maria Letizia Barreca
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Martina Pacetti
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Silvia Schenone
- Department of Pharmacy, University of Genoa, Viale Benedetto XV 3, 16132 Genoa, Italy
| | - Tiziano Bandiera
- D3 PharmaChemistry, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Anna Carbone
- Department of Pharmacy, University of Genoa, Viale Benedetto XV 3, 16132 Genoa, Italy
| | - Serena Massari
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
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18
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Multifaceted Nature of DNA Polymerase θ. Int J Mol Sci 2023; 24:ijms24043619. [PMID: 36835031 PMCID: PMC9962433 DOI: 10.3390/ijms24043619] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/26/2023] [Accepted: 02/02/2023] [Indexed: 02/15/2023] Open
Abstract
DNA polymerase θ belongs to the A family of DNA polymerases and plays a key role in DNA repair and damage tolerance, including double-strand break repair and DNA translesion synthesis. Pol θ is often overexpressed in cancer cells and promotes their resistance to chemotherapeutic agents. In this review, we discuss unique biochemical properties and structural features of Pol θ, its multiple roles in protection of genome stability and the potential of Pol θ as a target for cancer treatment.
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19
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Plasma Extracellular Vesicle Long RNA in Diagnosis and Prediction in Small Cell Lung Cancer. Cancers (Basel) 2022; 14:cancers14225493. [PMID: 36428585 PMCID: PMC9688902 DOI: 10.3390/cancers14225493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/23/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022] Open
Abstract
(1) Introduction: The aim of this study was to identify the plasma extracellular vesicle (EV)-specific transcriptional profile in small-cell lung cancer (SCLC) and to explore the application value of plasma EV long RNA (exLR) in SCLC treatment prediction and diagnosis. (2) Methods: Plasma samples were collected from 57 SCLC treatment-naive patients, 104 non-small-cell lung cancer (NSCLC) patients and 59 healthy participants. The SCLC patients were divided into chemo-sensitive and chemo-refractory groups based on the therapeutic effects. The exLR profiles of the plasma samples were analyzed by high-throughput sequencing. Bioinformatics approaches were used to investigate the differentially expressed exLRs and their biofunctions. Finally, a t-signature was constructed using logistic regression for SCLC treatment prediction and diagnosis. (3) Results: We obtained 220 plasma exLRs profiles in all the participants. Totals of 5787 and 1207 differentially expressed exLRs were identified between SCLC/healthy controls, between the chemo-sensitive/chemo-refractory groups, respectively. Furthermore, we constructed a t-signature that comprised ten exLRs, including EPCAM, CCNE2, CDC6, KRT8, LAMB1, CALB2, STMN1, UCHL1, HOXB7 and CDCA7, for SCLC treatment prediction and diagnosis. The exLR t-score effectively distinguished the chemo-sensitive from the chemo-refractory group (p = 9.268 × 10-9) with an area under the receiver operating characteristic curve (AUC) of 0.9091 (95% CI: 0.837 to 0.9811) and distinguished SCLC from healthy controls (AUC: 0.9643; 95% CI: 0.9256-1) and NSCLC (AUC: 0.721; 95% CI: 0.6384-0.8036). (4) Conclusions: This study firstly characterized the plasma exLR profiles of SCLC patients and verified the feasibility and value of identifying biomarkers based on exLR profiles in SCLC diagnosis and treatment prediction.
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20
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Liddiard K, Aston-Evans AN, Cleal K, Hendrickson E, Baird D. POLQ suppresses genome instability and alterations in DNA repeat tract lengths. NAR Cancer 2022; 4:zcac020. [PMID: 35774233 PMCID: PMC9241439 DOI: 10.1093/narcan/zcac020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/19/2022] [Accepted: 06/10/2022] [Indexed: 11/26/2022] Open
Abstract
DNA polymerase theta (POLQ) is a principal component of the alternative non-homologous end-joining (ANHEJ) DNA repair pathway that ligates DNA double-strand breaks. Utilizing independent models of POLQ insufficiency during telomere-driven crisis, we found that POLQ - /- cells are resistant to crisis-induced growth deceleration despite sustaining inter-chromosomal telomere fusion frequencies equivalent to wild-type (WT) cells. We recorded longer telomeres in POLQ - / - than WT cells pre- and post-crisis, notwithstanding elevated total telomere erosion and fusion rates. POLQ - /- cells emerging from crisis exhibited reduced incidence of clonal gross chromosomal abnormalities in accordance with increased genetic heterogeneity. High-throughput sequencing of telomere fusion amplicons from POLQ-deficient cells revealed significantly raised frequencies of inter-chromosomal fusions with correspondingly depreciated intra-chromosomal recombinations. Long-range interactions culminating in telomere fusions with centromere alpha-satellite repeats, as well as expansions in HSAT2 and HSAT3 satellite and contractions in ribosomal DNA repeats, were detected in POLQ - / - cells. In conjunction with the expanded telomere lengths of POLQ - /- cells, these results indicate a hitherto unrealized capacity of POLQ for regulation of repeat arrays within the genome. Our findings uncover novel considerations for the efficacy of POLQ inhibitors in clinical cancer interventions, where potential genome destabilizing consequences could drive clonal evolution and resistant disease.
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Affiliation(s)
- Kate Liddiard
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Alys N Aston-Evans
- Dementia Research Institute, School of Medicine, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff CF24 4HQ, UK
| | - Kez Cleal
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Duncan M Baird
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
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21
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DNA Polymerase Theta Plays a Critical Role in Pancreatic Cancer Development and Metastasis. Cancers (Basel) 2022; 14:cancers14174077. [PMID: 36077614 PMCID: PMC9454495 DOI: 10.3390/cancers14174077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC), due to its genomic heterogeneity and lack of effective treatment, despite decades of intensive research, will become the second leading cause of cancer-related deaths by 2030. Step-wise acquisition of mutations, due to genomic instability, is considered to drive the development of PDAC; the KRAS mutation occurs in 95 to 100% of human PDAC, and is already detectable in early premalignant lesions designated as pancreatic intraepithelial neoplasia (PanIN). This mutation is possibly the key event leading to genomic instability and PDAC development. Our study aimed to investigate the role of the error-prone DNA double-strand breaks (DSBs) repair pathway, alt-EJ, in the presence of the KRAS G12D mutation in pancreatic cancer development. Our findings show that oncogenic KRAS contributes to increasing the expression of Polθ, Lig3, and Mre11, key components of alt-EJ in both mouse and human PDAC models. We further confirm increased catalytic activity of alt-EJ in a mouse and human model of PDAC bearing the KRAS G12D mutation. Subsequently, we focused on estimating the impact of alt-EJ inactivation by polymerase theta (Polθ) deletion on pancreatic cancer development, and survival in genetically engineered mouse models (GEMMs) and cancer patients. Here, we show that even though Polθ deficiency does not fully prevent the development of pancreatic cancer, it significantly delays the onset of PanIN formation, prolongs the overall survival of experimental mice, and correlates with the overall survival of pancreatic cancer patients in the TCGA database. Our study clearly demonstrates the role of alt-EJ in the development of PDAC, and alt-EJ may be an attractive therapeutic target for pancreatic cancer patients.
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22
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Identifying General Tumor and Specific Lung Cancer Biomarkers by Transcriptomic Analysis. BIOLOGY 2022; 11:biology11071082. [PMID: 36101460 PMCID: PMC9313083 DOI: 10.3390/biology11071082] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/25/2022] [Accepted: 07/03/2022] [Indexed: 11/17/2022]
Abstract
The bioinformatic pipeline previously developed in our research laboratory is used to identify potential general and specific deregulated tumor genes and transcription factors related to the establishment and progression of tumoral diseases, now comparing lung cancer with other two types of cancer. Twenty microarray datasets were selected and analyzed separately to identify hub differentiated expressed genes and compared to identify all the deregulated genes and transcription factors in common between the three types of cancer and those unique to lung cancer. The winning DEGs analysis allowed to identify an important number of TFs deregulated in the majority of microarray datasets, which can become key biomarkers of general tumors and specific to lung cancer. A coexpression network was constructed for every dataset with all deregulated genes associated with lung cancer, according to DAVID’s tool enrichment analysis, and transcription factors capable of regulating them, according to oPOSSUM´s tool. Several genes and transcription factors are coexpressed in the networks, suggesting that they could be related to the establishment or progression of the tumoral pathology in any tissue and specifically in the lung. The comparison of the coexpression networks of lung cancer and other types of cancer allowed the identification of common connectivity patterns with deregulated genes and transcription factors correlated to important tumoral processes and signaling pathways that have not been studied yet to experimentally validate their role in lung cancer. The Kaplan–Meier estimator determined the association of thirteen deregulated top winning transcription factors with the survival of lung cancer patients. The coregulatory analysis identified two top winning transcription factors networks related to the regulatory control of gene expression in lung and breast cancer. Our transcriptomic analysis suggests that cancer has an important coregulatory network of transcription factors related to the acquisition of the hallmarks of cancer. Moreover, lung cancer has a group of genes and transcription factors unique to pulmonary tissue that are coexpressed during tumorigenesis and must be studied experimentally to fully understand their role in the pathogenesis within its very complex transcriptomic scenario. Therefore, the downstream bioinformatic analysis developed was able to identify a coregulatory metafirm of cancer in general and specific to lung cancer taking into account the great heterogeneity of the tumoral process at cellular and population levels.
