1
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Walczak-Szeffer A, Piastowska-Ciesielska AW. Endoplasmic reticulum stress as a target for retinoids in cancer treatment. Life Sci 2024; 352:122892. [PMID: 38971363 DOI: 10.1016/j.lfs.2024.122892] [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: 02/29/2024] [Revised: 06/21/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
Retinoids, natural and synthetic derivatives of vitamin A, have various regulatory activities including controlling cellular proliferation, differentiation, and death. Furthermore, they have been used to treat specific cancers with satisfying results. Nevertheless, retinoids have yet to be converted into effective systemic therapies for the majority of tumor types. Regulation of unfolded protein response signaling, and persistent activation of endoplasmic reticulum stress (ER-stress) are promising treatment methods for cancer. The present article reviews the current understanding of how vitamin A and its derivatives may aid to cause ER-stress-activated apoptosis, as well as therapeutic options for exploiting ER-stress for achieving beneficial goal. The therapeutic use of some retinoids discussed in this article was related to decreased disease recurrence and improved therapeutic outcomes via ER-stress activation and promotion, indicating that retinoids may play an important role in cancer treatment and prevention. More research is needed to expand the use of vitamin A derivatives in cancer therapy, either alone or in combination with unfolded protein response inducers.
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Affiliation(s)
- Anna Walczak-Szeffer
- Department of Cell Cultures and Genomic Analysis, Medical University of Lodz, Poland.
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2
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Schneider HE, Schmitt LM, Job A, Lankat-Buttgereit B, Gress T, Buchholz M, Gallmeier E. Synthetic lethality between ATR and POLA1 reveals a potential new target for individualized cancer therapy. Neoplasia 2024; 57:101038. [PMID: 39128273 DOI: 10.1016/j.neo.2024.101038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 08/06/2024] [Accepted: 08/06/2024] [Indexed: 08/13/2024]
Abstract
The ATR-CHK1 pathway plays a fundamental role in the DNA damage response and is therefore an attractive target in cancer therapy. The antitumorous effect of ATR inhibitors is at least partly caused by synthetic lethality between ATR and various DNA repair genes. In previous studies, we have identified members of the B-family DNA polymerases as potential lethal partner for ATR, i.e. POLD1 and PRIM1. In this study, we validated and characterized the synthetic lethality between ATR and POLA1. First, we applied a model of ATR-deficient DLD-1 human colorectal cancer cells to confirm synthetic lethality by using chemical POLA1 inhibition. Analyzing cell cycle and apoptotic markers via FACS and Western blotting, we were able to show that apoptosis and S phase arrest contributed to the increased sensitivity of ATR-deficient cancer cells towards POLA1 inhibitors. Importantly, siRNA-mediated POLA1 depletion in ATR-deficient cells caused similar effects in regard to impaired cell viability and cumulation of apoptotic markers, thus excluding toxic effects of chemical POLA1 inhibition. Conversely, we demonstrated that siRNA-mediated POLA1 depletion sensitized several cancer cell lines towards chemical inhibition of ATR and its main effector kinase CHK1. In conclusion, the synthetic lethality between ATR/CHK1 and POLA1 might represent a novel and promising approach for individualized cancer therapy: First, alterations of POLA1 could serve as a screening parameter for increased sensitivity towards ATR and CHK1 inhibitors. Second, alterations in the ATR-CHK1 pathway might predict in increased sensitivity towards POLA1 inhibitors.
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Affiliation(s)
- Hanna Elisabeth Schneider
- Center for Tumor Biology and Immunology, Department of Gastroenterology, Endocrinology and Metabolism, University Hospital of Marburg, Philipps-University Marburg, Marburg, Germany; Department of Medicine A - Hematology, Oncology and Pneumology, University Hospital Münster, Muenster, Germany
| | - Lisa-Maria Schmitt
- Center for Tumor Biology and Immunology, Department of Gastroenterology, Endocrinology and Metabolism, University Hospital of Marburg, Philipps-University Marburg, Marburg, Germany
| | - Albert Job
- Center for Tumor Biology and Immunology, Department of Gastroenterology, Endocrinology and Metabolism, University Hospital of Marburg, Philipps-University Marburg, Marburg, Germany
| | - Brigitte Lankat-Buttgereit
- Center for Tumor Biology and Immunology, Department of Gastroenterology, Endocrinology and Metabolism, University Hospital of Marburg, Philipps-University Marburg, Marburg, Germany
| | - Thomas Gress
- Center for Tumor Biology and Immunology, Department of Gastroenterology, Endocrinology and Metabolism, University Hospital of Marburg, Philipps-University Marburg, Marburg, Germany
| | - Malte Buchholz
- Center for Tumor Biology and Immunology, Department of Gastroenterology, Endocrinology and Metabolism, University Hospital of Marburg, Philipps-University Marburg, Marburg, Germany
| | - Eike Gallmeier
- Center for Tumor Biology and Immunology, Department of Gastroenterology, Endocrinology and Metabolism, University Hospital of Marburg, Philipps-University Marburg, Marburg, Germany; Department of Internal Medicine II - Gastroenterology, Oncology and Metabolism, Hospital Memmingen, Memmingen, Germany.
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3
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Wang J, Sadeghi CA, Le LV, Le Bouteiller M, Frock RL. ATM and 53BP1 regulate alternative end joining-mediated V(D)J recombination. SCIENCE ADVANCES 2024; 10:eadn4682. [PMID: 39083600 PMCID: PMC11290492 DOI: 10.1126/sciadv.adn4682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 06/11/2024] [Indexed: 08/02/2024]
Abstract
G0-G1 phase alternative end joining (A-EJ) is a recently defined mutagenic pathway characterized by resected deletion and translocation joints that are predominantly direct and are distinguished from A-EJ in cycling cells that rely much more on microhomology-mediated end joining (MMEJ). Using chemical and genetic approaches, we systematically evaluate potential A-EJ factors and DNA damage response (DDR) genes to support this mechanism by mapping the repair fates of RAG1/2-initiated double-strand breaks in the context of Igκ locus V-J recombination and chromosome translocation. Our findings highlight a polymerase theta-independent Parp1-XRCC1/LigIII axis as central A-EJ components, supported by 53BP1 in the context of an Ataxia-telangiectasia mutated (ATM)-activated DDR. Mechanistically, we demonstrate varied changes in short-range resection, MMEJ, and translocation, imposed by compromising specific DDR activities, which include polymerase alpha, Ataxia-telangiectasia and Rad3-related (ATR), DNA2, and Mre11. This study advances our understanding of DNA damage repair within the 53BP1 regulatory domain and the RAG1/2 postcleavage complex.
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Affiliation(s)
- Jinglong Wang
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cheyenne A. Sadeghi
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Long V. Le
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marie Le Bouteiller
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
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4
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Zhang R, He Z, Shi Y, Sun X, Chen X, Wang G, Zhang Y, Gao P, Wu Y, Lu S, Duan J, Sun S, Yang N, Fan W, Zhao K, Yang B, Xia Y, Zhang Y, Zhang Y, Yin H. Amplification editing enables efficient and precise duplication of DNA from short sequence to megabase and chromosomal scale. Cell 2024; 187:3936-3952.e19. [PMID: 38936359 DOI: 10.1016/j.cell.2024.05.056] [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: 12/25/2023] [Revised: 03/24/2024] [Accepted: 05/31/2024] [Indexed: 06/29/2024]
Abstract
Duplication is a foundation of molecular evolution and a driver of genomic and complex diseases. Here, we develop a genome editing tool named Amplification Editing (AE) that enables programmable DNA duplication with precision at chromosomal scale. AE can duplicate human genomes ranging from 20 bp to 100 Mb, a size comparable to human chromosomes. AE exhibits activity across various cell types, encompassing diploid, haploid, and primary cells. AE exhibited up to 73.0% efficiency for 1 Mb and 3.4% for 100 Mb duplications, respectively. Whole-genome sequencing and deep sequencing of the junctions of edited sequences confirm the precision of duplication. AE can create chromosomal microduplications within disease-relevant regions in embryonic stem cells, indicating its potential for generating cellular and animal models. AE is a precise and efficient tool for chromosomal engineering and DNA duplication, broadening the landscape of precision genome editing from an individual genetic locus to the chromosomal scale.
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Affiliation(s)
- Ruiwen Zhang
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China; Department of Rheumatology and Immunology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Zhou He
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Yajing Shi
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Xiangkun Sun
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Xinyu Chen
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Guoquan Wang
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Yizhou Zhang
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Pan Gao
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Ying Wu
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Shuhan Lu
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Junyi Duan
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Shangwu Sun
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Na Yang
- Center for Gene Diagnosis and Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Wei Fan
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Kaitao Zhao
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan 430071, China
| | - Bei Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yuchen Xia
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan 430071, China
| | - Yan Zhang
- Department of Clinical Laboratory, Institute of Translational Medicine, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Ying Zhang
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China; Department of Rheumatology and Immunology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Hao Yin
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China.
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5
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Vojnits K, Feng Z, Johnson P, Porras D, Manocha E, Vandersluis S, Pfammatter S, Thibault P, Bhatia M. Targeting of human cancer stem cells predicts efficacy and toxicity of FDA-approved oncology drugs. Cancer Lett 2024; 599:217108. [PMID: 38986735 DOI: 10.1016/j.canlet.2024.217108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 07/02/2024] [Accepted: 07/04/2024] [Indexed: 07/12/2024]
Abstract
Cancer remains the leading cause of death worldwide with approved oncology drugs continuing to have heterogenous patient responses and accompanied adverse effects (AEs) that limits effectiveness. Here, we examined >100 FDA-approved oncology drugs in the context of stemness using a surrogate model of transformed human pluripotent cancer stem cells (CSCs) vs. healthy stem cells (hSCs) capable of distinguishing abnormal self-renewal and differentiation. Although a proportion of these drugs had no effects (inactive), a larger portion affected CSCs (active), and a unique subset preferentially affected CSCs over hSCs (selective). Single cell gene expression and protein profiling of each drug's FDA recognized target provided a molecular correlation of responses in CSCs vs. hSCs. Uniquely, drugs selective for CSCs demonstrated clinical efficacy, measured by overall survival, and reduced AEs. Our findings reveal that while unintentional, half of anticancer drugs are active against CSCs and associated with improved clinical outcomes. Based on these findings, we suggest ability to target CSC targeting should be included as a property of early onco-therapeutic development.
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Affiliation(s)
- Kinga Vojnits
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON, Canada
| | - Zhuohang Feng
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON, Canada
| | - Paige Johnson
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON, Canada
| | - Deanna Porras
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON, Canada
| | - Ekta Manocha
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON, Canada
| | - Sean Vandersluis
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON, Canada
| | - Sibylle Pfammatter
- Department of Chemistry and Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC, Canada
| | - Pierre Thibault
- Department of Chemistry and Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC, Canada
| | - Mick Bhatia
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON, Canada.
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6
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Al-Wahaibi L, El-Emam AA, S. M. Abdelbaky M, Garcia-Granda S, Maurya A, Pal M, Siddiqui Z, Shukla R, Pathak SK, Srivastava R, Shukla VK, Prasad O, Sinha L. Structural Characterization, Spectroscopic Profile, Molecular Docking, ADMET Properties, Molecular Dynamics Simulation Studies, and Molecular Mechanics Generalized Born Surface Area Analysis of 5-(Adamantan-1-yl)-4-butyl-2,4-dihydro-3 H-1,2,4-triazole-3-thione as a Potential COX Inhibitor. ACS OMEGA 2024; 9:26651-26672. [PMID: 38911725 PMCID: PMC11191079 DOI: 10.1021/acsomega.4c03512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/25/2024]
Abstract
Employing a synergistic combination of theoretical density functional theory (DFT) and experimental techniques, we conducted a comprehensive analysis elucidating the structural and pharmacological attributes of 5-(adamantan-1-yl)-4-butyl-2,4-dihydro-3H-1,2,4-triazole-3-thione (5A4BT) as a potent COX inhibitor. The X-ray crystallographic data of 5A4BT showed the pivotal role played by weak interactions, notably π-π and C-H-π interactions, alongside hydrogen bonding, in orchestrating the intricate supramolecular architectures within the crystalline lattice. A quantitative analysis of the arrangement of the crystal structure, as well as both inter- and intramolecular interactions, was conducted using Hirshfeld surfaces and 2D fingerprint plots. Additionally, a comprehensive examination of the IR spectra was undertaken, employing both experimental methods and theoretical DFT techniques, to elucidate the vibrational characteristics of the compound. The strength of intermolecular N-H···S hydrogen bonding and charge transfer within the system was assessed through natural bonding orbital analysis. Moreover, Bader's atoms in molecules theory was employed to estimate the strength of intermolecular hydrogen bonds, revealing strong interactions within the 5A4BT dimer. The title compound exhibited binding affinities of -6.4 and -6.5 kcal/mol for COX1 (PDB 3KK6) and COX2 (1CX2) target proteins, respectively. For the first time, predictions regarding ADMET properties, drug-likeness, and toxicity, including favorable bioavailability, along with 100 ns molecular dynamics simulations, binding free energy, and energy decomposition per residue in the binding cavity of the protein from molecular mechanics generalized born surface area approach, collectively indicate the potential of 5A4BT as a nonselective COX inhibitor.
