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Cruz-León S, Majtner T, Hoffmann PC, Kreysing JP, Kehl S, Tuijtel MW, Schaefer SL, Geißler K, Beck M, Turoňová B, Hummer G. High-confidence 3D template matching for cryo-electron tomography. Nat Commun 2024; 15:3992. [PMID: 38734767 PMCID: PMC11088655 DOI: 10.1038/s41467-024-47839-8] [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: 10/31/2023] [Accepted: 04/12/2024] [Indexed: 05/13/2024] Open
Abstract
Visual proteomics attempts to build atlases of the molecular content of cells but the automated annotation of cryo electron tomograms remains challenging. Template matching (TM) and methods based on machine learning detect structural signatures of macromolecules. However, their applicability remains limited in terms of both the abundance and size of the molecular targets. Here we show that the performance of TM is greatly improved by using template-specific search parameter optimization and by including higher-resolution information. We establish a TM pipeline with systematically tuned parameters for the automated, objective and comprehensive identification of structures with confidence 10 to 100-fold above the noise level. We demonstrate high-fidelity and high-confidence localizations of nuclear pore complexes, vaults, ribosomes, proteasomes, fatty acid synthases, lipid membranes and microtubules, and individual subunits inside crowded eukaryotic cells. We provide software tools for the generic implementation of our method that is broadly applicable towards realizing visual proteomics.
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Affiliation(s)
- Sergio Cruz-León
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Tomáš Majtner
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Patrick C Hoffmann
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Jan Philipp Kreysing
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
- IMPRS on Cellular Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Sebastian Kehl
- Max Planck Computing and Data Facility, Gießenbachstraße 2, 85748, Garching, Germany
| | - Maarten W Tuijtel
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Stefan L Schaefer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Katharina Geißler
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
- IMPRS on Cellular Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Martin Beck
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany.
- Institute of Biochemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
| | - Beata Turoňová
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany.
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany.
- Institute of Biophysics, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
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2
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Li C, Gao M, Zha N, Guo G. The prognostic value and immunological role of MVP in pan-cancer study. Aging (Albany NY) 2024; 16:205802. [PMID: 38713157 DOI: 10.18632/aging.205802] [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: 06/19/2023] [Accepted: 04/08/2024] [Indexed: 05/08/2024]
Abstract
Major Vault Protein (MVP) has emerged as a potential prognostic and immunological biomarker in various cancer types. This pan-cancer study aimed to investigate expression of MVP and its correlation with clinical outcomes and immune infiltration across diverse cancer types. We conducted an analysis of extensive transcriptomic and clinical data from publicly available databases. Our findings unveiled a significant association between MVP expression and cancer progression, with higher expression levels predicting poorer overall survival in multiple cancer types. Importantly, MVP expression demonstrated a close relationship with immune infiltration in the tumor microenvironment, showing that higher expression levels were associated with increased immune cell infiltration. We further validated expression of MVP and function in cancer cell lines A549 and AGS. These compelling results suggest that MVP holds promise as a valuable biomarker for prognostic assessment and the development of immunotherapeutic strategies across various cancer types. Consequently, targeting MVP may offer a compelling therapeutic approach in the treatment of human cancers.
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Affiliation(s)
- Chunlin Li
- Department of Thoracic Surgery, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010010, China
| | - Min Gao
- Department of Thoracic Surgery, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010010, China
- Inner Mongolia Medical University, Hohhot 010010, China
| | - Nashunbayaer Zha
- Department of Thoracic Surgery, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010010, China
| | - Gang Guo
- Department of Thyroid and Breast Surgery, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010010, China
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3
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Avila-Bonilla RG, Martínez-Montero JP. Crosstalk between vault RNAs and innate immunity. Mol Biol Rep 2024; 51:387. [PMID: 38443657 PMCID: PMC10914904 DOI: 10.1007/s11033-024-09305-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: 11/15/2023] [Accepted: 01/31/2024] [Indexed: 03/07/2024]
Abstract
PURPOSE Vault (vt) RNAs are noncoding (nc) RNAs transcribed by RNA polymerase III (RNA Pol III) with 5'-triphosphate (5'-PPP) termini that play significant roles and are recognized by innate immune sensors, including retinoic acid-inducible protein 1 (RIG-I). In addition, vtRNAs adopt secondary structures that can be targets of interferon-inducible protein kinase R (PKR) and the oligoadenylate synthetase (OAS)/RNase L system, both of which are important for activating antiviral defenses. However, changes in the expression of vtRNAs have been associated with pathological processes that activate proinflammatory pathways, which influence cellular events such as differentiation, aging, autophagy, apoptosis, and drug resistance in cancer cells. RESULTS In this review, we summarized the biology of vtRNAs and focused on their interactions with the innate immune system. These findings provide insights into the diverse roles of vtRNAs and their correlation with various cellular processes to improve our understanding of their biological functions.
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Affiliation(s)
- Rodolfo Gamaliel Avila-Bonilla
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Departamento de Genética y Biología Molecular, Av. IPN 2508, 07360, Mexico City, Mexico.