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23
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Du K, Sun S, Jiang T, Liu T, Zuo X, Xia X, Liu X, Wang Y, Bu Y. E2F2 promotes lung adenocarcinoma progression through B-Myb- and FOXM1-facilitated core transcription regulatory circuitry. Int J Biol Sci 2022; 18:4151-4170. [PMID: 35844795 PMCID: PMC9274503 DOI: 10.7150/ijbs.72386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/14/2022] [Indexed: 11/15/2022] Open
Abstract
Lung adenocarcinoma (LUAD) causes severe cancer death worldwide. E2F2 is a canonical transcription factor implicated in transcription regulation, cell cycle and tumorigenesis. The role of E2F2 as well as its transcription regulatory network in LUAD remains obscure. In this study, we constructed a weighted gene co-expression network and identified several key modules and networks overrepresented in LUAD, including the E2F2-centered transcription regulatory network. Function analysis revealed that E2F2 overexpression accelerated cell growth, cell cycle progression and cell motility in LUAD cells whereas E2F2 knockdown inhibited these malignant phenotypes. Mechanistic investigations uncovered various E2F2-regulated downstream genes and oncogenic signaling pathways. Notably, three core transcription factors of E2F2, B-Myb and FOXM1 from the LUAD transcription regulatory network exhibited positive expression correlation, associated with each other, mutually transactivated each other, and regulated similar downstream gene cascades, hence constituting a consolidated core transcription regulatory circuitry. Moreover, E2F2 could promote and was essentially required for LUAD growth in orthotopic mouse models. Prognosis modeling revealed that a two-gene signature of E2F2 and PLK1 from the transcription regulatory circuitry remarkably stratified patients into low- and high-risk groups. Collectively, our results clarified the critical roles of E2F2 and the exquisite core transcription regulatory circuitry of E2F2/B-Myb/FOXM1 in LUAD progression.
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Affiliation(s)
- Kailong Du
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Shijie Sun
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Tinghui Jiang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Tao Liu
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Xiaofeng Zuo
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Xing Xia
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Xianjun Liu
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Yitao Wang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Youquan Bu
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
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24
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Segeren HA, Westendorp B. Mechanisms used by cancer cells to tolerate drug-induced replication stress. Cancer Lett 2022; 544:215804. [PMID: 35750276 DOI: 10.1016/j.canlet.2022.215804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/15/2022] [Accepted: 06/19/2022] [Indexed: 11/02/2022]
Abstract
Activation of oncogenes in cancer cells forces cell proliferation, leading to DNA replication stress (RS). As a consequence, cancer cells heavily rely on the intra S-phase checkpoint for survival. This fundamental principle formed the basis for the development of inhibitors against key players of the intra S-phase checkpoint, ATR and CHK1. These drugs are often combined with chemotherapeutic drugs that interfere with DNA replication to exacerbate RS and exhaust the intra S-phase checkpoint in cancer cells. However, drug resistance impedes efficient clinical use, suggesting that some cancer cells tolerate severe RS. In this review, we describe how an increased nucleotide pool, boosted stabilization and repair of stalled forks and firing of dormant origins fortify the RS response in cancer cells. Notably, the vast majority of the genes that confer RS tolerance are regulated by the E2F and NRF2 transcription factors. These transcriptional programs are frequently activated in cancer cells, allowing simultaneous activation of multiple tolerance avenues. We propose that the E2F and NRF2 transcriptional programs can be used as biomarker to select patients for treatment with RS-inducing drugs and as novel targets to kill RS-tolerant cancer cells. Together, this review aims to provide a framework to maximally exploit RS as an Achilles' heel of cancer cells.
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Affiliation(s)
- Hendrika A Segeren
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Bart Westendorp
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.
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25
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Drzewiecka M, Barszczewska-Pietraszek G, Czarny P, Skorski T, Śliwiński T. Synthetic Lethality Targeting Polθ. Genes (Basel) 2022; 13:genes13061101. [PMID: 35741863 PMCID: PMC9223150 DOI: 10.3390/genes13061101] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/06/2022] [Accepted: 06/11/2022] [Indexed: 01/27/2023] Open
Abstract
Research studies regarding synthetic lethality (SL) in human cells are primarily motivated by the potential of this phenomenon to be an effective, but at the same time, safe to the patient's anti-cancer chemotherapy. Among the factors that are targets for the induction of the synthetic lethality effect, those involved in DNA repair seem to be the most relevant. Specifically, when mutation in one of the canonical DNA double-strand break (DSB) repair pathways occurs, which is a frequent event in cancer cells, the alternative pathways may be a promising target for the elimination of abnormal cells. Currently, inhibiting RAD52 and/or PARP1 in the tumor cells that are deficient in the canonical repair pathways has been the potential target for inducing the effect of synthetic lethality. Unfortunately, the development of resistance to commonly used PARP1 inhibitors (PARPi) represents the greatest obstacle to working out a successful treatment protocol. DNA polymerase theta (Polθ), encoded by the POLQ gene, plays a key role in an alternative DSB repair pathway-theta-mediated end joining (TMEJ). Thus, it is a promising target in the treatment of tumors harboring deficiencies in homologous recombination repair (HRR), where its inhibition can induce SL. In this review, the authors discuss the current state of knowledge on Polθ as a potential target for synthetic lethality-based anticancer therapies.
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Affiliation(s)
- Małgorzata Drzewiecka
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lodz, Poland; (M.D.); (G.B.-P.)
| | - Gabriela Barszczewska-Pietraszek
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lodz, Poland; (M.D.); (G.B.-P.)
| | - Piotr Czarny
- Department of Medical Biochemistry, Medical University of Lodz, 92-216 Lodz, Poland;
| | - Tomasz Skorski
- Fels Cancer Institute for Personalized Medicine, Departament of Cancer and Cellular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
- Correspondence: (T.S.); (T.Ś.); Tel.: +1-215-707-9157 (T.S.); +48-42-635-44-86 (T.Ś.)
| | - Tomasz Śliwiński
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lodz, Poland; (M.D.); (G.B.-P.)
- Correspondence: (T.S.); (T.Ś.); Tel.: +1-215-707-9157 (T.S.); +48-42-635-44-86 (T.Ś.)
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26
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Vanson S, Li Y, Wood RD, Doublié S. Probing the structure and function of polymerase θ helicase-like domain. DNA Repair (Amst) 2022; 116:103358. [PMID: 35753097 PMCID: PMC10329254 DOI: 10.1016/j.dnarep.2022.103358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/09/2022] [Accepted: 06/09/2022] [Indexed: 11/19/2022]
Abstract
DNA Polymerase θ is the key actuator of the recently identified double-strand break repair pathway, theta-mediated end joining (TMEJ). It is the only known polymerase to have a 3-domain architecture containing an independently functional family A DNA polymerase tethered by a long central region to an N-terminal helicase-like domain (HLD). Full-length polymerase θ and the isolated HLD hydrolyze ATP in the presence of DNA, but no processive DNA duplex unwinding has been observed. Based on sequence and structure conservation, the HLD is classified as a member of helicase superfamily II and, more specifically, the Ski2-like family. The specific subdomain composition and organization most closely resemble that of archaeal DNA repair helicases Hel308 and Hjm. The underlying structural basis as to why the HLD is not able to processively unwind duplex DNA, despite its similarity to bona fide helicases, remains elusive. Activities of the HLD include ATP hydrolysis, protein displacement, and annealing of complementary DNA. These observations have led to speculation about the role of the HLD within the context of double-strand break repair via TMEJ, such as removal of single-stranded DNA binding proteins like RPA and RAD51 and microhomology alignment. This review summarizes the structural classification and organization of the polymerase θ HLD and its homologs and explores emerging data on its biochemical activities. We conclude with a simple, speculative model for the HLD's role in TMEJ.
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Affiliation(s)
- Scott Vanson
- Department of Microbiology and Molecular Genetics, University of Vermont, 89 Beaumont Ave, Burlington, VT 05405, USA
| | - Yuzhen Li
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Center, Houston, TX 77230, USA
| | - Richard D Wood
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Center, Houston, TX 77230, USA.
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, 89 Beaumont Ave, Burlington, VT 05405, USA.
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27
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Bermúdez-Guzmán L. Pan-cancer analysis of non-oncogene addiction to DNA repair. Sci Rep 2021; 11:23264. [PMID: 34853396 PMCID: PMC8636604 DOI: 10.1038/s41598-021-02773-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/23/2021] [Indexed: 12/26/2022] Open
Abstract
Cancer cells usually depend on the aberrant function of one or few driver genes to initiate and promote their malignancy, an attribute known as oncogene addiction. However, cancer cells might become dependent on the normal cellular functions of certain genes that are not oncogenes but ensure cell survival (non-oncogene addiction). The downregulation or silencing of DNA repair genes and the consequent genetic and epigenetic instability is key to promote malignancy, but the activation of the DNA-damage response (DDR) has been shown to become a type of non-oncogene addiction that critically supports tumour survival. In the present study, a systematic evaluation of DNA repair addiction at the pan-cancer level was performed using data derived from The Cancer Dependency Map and The Cancer Genome Atlas (TCGA). From 241 DDR genes, 59 were identified as commonly essential in cancer cell lines. However, large differences were observed in terms of dependency scores in 423 cell lines and transcriptomic alterations across 18 cancer types. Among these 59 commonly essential genes, 14 genes were exclusively associated with better overall patient survival and 19 with worse overall survival. Notably, a specific molecular signature among the latter, characterized by DDR genes like UBE2T, RFC4, POLQ, BRIP1, and H2AFX showing the weakest dependency scores, but significant upregulation was strongly associated with worse survival. The present study supports the existence and importance of non-oncogenic addiction to DNA repair in cancer and may facilitate the identification of prognostic biomarkers and therapeutic opportunities.