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Affiliation(s)
- Lamya
H. Al-Wahaibi
- Department
of Chemistry, College of Sciences, Princess
Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Ali A. El-Emam
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Mohammed S. M. Abdelbaky
- Department
of Physical and Analytical Chemistry, Faculty of Chemistry, Oviedo University-CINN, Oviedo 33006, Spain
| | - Santiago Garcia-Granda
- Department
of Physical and Analytical Chemistry, Faculty of Chemistry, Oviedo University-CINN, Oviedo 33006, Spain
| | - Anushree Maurya
- Department
of Physics, University of Lucknow, Lucknow 226007, Uttar Pradesh, India
| | - Mamta Pal
- Department
of Physics, University of Lucknow, Lucknow 226007, Uttar Pradesh, India
| | - Zohra Siddiqui
- Department
of Physics, University of Lucknow, Lucknow 226007, Uttar Pradesh, India
| | - Raj Shukla
- Department
of Physics, University of Lucknow, Lucknow 226007, Uttar Pradesh, India
| | - Shilendra K. Pathak
- Department
of Physics, M. M. M. P. G. College, Deoria 274502, Uttar Pradesh, India
| | - Ruchi Srivastava
- Department
of Physics, University of Lucknow, Lucknow 226007, Uttar Pradesh, India
| | - Vikas K. Shukla
- Department
of Physics, Maharishi University of Information
Technology, Lucknow 226013, Uttar Pradesh, India
| | - Onkar Prasad
- Department
of Physics, University of Lucknow, Lucknow 226007, Uttar Pradesh, India
| | - Leena Sinha
- Department
of Physics, University of Lucknow, Lucknow 226007, Uttar Pradesh, India
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7
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Powała K, Żołek T, Brown G, Kutner A. Molecular Interactions of Selective Agonists and Antagonists with the Retinoic Acid Receptor γ. Int J Mol Sci 2024; 25:6568. [PMID: 38928275 PMCID: PMC11203493 DOI: 10.3390/ijms25126568] [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: 05/21/2024] [Revised: 06/06/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
All-trans retinoic acid (ATRA), the major active metabolite of all-trans retinol (vitamin A), is a key hormonal signaling molecule. In the adult organism, ATRA has a widespread influence on processes that are crucial to the growth and differentiation of cells and, in turn, the acquisition of mature cell functions. Therefore, there is considerable potential in the use of retinoids to treat diseases. ATRA binds to the retinoic acid receptors (RAR) which, as activated by ATRA, selectively regulate gene expression. There are three main RAR isoforms, RARα, RARβ, and RARγ. They each have a distinct role, for example, RARα and RARγ regulate myeloid progenitor cell differentiation and hematopoietic stem cell maintenance, respectively. Hence, targeting an isoform is crucial to developing retinoid-based therapeutics. In principle, this is exemplified when ATRA is used to treat acute promyelocytic leukemia (PML) and target RARα within PML-RARα oncogenic fusion protein. ATRA with arsenic trioxide has provided a cure for the once highly fatal leukemia. Recent in vitro and in vivo studies of RARγ have revealed the potential use of agonists and antagonists to treat diseases as diverse as cancer, heterotopic ossification, psoriasis, and acne. During the final drug development there may be a need to design newer compounds with added modifications to improve solubility, pharmacokinetics, or potency. At the same time, it is important to retain isotype specificity and activity. Examination of the molecular interactions between RARγ agonists and the ligand binding domain of RARγ has revealed aspects to ligand binding that are crucial to RARγ selectivity and compound activity and key to designing newer compounds.
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Affiliation(s)
- Katarzyna Powała
- Department of Organic and Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha, 02-097 Warsaw, Poland
| | - Teresa Żołek
- Department of Organic and Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha, 02-097 Warsaw, Poland
| | - Geoffrey Brown
- School of Biomedical Sciences, Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK;
| | - Andrzej Kutner
- Department of Drug Chemistry Pharmaceutical and Biomedical Analysis, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha, 02-097 Warsaw, Poland;
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8
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Baranovskiy AG, Morstadt LM, Babayeva ND, Tahirov TH. Human primosome requires replication protein A when copying DNA with inverted repeats. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.11.584335. [PMID: 38559116 PMCID: PMC10979909 DOI: 10.1101/2024.03.11.584335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The human primosome, a four-subunit complex of primase and DNA polymerase alpha (Polα), initiates DNA synthesis on both chromosome strands by generating chimeric RNA-DNA primers for loading DNA polymerases delta and epsilon (Polε). Replication protein A (RPA) tightly binds to single-stranded DNA strands, protecting them from nucleolytic digestion and unauthorized transactions. We report here that RPA plays a critical role for the human primosome during DNA synthesis across inverted repeats prone to hairpin formation. On other alternatively structured DNA forming a G-quadruplex, RPA provides no assistance for primosome. A stimulatory effect of RPA on DNA synthesis across hairpins was also observed for the catalytic domain of Polα but not of Polε. The important factors for an efficient hairpin bypass by primosome are the high affinity of RPA to DNA based on four DNA-binding domains and the interaction of the winged-helix-turn-helix domain of RPA with Polα. Binding studies indicate that this interaction stabilizes the RPA/Polα complex on the primed template. This work provides insight into a cooperative action of RPA and primosome on DNA, which is critical for DNA synthesis across inverted repeats.
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9
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Deng J, Lai G, Zhang C, Li K, Zhu W, Xie B, Zhong X. A robust primary liver cancer subtype related to prognosis and drug response based on a multiple combined classifying strategy. Heliyon 2024; 10:e25570. [PMID: 38352751 PMCID: PMC10861988 DOI: 10.1016/j.heliyon.2024.e25570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 01/13/2024] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
The recurrence or resistance to treatment of primary liver cancer (PLL) is significantly related to the heterogeneity present within the tumor. In this study, we integrated prognosis risk score, mRNAsi index, and immune characteristics clustering to classify patients. The four subtypes obtained from the combined classification are associated with PLC's prognosis and drug response. In these subtypes, we observed mRNAsiH_ICCA subtype, the intersection between high mRNAsi and immune characteristics clustering A, had the worst prognosis. Specifically, immune characteristics clustering B (ICC_B) had high drug sensitivity in most drugs regardless of the value of mRNAsi. On the other hand, patients with low mRNAsi responded better to ten drugs including KU-55933 and NU7441, while patients with high mRNAsi might benefit from drugs like Leflunomide. By matching the specific characteristics of each combined subtype with the drug-induced cell line expression profile, we identified a group of potential therapeutic drugs that might regulate the expression of disease signature genes. We developed a feasible multiple combined typing strategy, hoping to guide therapeutic selection and promote the development of precision medicine.
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Affiliation(s)
- Jielian Deng
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Chongqing, China
- Medical Department, Yidu Cloud (Beijing) Technology Co., Beijing, China
| | - Guichuan Lai
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Cong Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Kangjie Li
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Wenyan Zhu
- Chongqing Engineering Research Center of Pharmaceutical Sciences, Chongqing Medical and Pharmaceutical College, Chongqing, China
- College of Pharmacy, Chongqing Medical University, Chongqing, China
- Medical Department, Yidu Cloud (Beijing) Technology Co., Beijing, China
| | - Biao Xie
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Xiaoni Zhong
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Chongqing, China
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10
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Rua-Fernandez J, Lovejoy CA, Mehta KPM, Paulin KA, Toudji YT, Giansanti C, Eichman BF, Cortez D. Self-reversal facilitates the resolution of HMCES DNA-protein crosslinks in cells. Cell Rep 2023; 42:113427. [PMID: 37950866 PMCID: PMC10842721 DOI: 10.1016/j.celrep.2023.113427] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 10/02/2023] [Accepted: 10/27/2023] [Indexed: 11/13/2023] Open
Abstract
Abasic sites are common DNA lesions stalling polymerases and threatening genome stability. When located in single-stranded DNA (ssDNA), they are shielded from aberrant processing by 5-hydroxymethyl cytosine, embryonic stem cell (ESC)-specific (HMCES) via a DNA-protein crosslink (DPC) that prevents double-strand breaks. Nevertheless, HMCES-DPCs must be removed to complete DNA repair. Here, we find that DNA polymerase α inhibition generates ssDNA abasic sites and HMCES-DPCs. These DPCs are resolved with a half-life of approximately 1.5 h. HMCES can catalyze its own DPC self-reversal reaction, which is dependent on glutamate 127 and is favored when the ssDNA is converted to duplex DNA. When the self-reversal mechanism is inactivated in cells, HMCES-DPC removal is delayed, cell proliferation is slowed, and cells become hypersensitive to DNA damage agents that increase AP (apurinic/apyrimidinic) site formation. In these circumstances, proteolysis may become an important mechanism of HMCES-DPC resolution. Thus, HMCES-DPC formation followed by self-reversal is an important mechanism for ssDNA AP site management.
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Affiliation(s)
- Jorge Rua-Fernandez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Courtney A Lovejoy
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Kavi P M Mehta
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Katherine A Paulin
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Yasmine T Toudji
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Celeste Giansanti
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Brandt F Eichman
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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11
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Nguyen TP, Fang M, Kim J, Wang B, Lin E, Khivansara V, Barrows N, Rivera-Cancel G, Goralski M, Cervantes CL, Xie S, Peterson JM, Povedano JM, Antczak MI, Posner BA, Harvey CJB, Naughton BT, McFadden DG, Ready JM, De Brabander JK, Nijhawan D. Inducible mismatch repair streamlines forward genetic approaches to target identification of cytotoxic small molecules. Cell Chem Biol 2023; 30:1453-1467.e8. [PMID: 37607550 PMCID: PMC10841267 DOI: 10.1016/j.chembiol.2023.07.017] [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: 02/16/2023] [Revised: 05/24/2023] [Accepted: 07/30/2023] [Indexed: 08/24/2023]
Abstract
Orphan cytotoxins are small molecules for which the mechanism of action (MoA) is either unknown or ambiguous. Unveiling the mechanism of these compounds may lead to useful tools for biological investigation and new therapeutic leads. In selected cases, the DNA mismatch repair-deficient colorectal cancer cell line, HCT116, has been used as a tool in forward genetic screens to identify compound-resistant mutations, which have ultimately led to target identification. To expand the utility of this approach, we engineered cancer cell lines with inducible mismatch repair deficits, thus providing temporal control over mutagenesis. By screening for compound resistance phenotypes in cells with low or high rates of mutagenesis, we increased both the specificity and sensitivity of identifying resistance mutations. Using this inducible mutagenesis system, we implicate targets for multiple orphan cytotoxins, including a natural product and compounds emerging from a high-throughput screen, thus providing a robust tool for future MoA studies.
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Affiliation(s)
- Thu P Nguyen
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Min Fang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiwoong Kim
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Baiyun Wang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Elisa Lin
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vishal Khivansara
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Neha Barrows
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Giomar Rivera-Cancel
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Maria Goralski
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Christopher L Cervantes
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shanhai Xie
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Johann M Peterson
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Juan Manuel Povedano
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Program in Molecular Medicine and Division of Endocrinology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Monika I Antczak
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bruce A Posner
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | | | - David G McFadden
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Program in Molecular Medicine and Division of Endocrinology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joseph M Ready
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jef K De Brabander
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Deepak Nijhawan
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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12
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Oli S, Kumar Chauhan H, Kumar Bisht A, Agnihotri S, Dobhal P. Bioactive compound, polyphenol content, and antioxidant activity of Asparagus racemosus Linn. root extract. Nat Prod Res 2023:1-6. [PMID: 37874669 DOI: 10.1080/14786419.2023.2272029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 10/07/2023] [Indexed: 10/26/2023]
Abstract
Asparagus racemosus Linn. is an ethnopharmacologically important plant having extensive uses in Ayurveda, Unani, and Siddha. This study was carried out to evaluate the chemical profile of A. racemosus Linn. using GC-MS and FT-IR analysis, and its polyphenol content and antioxidant effects. Plants were collected from Bhujiyaghat, Nainital (29.3159° N, 79.5245° E) in Kumaun Himalayas. GC-MS with FT-IR analysis identified multiple functional groups, including carboxylic acid derivatives. Methyl 11, 12-octadecadienoate, was screened as the major compounds by GC-MS. A. racemosus contains a high concentration of phenols (80.92 ± 0.57 mg of GAE/g of DW), flavonoids (58.22 ± 1.62 mg of QE/g of DW), and tannins (86.77 ± 0.81 mg of TAE/g of DW). DPPH (24.63 ± 0.21 g/ml) and FRAP (72.49483 ± 0.130549 mg of AAE/g of DW) assays revealed the presence of significant antioxidant activity in A. racemosus.
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Affiliation(s)
- Sheetal Oli
- Department of Botany, D.S.B Campus, Kumaun University, Nainital, India
| | | | - Anil Kumar Bisht
- Department of Botany, D.S.B Campus, Kumaun University, Nainital, India
| | - Saumya Agnihotri
- Department of Botany, D.S.B Campus, Kumaun University, Nainital, India
| | - Preeti Dobhal
- Department of Botany, D.S.B Campus, Kumaun University, Nainital, India
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13
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Rudd SG. Targeting pan-essential pathways in cancer with cytotoxic chemotherapy: challenges and opportunities. Cancer Chemother Pharmacol 2023; 92:241-251. [PMID: 37452860 PMCID: PMC10435635 DOI: 10.1007/s00280-023-04562-3] [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: 02/06/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023]
Abstract
Cytotoxic chemotherapy remains a key modality in cancer treatment. These therapies, successfully used for decades, continue to transform the lives of cancer patients daily. With the high attrition rate of current oncology drug development, combined with the knowledge that most new therapies do not displace standard-of-care treatments and that many healthcare systems cannot afford these new therapies; cytotoxic chemotherapies will remain an important component of cancer therapy for many years to come. The clinical value of these therapies is often under-appreciated within the pre-clinical cancer research community, where this diverse class of agents are often grouped together as non-specific cellular poisons killing tumor cells based solely upon proliferation rate; however, this is inaccurate. This review article seeks to reaffirm the importance of focusing research efforts upon improving our basic understanding of how these drugs work, discussing their ability to target pan-essential pathways in cancer cells, the relationship of this to the chemotherapeutic window, and highlighting basic science approaches that can be employed towards refining their use.
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Affiliation(s)
- Sean G Rudd
- Science For Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
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14
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El-Baba C, Ayache Z, Goli M, Hayar B, Kawtharani Z, Pisano C, Kobeissy F, Mechref Y, Darwiche N. The Antitumor Effect of the DNA Polymerase Alpha Inhibitor ST1926 in Glioblastoma: A Proteomics Approach. Int J Mol Sci 2023; 24:14069. [PMID: 37762371 PMCID: PMC10531065 DOI: 10.3390/ijms241814069] [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: 07/31/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Glioblastoma Multiforme (GBM) is the most aggressive form of malignant brain tumor. The median survival rate does not exceed two years, indicating an imminent need to develop novel therapies. The atypical adamantyl retinoid ST1926 induces apoptosis and growth inhibition in different cancer types. We have shown that ST1926 is an inhibitor of the catalytic subunit of DNA polymerase alpha (POLA1), which is involved in initiating DNA synthesis in eukaryotic cells. POLA1 levels are elevated in GBM versus normal brain tissues. Therefore, we studied the antitumor effects of ST1926 in several human GBM cell lines. We further explored the global protein expression profiles in GBM cell lines using liquid chromatography coupled with tandem mass spectrometry to identify new targets of ST1926. Low sub-micromolar concentrations of ST1926 potently decreased cell viability, induced cell damage and apoptosis, and reduced POLA1 protein levels in GBM cells. The proteomics profiles revealed 197 proteins significantly differentially altered upon ST1926 treatment of GBM cells involved in various cellular processes. We explored the differential gene and protein expression of significantly altered proteins in GBM compared to normal brain tissues.