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4
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Yu C, Zhu Q, Ma C, Luo C, Nie L, Cai H, Wang Q, Wang F, Ren H, Yan H, Xu K, Zhou L, Zhang C, Lu G, Lu Z, Zhu Y, Liu S. Major vault protein regulates tumor-associated macrophage polarization through interaction with signal transducer and activator of transcription 6. Front Immunol 2024; 14:1289795. [PMID: 38264642 PMCID: PMC10803552 DOI: 10.3389/fimmu.2023.1289795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/21/2023] [Indexed: 01/25/2024] Open
Abstract
Tumor-associated macrophages (TAMs) are critical in the tumor microenvironment (TME) of hepatocellular carcinoma (HCC). Major vault protein (MVP) mediates multidrug resistance, cell growth and development, and viral immunity. However, the relationship between MVP and TAMs polarization has not been clarified in HCC. We found that MVP significantly increased M2-TAMs infiltration levels in tumor tissues of HCC patients. MVP promoted HCC proliferation, metastasis, and invasion by regulating M2 polarization in vivo and in vitro. Mechanistically, MVP associated with signal transducer and activator of transcription 6 (STAT6) and enhanced STAT6 phosphorylation. STAT6 translocated from the cytosol to the nucleus and regulated M2 macrophage-associated gene transcription. These findings suggest that MVP modulates the macrophage M2 transcriptional program, revealing its potential role in the TAMs of TME.
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Affiliation(s)
- Chen Yu
- State Key Laboratory of Virology, Modern Virology Research Center, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan, China
| | - Qingmei Zhu
- State Key Laboratory of Virology, Modern Virology Research Center, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan, China
| | - Caijiao Ma
- State Key Laboratory of Virology, Modern Virology Research Center, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan, China
| | - Chuanjin Luo
- State Key Laboratory of Virology, Modern Virology Research Center, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan, China
| | - Longyu Nie
- State Key Laboratory of Virology, Modern Virology Research Center, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan, China
| | - Huanhuan Cai
- Institute of Myocardial Injury and Repair, Wuhan University, Wuhan, China
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Qiming Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Hunan, Changsha, China
| | - Fubing Wang
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
| | - Hong Ren
- Shanghai Children’s Medical Center, Affiliated Hospital to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huan Yan
- State Key Laboratory of Virology, Modern Virology Research Center, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan, China
| | - Ke Xu
- State Key Laboratory of Virology, Modern Virology Research Center, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan, China
| | - Li Zhou
- State Key Laboratory of Virology, Modern Virology Research Center, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan, China
| | - Caiyan Zhang
- Shanghai Children’s Medical Center, Affiliated Hospital to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guoping Lu
- Shanghai Children’s Medical Center, Affiliated Hospital to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhibing Lu
- Institute of Myocardial Injury and Repair, Wuhan University, Wuhan, China
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ying Zhu
- State Key Laboratory of Virology, Modern Virology Research Center, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan, China
| | - Shi Liu
- State Key Laboratory of Virology, Modern Virology Research Center, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, Wuhan, China
- Institute of Myocardial Injury and Repair, Wuhan University, Wuhan, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Hunan, Changsha, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
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5
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Frigon L, Pascal JM. Structural and biochemical analysis of the PARP1-homology region of PARP4/vault PARP. Nucleic Acids Res 2023; 51:12492-12507. [PMID: 37971310 PMCID: PMC10711553 DOI: 10.1093/nar/gkad1064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/19/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023] Open
Abstract
PARP4 is an ADP-ribosyltransferase that resides within the vault ribonucleoprotein organelle. Our knowledge of PARP4 structure and biochemistry is limited relative to other PARPs. PARP4 shares a region of homology with PARP1, an ADP-ribosyltransferase that produces poly(ADP-ribose) from NAD+ in response to binding DNA breaks. The PARP1-homology region of PARP4 includes a BRCT fold, a WGR domain, and the catalytic (CAT) domain. Here, we have determined X-ray structures of the PARP4 catalytic domain and performed biochemical analysis that together indicate an active site that is open to NAD+ interaction, in contrast to the closed conformation of the PARP1 catalytic domain that blocks access to substrate NAD+. We have also determined crystal structures of the minimal ADP-ribosyltransferase fold of PARP4 that illustrate active site alterations that restrict PARP4 to mono(ADP-ribose) rather than poly(ADP-ribose) modifications. We demonstrate that PARP4 interacts with vault RNA, and that the BRCT is primarily responsible for the interaction. However, the interaction does not lead to stimulation of mono(ADP-ribosylation) activity. The BRCT-WGR-CAT of PARP4 has lower activity than the CAT alone, suggesting that the BRCT and WGR domains regulate catalytic output. Our study provides first insights into PARP4 structure and regulation and expands understanding of PARP structural biochemistry.