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Affiliation(s)
- Luis Bermúdez-Guzmán
- Robotic Radiosurgery Center, International Cancer Center, San José, Costa Rica. .,Section of Genetics and Biotechnology, School of Biology, University of Costa Rica, San Pedro, San José, Costa Rica.
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28
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Prodhomme MK, Péricart S, Pommier RM, Morel AP, Brunac AC, Franchet C, Moyret-Lalle C, Brousset P, Puisieux A, Hoffmann JS, Tissier A. Opposite Roles for ZEB1 and TMEJ in the Regulation of Breast Cancer Genome Stability. Front Cell Dev Biol 2021; 9:727429. [PMID: 34458275 PMCID: PMC8388841 DOI: 10.3389/fcell.2021.727429] [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: 06/18/2021] [Accepted: 07/23/2021] [Indexed: 12/22/2022] Open
Abstract
Breast cancer cells frequently acquire mutations in faithful DNA repair genes, as exemplified by BRCA-deficiency. Moreover, overexpression of an inaccurate DNA repair pathway may also be at the origin of the genetic instability arising during the course of cancer progression. The specific gain in expression of POLQ, encoding the error-prone DNA polymerase Theta (POLθ) involved in theta-mediated end joining (TMEJ), is associated with a characteristic mutational signature. To gain insight into the mechanistic regulation of POLQ expression, this review briefly presents recent findings on the regulation of POLQ in the claudin-low breast tumor subtype, specifically expressing transcription factors involved in epithelial-to-mesenchymal transition (EMT) such as ZEB1 and displaying a paucity in genomic abnormality.
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Affiliation(s)
- Mélanie K Prodhomme
- INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Centre of Lyon, Équipe Labellisée Ligue Contre le Cancer, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France.,LabEx DEVweCAN, Université de Lyon, Lyon, France
| | - Sarah Péricart
- Laboratoire d'Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Toulouse, France
| | - Roxane M Pommier
- Gilles Thomas Bioinformatics Platform, Centre Léon Bérard, Cancer Research Centre of Lyon, Lyon, France
| | - Anne-Pierre Morel
- INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Centre of Lyon, Équipe Labellisée Ligue Contre le Cancer, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France.,LabEx DEVweCAN, Université de Lyon, Lyon, France
| | - Anne-Cécile Brunac
- Laboratoire d'Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Toulouse, France
| | - Camille Franchet
- Laboratoire d'Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Toulouse, France
| | - Caroline Moyret-Lalle
- INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Centre of Lyon, Équipe Labellisée Ligue Contre le Cancer, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France.,LabEx DEVweCAN, Université de Lyon, Lyon, France
| | - Pierre Brousset
- Laboratoire d'Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Toulouse, France
| | - Alain Puisieux
- INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Centre of Lyon, Équipe Labellisée Ligue Contre le Cancer, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Institut Curie, Versailles Saint-Quentin-en-Yvelines University, PSL Research University, Paris, France
| | - Jean-Sébastien Hoffmann
- Laboratoire d'Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Toulouse, France
| | - Agnès Tissier
- INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Centre of Lyon, Équipe Labellisée Ligue Contre le Cancer, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France.,LabEx DEVweCAN, Université de Lyon, Lyon, France
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29
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Wu K, Teng M, Zhou W, Lu F, Zhou Y, Zeng J, Yang J, Liu X, Zhang Y, Ding Y, Shen W. Wogonin Induces Cell Cycle Arrest and Apoptosis of Hepatocellular Carcinoma Cells by Activating Hippo Signalling. Anticancer Agents Med Chem 2021; 22:1551-1560. [PMID: 34431466 DOI: 10.2174/1871520621666210824105915] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/07/2021] [Accepted: 07/12/2021] [Indexed: 01/14/2023]
Abstract
OBJECTIVE The current study aimed to illustrate whether wogonin influences HCC cell cycle progression and apoptosis by regulating Hippo signaling. <P> Methods: The effects of wogonin on HCC cell viability, cell cycle progression and apoptosis were analyzed by utilizing CCK-8 and flow cytometry. RNA-seq was employed to analyze the expression profiles between wogonin-treated and control HCC cells, and the selected RNA-seq transcripts were validated by reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR). Immunofluorescence staining was performed to detect the distribution of YAP/TAZ in the nucleus and cytoplasm in HCC cells. Western blotting and human apoptosis array were performed to examine the expression of the indicated genes. <P> Results: We demonstrated that wogonin induced cell cycle arrest and apoptosis of HCC cell lines SMMC7721 and HCCLM3. RNA-seq analysis showed enrichment in genes associated with cell cycle progression and apoptosis following incubation with wogonin in HCC cells, and the pathways analysis further identified that Hippo signaling pathways highly altered in wogonin-treated cells. Specifically, wogonin increased the phosphorylation of MOB1 and LATS1, promoted translocation of endogenous YAP and TAZ from the nucleus to the cytoplasm, and facilitated phosphorylation of YAP and TAZ. Notably, overexpression of YAP or TAZ partially abrogated the wogonin-mediated HCC cell cycle arrest and apoptosis, and reversed wogonin-mediated suppression of Claspin. <P> Conclusion: Wogonin induced HCC cell cycle arrest and apoptosis probably by activating MOB1-LATS1 signaling to inhibit the activation of YAP and TAZ, and then decrease the expression of Claspin, suggesting that the understanding of the molecular mechanisms underlying wogonin-induced cell cycle arrest and apoptosis may be useful in HCC therapeutics.
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Affiliation(s)
- Keyan Wu
- Department of Cell Biology, School of Medicine of Yangzhou University, Yangzhou, Jiangsu. China
| | - Man Teng
- Department of Cell Biology, School of Medicine of Yangzhou University, Yangzhou, Jiangsu. China
| | - Wei Zhou
- Department of Cell Biology, School of Medicine of Yangzhou University, Yangzhou, Jiangsu. China
| | - Fanglin Lu
- Department of Cell Biology, School of Medicine of Yangzhou University, Yangzhou, Jiangsu. China
| | - Yang Zhou
- Department of Cell Biology, School of Medicine of Yangzhou University, Yangzhou, Jiangsu. China
| | - Jing Zeng
- Department of Cell Biology, School of Medicine of Yangzhou University, Yangzhou, Jiangsu. China
| | - Jie Yang
- Department of Cell Biology, School of Medicine of Yangzhou University, Yangzhou, Jiangsu. China
| | - Xinnong Liu
- Department of General Surgery, Affiliated Hospital of Yangzhou University, Yangzhou, Jiangsu. China
| | - Yu Zhang
- Department of Cell Biology, School of Medicine of Yangzhou University, Yangzhou, Jiangsu. China
| | - Yanbing Ding
- Department of Gastroenterology, Affiliated Hospital of Yangzhou University, Yangzhou, Jiangsu. China
| | - Weigan Shen
- Department of Cell Biology, School of Medicine of Yangzhou University, Yangzhou, Jiangsu. China
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30
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Lei J, Zhang D, Yao C, Ding S, Lu Z. Development of a Predictive Immune-Related Gene Signature Associated With Hepatocellular Carcinoma Patient Prognosis. Cancer Control 2021; 27:1073274820977114. [PMID: 33269615 PMCID: PMC8480351 DOI: 10.1177/1073274820977114] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background: Hepatocellular carcinoma (HCC) remains the third leader cancer-associated cause of death globally, but the etiological basis for this complex disease remains poorly clarified. The present study was thus conceptualized to define a prognostic immune-related gene (IRG) signature capable of predicting immunotherapy responsiveness and overall survival (OS) in patients with HCC. Methods: Five differentially expressed IRG associated with HCC were established the immune-related risk model through univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression analyses. Patients were separated at random into training and testing cohorts, after which the association between the identified IRG signature and OS was evaluated using the “survival” R package. In addition, maftools was leveraged to assess mutational data, with tumor mutation burden (TMB) scores being calculated as follows: (total mutations/total bases) × 106. Immune-related risk term abundance was quantified via “ssGSEA” algorithm using the “gsva” R package. Results: HCC patients were successfully stratified into low-risk and high-risk groups based upon a signature composed of 5 differentially expressed IRGs, with overall survival being significantly different between these 2 groups in training cohort, testing cohort and overall patient cohort (P = 1.745e-06, P = 1.888e-02, P = 4.281e-07). No association was observed between TMB and this IRG risk score in the overall patient cohort (P = 0.461). Notably, 19 out of 29 immune-related risk terms differed substantially in the overall patient dataset. These risk terms mainly included checkpoints, human leukocyte antigens, natural killer cells, dendritic cells, and major histocompatibility complex class I. Conclusion: In summary, an immune-related prognostic gene signature was successfully developed and used to predict survival outcomes and immune system status in patients with HCC. This signature has the potential to help guide immunotherapeutic treatment planning for patients affected by this deadly cancer.