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Affiliation(s)
- Chirine El-Baba
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut 1107 2020, Lebanon; (C.E.-B.); (Z.A.); (B.H.); (Z.K.); (F.K.)
| | - Zeinab Ayache
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut 1107 2020, Lebanon; (C.E.-B.); (Z.A.); (B.H.); (Z.K.); (F.K.)
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA;
| | - Berthe Hayar
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut 1107 2020, Lebanon; (C.E.-B.); (Z.A.); (B.H.); (Z.K.); (F.K.)
| | - Zeinab Kawtharani
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut 1107 2020, Lebanon; (C.E.-B.); (Z.A.); (B.H.); (Z.K.); (F.K.)
| | - Claudio Pisano
- Biogem, Institute of Molecular Biology and Genetics, 83031 Ariano Irpino, Italy;
| | - Firas Kobeissy
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut 1107 2020, Lebanon; (C.E.-B.); (Z.A.); (B.H.); (Z.K.); (F.K.)
- Department of Neurobiology, Center for Neurotrauma, Multiomics and Biomarkers (CNMB), Morehouse School of Medicine, 720 Westview Dr. SW, Atlanta, GA 30310, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA;
| | - Nadine Darwiche
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut 1107 2020, Lebanon; (C.E.-B.); (Z.A.); (B.H.); (Z.K.); (F.K.)
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15
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Zhao Y, Tabet D, Rubio Contreras D, Lao L, Kousholt AN, Weile J, Melo H, Hoeg L, Feng S, Coté AG, Lin ZY, Setiaputra D, Jonkers J, Gingras AC, Gómez Herreros F, Roth FP, Durocher D. Genome-scale mapping of DNA damage suppressors through phenotypic CRISPR-Cas9 screens. Mol Cell 2023; 83:2792-2809.e9. [PMID: 37478847 PMCID: PMC10530064 DOI: 10.1016/j.molcel.2023.06.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 04/18/2023] [Accepted: 06/21/2023] [Indexed: 07/23/2023]
Abstract
To maintain genome integrity, cells must accurately duplicate their genome and repair DNA lesions when they occur. To uncover genes that suppress DNA damage in human cells, we undertook flow-cytometry-based CRISPR-Cas9 screens that monitored DNA damage. We identified 160 genes whose mutation caused spontaneous DNA damage, a list enriched in essential genes, highlighting the importance of genomic integrity for cellular fitness. We also identified 227 genes whose mutation caused DNA damage in replication-perturbed cells. Among the genes characterized, we discovered that deoxyribose-phosphate aldolase DERA suppresses DNA damage caused by cytarabine (Ara-C) and that GNB1L, a gene implicated in 22q11.2 syndrome, promotes biogenesis of ATR and related phosphatidylinositol 3-kinase-related kinases (PIKKs). These results implicate defective PIKK biogenesis as a cause of some phenotypes associated with 22q11.2 syndrome. The phenotypic mapping of genes that suppress DNA damage therefore provides a rich resource to probe the cellular pathways that influence genome maintenance.
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Affiliation(s)
- Yichao Zhao
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Daniel Tabet
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | | | - Linjiang Lao
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Arne Nedergaard Kousholt
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Jochen Weile
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; Donnelly Centre and Department of Computer Science, University of Toronto, 160 College Street, Toronto M5S 3E1, Canada
| | - Henrique Melo
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Lisa Hoeg
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Sumin Feng
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Atina G Coté
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Dheva Setiaputra
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | | | - Frederick P Roth
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; Donnelly Centre and Department of Computer Science, University of Toronto, 160 College Street, Toronto M5S 3E1, Canada
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
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16
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Murai J, Ceribelli M, Fu H, Redon CE, Jo U, Murai Y, Aladjem MI, Thomas CJ, Pommier Y. Schlafen 11 (SLFN11) Kills Cancer Cells Undergoing Unscheduled Re-replication. Mol Cancer Ther 2023; 22:985-995. [PMID: 37216280 PMCID: PMC10524552 DOI: 10.1158/1535-7163.mct-22-0552] [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: 08/22/2022] [Revised: 09/24/2022] [Accepted: 05/16/2023] [Indexed: 05/24/2023]
Abstract
Schlafen 11 (SLFN11) is an increasingly prominent predictive biomarker and a molecular sensor for a wide range of clinical drugs: topoisomerases, PARP and replication inhibitors, and platinum derivatives. To expand the spectrum of drugs and pathways targeting SLFN11, we ran a high-throughput screen with 1,978 mechanistically annotated, oncology-focused compounds in two isogenic pairs of SLFN11-proficient and -deficient cells (CCRF-CEM and K562). We identified 29 hit compounds that selectively kill SLFN11-proficient cells, including not only previously known DNA-targeting agents, but also the neddylation inhibitor pevonedistat (MLN-4924) and the DNA polymerase α inhibitor AHPN/CD437, which both induced SLFN11 chromatin recruitment. By inactivating cullin-ring E3 ligases, pevonedistat acts as an anticancer agent partly by inducing unscheduled re-replication through supraphysiologic accumulation of CDT1, an essential factor for replication initiation. Unlike the known DNA-targeting agents and AHPN/CD437 that recruit SLFN11 onto chromatin in 4 hours, pevonedistat recruited SLFN11 at late time points (24 hours). While pevonedistat induced unscheduled re-replication in SLFN11-deficient cells after 24 hours, the re-replication was largely blocked in SLFN11-proficient cells. The positive correlation between sensitivity to pevonedistat and SLFN11 expression was also observed in non-isogenic cancer cells in three independent cancer cell databases (NCI-60, CTRP: Cancer Therapeutics Response Portal and GDSC: Genomic of Drug Sensitivity in Cancer). The present study reveals that SLFN11 not only detects stressed replication but also inhibits unscheduled re-replication induced by pevonedistat, thereby enhancing its anticancer efficacy. It also suggests SLFN11 as a potential predictive biomarker for pevonedistat in ongoing and future clinical trials.
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Affiliation(s)
- Junko Murai
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
- Department of Cell Growth and Tumor Regulation, Proteo-Science Center, Ehime University, Toon 791-0295, Japan
- Department of Biochemistry and Molecular Genetics, Ehime University Graduate School of Medicine, Toon 791-0295, Japan
| | - Michele Ceribelli
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Haiqing Fu
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Christophe E. Redon
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Ukhyun Jo
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yasuhisa Murai
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Mirit I. Aladjem
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Craig J. Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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17
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Liu L, Wang Q, Wu L, Zhang L, Huang Y, Yang H, Guo L, Fang Z, Wang X. Overexpression of POLA2 in hepatocellular carcinoma is involved in immune infiltration and predicts a poor prognosis. Cancer Cell Int 2023; 23:138. [PMID: 37452331 PMCID: PMC10349470 DOI: 10.1186/s12935-023-02949-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 05/16/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the second malignancy worldwide. POLA2 initiates DNA replication, regulates cell cycle and gene repair that promote tumorigenesis and disease progression. However, the prognostic and biological function roles of POLA2 in HCC had not been conclusively determined. METHODS The expression levels and prognosis role of POLA1 and POLA2 in HCC were analyzed based on TCGA-LIHC database and recruited 24 HCC patients. Gene mutations were analyzed using "maftools" package. POLA2 and immune cells correlations were analyzed by TIMER. POLA2 co-expressed genes functional enrichment were evaluated using Metascape. The mRNA and protein level of POLA2 was detected in HCC cells and tissues. Cell migration, invasion, proliferation, cell cycle and HCC cell lines derived xenograft model were performed to investigate POLA2 biological function. RESULTS POLA2 was significantly high expressed in HCC than in normal liver tissue in both TCGA-LIHC and our collected HCC samples. In validation cohort, POLA2 significantly related to tumor differentiation, tumor size and Ki-67 (p < 0.05). In TCGA-LIHC cohort, overexpression of POLA2 predicted a low OS and associated with different clinical stages. Multivariate Cox regression showed overexpression of POLA2 effectively distinguished the prognosis at different T, N, M, stages and grades of HCC. POLA2 expression correlated with mutation burden, immune cells infiltration and immune-associated genes expression of HCC. Functional enrichment revealed that POLA2 co-expressed genes were linked to cellular activity, plasma membrane protein complex and leukocyte activity, immune response-regulated cell surface receptor signaling pathway, and immune response-regulated signaling pathway. Moreover, POLA2 was also positively co-expressed with some immune checkpoints (CD274, CTL-4, HAVCR2, PDCD1, PDCD1LG2, TIGIT, and LAG3) (p < 0.001). Gene knockdown revealed that POLA2 promoted proliferation, migration, invasion, and cell cycle of SMMC-7721 and HepG2. The HCC xenograft tumor model also demonstrated remarkably tumor size inhibition, tumor proliferation inhibtion and tumor necrosis promotion when POLA2 knockdown. CONCLUSIONS POLA2 influenced immune microenvironment and tumor progression of HCC indicated that it might be a potential molecular marker for prognostic evaluation or a therapeutic target for HCC.
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Affiliation(s)
- Long Liu
- Department of Hepatobiliary Surgery, Taizhou Hospital of Zhejiang Province, Zhejiang University, Linhai, 317000, Zhejiang, China
| | - Qi Wang
- Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, 317000, Zhejiang, China
| | - Linjun Wu
- Department of Hepatobiliary Surgery, Taizhou Hospital of Zhejiang Province, Zhejiang University, Linhai, 317000, Zhejiang, China
- Taizhou Hospital Library, Wenzhou Medical University, Linhai, 317000, Zhejiang, China
| | - Lele Zhang
- Department of Medical Laboratory, School of Clinical Medicine, Ningxia Medical University, Yinchuan, 750004, China
| | - Yuxi Huang
- Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, 317000, Zhejiang, China
| | - Haihua Yang
- Department of Radiation Oncology, Taizhou Hospital of Zhejiang Province, Linhai, 317000, Zhejiang, China
- Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive, System Tumor of Zhejiang Province, Zhejiang, China
| | - Le Guo
- Department of Medical Laboratory, School of Clinical Medicine, Ningxia Medical University, Yinchuan, 750004, China
| | - Zheping Fang
- Department of Hepatobiliary Surgery, Taizhou Hospital of Zhejiang Province, Zhejiang University, Linhai, 317000, Zhejiang, China.
- Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, 317000, Zhejiang, China.
| | - Xuequan Wang
- Department of Radiation Oncology, Taizhou Hospital of Zhejiang Province, Linhai, 317000, Zhejiang, China.
- Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive, System Tumor of Zhejiang Province, Zhejiang, China.
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18
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Li Y, Chen Z, Peng J, Yuan C, Yan S, Yang N, Li P, Kong B. The splicing factor SNRPB promotes ovarian cancer progression through regulating aberrant exon skipping of POLA1 and BRCA2. Oncogene 2023:10.1038/s41388-023-02763-x. [PMID: 37391593 DOI: 10.1038/s41388-023-02763-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 06/08/2023] [Accepted: 06/22/2023] [Indexed: 07/02/2023]
Abstract
Splicing factors play a crucial role in the initiation and development of various human cancers. SNRPB, a core spliceosome component, regulates pre-mRNA alternative splicing. However, its function and underlying mechanism in ovarian cancer remain unclear. This study identified SNRPB as a critical driver of ovarian cancer through TCGA and CPTAC database analysis. SNRPB was highly upregulated in fresh frozen ovarian cancer tissues compared with normal fallopian tubes. Immunohistochemistry revealed that SNRPB expression was increased in formalin-fixed, paraffin-embedded ovarian cancer sections and was positively correlated with a poor prognosis for ovarian cancer. Functionally, SNRPB knockdown suppressed ovarian cancer cell proliferation and invasion, and overexpression exerted opposite effects. SNRPB expression increased after cisplatin treatment, and silencing SNRPB sensitized ovarian cancer cells to cisplatin. KEGG pathway analysis revealed that the differentially expressed genes (DEGs) were mainly enriched in DNA replication and homologous recombination, and almost all DEGs related to DNA replication and homologous recombination were downregulated after SNRPB knockdown according to RNA-seq. Exon 3 skipping of the DEGs DNA polymerase alpha 1 (POLA1) and BRCA2 was induced by SNRPB silencing. Exon 3 skipping of POLA1 yielded premature termination codons and led to nonsense-mediated RNA decay (NMD); exon 3 skipping of BRCA2 led to loss of the PALB2 binding domain, which is necessary for homologous recombination, and increased ovarian cancer cell cisplatin sensitivity. POLA1 or BRCA2 knockdown partially impaired the increased malignancy of SNRPB-overexpressing ovarian cancer cells. Moreover, miR-654-5p was found to reduce SNRPB mRNA expression by directly binding to the SNRPB 3'-UTR. Overall, SNRPB was identified as an important oncogenic driver that promotes ovarian cancer progression by repressing exon 3 skipping of POLA1 and BRCA2. Thus, SNRPB is a potential treatment target and prognostic marker for ovarian cancer.
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Affiliation(s)
- Yingwei Li
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China.
- Medical Integration and Practice Center, Cheeloo College of Medicine, Shandong University, Ji'nan 250012, Shandong Province, China.
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China.
| | - Zhongshao Chen
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China
| | - Jiali Peng
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China
| | - Cunzhong Yuan
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China
| | - Shi Yan
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China
| | - Ning Yang
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China
| | - Peng Li
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China
| | - Beihua Kong
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China.
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China.