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Affiliation(s)
- Léonie Frigon
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Qc H3T 1J4, Canada
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Qc H3T 1J4, Canada
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6
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Suskiewicz MJ, Prokhorova E, Rack JGM, Ahel I. ADP-ribosylation from molecular mechanisms to therapeutic implications. Cell 2023; 186:4475-4495. [PMID: 37832523 PMCID: PMC10789625 DOI: 10.1016/j.cell.2023.08.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 10/15/2023]
Abstract
ADP-ribosylation is a ubiquitous modification of biomolecules, including proteins and nucleic acids, that regulates various cellular functions in all kingdoms of life. The recent emergence of new technologies to study ADP-ribosylation has reshaped our understanding of the molecular mechanisms that govern the establishment, removal, and recognition of this modification, as well as its impact on cellular and organismal function. These advances have also revealed the intricate involvement of ADP-ribosylation in human physiology and pathology and the enormous potential that their manipulation holds for therapy. In this review, we present the state-of-the-art findings covering the work in structural biology, biochemistry, cell biology, and clinical aspects of ADP-ribosylation.
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Affiliation(s)
| | | | - Johannes G M Rack
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK; MRC Centre of Medical Mycology, University of Exeter, Exeter, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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7
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Suskiewicz MJ, Munnur D, Strømland Ø, Yang JC, Easton L, Chatrin C, Zhu K, Baretić D, Goffinont S, Schuller M, Wu WF, Elkins J, Ahel D, Sanyal S, Neuhaus D, Ahel I. Updated protein domain annotation of the PARP protein family sheds new light on biological function. Nucleic Acids Res 2023; 51:8217-8236. [PMID: 37326024 PMCID: PMC10450202 DOI: 10.1093/nar/gkad514] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/09/2023] [Accepted: 06/03/2023] [Indexed: 06/17/2023] Open
Abstract
AlphaFold2 and related computational tools have greatly aided studies of structural biology through their ability to accurately predict protein structures. In the present work, we explored AF2 structural models of the 17 canonical members of the human PARP protein family and supplemented this analysis with new experiments and an overview of recent published data. PARP proteins are typically involved in the modification of proteins and nucleic acids through mono or poly(ADP-ribosyl)ation, but this function can be modulated by the presence of various auxiliary protein domains. Our analysis provides a comprehensive view of the structured domains and long intrinsically disordered regions within human PARPs, offering a revised basis for understanding the function of these proteins. Among other functional insights, the study provides a model of PARP1 domain dynamics in the DNA-free and DNA-bound states and enhances the connection between ADP-ribosylation and RNA biology and between ADP-ribosylation and ubiquitin-like modifications by predicting putative RNA-binding domains and E2-related RWD domains in certain PARPs. In line with the bioinformatic analysis, we demonstrate for the first time PARP14's RNA-binding capability and RNA ADP-ribosylation activity in vitro. While our insights align with existing experimental data and are probably accurate, they need further validation through experiments.
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Affiliation(s)
| | - Deeksha Munnur
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Øyvind Strømland
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Ji-Chun Yang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Laura E Easton
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Chatrin Chatrin
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Domagoj Baretić
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | | | - Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Wing-Fung Wu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jonathan M Elkins
- Centre for Medicines Discovery, University of Oxford, Oxford OX3 7DQ, UK
| | - Dragana Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Sumana Sanyal
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - David Neuhaus
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
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8
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Hananya N, Ye X, Koren S, Muir T. A genetically encoded photoproximity labeling approach for mapping protein territories. Proc Natl Acad Sci U S A 2023; 120:e2219339120. [PMID: 37036999 PMCID: PMC10120045 DOI: 10.1073/pnas.2219339120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 03/07/2023] [Indexed: 04/12/2023] Open
Abstract
Studying dynamic biological processes requires approaches compatible with the lifetimes of the biochemical transactions under investigation, which can be very short. We describe a genetically encoded system that allows protein neighborhoods to be mapped using visible light. Our approach involves fusing an engineered flavoprotein to a protein of interest. Brief excitation of the fusion protein leads to the labeling of nearby proteins with cell-permeable probes. Mechanistic studies reveal different labeling pathways are operational depending on the nature of the exogenous probe that is employed. When combined with quantitative proteomics, this photoproximity labeling system generates "snapshots" of protein territories with high temporal and spatial resolution. The intrinsic fluorescence of the fusion domain permits correlated imaging and proteomics analyses, a capability that is exploited in several contexts, including defining the protein clients of the major vault protein. The technology should be broadly useful in the biomedical area.
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Affiliation(s)
- Nir Hananya
- Department of Chemistry, Princeton University, Princeton, NJ08544
| | - Xuanjia Ye
- Department of Chemistry, Princeton University, Princeton, NJ08544
| | - Shany Koren
- Department of Chemistry, Princeton University, Princeton, NJ08544
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Princeton, NJ08544
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9
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Addressing Critical Issues Related to Storage and Stability of the Vault Nanoparticle Expressed and Purified from Komagataella phaffi. Int J Mol Sci 2023; 24:ijms24044214. [PMID: 36835627 PMCID: PMC9959619 DOI: 10.3390/ijms24044214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/08/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
The vault nanoparticle is a eukaryotic assembly consisting of 78 copies of the 99-kDa major vault protein. They generate two cup-shaped symmetrical halves, which in vivo enclose protein and RNA molecules. Overall, this assembly is mainly involved in pro-survival and cytoprotective functions. It also holds a remarkable biotechnological potential for drug/gene delivery, thanks to its huge internal cavity and the absence of toxicity/immunogenicity. The available purification protocols are complex, partly because they use higher eukaryotes as expression systems. Here, we report a simplified procedure that combines human vault expression in the yeast Komagataella phaffii, as described in a recent report, and a purification process we have developed. This consists of RNase pretreatment followed by size-exclusion chromatography, which is far simpler than any other reported to date. Protein identity and purity was confirmed by SDS-PAGE, Western blot and transmission electron microscopy. We also found that the protein displayed a significant propensity to aggregate. We thus investigated this phenomenon and the related structural changes by Fourier-transform spectroscopy and dynamic light scattering, which led us to determine the most suitable storage conditions. In particular, the addition of either trehalose or Tween-20 ensured the best preservation of the protein in native, soluble form.