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Affiliation(s)
- Jiasheng Lei
- Department of Hepatobiliary Surgery, BengBu Medical College, BengBu, China
| | - Dengyong Zhang
- Department of Hepatobiliary Surgery, BengBu Medical College, BengBu, China
| | - Chao Yao
- Department of Hepatobiliary Surgery, BengBu Medical College, BengBu, China
| | - Sheng Ding
- Department of Hepatobiliary Surgery, BengBu Medical College, BengBu, China
| | - Zheng Lu
- Department of Hepatobiliary Surgery, BengBu Medical College, BengBu, China
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Cai C, Luo J, Liu Q, Liu Z, Zhao Y, Wu X, Yuegao Y, Lei Y, Lu J, Wang Y, Cai Z, Duan X, Lei M, Gu D, Liu Y. Claspin Overexpression Promotes Tumor Progression and Predicts Poor Clinical Outcome in Prostate Cancer. Genet Test Mol Biomarkers 2021; 25:131-139. [PMID: 33596143 DOI: 10.1089/gtmb.2020.0226] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background: Claspin (CLSPN) expression is acknowledged as a poor clinical prognostic factor in various tumors. However, the clinical characteristics and biological functions of CLSPN in prostate cancer (PCa) are still to be clarified. The aim of our study was to evaluate the association of CLSPN expression during PCa progression and its potential role in prognosis. Methods: We analyzed mRNA expression of the CLSPN gene with various clinicopathological features using the Cancer Genome Atlas and GSE21032 dataset. Immunohistochemical assays were used to detect the protein expression levels of CLSPN in human PCa tissue microarrays. Furthermore, we characterized the role of CLSPN in PCa progression through in vitro experiments using a CLSPN knockout. Results: Immunohistochemistry and public datasets revealed that CLSPN expression was increased in PCa with: a high Gleason score; advanced pathological stage; and positive surgical margins. In addition, upregulation of CLSPN was correlated with shorter biochemical recurrence (BCR)-free survival and overall survival. After we knocked-out CLSPN in DU145 and LNCaP cells, the in vitro phenotypic results showed that the ability of the knockouts to proliferate, migrate, and invade was attenuated; but that apoptosis was promoted. Conclusions: Our data support an oncogenic role for CLSPN in PCa progression. Moreover, increased CLSPN expression was identified as an independent factor in predicting bCR-free survival and disease-free survival in PCa patients.
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Affiliation(s)
- Chao Cai
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University and Guangdong Key Laboratory of Urology, Guangzhou, China
| | - Jiexin Luo
- Department of Urology, Affiliated Dongguan People's Hospital, Southern Medical University, Dongguan, China
| | - Qinwei Liu
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University and Guangdong Key Laboratory of Urology, Guangzhou, China
| | | | - Yan Zhao
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University and Guangdong Key Laboratory of Urology, Guangzhou, China
| | - Xiangkun Wu
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University and Guangdong Key Laboratory of Urology, Guangzhou, China
| | - Yuanzhi Yuegao
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University and Guangdong Key Laboratory of Urology, Guangzhou, China
| | - Yeci Lei
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University and Guangdong Key Laboratory of Urology, Guangzhou, China
| | - Jianming Lu
- Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Department of Urology, Guangzhou First People's Hospital, Guangzhou, China
| | - Ying Wang
- Medical Ultrasound Department, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhouda Cai
- Department of Andrology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Xiaolu Duan
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University and Guangdong Key Laboratory of Urology, Guangzhou, China
| | - Ming Lei
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University and Guangdong Key Laboratory of Urology, Guangzhou, China
| | - Di Gu
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University and Guangdong Key Laboratory of Urology, Guangzhou, China
| | - Yongda Liu
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University and Guangdong Key Laboratory of Urology, Guangzhou, China
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Huang R, Zhou PK. DNA damage repair: historical perspectives, mechanistic pathways and clinical translation for targeted cancer therapy. Signal Transduct Target Ther 2021; 6:254. [PMID: 34238917 PMCID: PMC8266832 DOI: 10.1038/s41392-021-00648-7] [Citation(s) in RCA: 289] [Impact Index Per Article: 96.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 04/28/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023] Open
Abstract
Genomic instability is the hallmark of various cancers with the increasing accumulation of DNA damage. The application of radiotherapy and chemotherapy in cancer treatment is typically based on this property of cancers. However, the adverse effects including normal tissues injury are also accompanied by the radiotherapy and chemotherapy. Targeted cancer therapy has the potential to suppress cancer cells' DNA damage response through tailoring therapy to cancer patients lacking specific DNA damage response functions. Obviously, understanding the broader role of DNA damage repair in cancers has became a basic and attractive strategy for targeted cancer therapy, in particular, raising novel hypothesis or theory in this field on the basis of previous scientists' findings would be important for future promising druggable emerging targets. In this review, we first illustrate the timeline steps for the understanding the roles of DNA damage repair in the promotion of cancer and cancer therapy developed, then we summarize the mechanisms regarding DNA damage repair associated with targeted cancer therapy, highlighting the specific proteins behind targeting DNA damage repair that initiate functioning abnormally duo to extrinsic harm by environmental DNA damage factors, also, the DNA damage baseline drift leads to the harmful intrinsic targeted cancer therapy. In addition, clinical therapeutic drugs for DNA damage and repair including therapeutic effects, as well as the strategy and scheme of relative clinical trials were intensive discussed. Based on this background, we suggest two hypotheses, namely "environmental gear selection" to describe DNA damage repair pathway evolution, and "DNA damage baseline drift", which may play a magnified role in mediating repair during cancer treatment. This two new hypothesis would shed new light on targeted cancer therapy, provide a much better or more comprehensive holistic view and also promote the development of new research direction and new overcoming strategies for patients.
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Affiliation(s)
- Ruixue Huang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, Hunan, China
| | - Ping-Kun Zhou
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing, China.
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Ray U, Raghavan SC. Understanding the DNA double-strand break repair and its therapeutic implications. DNA Repair (Amst) 2021; 106:103177. [PMID: 34325086 DOI: 10.1016/j.dnarep.2021.103177] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 06/25/2021] [Accepted: 07/07/2021] [Indexed: 10/20/2022]
Abstract
Repair of DNA double-strand breaks (DSBs) and its regulation are tightly integrated inside cells. Homologous recombination, nonhomologous end joining and microhomology mediated end joining are three major DSB repair pathways in mammalian cells. Targeting proteins associated with these repair pathways using small molecule inhibitors can prove effective in tumors, especially those with deregulated repair. Sensitization of cancer to current age therapy including radio and chemotherapy, using small molecule inhibitors is promising and warrant further development. Although several are under clinical trial, till date no repair inhibitor is approved for commercial use in cancer patients, with the exception of PARP inhibitors targeting single-strand break repair. Based on molecular profiling of repair proteins, better prognostic and therapeutic output can be achieved in patients. In the present review, we highlight the different mechanisms of DSB repair, chromatin dynamics to provide repair accessibility and modulation of inhibitors in association with molecular profiling and current gold standard treatment modalities for cancer.
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Affiliation(s)
- Ujjayinee Ray
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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34
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Ngoi NYL, Pham MM, Tan DSP, Yap TA. Targeting the replication stress response through synthetic lethal strategies in cancer medicine. Trends Cancer 2021; 7:930-957. [PMID: 34215565 DOI: 10.1016/j.trecan.2021.06.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 12/11/2022]
Abstract
The replication stress response (RSR) involves a downstream kinase cascade comprising ataxia telangiectasia-mutated (ATM), ATM and rad3-related (ATR), checkpoint kinases 1 and 2 (CHK1/2), and WEE1-like protein kinase (WEE1), which cooperate to arrest the cell cycle, protect stalled forks, and allow time for replication fork repair. In the presence of elevated replicative stress, cancers are increasingly dependent on RSR to maintain genomic integrity. An increasing number of drug candidates targeting key RSR nodes, as monotherapy through synthetic lethality, or through rational combinations with immune checkpoint inhibitors and targeted therapies, are demonstrating promising efficacy in early phase trials. RSR targeting is also showing potential in reversing PARP inhibitor resistance, an important area of unmet clinical need. In this review, we introduce the concept of targeting the RSR, detail the current landscape of monotherapy and combination strategies, and discuss emerging therapeutic approaches, such as targeting Polθ.