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19
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Rua-Fernandez J, Lovejoy CA, Mehta KPM, Paulin KA, Toudji YT, Eichman BF, Cortez D. Self-reversal facilitates the resolution of HMCES-DNA protein crosslinks in cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544844. [PMID: 37398432 PMCID: PMC10312715 DOI: 10.1101/2023.06.14.544844] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Abasic sites are common DNA lesions that stall polymerases and threaten genome stability. When located in single-stranded DNA (ssDNA), they are shielded from aberrant processing by HMCES via a DNA-protein crosslink (DPC) that prevents double-strand breaks. Nevertheless, the HMCES-DPC must be removed to complete DNA repair. Here, we found that DNA polymerase α inhibition generates ssDNA abasic sites and HMCES-DPCs. These DPCs are resolved with a half-life of approximately 1.5 hours. Resolution does not require the proteasome or SPRTN protease. Instead, HMCES-DPC self-reversal is important for resolution. Biochemically, self-reversal is favored when the ssDNA is converted to duplex DNA. When the self-reversal mechanism is inactivated, HMCES-DPC removal is delayed, cell proliferation is slowed, and cells become hypersensitive to DNA damage agents that increase AP site formation. Thus, HMCES-DPC formation followed by self-reversal is an important mechanism for ssDNA AP site management.
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20
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Tian C, Zhou J, Li X, Gao Y, Wen Q, Kang X, Wang N, Yao Y, Jiang J, Song G, Zhang T, Hu S, Liao J, Yu C, Wang Z, Liu X, Pei X, Chan K, Liu Z, Gan H. Impaired histone inheritance promotes tumor progression. Nat Commun 2023; 14:3429. [PMID: 37301892 PMCID: PMC10257670 DOI: 10.1038/s41467-023-39185-y] [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: 10/20/2022] [Accepted: 06/02/2023] [Indexed: 06/12/2023] Open
Abstract
Faithful inheritance of parental histones is essential to maintain epigenetic information and cellular identity during cell division. Parental histones are evenly deposited onto the replicating DNA of sister chromatids in a process dependent on the MCM2 subunit of DNA helicase. However, the impact of aberrant parental histone partition on human disease such as cancer is largely unknown. In this study, we construct a model of impaired histone inheritance by introducing MCM2-2A mutation (defective in parental histone binding) in MCF-7 breast cancer cells. The resulting impaired histone inheritance reprograms the histone modification landscapes of progeny cells, especially the repressive histone mark H3K27me3. Lower H3K27me3 levels derepress the expression of genes associated with development, cell proliferation, and epithelial to mesenchymal transition. These epigenetic changes confer fitness advantages to some newly emerged subclones and consequently promote tumor growth and metastasis after orthotopic implantation. In summary, our results indicate that impaired inheritance of parental histones can drive tumor progression.
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Affiliation(s)
- Congcong Tian
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Jiaqi Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Xinran Li
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Yuan Gao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Qing Wen
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Xing Kang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Nan Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Yuan Yao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Jiuhang Jiang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
- College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, 510642, Guangzhou, Guangdong, China
| | - Guibing Song
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
- College of Animal Science and Technology, Northwest A&F University, 712100, Shaanxi, Angling, China
| | - Tianjun Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Suili Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
- College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, 510642, Guangzhou, Guangdong, China
| | - JingYi Liao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Chuanhe Yu
- Hormel Institute, University of Minnesota, Austin, MN, 55912, USA
| | - Zhiquan Wang
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Xiangyu Liu
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Health Science Center, 518060, Shenzhen, China
| | - Xinhai Pei
- Department of Anatomy and Histology, Shenzhen University Health Science Center, 518060, Shenzhen, China
| | - Kuiming Chan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong Special Administration Region, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, 518172, Shenzhen, China
| | - Zichuan Liu
- School of Pharmaceutical Science and Technology, Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, 300072, Tianjin, China
| | - Haiyun Gan
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China.
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21
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Huang XW, Pan W, Zhong MZ, Chhonker YS, Steele AD, Keohane CE, Mishra B, Felix Raj Lucas LO, Murry DJ, Ausubel FM, Wuest WM, Li CX, Mylonakis E. Biological Evaluation of the Antibacterial Retinoid CD437 in Cutibacterium acnes Infection. Antimicrob Agents Chemother 2023; 67:e0167922. [PMID: 36943064 PMCID: PMC10112217 DOI: 10.1128/aac.01679-22] [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: 12/15/2022] [Accepted: 02/24/2023] [Indexed: 03/23/2023] Open
Abstract
Acne vulgaris is a complex skin disease involving infection by Cutibacterium acnes, inflammation, and hyperkeratinization. We evaluated the activity of the retinoid 6-[3-(adamantyl)-4-hydroxyphenyl]-2-naphthalene carboxylic acid (CD437) and 16 other retinoid analogs as potential anti-C. acnes compounds and found that CD437 displayed the highest antimicrobial activity with an MIC against C. acnes (ATCC 6919 and HM-513) of 1 μg/mL. CD437 demonstrated an MBC of 2 μg/mL compared to up to 64 μg/mL for the retinoid adapalene and up to 16 μg/mL for tetracycline, which are commonly used clinically to treat acne. Membrane permeability assays demonstrated that exposure of C. acnes ATCC 6919 to CD437 damaged the integrity of C. acnes ATCC 6919 bacterial membranes, and this finding was confirmed with scanning electron microscopy. Additionally, CD437 downregulated the expression of C. acnes ATCC 6919 virulence factors, including the genes encoding Christie-Atkins-Munch-Petersen factor 1 (CAMP1), CAMP2, glycerol-ester hydrolase B (GehB), sialidase B, and neuraminidase. In a mouse skin infection model of C. acnes ATCC 6919, topical treatment with CD437 ameliorated skin lesions and reduced the bacterial burden in situ (P < 0.001). In human NHEK primary cells, CD437 reduced the transcriptional levels of the coding genes for inflammatory cytokines (interleukin-1α, ~10-fold; interleukin-6, ~20-fold; interleukin-8, ~30-fold; and tumor necrosis factor-alpha, ~6-fold) and downregulated the transcriptional levels of KRT10 (~10-fold), FLG (~4-fold), and TGM1 (~2-fold), indicating that CD437 can diminish inflammation and hyperkeratinization. In summary, CD437 deserves further attention for its dual function as a potential acne therapeutic that potentially acts on both the pathogen and the host.
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Affiliation(s)
- Xiao-wen Huang
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Wen Pan
- Division of Infectious Diseases, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Mei-zhen Zhong
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yashpal Singh Chhonker
- Department of Pharmacy Practice and Science, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Andrew D. Steele
- Department of Chemistry, Emory University, Atlanta, Georgia, USA
| | | | - Biswajit Mishra
- Division of Infectious Diseases, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Lewis Oscar Felix Raj Lucas
- Division of Infectious Diseases, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Daryl J. Murry
- Department of Pharmacy Practice and Science, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Frederick M. Ausubel
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - William M. Wuest
- Department of Chemistry, Emory University, Atlanta, Georgia, USA
- Emory Antibiotic Resistance Center, Emory University, Atlanta, Georgia, USA
| | - Chang-xing Li
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Eleftherios Mylonakis
- Division of Infectious Diseases, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
- Department of Medicine, Houston Methodist Hospital and Academic Institute, Houston, Texas, USA
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22
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He Q, Baranovskiy AG, Morstadt LM, Lisova AE, Babayeva ND, Lusk BL, Lim CJ, Tahirov TH. Structures of human primosome elongation complexes. Nat Struct Mol Biol 2023; 30:579-583. [PMID: 37069376 PMCID: PMC10268227 DOI: 10.1038/s41594-023-00971-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 03/20/2023] [Indexed: 04/19/2023]
Abstract
The synthesis of RNA-DNA primer by primosome requires coordination between primase and DNA polymerase α subunits, which is accompanied by unknown architectural rearrangements of multiple domains. Using cryogenic electron microscopy, we solved a 3.6 Å human primosome structure caught at an early stage of RNA primer elongation with deoxynucleotides. The structure confirms a long-standing role of primase large subunit and reveals new insights into how primosome is limited to synthesizing short RNA-DNA primers.
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Affiliation(s)
- Qixiang He
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Andrey G Baranovskiy
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Lucia M Morstadt
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Alisa E Lisova
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Nigar D Babayeva
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Benjamin L Lusk
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ci Ji Lim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - Tahir H Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA.
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23
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Al-Omary FM, Alvarez N, Al-Rasheed LS, Veiga N, Hassan HM, El-Emam AA. Novel Adamantane-Linked Isothiourea Derivatives as Potential Chemotherapeutic Agents: Synthesis, Structural Insights, and Antimicrobial/Anti-Proliferative Profiles. ACS OMEGA 2023; 8:13465-13477. [PMID: 37065023 PMCID: PMC10099428 DOI: 10.1021/acsomega.3c01469] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
In this study, two adamantane-linked isothiourea derivatives containing a common 4-chlorophenyl substituent coupled with 4-nitrobenzyl or 4-bromobenzyl moieties were synthesized. Both derivatives were characterized, in the solid state and in solution, through a synergistic combination of experimental and in silico techniques, and the results are of great value for the chemical and structural characterization of related compounds. The crystal structures of both derivatives were analyzed in depth, including Hirshfeld surface analysis and lattice energy calculations, revealing a predominant dispersive component of the total energy that stabilizes crystal packing. Both compounds showed potent broad-spectrum antibacterial activity and moderate activity against the pathogenic fungus Candida albicans. In addition, in vitro anti-proliferative activity assays showed that the 4-bromobenzyl analogue displays higher activity than the 4-nitrobenzyl one, with IC50 values under 30 μM against five human cancer cell lines. Our results give evidence of the potential of the adamantane/isothiourea combination to render auspicious scaffolds for new potential chemotherapeutic agents.
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Affiliation(s)
- Fatmah
A. M. Al-Omary
- Department
of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Natalia Alvarez
- Química
Inorgánica, Facultad de Química, Universidad de la República, Av. General Flores 2124, Montevideo 11800, Uruguay
| | - Lamees S. Al-Rasheed
- Department
of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Nicolás Veiga
- Química
Inorgánica, Facultad de Química, Universidad de la República, Av. General Flores 2124, Montevideo 11800, Uruguay
| | - Hanan M. Hassan
- Department
of Pharmacology and Biochemistry, Faculty of Pharmacy, Delta University for Science and Technology, International Costal Road, Gamasa
City, Mansoura 11152, Egypt
| | - Ali A. El-Emam
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
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24
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Saha LK, Saha S, Yang X, Huang SYN, Sun Y, Jo U, Pommier Y. Replication-associated formation and repair of human topoisomerase IIIα cleavage complexes. Nat Commun 2023; 14:1925. [PMID: 37024461 PMCID: PMC10079683 DOI: 10.1038/s41467-023-37498-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 03/08/2023] [Indexed: 04/08/2023] Open
Abstract
Topoisomerase IIIα (TOP3A) belongs to the conserved Type IA family of DNA topoisomerases. Here we report that human TOP3A is associated with DNA replication forks and that a "self-trapping" TOP3A mutant (TOP3A-R364W) generates cellular TOP3A DNA cleavage complexes (TOP3Accs). We show that trapped TOP3Accs that interfere with replication, induce DNA damage and genome instability. To elucidate how TOP3Accs are repaired, we explored the role of Spartan (SPRTN), the metalloprotease associated with DNA replication, which digests proteins forming DNA-protein crosslinks (DPCs). We find that SPRTN-deficient cells show elevated TOP3Accs, whereas overexpression of SPRTN lowers cellular TOP3Accs. SPRTN is deubiquitinated and epistatic with TDP2 in response to TOP3Accs. In addition, we found that MRE11 can excise TOP3Accs, and that cell cycle determines the preference for the SPRTN-TDP2 vs. the ATM-MRE11 pathways, in S vs. G2, respectively. Our study highlights the prevalence of TOP3Accs repair mechanisms to ensure normal DNA replication.
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Affiliation(s)
- Liton Kumar Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Sourav Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Xi Yang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Shar-Yin Naomi Huang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Yilun Sun
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Ukhyun Jo
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
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25
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Nguyen TP, Fang M, Kim J, Wang B, Lin E, Khivansara V, Barrows N, Rivera-Cancel G, Goralski M, Cervantes CL, Xie S, Peterson JM, Povedano JM, Antczak MI, Posner BA, McFadden DG, Ready JM, De Brabander JK, Nijhawan D. Inducible mismatch repair streamlines forward genetic approaches to target identification of cytotoxic small molecules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.21.529401. [PMID: 36865268 PMCID: PMC9980046 DOI: 10.1101/2023.02.21.529401] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Orphan cytotoxins are small molecules for which the mechanism of action (MoA) is either unknown or ambiguous. Unveiling the mechanism of these compounds may lead to useful tools for biological investigation and in some cases, new therapeutic leads. In select cases, the DNA mismatch repair-deficient colorectal cancer cell line, HCT116, has been used as a tool in forward genetic screens to identify compound-resistant mutations, which have ultimately led to target identification. To expand the utility of this approach, we engineered cancer cell lines with inducible mismatch repair deficits, thus providing temporal control over mutagenesis. By screening for compound resistance phenotypes in cells with low or high rates of mutagenesis, we increased both the specificity and sensitivity of identifying resistance mutations. Using this inducible mutagenesis system, we implicate targets for multiple orphan cytotoxins, including a natural product and compounds emerging from a high-throughput screen, thus providing a robust tool for future MoA studies.
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26
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Warda ET, El-Ashmawy MB, Habib ESE, Abdelbaky MSM, Garcia-Granda S, Thamotharan S, El-Emam AA. Synthesis and in vitro antibacterial, antifungal, anti-proliferative activities of novel adamantane-containing thiazole compounds. Sci Rep 2022; 12:21058. [PMID: 36474013 PMCID: PMC9726863 DOI: 10.1038/s41598-022-25390-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
A series of (Z)-N-(adamantan-1-yl)-3,4-diarylthiazol-2(3H)-imines (5a-r) was synthesized via condensation of 1-(adamantan-1-yl)-3-arylthioureas (3a-c) with various aryl bromomethyl ketones (4a-f). The structures of the synthesized compounds were characterized by 1H NMR, 13C NMR and by X-ray crystallography. The in vitro inhibitory activities of the synthesized compounds were assessed against a panel of Gram-positive and Gram-negative bacteria, and pathogenic fungi. Compounds 5c, 5g, 5l, 5m, and 5q displayed potent broad-spectrum antibacterial activity, while compounds 5a and 5o showed activity against the tested Gram-positive bacteria. Compounds 5b, 5l and 5q displayed potent antifungal activity against Candida albicans. In addition, the synthesized compounds were evaluated for anti-proliferative activity towards five human tumor cell lines. The optimal anti-proliferative activity was attained by compounds 5e and 5k which showed potent inhibitory activity against all the tested cell lines. Molecular docking analysis reveals that compounds 5e and 5k can occupy the positions of NAD cofactor and the histone deacetylase inhibitor EX527 at the active site of SIRT1 enzyme.