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10
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Aljabali AAA, Rezigue M, Alsharedeh RH, Obeid MA, Mishra V, Serrano-Aroca Á, Tambuwala MM. Protein-Based Drug Delivery Nanomedicine Platforms: Recent Developments. Pharm Nanotechnol 2022; 10:257-267. [PMID: 35980061 DOI: 10.2174/2211738510666220817120307] [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: 02/21/2022] [Revised: 04/08/2022] [Accepted: 04/26/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND Naturally occurring protein cages, both viral and non-viral assemblies, have been developed for various pharmaceutical applications. Protein cages are ideal platforms as they are compatible, biodegradable, bioavailable, and amenable to chemical and genetic modification to impart new functionalities for selective targeting or tracking of proteins. The ferritin/ apoferritin protein cage, plant-derived viral capsids, the small Heat shock protein, albumin, soy and whey protein, collagen, and gelatin have all been exploited and characterized as drugdelivery vehicles. Protein cages come in many shapes and types with unique features such as unmatched uniformity, size, and conjugations. OBJECTIVES The recent strategic development of drug delivery will be covered in this review, emphasizing polymer-based, specifically protein-based, drug delivery nanomedicine platforms. The potential and drawbacks of each kind of protein-based drug-delivery system will also be highlighted. METHODS Research examining the usability of nanomaterials in the pharmaceutical and medical sectors were identified by employing bibliographic databases and web search engines. RESULTS Rings, tubes, and cages are unique protein structures that occur in the biological environment and might serve as building blocks for nanomachines. Furthermore, numerous virions can undergo reversible structural conformational changes that open or close gated pores, allowing customizable accessibility to their core and ideal delivery vehicles. CONCLUSION Protein cages' biocompatibility and their ability to be precisely engineered indicate they have significant potential in drug delivery and intracellular administration.
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Affiliation(s)
- Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, Irbid 21163 - P.O. BOX 566, Jordan
| | - Meriem Rezigue
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, Irbid 21163 - P.O. BOX 566, Jordan
| | - Rawan H Alsharedeh
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, Irbid 21163 - P.O. BOX 566, Jordan
| | - Mohammad A Obeid
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, Irbid 21163 - P.O. BOX 566, Jordan
| | - Vijay Mishra
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara 144411, India
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia, San Vicente Mártir, 46001 Valencia, Spain
| | - Murtaza M Tambuwala
- Lincoln Medical School, University of Lincoln, Brayford Pool Campus, Lincoln LN6 7TS, England, UK
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11
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Li P, Lei Y, Qi J, Liu W, Yao K. Functional roles of ADP-ribosylation writers, readers and erasers. Front Cell Dev Biol 2022; 10:941356. [PMID: 36035988 PMCID: PMC9404506 DOI: 10.3389/fcell.2022.941356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
ADP-ribosylation is a reversible post-translational modification (PTM) tightly regulated by the dynamic interplay between its writers, readers and erasers. As an intricate and versatile PTM, ADP-ribosylation plays critical roles in various physiological and pathological processes. In this review, we discuss the major players involved in the ADP-ribosylation cycle, which may facilitate the investigation of the ADP-ribosylation function and contribute to the understanding and treatment of ADP-ribosylation associated disease.
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12
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Small but Powerful: The Human Vault RNAs as Multifaceted Modulators of Pro-Survival Characteristics and Tumorigenesis. Cancers (Basel) 2022; 14:cancers14112787. [PMID: 35681764 PMCID: PMC9179338 DOI: 10.3390/cancers14112787] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/23/2022] [Accepted: 06/01/2022] [Indexed: 12/04/2022] Open
Abstract
Simple Summary Small non-protein-coding RNAs have been recognized as valuable regulators of gene expression in all three domains of life. Particularly in multicellular organisms, ncRNAs-mediated gene expression control has evolved as a central principle of cellular homeostasis. Thus, it is not surprising that non-coding RNA misregulation has been linked to various diseases. Here, we review the contributions of the four human vault RNAs to cellular proliferation, apoptosis and cancer biology. Abstract The importance of non-coding RNAs for regulating gene expression has been uncovered in model systems spanning all three domains of life. More recently, their involvement in modulating signal transduction, cell proliferation, tumorigenesis and cancer progression has also made them promising tools and targets for oncotherapy. Recent studies revealed a class of highly conserved small ncRNAs, namely vault RNAs, as regulators of several cellular homeostasis mechanisms. The human genome encodes four vault RNA paralogs that share significant sequence and structural similarities, yet they seem to possess distinct roles in mammalian cells. The alteration of vault RNA expression levels has frequently been observed in cancer tissues, thus hinting at a putative role in orchestrating pro-survival characteristics. Over the last decade, significant advances have been achieved in clarifying the relationship between vault RNA and cellular mechanisms involved in cancer development. It became increasingly clear that vault RNAs are involved in controlling apoptosis, lysosome biogenesis and function, as well as autophagy in several malignant cell lines, most likely by modulating signaling pathways (e.g., the pro-survival MAPK cascade). In this review, we discuss the identified and known functions of the human vault RNAs in the context of cell proliferation, tumorigenesis and chemotherapy resistance.