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Affiliation(s)
- Natalie Y L Ngoi
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore
| | - Melissa M Pham
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David S P Tan
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore
| | - Timothy A Yap
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Khalifa Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; The Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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35
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Depletion of DNA Polymerase Theta Inhibits Tumor Growth and Promotes Genome Instability through the cGAS-STING-ISG Pathway in Esophageal Squamous Cell Carcinoma. Cancers (Basel) 2021; 13:cancers13133204. [PMID: 34206946 PMCID: PMC8268317 DOI: 10.3390/cancers13133204] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/13/2021] [Accepted: 06/23/2021] [Indexed: 12/30/2022] Open
Abstract
Simple Summary DNA polymerase theta, encoded by the human POLQ gene, is upregulated in several cancers and is associated with poor clinical outcomes. The importance of POLQ, however, has yet to be elucidated in esophageal cancer. In this study, we explored the functional impacts of POLQ and looked into its underlying mechanisms. POLQ was overexpressed in esophageal squamous cell carcinoma (ESCC) tumors associated with unfavorable prognosis and contributed to malignant phenotypes by promoting genome stability, suggesting that targeting polymerase theta may provide a potential therapeutic approach for improving ESCC management. Abstract Overexpression of the specialized DNA polymerase theta (POLQ) is frequent in breast, colon and lung cancers and has been correlated with unfavorable clinical outcomes. Here, we aimed to determine the importance and functional role of POLQ in esophageal squamous cell carcinoma (ESCC). Integrated analysis of four RNA-seq datasets showed POLQ was predominantly upregulated in ESCC tumors. High expression of POLQ was also observed in a cohort of 25 Hong Kong ESCC patients and negatively correlated with ESCC patient survival. POLQ knockout (KO) ESCC cells were sensitized to multiple genotoxic agents. Both rH2AX foci staining and the comet assay indicated a higher level of genomic instability in POLQ-depleted cells. Double KO of POLQ and FANCD2, known to promote POLQ recruitment at sites of damage, significantly impaired cell proliferation both in vitro and in vivo, as compared to either single POLQ or FANCD2 KOs. A significantly increased number of micronuclei was observed in POLQ and/or FANCD2 KO ESCC cells. Loss of POLQ and/or FANCD2 also resulted in the activation of cGAS and upregulation of interferon-stimulated genes (ISGs). Our results suggest that high abundance of POLQ in ESCC contributes to the malignant phenotype through genome instability and activation of the cGAS pathway.
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Matos-Rodrigues G, Guirouilh-Barbat J, Martini E, Lopez BS. Homologous recombination, cancer and the 'RAD51 paradox'. NAR Cancer 2021; 3:zcab016. [PMID: 34316706 PMCID: PMC8209977 DOI: 10.1093/narcan/zcab016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/08/2021] [Accepted: 04/20/2021] [Indexed: 01/22/2023] Open
Abstract
Genetic instability is a hallmark of cancer cells. Homologous recombination (HR) plays key roles in genome stability and variability due to its roles in DNA double-strand break and interstrand crosslink repair, and in the protection and resumption of arrested replication forks. HR deficiency leads to genetic instability, and, as expected, many HR genes are downregulated in cancer cells. The link between HR deficiency and cancer predisposition is exemplified by familial breast and ovarian cancers and by some subgroups of Fanconi anaemia syndromes. Surprisingly, although RAD51 plays a pivotal role in HR, i.e., homology search and in strand exchange with a homologous DNA partner, almost no inactivating mutations of RAD51 have been associated with cancer predisposition; on the contrary, overexpression of RAD51 is associated with a poor prognosis in different types of tumours. Taken together, these data highlight the fact that RAD51 differs from its HR partners with regard to cancer susceptibility and expose what we call the ‘RAD51 paradox’. Here, we catalogue the dysregulations of HR genes in human pathologies, including cancer and Fanconi anaemia or congenital mirror movement syndromes, and we discuss the RAD51 paradox.
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Affiliation(s)
- Gabriel Matos-Rodrigues
- Université de Paris, INSERM U1016, UMR 8104 CNRS, Institut Cochin, Equipe Labellisée Ligue Contre le Cancer, F-75014, France
| | - Josée Guirouilh-Barbat
- Université de Paris, INSERM U1016, UMR 8104 CNRS, Institut Cochin, Equipe Labellisée Ligue Contre le Cancer, F-75014, France
| | - Emmanuelle Martini
- Université de Paris and Université Paris-Saclay, Laboratory of Development of the Gonads, IRCM/IBFJ CEA, UMR Genetic Stability, Stem Cells and Radiation, F-92265 Fontenay aux Roses, France
| | - Bernard S Lopez
- Université de Paris, INSERM U1016, UMR 8104 CNRS, Institut Cochin, Equipe Labellisée Ligue Contre le Cancer, F-75014, France
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37
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Replication Stress, Genomic Instability, and Replication Timing: A Complex Relationship. Int J Mol Sci 2021; 22:ijms22094764. [PMID: 33946274 PMCID: PMC8125245 DOI: 10.3390/ijms22094764] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 12/29/2022] Open
Abstract
The replication-timing program constitutes a key element of the organization and coordination of numerous nuclear processes in eukaryotes. This program is established at a crucial moment in the cell cycle and occurs simultaneously with the organization of the genome, thus indicating the vital significance of this process. With recent technological achievements of high-throughput approaches, a very strong link has been confirmed between replication timing, transcriptional activity, the epigenetic and mutational landscape, and the 3D organization of the genome. There is also a clear relationship between replication stress, replication timing, and genomic instability, but the extent to which they are mutually linked to each other is unclear. Recent evidence has shown that replication timing is affected in cancer cells, although the cause and consequence of this effect remain unknown. However, in-depth studies remain to be performed to characterize the molecular mechanisms of replication-timing regulation and clearly identify different cis- and trans-acting factors. The results of these studies will potentially facilitate the discovery of new therapeutic pathways, particularly for personalized medicine, or new biomarkers. This review focuses on the complex relationship between replication timing, replication stress, and genomic instability.
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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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Schrempf A, Slyskova J, Loizou JI. Targeting the DNA Repair Enzyme Polymerase θ in Cancer Therapy. Trends Cancer 2021; 7:98-111. [PMID: 33109489 DOI: 10.1016/j.trecan.2020.09.007] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/21/2020] [Accepted: 09/28/2020] [Indexed: 12/21/2022]
Abstract
Targeted cancer therapies represent a milestone towards personalized treatment as they function via inhibition of cancer-specific alterations. Polymerase θ (POLQ), an error-prone translesion polymerase, also involved in DNA double-strand break (DSB) repair, is often upregulated in cancer. POLQ is synthetic lethal with various DNA repair genes, including known cancer drivers such as BRCA1/2, making it essential in homologous recombination-deficient cancers. Thus, POLQ represents a promising target in cancer therapy and efforts for the development of POLQ inhibitors are actively underway with first clinical trials due to start in 2021. This review summarizes the journey of POLQ from a backup DNA repair enzyme to a promising therapeutic target for cancer treatment.
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Affiliation(s)
- Anna Schrempf
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria; Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Jana Slyskova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria; Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria.
| | - Joanna I Loizou
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria; Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria.
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Kuei CH, Lin HY, Lin MH, Lee HH, Lin CH, Lee WJ, Chen YL, Lu LS, Zheng JQ, Hung RC, Chiu HW, Chen KC, Lin YF. DNA polymerase theta repression enhances the docetaxel responsiveness in metastatic castration-resistant prostate cancer. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165954. [PMID: 32877750 DOI: 10.1016/j.bbadis.2020.165954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/21/2020] [Accepted: 08/26/2020] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Docetaxel remains a main treatment for metastatic castration-resistant prostate cancer (mCRPC); however, the development of docetaxel resistance has been found in some mCRPC patients. The aim of this work is to identify an effective biomarker for predicting therapeutic effectiveness of docetaxel in mCRPC patients. METHODS We examined DNA polymerase theta (POLQ) expression in The Cancer Genome Atlas (TCGA) database and Tissue microarray. Kaplan-Meier analyses were performed to estimate the prognostic significance of POLQ. A series of functional analyses were conducted in cell lines and xenograft models. Regulated pathways were predicted by Geneset Enrichment Analysis (GSEA) software and further investigated by luciferase reporter and RT-PCR assays. RESULTS We found that POLQ mRNA levels in CRPC tissues was significantly higher than that of other DNA polymerases in non-CRPC prostate tissues. POLQ upregulation was extensively detected in mCRPC and strongly predicted a poor prognosis. POLQ knockdown enhanced docetaxel sensitivity in a cell-based cytotoxicity assay and promoted the therapeutic effect on the tumor growth of metastatic PC-3M cells in xenograft models. The computational simulation by GSEA software significantly predicted the association between POLQ upregulation and the activation of E2F/G2M checkpoint-related pathways. Moreover, luciferase reporter and RT-PCR assays demonstrated that POLQ knockdown downregulated the transcriptional regulatory activity of E2F and repressed E2F/G2M checkpoint-regulated CDK1 in mCRPC cells. CONCLUSION Our results suggest that POLQ serves as a predictive factor for poor docetaxel response and provide a novel strategy to enhance the anticancer effects of docetaxel therapy by targeting POLQ in mCRPC patients.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- DNA-Directed DNA Polymerase/genetics
- DNA-Directed DNA Polymerase/metabolism
- Docetaxel/pharmacology
- Humans
- Male
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Neoplasms, Experimental/drug therapy
- Neoplasms, Experimental/metabolism
- Neoplasms, Experimental/pathology
- PC-3 Cells
- Prostatic Neoplasms, Castration-Resistant/drug therapy
- Prostatic Neoplasms, Castration-Resistant/metabolism
- Prostatic Neoplasms, Castration-Resistant/pathology
- RNA, Messenger/drug effects
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Tumor Cells, Cultured
- DNA Polymerase theta
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Affiliation(s)
- Chia-Hao Kuei
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; Department of Urology, Division of Surgery, Cardinal Tien Hospital, Xindian District, New Taipei City 23148, Taiwan
| | - Hui-Yu Lin
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; Department of Breast Surgery and General Surgery, Division of Surgery, Cardinal Tien Hospital, Xindian district, New Taipei City 23148, Taiwan
| | - Min-Hsuan Lin
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Hsun-Hua Lee
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; Department of Neurology, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23148, Taiwan; Department of Neurology, School of Medicine, College of Medicine, Taipei Medical University, New Taipei City 23561, Taiwan; Department of Neurology, Vertigo and Balance Impairment Center, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan; Taipei Neuroscience Institute, Taipei Medical University, New Taipei City 23561, Taiwan
| | - Che-Hsuan Lin
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; Department of Otolaryngology, Taipei Medical University Hospital, Taipei Medical University, Taipei 11031, Taiwan
| | - Wei-Jiunn Lee
- Department of Urology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; Department of Medical Education and Research, Wan Fang Hospital, Taipei Medical University, Taipei 11696, Taiwan
| | - Yen-Lin Chen
- Department of Pathology, Cardinal Tien Hospital, School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City 23148, Taiwan
| | - Long-Sheng Lu
- Department of Radiation Oncology, Taipei Medical University Hospital, Taipei 11031, Taiwan
| | - Jing-Quan Zheng
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; Department of Chest Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
| | - Ruei-Chen Hung
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Hui-Wen Chiu
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; Division of Nephrology, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan; TMU Research Center of Urology and Kidney, Taipei Medical University, Taipei, Taiwan
| | - Kuan-Chou Chen
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; Department of Urology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; Department of Urology, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
| | - Yuan-Feng Lin
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; Cell Physiology and Molecular Image Research Center, Wan Fang Hospital, Taipei Medical University, Taipei 11696, Taiwan.