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Affiliation(s)
- Eman T. Warda
- grid.10251.370000000103426662Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516 Egypt
| | - Mahmoud B. El-Ashmawy
- grid.10251.370000000103426662Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516 Egypt
| | - El-Sayed E. Habib
- grid.10251.370000000103426662Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, 35516 Egypt
| | - Mohammed S. M. Abdelbaky
- grid.10863.3c0000 0001 2164 6351Department of Physical and Analytical Chemistry, Faculty of Chemistry, Oviedo University-CINN, 33006 Oviedo, Spain
| | - Santiago Garcia-Granda
- grid.10863.3c0000 0001 2164 6351Department of Physical and Analytical Chemistry, Faculty of Chemistry, Oviedo University-CINN, 33006 Oviedo, Spain
| | - Subbiah Thamotharan
- grid.412423.20000 0001 0369 3226Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, 613 401 India
| | - Ali A. El-Emam
- grid.10251.370000000103426662Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516 Egypt
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27
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Lisova AE, Baranovskiy AG, Morstadt LM, Babayeva ND, Tahirov T. Human DNA polymerase α has a strong mutagenic potential at the initial steps of DNA synthesis. Nucleic Acids Res 2022; 50:12266-12273. [PMID: 36454017 PMCID: PMC9757036 DOI: 10.1093/nar/gkac1101] [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: 08/12/2022] [Revised: 09/16/2022] [Accepted: 11/10/2022] [Indexed: 12/05/2022] Open
Abstract
DNA polymerase α (Polα) is essential for DNA replication initiation and makes a notable contribution to genome mutagenesis. The activity and fidelity of Polα during the early steps of DNA replication have not been well studied. Here we show that at the beginning of DNA synthesis, when extending the RNA primer received from primase, Polα is more mutagenic than during the later DNA elongation steps. Kinetic and binding studies revealed substantially higher activity and affinity to the template:primer when Polα interacts with ribonucleotides of a chimeric RNA-DNA primer. Polα activity greatly varies during first six steps of DNA synthesis, and the bias in the rates of correct and incorrect dNTP incorporation leads to impaired fidelity, especially upon the second step of RNA primer extension. Furthermore, increased activity and stability of Polα/template:primer complexes containing RNA-DNA primers result in higher efficiency of mismatch extension.
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Affiliation(s)
| | | | - Lucia M Morstadt
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Nigar D Babayeva
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Tahir H Tahirov
- To whom correspondence should be addressed. Tel: +1 402 559 7608; Fax: +1 402 559 3739;
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28
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Mann A, Ramirez-Otero MA, De Antoni A, Hanthi YW, Sannino V, Baldi G, Falbo L, Schrempf A, Bernardo S, Loizou J, Costanzo V. POLθ prevents MRE11-NBS1-CtIP-dependent fork breakage in the absence of BRCA2/RAD51 by filling lagging-strand gaps. Mol Cell 2022; 82:4218-4231.e8. [PMID: 36400008 DOI: 10.1016/j.molcel.2022.09.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/16/2022] [Accepted: 09/09/2022] [Indexed: 11/18/2022]
Abstract
POLθ promotes repair of DNA double-strand breaks (DSBs) resulting from collapsed forks in homologous recombination (HR) defective tumors. Inactivation of POLθ results in synthetic lethality with the loss of HR genes BRCA1/2, which induces under-replicated DNA accumulation. However, it is unclear whether POLθ-dependent DNA replication prevents HR-deficiency-associated lethality. Here, we isolated Xenopus laevis POLθ and showed that it processes stalled Okazaki fragments, directly visualized by electron microscopy, thereby suppressing ssDNA gaps accumulating on lagging strands in the absence of RAD51 and preventing fork reversal. Inhibition of POLθ DNA polymerase activity leaves fork gaps unprotected, enabling their cleavage by the MRE11-NBS1-CtIP endonuclease, which produces broken forks with asymmetric single-ended DSBs, hampering BRCA2-defective cell survival. These results reveal a POLθ-dependent genome protection function preventing stalled forks rupture and highlight possible resistance mechanisms to POLθ inhibitors.
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Affiliation(s)
- Anjali Mann
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Miguel Angel Ramirez-Otero
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Anna De Antoni
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Yodhara Wijesekara Hanthi
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Vincenzo Sannino
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Giorgio Baldi
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Lucia Falbo
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Anna Schrempf
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Centre, Medical University of Vienna, Vienna, Austria
| | - Sara Bernardo
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Centre, Medical University of Vienna, Vienna, Austria
| | - Joanna Loizou
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Centre, Medical University of Vienna, Vienna, Austria
| | - Vincenzo Costanzo
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy.
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29
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Zhang J, Chan DW, Lin SY. Exploiting DNA Replication Stress as a Therapeutic Strategy for Breast Cancer. Biomedicines 2022; 10:2775. [PMID: 36359297 PMCID: PMC9687274 DOI: 10.3390/biomedicines10112775] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/19/2022] [Accepted: 10/27/2022] [Indexed: 09/19/2023] Open
Abstract
Proliferating cells rely on DNA replication to ensure accurate genome duplication. Cancer cells, including breast cancer cells, exhibit elevated replication stress (RS) due to the uncontrolled oncogenic activation, loss of key tumor suppressors, and defects in the DNA repair machinery. This intrinsic vulnerability provides a great opportunity for therapeutic exploitation. An increasing number of drug candidates targeting RS in breast cancer are demonstrating promising efficacy in preclinical and early clinical trials. However, unresolved challenges lie in balancing the toxicity of these drugs while maintaining clinical efficacy. Furthermore, biomarkers of RS are urgently required to guide patient selection. In this review, we introduce the concept of targeting RS, detail the current therapies that target RS, and highlight the integration of RS with immunotherapies for breast cancer treatment. Additionally, we discuss the potential biomarkers to optimizing the efficacy of these therapies. Together, the continuous advances in our knowledge of targeting RS would benefit more patients with breast cancer.
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Affiliation(s)
- Jing Zhang
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Shiaw-Yih Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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30
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Abdelaal MR, Ibrahim E, Elnagar MR, Soror SH, Haffez H. Augmented Therapeutic Potential of EC-Synthetic Retinoids in Caco-2 Cancer Cells Using an In Vitro Approach. Int J Mol Sci 2022; 23:ijms23169442. [PMID: 36012706 PMCID: PMC9409216 DOI: 10.3390/ijms23169442] [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: 07/02/2022] [Revised: 07/29/2022] [Accepted: 08/05/2022] [Indexed: 11/16/2022] Open
Abstract
Colorectal cancer therapies have produced promising clinical responses, but tumor cells rapidly develop resistance to these drugs. It has been previously shown that EC19 and EC23, two EC-synthetic retinoids, have single-agent preclinical anticancer activity in colorectal carcinoma. Here, isobologram analysis revealed that they have synergistic cytotoxicity with retinoic acid receptor (RAR) isoform-selective agonistic retinoids such as AC261066 (RARβ2-selective agonist) and CD437 (RARγ-selective agonist) in Caco-2 cells. This synergism was confirmed by calculating the combination index (lower than 1) and the dose reduction index (higher than 1). Flow cytometry of combinatorial IC50 (the concentration causing 50% cell death) confirmed the cell cycle arrest at the SubG0-G1 phase with potentiated apoptotic and necrotic effects. The reported synergistic anticancer activity can be attributed to their ability to reduce the expression of ATP-binding cassette (ABC) transporters including P-glycoprotein (P-gp1), breast cancer resistance protein (BCRP) and multi-drug resistance-associated protein-1 (MRP1) and Heat Shock Protein 70 (Hsp70). This adds up to the apoptosis-promoting activity of EC19 and EC23, as shown by the increased Caspase-3/7 activities and DNA fragmentation leading to DNA double-strand breaks. This study sheds the light on the possible use of EC-synthetic retinoids in the rescue of multi-drug resistance in colorectal cancer using Caco-2 as a model and suggests new promising combinations between different synthetic retinoids. The current in vitro results pave the way for future studies on these compounds as possible cures for colorectal carcinoma.
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Affiliation(s)
- Mohamed R. Abdelaal
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, Helwan University, Cairo 11795, Egypt
- Center of Scientific Excellence “Helwan Structural Biology Research, (HSBR)”, Helwan University, Cairo 11795, Egypt
| | - Esraa Ibrahim
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, Helwan University, Cairo 11795, Egypt
- Center of Scientific Excellence “Helwan Structural Biology Research, (HSBR)”, Helwan University, Cairo 11795, Egypt
| | - Mohamed R. Elnagar
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Al-Azhar University, Cairo 11823, Egypt
| | - Sameh H. Soror
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, Helwan University, Cairo 11795, Egypt
- Center of Scientific Excellence “Helwan Structural Biology Research, (HSBR)”, Helwan University, Cairo 11795, Egypt
| | - Hesham Haffez
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, Helwan University, Cairo 11795, Egypt
- Center of Scientific Excellence “Helwan Structural Biology Research, (HSBR)”, Helwan University, Cairo 11795, Egypt
- Correspondence: ; Tel.: +20-1094-970-173
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31
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Povedano JM, Li V, Lake KE, Bai X, Rallabandi R, Kim J, Xie Y, De Brabander JK, McFadden DG. TK216 targets microtubules in Ewing sarcoma cells. Cell Chem Biol 2022; 29:1325-1332.e4. [PMID: 35803262 PMCID: PMC9394687 DOI: 10.1016/j.chembiol.2022.06.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 05/02/2022] [Accepted: 06/15/2022] [Indexed: 11/12/2022]
Abstract
Ewing sarcoma (EWS) is a pediatric malignancy driven by the EWSR1-FLI1 fusion protein formed by the chromosomal translocation t(11; 22). The small molecule TK216 was developed as a first-in-class direct EWSR1-FLI1 inhibitor and is in phase II clinical trials in combination with vincristine for patients with EWS. However, TK216 exhibits anti-cancer activity against cancer cell lines and xenografts that do not express EWSR1-FLI1, and the mechanism underlying cytotoxicity remains unresolved. We apply a forward-genetics screening platform utilizing engineered hypermutation in EWS cell lines and identify recurrent mutations in TUBA1B, encoding ⍺-tubulin, that prove sufficient to drive resistance to TK216. Using reconstituted microtubule (MT) polymerization in vitro and cell-based chemical probe competition assays, we demonstrate that TK216 acts as an MT destabilizing agent. This work defines the mechanism of cytotoxicity of TK216, explains the synergy observed with vincristine, and calls for a reexamination of ongoing clinical trials with TK216. Recurrent TUBA1B mutations were identified in TK216-resistant Ewing sarcoma cells TUBA1B mutations independently drove resistance to TK216 TK216 suppressed tubulin polymerization in vitro in a stereo-selective manner TK216 and vincristine act on microtubules through distinct binding mechanisms
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Affiliation(s)
- Juan Manuel Povedano
- Department of Internal Medicine, Division of Endocrinology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Vicky Li
- Department of Internal Medicine, Division of Endocrinology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Katherine E Lake
- Department of Internal Medicine, Division of Endocrinology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Xin Bai
- Department of Internal Medicine, Division of Endocrinology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Rameshu Rallabandi
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA; Program in Molecular Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Jiwoong Kim
- Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Yang Xie
- Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Jef K De Brabander
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA; Program in Molecular Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - David G McFadden
- Department of Internal Medicine, Division of Endocrinology, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA; Program in Molecular Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA.
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32
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Baranovskiy AG, Lisova AE, Morstadt LM, Babayeva ND, Tahirov TH. Insight into RNA-DNA primer length counting by human primosome. Nucleic Acids Res 2022; 50:6264-6270. [PMID: 35689638 PMCID: PMC9226528 DOI: 10.1093/nar/gkac492] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/19/2022] [Accepted: 06/08/2022] [Indexed: 11/15/2022] Open
Abstract
The human primosome, a four-subunit complex of primase and DNA polymerase alpha (Polα), synthesizes chimeric RNA–DNA primers of a limited length for DNA polymerases delta and epsilon to initiate DNA replication on both chromosome strands. Despite recent structural insights into the action of its two catalytic centers, the mechanism of DNA synthesis termination is still unclear. Here we report results of functional and structural studies revealing how the human primosome counts RNA–DNA primer length and timely terminates DNA elongation. Using a single-turnover primer extension assay, we defined two factors that determine a mature primer length (∼35-mer): (i) a tight interaction of the C-terminal domain of the DNA primase large subunit (p58C) with the primer 5′-end, and (ii) flexible tethering of p58C and the DNA polymerase alpha catalytic core domain (p180core) to the primosome platform domain by extended linkers. The obtained data allow us to conclude that p58C is a key regulator of all steps of RNA–DNA primer synthesis. The above-described findings provide a notable insight into the mechanism of DNA synthesis termination by a eukaryotic primosome, an important process for ensuring successful primer handover to replication DNA polymerases and for maintaining genome integrity.