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13
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Lin A, Piehowski PD, Tsai CF, Makushok T, Yi L, Diaz U, Yan C, Summers D, Sood P, Smith RD, Liu T, Marshall WF. Determining protein polarization proteome-wide using physical dissection of individual Stentor coeruleus cells. Curr Biol 2022; 32:2300-2308.e4. [PMID: 35447087 PMCID: PMC9133221 DOI: 10.1016/j.cub.2022.03.078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/08/2022] [Accepted: 03/30/2022] [Indexed: 12/18/2022]
Abstract
Cellular components are non-randomly arranged with respect to the shape and polarity of the whole cell.1-4 Patterning within cells can extend down to the level of individual proteins and mRNA.5,6 But how much of the proteome is actually localized with respect to cell polarity axes? Proteomics combined with cellular fractionation7-11 has shown that most proteins localize to one or more organelles but does not tell us how many proteins have a polarized localization with respect to the large-scale polarity axes of the intact cell. Genome-wide localization studies in yeast12-15 found that only a few percent of proteins have a localized position relative to the cell polarity axis defined by sites of polarized cell growth. Here, we describe an approach for analyzing protein distribution within a cell with a visibly obvious global patterning-the giant ciliate Stentor coeruleus.16,17 Ciliates, including Stentor, have highly polarized cell shapes with visible surface patterning.1,18 A Stentor cell is roughly 2 mm long, allowing a "proteomic dissection" in which microsurgery is used to separate cellular fragments along the anterior-posterior axis, followed by comparative proteomic analysis. In our analysis, 25% of the proteome, including signaling proteins, centrin/SFI proteins, and GAS2 orthologs, shows a polarized location along the cell's anterior-posterior axis. We conclude that a large proportion of all proteins are polarized with respect to global cell polarity axes and that proteomic dissection provides a simple and effective approach for spatial proteomics.
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Affiliation(s)
- Athena Lin
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Paul D Piehowski
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Chia-Feng Tsai
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Tatyana Makushok
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lian Yi
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Ulises Diaz
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Connie Yan
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Diana Summers
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Pranidhi Sood
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Richard D Smith
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Tao Liu
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Wallace F Marshall
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, United States of America.
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14
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Poly (ADP-ribose) polymerase: An Overview of Mechanistic Approaches and Therapeutic Opportunities in the Management of Stroke. Neurochem Res 2022; 47:1830-1852. [PMID: 35437712 DOI: 10.1007/s11064-022-03595-z] [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: 12/21/2021] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 10/18/2022]
Abstract
Stroke is one of the leading causes of morbidity and mortality accompanied by blood supply loss to a particular brain area. Several mechanistic approaches such as inhibition of poly (ADP-ribose) polymerase, therapies against tissue thrombosis, and neutrophils lead to stroke's therapeutic intervention. Evidence obtained with the poly (ADP-ribose) polymerase (PARP) inhibition and animals having a deficiency of PARP enzymes; represented the role of PARP in cerebral stroke, ischemia/reperfusion, and neurotrauma. PARP is a nuclear enzyme superfamily with various isoforms, each with different structural domains and functions, and out of all, PARP-1 is the best-characterized member. It has been shown to perform multiple physiological as well as pathological processes, including its role in inflammation, oxidative stress, apoptosis, and mitochondrial dysfunction. The enzyme interacts with NF-κB, p53, and other transcriptional factors to regulate survival and cell death and modulates multiple downstream signaling pathways. Clinical trials have also been conducted using PARP inhibitors for numerous disorders and have shown positive results. However, additional information is yet to be established for the therapeutic intervention of PARP inhibitors in stroke. These agents' utilization appears to be challenging due to their unknown potential long-term side effects. PARP activity increased during ischemia, but its inhibition provided significant neuroprotection. Despite the increased interest in PARP as a pharmacological modulator for novel therapeutic therapies, the current review focused on stroke and poly ADP-ribosylation.