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Implications of CLSPN Variants in Cellular Function and Susceptibility to Cancer. Cancers (Basel) 2020; 12:cancers12092396. [PMID: 32847043 PMCID: PMC7565888 DOI: 10.3390/cancers12092396] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/05/2020] [Accepted: 08/20/2020] [Indexed: 11/28/2022] Open
Abstract
Claspin is a multifunctional protein that participates in physiological processes essential for cell homeostasis that are often defective in cancer, namely due to genetic changes. It is conceivable that Claspin gene (CLSPN) alterations may contribute to cancer development. Therefore, CLSPN germline alterations were characterized in sporadic and familial breast cancer and glioma samples, as well as in six cancer cell lines. Their association to cancer susceptibility and functional impact were investigated. Eight variants were identified (c.-68C>T, c.17G>A, c.1574A>G, c.2230T>C, c.2028+16G>A, c.3595-3597del, and c.3839C>T). CLSPN c.1574A>G (p.Asn525Ser) was significantly associated with breast cancer and was shown to cause partial exon skipping and decreased Claspin expression and Chk1 activation in a minigene splicing assay and in signalling experiments, respectively. CLSPN c.2028+16G>A was significantly associated with familial breast cancer and glioma, whereas c.2230T>C (p.Ser744Pro), was exclusively detected in breast cancer and glioma patients, but not in healthy controls. The remaining variants lacked a significant association with cancer. Nevertheless, the c.-68C>T promoter variant increased transcriptional activity in a luciferase assay. In conclusion, some of the CLSPN variants identified in the present study appear to modulate Claspin’s function by altering CLSPN transcription and RNA processing, as well as Chk1 activation.
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Laporte GA, Leguisamo NM, Gloria HDCE, Azambuja DB, Kalil AN, Saffi J. The role of double-strand break repair, translesion synthesis, and interstrand crosslinks in colorectal cancer progression-clinicopathological data and survival. J Surg Oncol 2020; 121:906-916. [PMID: 31650563 DOI: 10.1002/jso.25737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 10/08/2019] [Indexed: 12/24/2022]
Abstract
BACKGROUND AND OBJECTIVES DNA repair is a new and important pathway that explains colorectal carcinogenesis. This study will evaluate the prognostic value of molecular modulation of double-strand break repair (XRCC2 and XRCC5); DNA damage tolerance/translesion synthesis (POLH, POLK, and POLQ), and interstrand crosslink repair (DCLRE1A) in sporadic colorectal cancer (CRC). METHODS Tumor specimens and matched healthy mucosal tissues from 47 patients with CRC who underwent surgery were assessed for gene expression of XRCC2, XRCC5, POLH, POLK, POLQ, and DCLRE1A; protein expression of Polk, Ku80, p53, Ki67, and mismatch repair MLH1 and MSH2 components; CpG island promoter methylation of XRCC5, POLH, POLK, POLQ, and DCLRE1A was performed. RESULTS Neoplastic tissues exhibited induction of POLK (P < .001) and DCLRE1A (P < .001) expression and low expression of POLH (P < .001) and POLQ (P < .001) in comparison to healthy paired mucosa. Low expression of POLH was associated with mucinous histology and T1-T2 tumors (P = .038); low tumor expression of POLK was associated with distant metastases (P = .042). CRC harboring POLK promoter methylation exhibited better disease-free survival (DFS) (P = .005). CONCLUSIONS This study demonstrated that low expression or unmethylated POLH and POLK were related to worse biological behavior tumors. However, POLK methylation was associated with better DFS. POLK and POLH are potential prognostic biomarkers in CRC.
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Affiliation(s)
- Gustavo A Laporte
- Division of Surgical Oncology, Santa Rita Hospital/ISCMPA, Porto Alegre, Brazil
- Laboratory of Genetic Toxicology, Federal University of Health Sciences of Porto Alegre/UFCSPA, Porto Alegre, Rio Grande do Sul, Brazil
| | - Natália M Leguisamo
- Laboratory of Genetic Toxicology, Federal University of Health Sciences of Porto Alegre/UFCSPA, Porto Alegre, Rio Grande do Sul, Brazil
- Institute of Cardiology of Rio Grande do Sul, University Foundation of Cardiology, Porto Alegre, Brazil
| | - Helena de Castro E Gloria
- Laboratory of Genetic Toxicology, Federal University of Health Sciences of Porto Alegre/UFCSPA, Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Antonio N Kalil
- Division of Surgical Oncology, Santa Rita Hospital/ISCMPA, Porto Alegre, Brazil
| | - Jenifer Saffi
- Laboratory of Genetic Toxicology, Federal University of Health Sciences of Porto Alegre/UFCSPA, Porto Alegre, Rio Grande do Sul, Brazil
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When RAD52 Allows Mitosis to Accept Unscheduled DNA Synthesis. Cancers (Basel) 2019; 12:cancers12010026. [PMID: 31861741 PMCID: PMC7017103 DOI: 10.3390/cancers12010026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 12/15/2022] Open
Abstract
Faithful duplication of the human genome during the S phase of cell cycle and accurate segregation of sister chromatids in mitosis are essential for the maintenance of chromosome stability from one generation of cells to the next. Cells that are copying their DNA in preparation for division can suffer from ‘replication stress’ (RS) due to various external or endogenous impediments that slow or stall replication forks. RS is a major cause of pathologies including cancer, premature ageing and other disorders associated with genomic instability. It particularly affects genomic loci where progression of replication forks is intrinsically slow or problematic, such as common fragile site (CFS), telomeres, and repetitive sequences. Although the eukaryotic cell cycle is conventionally thought of as several separate steps, each of which must be completed before the next one is initiated, it is now accepted that incompletely replicated chromosomal domains generated in S phase upon RS at these genomic loci can result in late DNA synthesis in G2/M. In 2013, during investigations into the mechanism by which the specialized DNA polymerase eta (Pol η) contributes to the replication and stability of CFS, we unveiled that indeed some DNA synthesis was still occurring in early mitosis at these loci. This surprising observation of mitotic DNA synthesis that differs fundamentally from canonical semi-conservative DNA replication in S-phase has been then confirmed, called “MiDAS”and believed to counteract potentially lethal chromosome mis-segregation and non-disjunction. While other contributions in this Special Issue of Cancers focus on the role of RAS52RAD52 during MiDAS, this review emphases on the discovery of MiDAS and its molecular effectors.
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Wickersham KE, Hodges TK, Edelman MJ, Song Y, Nan M, Dorsey SG. Differential Gene Expression in Erlotinib-Treated Fibroblasts. Nurs Res 2019; 68:110-126. [PMID: 30540703 PMCID: PMC7580303 DOI: 10.1097/nnr.0000000000000330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
BACKGROUND Therapies targeting the epidermal growth factor receptor (EGFR) result in a painful rash, the most common and debilitating toxicity among patients with non-small cell lung cancer (NSCLC) who take EGFR tyrosine kinase inhibitor (TKI) therapy; however, predicting the development and the severity of the rash is difficult. OBJECTIVE The aim of this study was to examine how erlotinib-an EGFR TKI that NSCLC patients take to stop or slow tumor growth-altered the transcriptome of dermal fibroblasts. METHODS Dermal fibroblasts (ATCC PCS-201-012) were seeded in cell culture flasks, grown under standard conditions, and transferred to cell culture dishes. Cells were treated once daily for 3 days with erlotinib 100 nM (n = 5), erlotinib 1 μM (n = 5), vehicle 1 μM (dimethyl sulfoxide) (n = 5), or no treatment (n = 5). Total RNA was extracted using a standard TRIzol method and hybridized using Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays. Raw intensities generated from the arrays were normalized using a Robust Multiarray Average method and analyzed using analysis of variance in Limma R software. Differentially expressed genes were analyzed using Ingenuity Pathway Analysis to identify canonical or noncanonical signaling pathways enriched in this dataset. RESULTS We selected genes for investigation based on their potential role in wound healing (AQP3), rash development (CCL2), fibroblast activation (PALLD), cancer and cancer progression (GDF-15, SLC7A11, MMP12, and DIRAS3), and cell cycle control (CDC6). We were able to validate four of these genes by both Western blot analysis and quantitative polymerase chain reaction (MMP12, CCL2, CDC6, and SLC7A11). DISCUSSION If found predictive of rash in future studies using patient samples, our findings may help to identify those at risk for severe rash so that (a) the dose of EGFR TKI therapy may be adjusted; (b) additional treatments for the rash can be developed; and/or (c) precise, patient-centered interventions can be developed so that patients with cancer can better self-manage their rash and adhere to EGFR TKI treatment.