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Affiliation(s)
- Andrey G Baranovskiy
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center. University of Nebraska Medical Center, Omaha, NE, USA
| | - Alisa E Lisova
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center. University of Nebraska Medical Center, Omaha, NE, USA
| | - Lucia M Morstadt
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center. University of Nebraska Medical Center, Omaha, NE, USA
| | - Nigar D Babayeva
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center. University of Nebraska Medical Center, Omaha, NE, USA
| | - Tahir H Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center. University of Nebraska Medical Center, Omaha, NE, USA
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33
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Baraniya D, Chitrala KN, Al-Hebshi NN. Global transcriptional response of oral squamous cell carcinoma cell lines to health-associated oral bacteria - an in vitro study. J Oral Microbiol 2022; 14:2073866. [PMID: 35600164 PMCID: PMC9116255 DOI: 10.1080/20002297.2022.2073866] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Divyashri Baraniya
- Oral Microbiome Research Laboratory, Maurice H. Kornberg School of Dentistry, Temple University, Philadelphia, USA
| | - Kumaraswamy Naidu Chitrala
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, USA
| | - Nezar Noor Al-Hebshi
- Oral Microbiome Research Laboratory, Maurice H. Kornberg School of Dentistry, Temple University, Philadelphia, USA
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Temple University Health System, Philadelphia, USA
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34
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Ciereszko A, Dietrich MA, Słowińska M, Nynca J, Ciborowski M, Kaczmarek MM, Myszczyński K, Kiśluk J, Majewska A, Michalska-Falkowska A, Kodzik N, Reszeć J, Sierko E, Nikliński J. Application of two-dimensional difference gel electrophoresis to identify protein changes between center, margin, and adjacent non-tumor tissues obtained from non-small-cell lung cancer with adenocarcinoma or squamous cell carcinoma subtype. PLoS One 2022; 17:e0268073. [PMID: 35512017 PMCID: PMC9071164 DOI: 10.1371/journal.pone.0268073] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/21/2022] [Indexed: 12/12/2022] Open
Abstract
Lung cancer is responsible for the most cancer-related mortality worldwide and the mechanism of its development is poorly understood. Proteomics has become a powerful tool offering vital knowledge related to cancer development. Using a two-dimensional difference gel electrophoresis (2D-DIGE) approach, we sought to compare tissue samples from non-small-cell lung cancer (NSCLC) patients taken from the tumor center and tumor margin. Two subtypes of NSCLC, adenocarcinoma (ADC) and squamous cell carcinoma (SCC) were compared. Data are available via ProteomeXchange with identifier PXD032736 and PXD032962 for ADC and SCC, respectively. For ADC proteins, 26 significant canonical pathways were identified, including Rho signaling pathways, a semaphorin neuronal repulsive signaling pathway, and epithelial adherens junction signaling. For SCC proteins, nine significant canonical pathways were identified, including hypoxia-inducible factor-1α signaling, thyroid hormone biosynthesis, and phagosome maturation. Proteins differentiating the tumor center and tumor margin were linked to cancer invasion and progression, including cell migration, adhesion and invasion, cytoskeletal structure, protein folding, anaerobic metabolism, tumor angiogenesis, EMC transition, epithelial adherens junctions, and inflammatory responses. In conclusion, we identified several proteins that are important for the better characterization of tumor development and molecular specificity of both lung cancer subtypes. We also identified proteins that may be important as biomarkers and/or targets for anticancer therapy.
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Affiliation(s)
- Andrzej Ciereszko
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
- * E-mail:
| | - Mariola A. Dietrich
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Mariola Słowińska
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Joanna Nynca
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Michał Ciborowski
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Monika M. Kaczmarek
- Molecular Biology Laboratory, Institute of Animal Reproduction and Food Research Polish Academy of Sciences, Olsztyn, Poland
| | - Kamil Myszczyński
- Molecular Biology Laboratory, Institute of Animal Reproduction and Food Research Polish Academy of Sciences, Olsztyn, Poland
| | - Joanna Kiśluk
- Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
| | - Anna Majewska
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | | | - Natalia Kodzik
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Joanna Reszeć
- Department of Medical Pathomorphology, Medical University of Bialystok, Bialystok, Poland
| | - Ewa Sierko
- Department of Oncology, Medical University of Bialystok, Bialystok, Poland
| | - Jacek Nikliński
- Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
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35
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Baranovskiy AG, Babayeva ND, Lisova AE, Morstadt LM, Tahirov TH. Structural and functional insight into mismatch extension by human DNA polymerase α. Proc Natl Acad Sci U S A 2022; 119:e2111744119. [PMID: 35467978 PMCID: PMC9169922 DOI: 10.1073/pnas.2111744119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 03/08/2022] [Indexed: 12/11/2022] Open
Abstract
Human DNA polymerase α (Polα) does not possess proofreading ability and plays an important role in genome replication and mutagenesis. Polα extends the RNA primers generated by primase and provides a springboard for loading other replication factors. Here we provide the structural and functional analysis of the human Polα interaction with a mismatched template:primer. The structure of the human Polα catalytic domain in the complex with an incoming deoxycytidine triphosphate (dCTP) and the template:primer containing a T-C mismatch at the growing primer terminus was solved at a 2.9 Å resolution. It revealed the absence of significant distortions in the active site and in the conformation of the substrates, except the primer 3′-end. The T-C mismatch acquired a planar geometry where both nucleotides moved toward each other by 0.4 Å and 0.7 Å, respectively, and made one hydrogen bond. The binding studies conducted at a physiological salt concentration revealed that Polα has a low affinity to DNA and is not able to discriminate against a mispaired template:primer in the absence of deoxynucleotide triphosphate (dNTP). Strikingly, in the presence of cognate dNTP, Polα showed a more than 10-fold higher selectivity for a correct duplex versus a mismatched one. According to pre-steady-state kinetic studies, human Polα extends the T-C mismatch with a 249-fold lower efficiency due to reduction of the polymerization rate constant by 38-fold and reduced affinity to the incoming nucleotide by 6.6-fold. Thus, a mismatch at the postinsertion site affects all factors important for primer extension: affinity to both substrates and the rate of DNA polymerization.
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Affiliation(s)
- Andrey G. Baranovskiy
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198
| | - Nigar D. Babayeva
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198
| | - Alisa E. Lisova
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198
| | - Lucia M. Morstadt
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198
| | - Tahir H. Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198
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36
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Mehta KPM, Thada V, Zhao R, Krishnamoorthy A, Leser M, Lindsey Rose K, Cortez D. CHK1 phosphorylates PRIMPOL to promote replication stress tolerance. SCIENCE ADVANCES 2022; 8:eabm0314. [PMID: 35353580 PMCID: PMC8967226 DOI: 10.1126/sciadv.abm0314] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 02/07/2022] [Indexed: 05/02/2023]
Abstract
Replication-coupled DNA repair and damage tolerance mechanisms overcome replication stress challenges and complete DNA synthesis. These pathways include fork reversal, translesion synthesis, and repriming by specialized polymerases such as PRIMPOL. Here, we investigated how these pathways are used and regulated in response to varying replication stresses. Blocking lagging-strand priming using a POLα inhibitor slows both leading- and lagging-strand synthesis due in part to RAD51-, HLTF-, and ZRANB3-mediated, but SMARCAL1-independent, fork reversal. ATR is activated, but CHK1 signaling is dampened compared to stalling both the leading and lagging strands with hydroxyurea. Increasing CHK1 activation by overexpressing CLASPIN in POLα-inhibited cells promotes replication elongation through PRIMPOL-dependent repriming. CHK1 phosphorylates PRIMPOL to promote repriming irrespective of the type of replication stress, and this phosphorylation is important for cellular resistance to DNA damage. However, PRIMPOL activation comes at the expense of single-strand gap formation, and constitutive PRIMPOL activity results in reduced cell fitness.
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Affiliation(s)
| | - Vaughn Thada
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37237, USA
| | - Runxiang Zhao
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37237, USA
| | - Archana Krishnamoorthy
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37237, USA
| | - Micheal Leser
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37237, USA
| | - Kristie Lindsey Rose
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37237, USA
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37
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Al-Wahaibi LH, Asokan KV, Al-Shaalan NH, Tawfik SS, Hassan HM, El-Emam AA, Percino MJ, Thamotharan S. Supramolecular Self-Assembly Mediated by Multiple Hydrogen Bonds and the Importance of C-S···N Chalcogen Bonds in N'-(Adamantan-2-ylidene)hydrazide Derivatives. ACS OMEGA 2022; 7:10608-10621. [PMID: 35382346 PMCID: PMC8973099 DOI: 10.1021/acsomega.2c00159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 02/23/2022] [Indexed: 12/02/2022]
Abstract
![]()
The present article
comprehensively examines six N′-(adamantan-2-ylidene)hydrazide
derivatives using the Hirshfeld
surface analysis, PIXEL energy for molecular dimers, lattice energies
for crystal packing, and topological analysis for intramolecular and
intermolecular interactions. The crystal structure of one of the N′-(adamantan-2-ylidene)hydrazide derivatives, namely, N′-(adamantan-2-ylidene)-5-bromothiophene-2-carbohydrazide 1, C15H17N2OSBr, has been
determined and analyzed in detail along with five closely related
structures. The molecular conformation of 1 is locked
by an intramolecular C–S···N chalcogen bond
as found in one of its closely related structure, namely, N′-(adamantan-2-ylidene)thiophene-2-carbohydrazide.
Furthermore, a detailed potential energy surface scan analysis has
been performed to highlight the importance of a chalcogen bond. Two
of these compounds possess syn-orientation for amide units, whereas
the corresponding moiety exhibits anti-conformations in the remaining
four structures. The Hirshfeld surface and its decomposed fingerprint
plots provide a qualitative picture of acyl substituent effects on
the intermolecular interactions toward crystal packing of these six
structures. Intermolecular interaction energies for dimers observed
in these structures calculated by density functional theory (B97D3/def2-TZVP)
and PIXEL (MP2/6-31G**) methods are comparable. This study also identifies
that multiple hydrogen bonds, including N/C–H···O/N
and C–H···π interactions, are collectively
responsible for a self-assembled synthon. The nature and strength
of these interactions have been studied using atoms in molecule topological
analysis. The in vitro antiproliferative activity
of compound 1 was assessed against five human tumor cell
lines and showed marked antiproliferative activity.
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Affiliation(s)
- Lamya H. Al-Wahaibi
- Department of Chemistry, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Karthick Vishal Asokan
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur 613401, India
| | - Nora H. Al-Shaalan
- Department of Chemistry, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Samar S. Tawfik
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Hanan M. Hassan
- Department of Pharmacology and Biochemistry, Faculty of Pharmacy, Delta University for Science and Technology, International Costal Road, Gamasa City, Mansoura 11152, Egypt
| | - Ali A. El-Emam
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - M. Judith Percino
- Unidad de Polímeros y Electrónica Orgánica, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Val3-Ecocampus Valsequillo, Independencia O2 Sur 50, San Pedro Zacachimalpa, Puebla 72960, Mexico
| | - Subbiah Thamotharan
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur 613401, India
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38
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Feng Z, Li L, Tu Y, Shu X, Zhang Y, Zeng Q, Luo L, Wu A, Chen W, Cao Y, Li Z. Identification of Circular RNA-Based Immunomodulatory Networks in Colorectal Cancer. Front Oncol 2022; 11:779706. [PMID: 35155186 PMCID: PMC8833313 DOI: 10.3389/fonc.2021.779706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 12/30/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Circular RNAs (circRNAs) have been recently proposed as hub molecules in various diseases, especially in tumours. We found that circRNAs derived from ribonuclease P RNA component H1 (RPPH1) were highly expressed in colorectal cancer (CRC) samples from Gene Expression Omnibus (GEO) datasets. OBJECTIVE We sought to identify new circRNAs derived from RPPH1 and investigate their regulation of the competing endogenous RNA (ceRNA) and RNA binding protein (RBP) networks of CRC immune infiltration. METHODS The circRNA expression profiles miRNA and mRNA data were extracted from the GEO and The Cancer Genome Atlas (TCGA) datasets, respectively. The differentially expressed (DE) RNAs were identified using R software and online server tools, and the circRNA-miRNA-mRNA and circRNA-protein networks were constructed using Cytoscape. The relationship between targeted genes and immune infiltration was identified using the GEPIA2 and TIMER2 online server tools. RESULTS A ceRNA network, including eight circRNAs, five miRNAs, and six mRNAs, was revealed. Moreover, a circRNA-protein network, including eight circRNAs and 49 proteins, was established. The targeted genes, ENOX1, NCAM1, SAMD4A, and ZC3H10, are closely related to CRC tumour-infiltrating macrophages. CONCLUSIONS We analysed the characteristics of circRNA from RPPH1 as competing for endogenous RNA binding miRNA or protein in CRC macrophage infiltration. The results point towards the development of a new diagnostic and therapeutic paradigm for CRC.
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Affiliation(s)
- Zongfeng Feng
- Department of General Surgery, First Affiliated Hospital of Nanchang University, Nanchang, China.,Laboratory of Digestive Surgery, Nanchang University, Nanchang, China.,Medical Innovation Center, the First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Leyan Li
- Laboratory of Digestive Surgery, Nanchang University, Nanchang, China.,Medical Innovation Center, the First Affiliated Hospital of Nanchang University, Nanchang, China.,Queen Mary School, Medical Department of Nanchang University, Nanchang, China
| | - Yi Tu
- Department of Pathology, the First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xufeng Shu
- Department of General Surgery, First Affiliated Hospital of Nanchang University, Nanchang, China.,Laboratory of Digestive Surgery, Nanchang University, Nanchang, China.,Medical Innovation Center, the First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yang Zhang
- Department of General Surgery, First Affiliated Hospital of Nanchang University, Nanchang, China.,Laboratory of Digestive Surgery, Nanchang University, Nanchang, China.,Medical Innovation Center, the First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Qingwen Zeng
- Department of General Surgery, First Affiliated Hospital of Nanchang University, Nanchang, China.,Laboratory of Digestive Surgery, Nanchang University, Nanchang, China.,Medical Innovation Center, the First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Lianghua Luo
- Department of General Surgery, First Affiliated Hospital of Nanchang University, Nanchang, China.,Laboratory of Digestive Surgery, Nanchang University, Nanchang, China.,Medical Innovation Center, the First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Ahao Wu
- Department of General Surgery, First Affiliated Hospital of Nanchang University, Nanchang, China.,Laboratory of Digestive Surgery, Nanchang University, Nanchang, China
| | - Wenzheng Chen
- Department of General Surgery, First Affiliated Hospital of Nanchang University, Nanchang, China.,Laboratory of Digestive Surgery, Nanchang University, Nanchang, China.,Medical Innovation Center, the First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yi Cao
- Department of General Surgery, First Affiliated Hospital of Nanchang University, Nanchang, China.,Laboratory of Digestive Surgery, Nanchang University, Nanchang, China.,Medical Innovation Center, the First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhengrong Li
- Department of General Surgery, First Affiliated Hospital of Nanchang University, Nanchang, China.,Laboratory of Digestive Surgery, Nanchang University, Nanchang, China.,Medical Innovation Center, the First Affiliated Hospital of Nanchang University, Nanchang, China
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39
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Mirman Z, Sasi NK, King A, Chapman JR, de Lange T. 53BP1-shieldin-dependent DSB processing in BRCA1-deficient cells requires CST-Polα-primase fill-in synthesis. Nat Cell Biol 2022; 24:51-61. [PMID: 35027730 PMCID: PMC8849574 DOI: 10.1038/s41556-021-00812-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 11/09/2021] [Indexed: 12/19/2022]
Abstract
The efficacy of poly(ADP)-ribose polymerase 1 inhibition (PARPi) in BRCA1-deficient cells depends on 53BP1 and shieldin, which have been proposed to limit single-stranded DNA at double-strand breaks (DSBs) by blocking resection and/or through CST-Polα-primase-mediated fill-in. We show that primase (like 53BP1-shieldin and CST-Polα) promotes radial chromosome formation in PARPi-treated BRCA1-deficient cells and demonstrate shieldin-CST-Polα-primase-dependent incorporation of BrdU at DSBs. In the absence of 53BP1 or shieldin, radial formation in BRCA1-deficient cells was restored by the tethering of CST near DSBs, arguing that in this context, shieldin acts primarily by recruiting CST. Furthermore, a SHLD1 mutant defective in CST binding (SHLD1Δ) was non-functional in BRCA1-deficient cells and its function was restored after reconnecting SHLD1Δ to CST. Interestingly, at dysfunctional telomeres and at DNA breaks in class switch recombination where CST has been implicated, SHLD1Δ was fully functional, perhaps because these DNA ends carry CST recognition sites that afford SHLD1-independent binding of CST. These data establish that in BRCA1-deficient cells, CST-Polα-primase is the major effector of shieldin-dependent DSB processing.