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15
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Manco G, Lacerra G, Porzio E, Catara G. ADP-Ribosylation Post-Translational Modification: An Overview with a Focus on RNA Biology and New Pharmacological Perspectives. Biomolecules 2022; 12:biom12030443. [PMID: 35327636 PMCID: PMC8946771 DOI: 10.3390/biom12030443] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/02/2022] [Accepted: 03/10/2022] [Indexed: 02/04/2023] Open
Abstract
Cellular functions are regulated through the gene expression program by the transcription of new messenger RNAs (mRNAs), alternative RNA splicing, and protein synthesis. To this end, the post-translational modifications (PTMs) of proteins add another layer of complexity, creating a continuously fine-tuned regulatory network. ADP-ribosylation (ADPr) is an ancient reversible modification of cellular macromolecules, regulating a multitude of key functional processes as diverse as DNA damage repair (DDR), transcriptional regulation, intracellular transport, immune and stress responses, and cell survival. Additionally, due to the emerging role of ADP-ribosylation in pathological processes, ADP-ribosyltransferases (ARTs), the enzymes involved in ADPr, are attracting growing interest as new drug targets. In this review, an overview of human ARTs and their related biological functions is provided, mainly focusing on the regulation of ADP-ribosyltransferase Diphtheria toxin-like enzymes (ARTD)-dependent RNA functions. Finally, in order to unravel novel gene functional relationships, we propose the analysis of an inventory of human gene clusters, including ARTDs, which share conserved sequences at 3′ untranslated regions (UTRs).
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Affiliation(s)
- Giuseppe Manco
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy;
- Correspondence: (G.M.); (G.C.)
| | - Giuseppina Lacerra
- Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy;
| | - Elena Porzio
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy;
| | - Giuliana Catara
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy;
- Correspondence: (G.M.); (G.C.)
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16
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Guerra P, González-Alamos M, Llauró A, Casañas A, Querol-Audí J, de Pablo PJ, Verdaguer N. Symmetry disruption commits vault particles to disassembly. SCIENCE ADVANCES 2022; 8:eabj7795. [PMID: 35138889 PMCID: PMC8827651 DOI: 10.1126/sciadv.abj7795] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Vaults are ubiquitous ribonucleoprotein particles involved in a diversity of cellular processes, with promising applications as nanodevices for delivery of multiple cargos. The vault shell is assembled by the symmetrical association of multiple copies of the major vault protein that, initially, generates half vaults. The pairwise, anti-parallel association of two half vaults produces whole vaults. Here, using a combination of vault recombinant reconstitution and structural techniques, we characterized the molecular determinants for the vault opening process. This process commences with a relaxation of the vault waist, causing the expansion of the inner cavity. Then, local disengagement of amino-terminal domains at the vault midsection seeds a conformational change that leads to the aperture, facilitating access to the inner cavity where cargo is hosted. These results inform a hitherto uncharacterized step of the vault cycle and will aid current engineering efforts leveraging vault for tailored cargo delivery.
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Affiliation(s)
- Pablo Guerra
- Structural Biology Department, Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri i Reixac 15, E-08028 Barcelona, Spain
| | - María González-Alamos
- Structural Biology Department, Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri i Reixac 15, E-08028 Barcelona, Spain
| | - Aida Llauró
- Department of Condensed Matter Physics, Autonomous University of Madrid, Madrid 28049, Spain
| | - Arnau Casañas
- Structural Biology Department, Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri i Reixac 15, E-08028 Barcelona, Spain
| | - Jordi Querol-Audí
- Structural Biology Department, Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri i Reixac 15, E-08028 Barcelona, Spain
| | - Pedro J. de Pablo
- Department of Condensed Matter Physics, Autonomous University of Madrid, Madrid 28049, Spain
| | - Núria Verdaguer
- Structural Biology Department, Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri i Reixac 15, E-08028 Barcelona, Spain
- Corresponding author.
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17
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Richard IA, Burgess JT, O'Byrne KJ, Bolderson E. Beyond PARP1: The Potential of Other Members of the Poly (ADP-Ribose) Polymerase Family in DNA Repair and Cancer Therapeutics. Front Cell Dev Biol 2022; 9:801200. [PMID: 35096828 PMCID: PMC8795897 DOI: 10.3389/fcell.2021.801200] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/21/2021] [Indexed: 01/22/2023] Open
Abstract
The proteins within the Poly-ADP Ribose Polymerase (PARP) family encompass a diverse and integral set of cellular functions. PARP1 and PARP2 have been extensively studied for their roles in DNA repair and as targets for cancer therapeutics. Several PARP inhibitors (PARPi) have been approved for clinical use, however, while their efficacy is promising, tumours readily develop PARPi resistance. Many other members of the PARP protein family share catalytic domain homology with PARP1/2, however, these proteins are comparatively understudied, particularly in the context of DNA damage repair and tumourigenesis. This review explores the functions of PARP4,6-16 and discusses the current knowledge of the potential roles these proteins may play in DNA damage repair and as targets for cancer therapeutics.