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Affiliation(s)
- Karen E Wickersham
- Karen E. Wickersham, PhD, RN, was Assistant Professor, School of Nursing, University of Maryland, Baltimore; now Assistant Professor, University of South Carolina, College of Nursing, Columbia, South Carolina. Theresa K. Hodges, PhD, is Bioinformatics Analyst I, Institute for Genome Sciences, School of Medicine, University of Maryland, Baltimore, Maryland. Martin J. Edelman, MD, was Director, Medical Thoracic Oncology, University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, Maryland; now Professor and Chair, Department of Hematology/Oncology; Deputy Director, Cancer Center for Clinical Research; and G. Morris Dorrance Jr. Chair in Medical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania. Yang Song, PhD, is Bioinformatics Analyst II, Institute for Genome Sciences, School of Medicine, University of Maryland, Baltimore, Maryland. Mintong Nan, BS, was Laboratory Research Technician, Department of Pain and Translational Symptom Science, University of Maryland, Baltimore, School of Nursing, Baltimore, Maryland. Susan G. Dorsey, PhD, RN, FAAN, is Professor and Chair, Department of Pain and Translational Symptom Science, University of Maryland, Baltimore, School of Nursing, Baltimore, Maryland; and PhD Student at the University of Maryland
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Li R, Liu Y, Wang T, Tang J, Xie L, Yao Z, Li K, Liao Y, Zhou L, Geng Z, Huang Z, Yang Z, Han L. The characteristics of lung cancer in Xuanwei County: A review of differentially expressed genes and noncoding RNAs on cell proliferation and migration. Biomed Pharmacother 2019; 119:109312. [PMID: 31518876 DOI: 10.1016/j.biopha.2019.109312] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 07/27/2019] [Accepted: 07/31/2019] [Indexed: 12/15/2022] Open
Abstract
The occurrence of lung cancers is the highest in Xuanwei County, Yunnan province, China, especially among nonsmoking women. Domestic combustion of smoky coal induces serious indoor air pollution and is considered to be the main cause of human lung cancers. The occurrence of lung cancer in Xuanwei County has unique characteristics, such as the high morbidity in nonsmoking women or people with no family history. In the present review, we summarize advances in identification of differentially expressed genes, regulatory lncRNAs and miRNAs in cell proliferation and migration of lung cancers in Xuanwei County. Moreover, several regulatory differentially expressed genes (DEGs) or noncoding RNAs have diagnostic and prognostic significance for lung cancers in Xuanwei County and have the potential to serve as biomarkers.
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Affiliation(s)
- Rong Li
- Department of Medical Oncology, The Third Affiliated Hospital of Kunming Medical University (Cancer Hospital of Yunnan Province), Kunming, Yunnan, 650118, China
| | - Yan Liu
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Cancer Hospital of Yunnan Province), Kunming, Yunnan, 650118, China
| | - Tiying Wang
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Cancer Hospital of Yunnan Province), Kunming, Yunnan, 650118, China
| | - Jiadai Tang
- Department of Medical Oncology, The Third Affiliated Hospital of Kunming Medical University (Cancer Hospital of Yunnan Province), Kunming, Yunnan, 650118, China
| | - Lin Xie
- Department of Medical Oncology, The Third Affiliated Hospital of Kunming Medical University (Cancer Hospital of Yunnan Province), Kunming, Yunnan, 650118, China.
| | - Zhihong Yao
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Cancer Hospital of Yunnan Province), Kunming, Yunnan, 650118, China
| | - Kechen Li
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Cancer Hospital of Yunnan Province), Kunming, Yunnan, 650118, China
| | - Yedan Liao
- Department of Medical Oncology, The Third Affiliated Hospital of Kunming Medical University (Cancer Hospital of Yunnan Province), Kunming, Yunnan, 650118, China
| | - Ling Zhou
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Cancer Hospital of Yunnan Province), Kunming, Yunnan, 650118, China
| | - Zhenqin Geng
- Department of Medical Oncology, The Third Affiliated Hospital of Kunming Medical University (Cancer Hospital of Yunnan Province), Kunming, Yunnan, 650118, China
| | - Zeyong Huang
- Medical School, Kunming University of Science and Technology, Kunming, Yunnan, 650504, China
| | - Zuozhang Yang
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Cancer Hospital of Yunnan Province), Kunming, Yunnan, 650118, China.
| | - Lei Han
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Cancer Hospital of Yunnan Province), Kunming, Yunnan, 650118, China
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Liu Q, Lopez K, Murnane J, Humphrey T, Barcellos-Hoff MH. Misrepair in Context: TGFβ Regulation of DNA Repair. Front Oncol 2019; 9:799. [PMID: 31552165 PMCID: PMC6736563 DOI: 10.3389/fonc.2019.00799] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/06/2019] [Indexed: 12/13/2022] Open
Abstract
Repair of DNA damage protects genomic integrity, which is key to tissue functional integrity. In cancer, the type and fidelity of DNA damage response is the fundamental basis for clinical response to cytotoxic therapy. Here we consider the contribution of transforming growth factor-beta (TGFβ), a ubiquitous, pleotropic cytokine that is abundant in the tumor microenvironment, to therapeutic response. The action of TGFβ is best illustrated in head and neck squamous cell carcinoma (HNSCC). Survival of HNSCC patients with human papilloma virus (HPV) positive cancer is more than double compared to those with HPV-negative HNSCC. Notably, HPV infection profoundly impairs TGFβ signaling. HPV blockade of TGFβ signaling, or pharmaceutical TGFβ inhibition that phenocopies HPV infection, shifts cancer cells from error-free homologous-recombination DNA double-strand-break (DSB) repair to error-prone alternative end-joining (altEJ). Cells using altEJ are more sensitive to standard of care radiotherapy and cisplatin, and are sensitized to PARP inhibitors. Hence, HPV-positive HNSCC is an experiment of nature that provides a strong rationale for the use of TGFβ inhibitors for optimal therapeutic combinations that improve patient outcome.
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Affiliation(s)
- Qi Liu
- Department of Radiation Oncology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States.,Institute of Biomedical Engineering, Peking University Shenzhen Graduate School, Shenzhen, China.,Shenzhen Bay Laboratory (SZBL), Shenzhen, China
| | - Kirsten Lopez
- Department of Oncology, CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | - John Murnane
- Department of Radiation Oncology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
| | - Timothy Humphrey
- Department of Oncology, CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | - Mary Helen Barcellos-Hoff
- Department of Radiation Oncology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
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Stratmann JA, Sebastian M. Polo-like kinase 1 inhibition in NSCLC: mechanism of action and emerging predictive biomarkers. LUNG CANCER-TARGETS AND THERAPY 2019; 10:67-80. [PMID: 31308774 PMCID: PMC6612950 DOI: 10.2147/lctt.s177618] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 05/24/2019] [Indexed: 12/16/2022]
Abstract
Non-small cell lung cancer (NSCLC) is the leading cause of cancer death worldwide. Due to often unspecific disease symptoms, locally advanced or metastatic disease is diagnosed in the majority of all cases. Palliative treatment options comprise of conventional cytotoxic agents, immunotherapy with checkpoint inhibitors and the use of specific small-molecule tyrosine kinase inhibitors (TKI). However, these TKIs are mainly restricted to a small proportion of patients with lung cancer that harbor activating driver mutations. Still, the effectiveness and favorable safety profile of these compounds have prompted a systematic search for specific driver mechanisms of tumorigenesis and moreover the development of corresponding kinase inhibitors. In recent years, the Polo-like kinase (PLK) family has emerged as a key regulator in mitotic regulation. Its role in cell proliferation and the frequently observed overexpression in various tumor entities have raised much interest in basic and clinical oncology aiming to attenuate tumor growth by targeting the PLK. In this review, we give a comprehensive summary on the (pre-) clinical development of the different types of PLK inhibitors in lung cancer and summarize their mechanisms of action, safety and efficacy data and give an overview on translational research aiming to identify predictive biomarkers for a rational use of PLK inhibitors.