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Affiliation(s)
- Zachary Mirman
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY, USA
| | - Nanda Kumar Sasi
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY, USA
| | - Ashleigh King
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - J Ross Chapman
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Titia de Lange
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY, USA.
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40
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Dallavalle S, Musso L, Cincinelli R, Darwiche N, Gervasoni S, Vistoli G, Guglielmi MB, La Porta I, Pizzulo M, Modica E, Prosperi F, Signorino G, Colelli F, Cardile F, Fucci A, D'Andrea EL, Riccio A, Pisano C. Antitumor activity of novel POLA1-HDAC11 dual inhibitors. Eur J Med Chem 2021; 228:113971. [PMID: 34772529 DOI: 10.1016/j.ejmech.2021.113971] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 10/29/2021] [Accepted: 10/31/2021] [Indexed: 12/27/2022]
Abstract
Hybrid molecules targeting simultaneously DNA polymerase α (POLA1) and histone deacetylases (HDACs) were designed and synthesized to exploit a potential synergy of action. Among a library of screened molecules, MIR002 and GEM144 showed antiproliferative activity at nanomolar concentrations on a panel of human solid and haematological cancer cell lines. In vitro functional assays confirmed that these molecules inhibited POLA1 primer extension activity, as well as HDAC11. Molecular docking studies also supported these findings. Mechanistically, MIR002 and GEM144 induced acetylation of p53, activation of p21, G1/S cell cycle arrest, and apoptosis. Oral administration of these inhibitors confirmed their antitumor activity in in vivo models. In human non-small cancer cell (H460) xenografted in nude mice MIR002 at 50 mg/kg, Bid (qd × 5 × 3w) inhibited tumor growth (TGI = 61%). More interestingly, in POLA1 inhibitor resistant cells (H460-R9A), the in vivo combination of MIR002 with cisplatin showed an additive antitumor effect with complete disappearance of tumor masses in two animals at the end of the treatment. Moreover, in two human orthotopic malignant pleural mesothelioma xenografts (MM473 and MM487), oral treatments with MIR002 and GEM144 confirmed their significant antitumor activity (TGI = 72-77%). Consistently with recent results that have shown an inverse correlation between POLA1 expression and type I interferon levels, MIR002 significantly upregulated interferon-α in immunocompetent mice.
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Affiliation(s)
- Sabrina Dallavalle
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy.
| | - Loana Musso
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy
| | - Raffaella Cincinelli
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy
| | - Nadine Darwiche
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Silvia Gervasoni
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, via Mangiagalli 25, Milano, 20133, Italy
| | - Giulio Vistoli
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, via Mangiagalli 25, Milano, 20133, Italy
| | - Mario B Guglielmi
- Biogem, Institute of Molecular Biology and Genetics, Via Camporeale, 83031 Ariano Irpino(AV), Italy
| | - Ilaria La Porta
- Biogem, Institute of Molecular Biology and Genetics, Via Camporeale, 83031 Ariano Irpino(AV), Italy
| | - Maddalena Pizzulo
- Biogem, Institute of Molecular Biology and Genetics, Via Camporeale, 83031 Ariano Irpino(AV), Italy
| | - Elisa Modica
- Biogem, Institute of Molecular Biology and Genetics, Via Camporeale, 83031 Ariano Irpino(AV), Italy
| | - Federica Prosperi
- Biogem, Institute of Molecular Biology and Genetics, Via Camporeale, 83031 Ariano Irpino(AV), Italy
| | - Giacomo Signorino
- Biogem, Institute of Molecular Biology and Genetics, Via Camporeale, 83031 Ariano Irpino(AV), Italy
| | - Fabiana Colelli
- Biogem, Institute of Molecular Biology and Genetics, Via Camporeale, 83031 Ariano Irpino(AV), Italy
| | - Francesco Cardile
- Biogem, Institute of Molecular Biology and Genetics, Via Camporeale, 83031 Ariano Irpino(AV), Italy
| | - Alessandra Fucci
- Biogem, Institute of Molecular Biology and Genetics, Via Camporeale, 83031 Ariano Irpino(AV), Italy
| | - Egildo Luca D'Andrea
- Biogem, Institute of Molecular Biology and Genetics, Via Camporeale, 83031 Ariano Irpino(AV), Italy
| | - Assunta Riccio
- Biogem, Institute of Molecular Biology and Genetics, Via Camporeale, 83031 Ariano Irpino(AV), Italy
| | - Claudio Pisano
- Biogem, Institute of Molecular Biology and Genetics, Via Camporeale, 83031 Ariano Irpino(AV), Italy.
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41
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Al-Mutairi A, Alagappan K, Blacque O, Al-Alshaikh MA, El-Emam AA, Percino MJ, Thamotharan S. Crystallographic and Theoretical Exploration of Weak Hydrogen Bonds in Arylmethyl N'-(adamantan-1-yl)piperidine-1-carbothioimidates and Molecular Docking Analysis. ACS OMEGA 2021; 6:27026-27037. [PMID: 34693122 PMCID: PMC8529591 DOI: 10.1021/acsomega.1c03559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/24/2021] [Indexed: 12/23/2022]
Abstract
Crystal structures of two potential chemotherapeutic agents, namely 4-nitrobenzyl N'-(adamantan-1-yl)piperidine-1-carbothioimidate 1 and 4-bromobenzyl N'-(adamantan-1-yl)piperidine-1-carbothioimidate 2, have been analyzed in detail. X-ray analysis reveals that the molecular conformations of these compounds are strikingly different. These two structures are compared with two of their closely related structures. In the related structures, morpholine replaces piperidine. Based on the Hirshfeld surface analysis and two-dimensional (2D) fingerprint plots, we describe the effects of piperidine/morpholine and Br/NO2 groups on the intermolecular interactions. An analysis of the CLP-PIXEL energy provides insight into the energetics of the dimers observed in the title compounds and their related structures. Compound 1 stabilizes with bifurcated C-H···S, C-H···O, and O(lp)···C(π) interactions, whereas compound 2 stabilizes with C-H···N, C-H···Br, and C-H···C interactions. The energy frameworks for the crystal structures of the title compounds reveal differences. The atoms-in-molecules (AIM) analysis was performed to confirm the intermolecular interactions found in the crystal structures of 1 and 2. Additionally, docking analysis suggests that the title compounds bind at the active site of human sphingosine kinase 1, a well-known cancer target.
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Affiliation(s)
- Aamal
A. Al-Mutairi
- Department
of Chemistry, College of Sciences, Imam
Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
| | - Kowsalya Alagappan
- Biomolecular
Crystallography Laboratory, Department of Bioinformatics, School of
Chemical and Biotechnology, SASTRA Deemed
University, Thanjavur 613401, India
| | - Olivier Blacque
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Monirah A. Al-Alshaikh
- Department
of Chemistry, College of Sciences, King
Saud University, Riyadh 11451, Saudi Arabia
| | - Ali A. El-Emam
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - M. Judith Percino
- Unidad de
Polímeros y Electrónica Orgánica, Instituto de
Ciencias, Benemérita Universidad
Autónoma de Puebla, Val3-Ecocampus Valsequillo, Independencia O2 Sur 50, San Pedro Zacachimalpa, Puebla C.P.72960, Mexico
| | - Subbiah Thamotharan
- Biomolecular
Crystallography Laboratory, Department of Bioinformatics, School of
Chemical and Biotechnology, SASTRA Deemed
University, Thanjavur 613401, India
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42
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The unfolding role of ceramide in coordinating retinoid-based cancer therapy. Biochem J 2021; 478:3621-3642. [PMID: 34648006 DOI: 10.1042/bcj20210368] [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: 05/18/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 12/30/2022]
Abstract
Sphingolipid-mediated regulation in cancer development and treatment is largely ceramide-centered with the complex sphingolipid metabolic pathways unfolding as attractive targets for anticancer drug discovery. The dynamic interconversion of sphingolipids is tightly controlled at the level of enzymes and cellular compartments in response to endogenous or exogenous stimuli, such as anticancer drugs, including retinoids. Over the past two decades, evidence emerged that retinoids owe part of their potency in cancer therapy to modulation of sphingolipid metabolism and ceramide generation. Ceramide has been proposed as a 'tumor-suppressor lipid' that orchestrates cell growth, cell cycle arrest, cell death, senescence, autophagy, and metastasis. There is accumulating evidence that cancer development is promoted by the dysregulation of tumor-promoting sphingolipids whereas cancer treatments can kill tumor cells by inducing the accumulation of endogenous ceramide levels. Resistance to cancer therapy may develop due to a disrupted equilibrium between the opposing roles of tumor-suppressor and tumor-promoter sphingolipids. Despite the undulating effect and complexity of sphingolipid pathways, there are emerging opportunities for a plethora of enzyme-targeted therapeutic interventions that overcome resistance resulting from perturbed sphingolipid pathways. Here, we have revisited the interconnectivity of sphingolipid metabolism and the instrumental role of ceramide-biosynthetic and degradative enzymes, including bioactive sphingolipid products, how they closely relate to cancer treatment and pathogenesis, and the interplay with retinoid signaling in cancer. We focused on retinoid targeting, alone or in combination, of sphingolipid metabolism nodes in cancer to enhance ceramide-based therapeutics. Retinoid and ceramide-based cancer therapy using novel strategies such as combination treatments, synthetic retinoids, ceramide modulators, and delivery formulations hold promise in the battle against cancer.
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43
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Osman DA, Macías MA, Al-Wahaibi LH, Al-Shaalan NH, Zondagh LS, Joubert J, Garcia-Granda S, El-Emam AA. Structural Insights and Docking Analysis of Adamantane-Linked 1,2,4-Triazole Derivatives as Potential 11β-HSD1 Inhibitors. Molecules 2021; 26:5335. [PMID: 34500764 PMCID: PMC8433897 DOI: 10.3390/molecules26175335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 11/21/2022] Open
Abstract
The solid-state structural analysis and docking studies of three adamantane-linked 1,2,4-triazole derivatives are presented. Crystal structure analyses revealed that compound 2 crystallizes in the triclinic P-1 space group, while compounds 1 and 3 crystallize in the same monoclinic P21/c space group. Since the only difference between them is the para substitution on the aryl group, the electronic nature of these NO2 and halogen groups seems to have no influence over the formation of the solid. However, a probable correlation with the size of the groups is not discarded due to the similar intermolecular disposition between the NO2/Cl substituted molecules. Despite the similarities, CE-B3LYP energy model calculations show that pairwise interaction energies vary between them, and therefore the total packing energy is affected. HOMO-LUMO calculated energies show that the NO2 group influences the reactivity properties characterizing the molecule as soft and with the best disposition to accept electrons. Further, in silico studies predicted that the compounds might be able to inhibit the 11β-HSD1 enzyme, which is implicated in obesity and diabetes. Self- and cross-docking experiments revealed that a number of non-native 11β-HSD1 inhibitors were able to accurately dock within the 11β-HSD1 X-ray structure 4C7J. The molecular docking of the adamantane-linked 1,2,4-triazoles have similar predicted binding affinity scores compared to the 4C7J native ligand 4YQ. However, they were unable to form interactions with key active site residues. Based on these docking results, a series of potentially improved compounds were designed using computer aided drug design tools. The docking results of the new compounds showed similar predicted 11β-HSD1 binding affinity scores as well as interactions to a known potent 11β-HSD1 inhibitor.
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Affiliation(s)
- Doaa A. Osman
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, Oviedo University-CINN, 33006 Oviedo, Spain; (D.A.O.); (S.G.-G.)
| | - Mario A. Macías
- Crystallography and Chemistry of Materials, CrisQuimMat, Department of Chemistry, Universidad de Los Andes, Carrera 1 No. 18A-10, Bogotá 111711, Colombia;
| | - Lamya H. Al-Wahaibi
- Department of Chemistry, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia;
| | - Nora H. Al-Shaalan
- Department of Chemistry, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia;
| | - Luke S. Zondagh
- Pharmaceutical Chemistry, School of Pharmacy, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (L.S.Z.); (J.J.)
| | - Jacques Joubert
- Pharmaceutical Chemistry, School of Pharmacy, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (L.S.Z.); (J.J.)
| | - Santiago Garcia-Granda
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, Oviedo University-CINN, 33006 Oviedo, Spain; (D.A.O.); (S.G.-G.)
| | - Ali A. El-Emam
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
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44
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Schimmel J, Muñoz-Subirana N, Kool H, van Schendel R, Tijsterman M. Small tandem DNA duplications result from CST-guided Pol α-primase action at DNA break termini. Nat Commun 2021; 12:4843. [PMID: 34376693 PMCID: PMC8355091 DOI: 10.1038/s41467-021-25154-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 07/20/2021] [Indexed: 12/11/2022] Open
Abstract
Small tandem duplications of DNA occur frequently in the human genome and are implicated in the aetiology of certain human cancers. Recent studies have suggested that DNA double-strand breaks are causal to this mutational class, but the underlying mechanism remains elusive. Here, we identify a crucial role for DNA polymerase α (Pol α)-primase in tandem duplication formation at breaks having complementary 3′ ssDNA protrusions. By including so-called primase deserts in CRISPR/Cas9-induced DNA break configurations, we reveal that fill-in synthesis preferentially starts at the 3′ tip, and find this activity to be dependent on 53BP1, and the CTC1-STN1-TEN1 (CST) and Shieldin complexes. This axis generates near-blunt ends specifically at DNA breaks with 3′ overhangs, which are subsequently repaired by non-homologous end-joining. Our study provides a mechanistic explanation for a mutational signature abundantly observed in the genomes of species and cancer cells. Error-prone repair of DNA double-strand breaks have been implied to cause cancer-associated genome alterations, but the mechanism of their formation remains unclear. Here the authors find that DNA polymerase α primase plays part in tandem duplication formation at CRISPR/Cas9-induced complementary 3′ ssDNA protrusions.