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Affiliation(s)
- Iain A Richard
- Cancer and Ageing Research Program (CARP), Centre for Genomics and Personalised Health (CGPH), Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Joshua T Burgess
- Cancer and Ageing Research Program (CARP), Centre for Genomics and Personalised Health (CGPH), Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Kenneth J O'Byrne
- Cancer and Ageing Research Program (CARP), Centre for Genomics and Personalised Health (CGPH), Queensland University of Technology (QUT), Brisbane, QLD, Australia.,Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Emma Bolderson
- Cancer and Ageing Research Program (CARP), Centre for Genomics and Personalised Health (CGPH), Queensland University of Technology (QUT), Brisbane, QLD, Australia
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18
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Martina L, Asselman C, Thery F, Boucher K, Delhaye L, Maia TM, Dermaut B, Eyckerman S, Impens F. Proteome Profiling of RNF213 Depleted Cells Reveals Nitric Oxide Regulator DDAH1 Antilisterial Activity. Front Cell Infect Microbiol 2021; 11:735416. [PMID: 34804992 PMCID: PMC8595287 DOI: 10.3389/fcimb.2021.735416] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/08/2021] [Indexed: 01/25/2023] Open
Abstract
RNF213 is a large, poorly characterized interferon-induced protein. Mutations in RNF213 are associated with predisposition for Moyamoya disease (MMD), a rare cerebrovascular disorder. Recently, RNF213 was found to have broad antimicrobial activity in vitro and in vivo, yet the molecular mechanisms behind this function remain unclear. Using mass spectrometry-based proteomics and validation by real-time PCR we report here that knockdown of RNF213 leads to transcriptional upregulation of MVP and downregulation of CYR61, in line with reported pro- and anti-bacterial activities of these proteins. Knockdown of RNF213 also results in downregulation of DDAH1, which we discover to exert antimicrobial activity against Listeria monocytogenes infection. DDAH1 regulates production of nitric oxide (NO), a molecule with both vascular and antimicrobial effects. We show that NO production is reduced in macrophages from RNF213 KO mice, suggesting that RNF213 controls Listeria infection through regulation of DDAH1 transcription and production of NO. Our findings propose a potential mechanism for the antilisterial activity of RNF213 and highlight NO as a potential link between RNF213-mediated immune responses and the development of MMD.
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Affiliation(s)
- Lia Martina
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Caroline Asselman
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Fabien Thery
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Katie Boucher
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,VIB Proteomics Core, VIB, Ghent, Belgium
| | - Louis Delhaye
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Teresa M Maia
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,VIB Proteomics Core, VIB, Ghent, Belgium
| | - Bart Dermaut
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Sven Eyckerman
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Francis Impens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,VIB Proteomics Core, VIB, Ghent, Belgium
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19
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Kirby IT, Person A, Cohen M. Rational design of selective inhibitors of PARP4. RSC Med Chem 2021; 12:1950-1957. [PMID: 34825190 DOI: 10.1039/d1md00195g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 10/01/2021] [Indexed: 12/22/2022] Open
Abstract
PARPs (PARP1-16 in humans) are a large family of ADP-ribosyltransferases (ARTs) that have diverse roles in cellular physiology and pathophysiology. Most PARP family members mediate mono-ADP-ribosylation (MARylation) of targets. The function of PARP-mediated MARylation in cells is poorly characterized, due in large part to the paucity of selective small molecule inhibitors of the catalytic activity of individual PARP enzymes. Herein we describe the rational design of selective small molecule inhibitors of PARP4 (also known as vPARP). These inhibitors are based on a quinazolin-4(3H)-one scaffold, and contain substituents at the C-8 position designed to exploit a unique threonine (Thr484, human PARP4 numbering) in the PARP4 nicotinamide sub-pocket. Our most potent analog, AEP07, which contains an iodine at the C-8 position, is at least 12-fold selective over other PARP family members. AEP07 will serve as a useful lead compound for the further development of PARP4 inhibitors that can be used to probe the cellular functions of PARP4 catalytic activity.
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Affiliation(s)
- Ilsa T Kirby
- Initial Therapeutics South San Francisco CA 94080 USA
| | - Ashley Person
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health Bethesda MD 20892 USA
| | - Michael Cohen
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University Portland OR 97239 USA
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20
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Goel D, Sinha S. Naturally occurring protein nano compartments: basic structure, function, and genetic engineering. NANO EXPRESS 2021. [DOI: 10.1088/2632-959x/ac2c93] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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21
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Pillay N, Brady RM, Dey M, Morgan RD, Taylor SS. DNA replication stress and emerging prospects for PARG inhibitors in ovarian cancer therapy. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 163:160-170. [PMID: 33524442 DOI: 10.1016/j.pbiomolbio.2021.01.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 01/13/2021] [Accepted: 01/19/2021] [Indexed: 02/07/2023]
Abstract
Poly (ADP-ribosyl)ation has central functions in maintaining genome stability, including facilitating DNA replication and repair. In cancer cells these processes are frequently disrupted, and thus interfering with poly (ADP-ribosyl)ation can exacerbate inherent genome instability and induce selective cytotoxicity. Indeed, inhibitors of poly (ADP-ribose) polymerase (PARP) are having a major clinical impact in treating women with BRCA-mutant ovarian cancer, based on a defect in homologous recombination. However, only around half of ovarian cancers harbour defects in homologous recombination, and most sensitive tumours eventually acquire PARP inhibitor resistance with treatment. Thus, there is a pressing need to develop alternative treatment strategies to target tumours with both inherent and acquired resistance to PARP inhibition. Several novel inhibitors of poly (ADP-ribose)glycohydrolase (PARG) have been described, with promising anti-cancer activity in vitro that is distinct from PARP inhibitors. Here we discuss, the role of poly (ADP-ribosyl)ation in genome stability, and the potential for PARG inhibitors as a complementary strategy to PARP inhibitors in the treatment of ovarian cancer.