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Affiliation(s)
- Jan A Stratmann
- Department of Internal Medicine II, University Clinic of Frankfurt, 60596 Frankfurt, Germany
| | - Martin Sebastian
- Department of Internal Medicine II, University Clinic of Frankfurt, 60596 Frankfurt, Germany
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POLQ Overexpression Is Associated with an Increased Somatic Mutation Load and PLK4 Overexpression in Lung Adenocarcinoma. Cancers (Basel) 2019; 11:cancers11050722. [PMID: 31137743 PMCID: PMC6562496 DOI: 10.3390/cancers11050722] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/16/2019] [Accepted: 05/22/2019] [Indexed: 01/23/2023] Open
Abstract
DNA Polymerase Theta (POLQ) is a DNA polymerase involved in error-prone translesion DNA synthesis (TLS) and error-prone repair of DNA double-strand breaks (DSBs). In the present study, we examined whether abnormal POLQ expression may be involved in the pathogenesis of lung adenocarcinoma (LAC). First, we found overexpression of POLQ at both the mRNA and protein levels in LAC, using data from the Cancer Genome Atlas (TCGA) database and by immunohistochemical analysis of our LAC series. POLQ overexpression was associated with an advanced pathologic stage and an increased total number of somatic mutations in LAC. When H1299 human lung cancer cell clones overexpressing POLQ were established and examined, the clones showed resistance to a DSB-inducing chemical in the clonogenic assay and an increased frequency of mutations in the supF forward mutation assay. Further analysis revealed that POLQ overexpression was also positively correlated with Polo Like Kinase 4 (PLK4) overexpression in LAC, and that PLK4 overexpression in the POLQ-overexpressing H1299 cells induced centrosome amplification. Finally, analysis of the TCGA data revealed that POLQ overexpression was associated with an increased somatic mutation load and PLK4 overexpression in diverse human cancers; on the other hand, overexpressions of nine TLS polymerases other than POLQ were associated with an increased somatic mutation load at a much lower frequency. Thus, POLQ overexpression is associated with advanced pathologic stage, increased somatic mutation load, and PLK4 overexpression, the last inducing centrosome amplification, in LAC, suggesting that POLQ overexpression is involved in the pathogenesis of LAC.
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Bianco JN, Bergoglio V, Lin YL, Pillaire MJ, Schmitz AL, Gilhodes J, Lusque A, Mazières J, Lacroix-Triki M, Roumeliotis TI, Choudhary J, Moreaux J, Hoffmann JS, Tourrière H, Pasero P. Overexpression of Claspin and Timeless protects cancer cells from replication stress in a checkpoint-independent manner. Nat Commun 2019; 10:910. [PMID: 30796221 PMCID: PMC6385232 DOI: 10.1038/s41467-019-08886-8] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/05/2019] [Indexed: 12/31/2022] Open
Abstract
Oncogene-induced replication stress (RS) promotes cancer development but also impedes tumor growth by activating anti-cancer barriers. To determine how cancer cells adapt to RS, we have monitored the expression of different components of the ATR-CHK1 pathway in primary tumor samples. We show that unlike upstream components of the pathway, the checkpoint mediators Claspin and Timeless are overexpressed in a coordinated manner. Remarkably, reducing the levels of Claspin and Timeless in HCT116 cells to pretumoral levels impeded fork progression without affecting checkpoint signaling. These data indicate that high level of Claspin and Timeless increase RS tolerance by protecting replication forks in cancer cells. Moreover, we report that primary fibroblasts adapt to oncogene-induced RS by spontaneously overexpressing Claspin and Timeless, independently of ATR signaling. Altogether, these data indicate that enhanced levels of Claspin and Timeless represent a gain of function that protects cancer cells from of oncogene-induced RS in a checkpoint-independent manner.
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Affiliation(s)
- Julien N Bianco
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, 34396, Montpellier, France.,Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Valérie Bergoglio
- Cancer Research Center of Toulouse, INSERM U1037, CNRS ERL5294, University of Toulouse 3, 31037, Toulouse, France
| | - Yea-Lih Lin
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, 34396, Montpellier, France
| | - Marie-Jeanne Pillaire
- Cancer Research Center of Toulouse, INSERM U1037, CNRS ERL5294, University of Toulouse 3, 31037, Toulouse, France
| | - Anne-Lyne Schmitz
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, 34396, Montpellier, France
| | - Julia Gilhodes
- Clinical trials Office - Biostatistics Unit, Institute Claudius Regaud, Institute Universitaire du Cancer Toulouse-Oncopole (IUCT-O), 31100, Toulouse, France
| | - Amelie Lusque
- Clinical trials Office - Biostatistics Unit, Institute Claudius Regaud, Institute Universitaire du Cancer Toulouse-Oncopole (IUCT-O), 31100, Toulouse, France
| | - Julien Mazières
- Thoracic Oncology Department, Toulouse University Hospital, University Paul Sabatier, 31062, Toulouse, France
| | | | | | | | - Jérôme Moreaux
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, 34396, Montpellier, France
| | - Jean-Sébastien Hoffmann
- Cancer Research Center of Toulouse, INSERM U1037, CNRS ERL5294, University of Toulouse 3, 31037, Toulouse, France
| | - Hélène Tourrière
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, 34396, Montpellier, France.
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, 34396, Montpellier, France.
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Jiraskova K, Hughes DJ, Brezina S, Gumpenberger T, Veskrnova V, Buchler T, Schneiderova M, Levy M, Liska V, Vodenkova S, Di Gaetano C, Naccarati A, Pardini B, Vymetalkova V, Gsur A, Vodicka P. Functional Polymorphisms in DNA Repair Genes Are Associated with Sporadic Colorectal Cancer Susceptibility and Clinical Outcome. Int J Mol Sci 2018; 20:E97. [PMID: 30591675 PMCID: PMC6337670 DOI: 10.3390/ijms20010097] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 12/18/2018] [Accepted: 12/21/2018] [Indexed: 02/06/2023] Open
Abstract
DNA repair processes are involved in both the onset and treatment efficacy of colorectal cancer (CRC). A change of a single nucleotide causing an amino acid substitution in the corresponding protein may alter the efficiency of DNA repair, thus modifying the CRC susceptibility and clinical outcome. We performed a candidate gene approach in order to analyze the association of non-synonymous single nucleotide polymorphisms (nsSNPs) in the genes covering the main DNA repair pathways with CRC risk and clinical outcome modifications. Our candidate polymorphisms were selected according to the foremost genomic and functional prediction databases. Sixteen nsSNPs in 12 DNA repair genes were evaluated in cohorts from the Czech Republic and Austria. Apart from the tumor-node-metastasis (TNM) stage, which occurred as the main prognostic factor in all of the performed analyses, we observed several significant associations of different nsSNPs with survival and clinical outcomes in both cohorts. However, only some of the genes (REV3L, POLQ, and NEIL3) were prominently defined as prediction factors in the classification and regression tree analysis; therefore, the study suggests their association for patient survival. In summary, we provide observational and bioinformatics evidence that even subtle alterations in specific proteins of the DNA repair pathways may contribute to CRC susceptibility and clinical outcome.
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Affiliation(s)
- Katerina Jiraskova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic.
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic.
| | - David J Hughes
- Cancer Biology and Therapeutics Group, UCD Conway Institute, University College Dublin, Dublin 4, Ireland.
| | - Stefanie Brezina
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Borschkegasse 8a, A-1090 Vienna, Austria.
| | - Tanja Gumpenberger
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Borschkegasse 8a, A-1090 Vienna, Austria.
| | - Veronika Veskrnova
- Department of Oncology, First Faculty of Medicine, Charles University and Thomayer Hospital, Videnska 800, 140 59 Prague, Czech Republic.
| | - Tomas Buchler
- Department of Oncology, First Faculty of Medicine, Charles University and Thomayer Hospital, Videnska 800, 140 59 Prague, Czech Republic.
| | - Michaela Schneiderova
- Department of Surgery, General University Hospital in Prague, U Nemocnice 499/2, 128 08 Prague, Czech Republic.
| | - Miroslav Levy
- Department of Surgery, First Faculty of Medicine, Charles University and Thomayer Hospital, Thomayerova 815/5, 140 00 Prague, Czech Republic.
| | - Vaclav Liska
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University in Prague, 323 00 Pilsen, Czech Republic.
- Department of Surgery, Medical School in Pilsen, Charles University, Alej svobody 80, 304 600 Pilsen, Czech Republic.
| | - Sona Vodenkova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic.
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic.
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Ruska 2411/87, 100 00 Prague, Czech Republic.
| | - Cornelia Di Gaetano
- Molecular and Genetic Epidemiology; Genomic Variation in Human Populations and Complex Diseases, IIGM Italian Institute for Genomic Medicine, Via Nizza 52, 10126 Turin, Italy.
- Department of Medical Sciences, University of Turin, Corso Dogliotti 14, 10126 Turin, Italy.
| | - Alessio Naccarati
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic.
- Molecular and Genetic Epidemiology; Genomic Variation in Human Populations and Complex Diseases, IIGM Italian Institute for Genomic Medicine, Via Nizza 52, 10126 Turin, Italy.
| | - Barbara Pardini
- Molecular and Genetic Epidemiology; Genomic Variation in Human Populations and Complex Diseases, IIGM Italian Institute for Genomic Medicine, Via Nizza 52, 10126 Turin, Italy.
- Department of Medical Sciences, University of Turin, Corso Dogliotti 14, 10126 Turin, Italy.
| | - Veronika Vymetalkova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic.
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic.
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University in Prague, 323 00 Pilsen, Czech Republic.
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Borschkegasse 8a, A-1090 Vienna, Austria.
| | - Pavel Vodicka
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic.
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic.
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University in Prague, 323 00 Pilsen, Czech Republic.
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