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Affiliation(s)
- Joost Schimmel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Núria Muñoz-Subirana
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Hanneke Kool
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Robin van Schendel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands. .,Institute of Biology Leiden, Leiden University, Leiden, The Netherlands.
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45
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Wang Y, Chen Y, Wang C, Yang M, Wang Y, Bao L, Wang JE, Kim B, Chan KY, Xu W, Capota E, Ortega J, Nijhawan D, Li GM, Luo W, Wang Y. MIF is a 3' flap nuclease that facilitates DNA replication and promotes tumor growth. Nat Commun 2021; 12:2954. [PMID: 34012010 PMCID: PMC8134555 DOI: 10.1038/s41467-021-23264-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 04/20/2021] [Indexed: 11/13/2022] Open
Abstract
How cancer cells cope with high levels of replication stress during rapid proliferation is currently unclear. Here, we show that macrophage migration inhibitory factor (MIF) is a 3’ flap nuclease that translocates to the nucleus in S phase. Poly(ADP-ribose) polymerase 1 co-localizes with MIF to the DNA replication fork, where MIF nuclease activity is required to resolve replication stress and facilitates tumor growth. MIF loss in cancer cells leads to mutation frequency increases, cell cycle delays and DNA synthesis and cell growth inhibition, which can be rescued by restoring MIF, but not nuclease-deficient MIF mutant. MIF is significantly upregulated in breast tumors and correlates with poor overall survival in patients. We propose that MIF is a unique 3’ nuclease, excises flaps at the immediate 3’ end during DNA synthesis and favors cancer cells evading replication stress-induced threat for their growth. Replication stress is associated with cancer formation and progression. Here the authors reveal that the macrophage migration inhibitory factor (MIF) functions as 3’ flap nuclease involved in resolving replication stress affecting overall tumor progression.
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Affiliation(s)
- Yijie Wang
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yan Chen
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Chenliang Wang
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Mingming Yang
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yanan Wang
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Lei Bao
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jennifer E Wang
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - BongWoo Kim
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Kara Y Chan
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Weizhi Xu
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Emanuela Capota
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Janice Ortega
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Deepak Nijhawan
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Guo-Min Li
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Weibo Luo
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yingfei Wang
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA. .,Department of Neurology, UT Southwestern Medical Center, Dallas, TX, USA.
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46
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Restoration of ceramide de novo synthesis by the synthetic retinoid ST1926 as it induces adult T-cell leukemia cell death. Biosci Rep 2021; 40:226649. [PMID: 33048123 PMCID: PMC7593536 DOI: 10.1042/bsr20200050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 09/21/2020] [Accepted: 09/30/2020] [Indexed: 01/15/2023] Open
Abstract
Ceramide (Cer) is a bioactive cellular lipid with compartmentalized and tightly regulated levels. Distinct metabolic pathways lead to the generation of Cer species with distinguishable roles in oncogenesis. Deregulation of Cer pathways has emerged as an important mechanism for acquired chemotherapeutic resistance. Adult T-cell leukemia (ATL) cells are defective in Cer synthesis. ATL is an aggressive neoplasm that develops following infection with human T-cell lymphotropic virus-1 (HTLV-1) where the viral oncogene Tax contributes to the pathogenesis of the disease. ATL cells, resistant to all-trans-retinoic acid, are sensitive to pharmacologically achievable concentrations of the synthetic retinoid ST1926. We studied the effects of ST1926 on Cer pathways in ATL cells. ST1926 treatment resulted in early Tax oncoprotein degradation in HTLV-1-treated cells. ST1926 induced cell death and a dose- and time-dependent accumulation of Cer in malignant T cells. The kinetics and degree of Cer production showed an early response upon ST1926 treatment. ST1926 enhanced de novo Cer synthesis via activation of ceramide synthase CerS(s) without inhibiting dihydroceramide desaturase, thereby accumulating Cer rather than the less bioactive dihydroceramide. Using labeling experiments with the unnatural 17-carbon sphinganine and measuring the generated Cer species, we showed that ST1926 preferentially induces the activities of a distinct set of CerS(s). We detected a delay in cell death response and interruption of Cer generation in response to ST1926 in Molt-4 cells overexpressing Bcl-2. These results highlight the potential role of ST1926 in inducing Cer levels, thus lowering the threshold for cell death in ATL cells.
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47
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Ercilla A, Benada J, Amitash S, Zonderland G, Baldi G, Somyajit K, Ochs F, Costanzo V, Lukas J, Toledo L. Physiological Tolerance to ssDNA Enables Strand Uncoupling during DNA Replication. Cell Rep 2021; 30:2416-2429.e7. [PMID: 32075739 DOI: 10.1016/j.celrep.2020.01.067] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 12/17/2019] [Accepted: 01/22/2020] [Indexed: 12/20/2022] Open
Abstract
It has been long assumed that normally leading strand synthesis must proceed coordinated with the lagging strand to prevent strand uncoupling and the pathological accumulation of single-stranded DNA (ssDNA) in the cell, a dogma recently challenged by in vitro studies in prokaryotes. Here, we report that human DNA polymerases can function independently at each strand in vivo and that the resulting strand uncoupling is supported physiologically by a cellular tolerance to ssDNA. Active forks rapidly accumulate ssDNA at the lagging strand when POLA1 is inhibited without triggering a stress response, despite ssDNA formation being considered a hallmark of replication stress. Acute POLA1 inhibition causes a lethal RPA exhaustion, but cells can duplicate their DNA with limited POLA1 activity and exacerbated strand uncoupling as long as RPA molecules suffice to protect the elevated ssDNA. Although robust, this uncoupled mode of DNA replication is also an in-built weakness that can be targeted for cancer treatment.
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Affiliation(s)
- Amaia Ercilla
- Center for Chromosome Stability, Institute for Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Jan Benada
- Center for Chromosome Stability, Institute for Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Sampath Amitash
- Center for Chromosome Stability, Institute for Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Gijs Zonderland
- Center for Chromosome Stability, Institute for Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Giorgio Baldi
- DNA Metabolism Laboratory, FIRC Institute for Molecular Oncology (IFOM), Milan 20139, Italy
| | - Kumar Somyajit
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Fena Ochs
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Vincenzo Costanzo
- DNA Metabolism Laboratory, FIRC Institute for Molecular Oncology (IFOM), Milan 20139, Italy
| | - Jiri Lukas
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Luis Toledo
- Center for Chromosome Stability, Institute for Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark.
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48
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Al-Wahaibi L, Grandhi DS, Tawfik SS, Al-Shaalan NH, Elmorsy MA, El-Emam AA, Percino MJ, Thamotharan S. Probing the Effect of Halogen Substituents (Br, Cl, and F) on the Non-covalent Interactions in 1-(Adamantan-1-yl)-3-arylthiourea Derivatives: A Theoretical Study. ACS OMEGA 2021; 6:4816-4830. [PMID: 33644590 PMCID: PMC7905817 DOI: 10.1021/acsomega.0c05793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 02/02/2021] [Indexed: 12/20/2022]
Abstract
The effect of halogen substituents (X = Br, Cl, and F) on the crystal packing and intra- and intermolecular interactions in four adamantane-thiourea hybrid derivatives is investigated using different theoretical tools. The bromo and chloro derivatives exhibit 3D isostructurality as evident from lattice parameters, molecular conformation, and crystal packing. The density functional theory study suggests that the molecular conformation of the parent (unsubstituted) and fluoro derivatives exhibits a stable low energy anti-syn conformation. In contrast, bromo and chloro derivatives adopt stable and relatively high energy minima on their potential energy surfaces. Hirshfeld surface analysis reveals the effect of halogen substituents on the intermolecular contacts. The halogen atoms mainly reduce the contribution of H···H contacts toward crystal packing. PIXEL energy analysis indicates the strong dimer formed by N-H···S hydrogen bonds in all four structures. It also revealed that a vast number of H···H contacts observed in different dimers of these structures either presented along with other conventional interactions or solely stabilize the dimeric topology. The topological parameters for intermolecular interactions in these structures suggest an intermediate bonding character between shared and closed-shell interactions for N-H···S hydrogen bonds in the parent and chloro derivatives. In contrast, the N-H···S hydrogen bond in other structures is of a closed-shell interaction. Among four derivatives, the fluoro derivative is weakly packed in the solid state based on the PIXEL method's lattice energy calculation.
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Affiliation(s)
- Lamya
H. Al-Wahaibi
- Department
of Chemistry, College of Sciences, Princess
Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Divya Sri Grandhi
- Biomolecular
Crystallography Laboratory, Department of Bioinformatics, School of
Chemical and Biotechnology, SASTRA Deemed
University, Thanjavur 613 401, India
| | - Samar S. Tawfik
- Department
of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Nora H. Al-Shaalan
- Department
of Chemistry, College of Sciences, Princess
Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Mohammed A. Elmorsy
- Department
of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Ali A. El-Emam
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - M. Judith Percino
- Unidad
de Polímeros y Electrónica Orgánica, Instituto
de Ciencias, Benemérita Universidad
Autónoma de Puebla, Val3-Ecocampus Valsequillo, Independencia O2 Sur 50, San Pedro Zacachimalpa, Puebla CP 72960, Mexico
| | - Subbiah Thamotharan
- Biomolecular
Crystallography Laboratory, Department of Bioinformatics, School of
Chemical and Biotechnology, SASTRA Deemed
University, Thanjavur 613 401, India
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49
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Hassan HM, Al-Wahaibi LH, Shehatou GS, El-Emam AA. Adamantane-linked isothiourea derivatives suppress the growth of experimental hepatocellular carcinoma via inhibition of TLR4-MyD88-NF-κB signaling. Am J Cancer Res 2021; 11:350-369. [PMID: 33575076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 12/11/2020] [Indexed: 12/24/2022] Open
Abstract
In this study, in vitro cytotoxic effects of seven adamantyl isothiourea derivatives were evaluated against five human tumor cell lines using the MTT assay. Compounds 5 and 6 were found to be the most active derivatives particularly against hepatocellular carcinoma (HCC). To decipher the potential mechanisms involved, in vivo studies were conducted in rats by inducing HCC via chronic thioacetamide (TAA) administration (200 mg/kg, i.p., twice weekly) for 16 weeks. Compounds 5 and 6 were administered to HCC rats, at a dose of 10 mg/kg/day, for further 2 weeks. In vitro and in vivo antitumor activities of compounds 5 and 6 were compared to those of the anticancer drug doxorubicin (DOXO). In the HCC rat model, compounds 5 and 6 significantly reduced serum levels of ALT, AST with ALP and α-fetoprotein. H & E and Masson trichrome staining revealed that both compounds suppressed hepatocyte tumorigenesis and diminished fibrosis, inflammation and other histopathological alterations. Mechanistically, compounds 5 and 6 markedly decreased protein expression levels of α-SMA, sEH, p-NF-κB p65, TLR4, MyD88, TRAF-6, TNF-α, IL-1β and TGF-β1, whereas they increased caspase-3 expression in liver tissues of HCC rats. In most analyses, the effects of compound 6 were more comparable to DOXO than compound 5. These findings suggested that the compounds 5 and 6 displayed in vitro and in vivo cytotoxic potential against HCC, probably via inhibition of TLR4-MyD88-NF-κB signaling.
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Affiliation(s)
- Hanan M Hassan
- Department of Pharmacology and Biochemistry, Faculty of Pharmacy, Delta University for Science and Technology International Costal Road, Gamasa 11152, Mansoura, Egypt
| | - Lamya H Al-Wahaibi
- Department of Chemistry, College of Sciences, Princess Nourah bint Abdulrahman University Riyadh 11671, Saudi Arabia
| | - George Sg Shehatou
- Department of Pharmacology and Biochemistry, Faculty of Pharmacy, Delta University for Science and Technology International Costal Road, Gamasa 11152, Mansoura, Egypt.,Department of Pharmacology and Toxicology, Faculty of Pharmacy, Mansoura University Mansoura 35516, Egypt
| | - Ali A El-Emam
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University Mansoura 35516, Egypt
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50
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Shilkin ES, Boldinova EO, Stolyarenko AD, Goncharova RI, Chuprov-Netochin RN, Smal MP, Makarova AV. Translesion DNA Synthesis and Reinitiation of DNA Synthesis in Chemotherapy Resistance. BIOCHEMISTRY (MOSCOW) 2021; 85:869-882. [PMID: 33045948 DOI: 10.1134/s0006297920080039] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Many chemotherapy drugs block tumor cell division by damaging DNA. DNA polymerases eta (Pol η), iota (Pol ι), kappa (Pol κ), REV1 of the Y-family and zeta (Pol ζ) of the B-family efficiently incorporate nucleotides opposite a number of DNA lesions during translesion DNA synthesis. Primase-polymerase PrimPol and the Pol α-primase complex reinitiate DNA synthesis downstream of the damaged sites using their DNA primase activity. These enzymes can decrease the efficacy of chemotherapy drugs, contribute to the survival of tumor cells and to the progression of malignant diseases. DNA polymerases are promising targets for increasing the effectiveness of chemotherapy, and mutations and polymorphisms in some DNA polymerases can serve as additional prognostic markers in a number of oncological disorders.
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Affiliation(s)
- E S Shilkin
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - E O Boldinova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - A D Stolyarenko
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - R I Goncharova
- Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Minsk, 220072, Republic of Belarus
| | - R N Chuprov-Netochin
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - M P Smal
- Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Minsk, 220072, Republic of Belarus.
| | - A V Makarova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.
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