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Affiliation(s)
- Nisha Pillay
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Wilmslow Rd, Manchester, M20 4GJ, UK; Divisions of Structural Biology & Cancer Biology, The Institute of Cancer Research (ICR), London, SW7 3RP, UK
| | - Rosie M Brady
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Wilmslow Rd, Manchester, M20 4GJ, UK
| | - Malini Dey
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Wilmslow Rd, Manchester, M20 4GJ, UK
| | - Robert D Morgan
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Wilmslow Rd, Manchester, M20 4GJ, UK; Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Rd, Manchester, M20 4BX, UK
| | - Stephen S Taylor
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Wilmslow Rd, Manchester, M20 4GJ, UK.
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22
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Demény MA, Virág L. The PARP Enzyme Family and the Hallmarks of Cancer Part 2: Hallmarks Related to Cancer Host Interactions. Cancers (Basel) 2021; 13:2057. [PMID: 33923319 PMCID: PMC8123211 DOI: 10.3390/cancers13092057] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/07/2021] [Accepted: 04/21/2021] [Indexed: 12/12/2022] Open
Abstract
Poly (ADP-ribose) polymerases (PARPs) modify target proteins with a single ADP-ribose unit or with a poly (ADP-ribose) (PAR) polymer. PARP inhibitors (PARPis) recently became clinically available for the treatment of BRCA1/2 deficient tumors via the synthetic lethality paradigm. This personalized treatment primarily targets DNA damage-responsive PARPs (PARP1-3). However, the biological roles of PARP family member enzymes are broad; therefore, the effects of PARPis should be viewed in a much wider context, which includes complex effects on all known hallmarks of cancer. In the companion paper (part 1) to this review, we presented the fundamental roles of PARPs in intrinsic cancer cell hallmarks, such as uncontrolled proliferation, evasion of growth suppressors, cell death resistance, genome instability, replicative immortality, and reprogrammed metabolism. In the second part of this review, we present evidence linking PARPs to cancer-associated inflammation, anti-cancer immune response, invasion, and metastasis. A comprehensive overview of the roles of PARPs can facilitate the identification of novel cancer treatment opportunities and barriers limiting the efficacy of PARPi compounds.
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Affiliation(s)
- Máté A. Demény
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- MTA-DE Cell Biology and Signaling Research Group, 4032 Debrecen, Hungary
| | - László Virág
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- MTA-DE Cell Biology and Signaling Research Group, 4032 Debrecen, Hungary
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23
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Immunoediting role for major vault protein in apoptotic signaling induced by bacterial N-acyl homoserine lactones. Proc Natl Acad Sci U S A 2021; 118:2012529118. [PMID: 33723037 PMCID: PMC8000436 DOI: 10.1073/pnas.2012529118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The major vault protein (MVP) mediates diverse cellular responses, including cancer cell resistance to chemotherapy and protection against inflammatory responses to Pseudomonas aeruginosa Here, we report the use of photoactive probes to identify MVP as a target of the N-(3-oxo-dodecanoyl) homoserine lactone (C12), a quorum sensing signal of certain proteobacteria including P. aeruginosa. A treatment of normal and cancer cells with C12 or other N-acyl homoserine lactones (AHLs) results in rapid translocation of MVP into lipid raft (LR) membrane fractions. Like AHLs, inflammatory stimuli also induce LR-localization of MVP, but the C12 stimulation reprograms (functionalizes) bioactivity of the plasma membrane by recruiting death receptors, their apoptotic adaptors, and caspase-8 into LR. These functionalized membranes control AHL-induced signaling processes, in that MVP adjusts the protein kinase p38 pathway to attenuate programmed cell death. Since MVP is the structural core of large particles termed vaults, our findings suggest a mechanism in which MVP vaults act as sentinels that fine-tune inflammation-activated processes such as apoptotic signaling mediated by immunosurveillance cytokines including tumor necrosis factor-related apoptosis inducing ligand (TRAIL).
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24
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Frascotti G, Galbiati E, Mazzucchelli M, Pozzi M, Salvioni L, Vertemara J, Tortora P. The Vault Nanoparticle: A Gigantic Ribonucleoprotein Assembly Involved in Diverse Physiological and Pathological Phenomena and an Ideal Nanovector for Drug Delivery and Therapy. Cancers (Basel) 2021; 13:cancers13040707. [PMID: 33572350 PMCID: PMC7916137 DOI: 10.3390/cancers13040707] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/03/2021] [Accepted: 02/03/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary In recent decades, a molecular complex referred to as vault nanoparticle has attracted much attention by the scientific community, due to its unique properties. At the molecular scale, it is a huge assembly consisting of 78 97-kDa polypeptide chains enclosing an internal cavity, wherein enzymes involved in DNA integrity maintenance and some small noncoding RNAs are accommodated. Basically, two reasons justify this interest. On the one hand, this complex represents an ideal tool for the targeted delivery of drugs, provided it is suitably engineered, either chemically or genetically; on the other hand, it has been shown to be involved in several cellular pathways and mechanisms that most often result in multidrug resistance. It is therefore expected that a better understanding of the physiological roles of this ribonucleoproteic complex may help develop new therapeutic strategies capable of coping with cancer progression. Here, we provide a comprehensive review of the current knowledge. Abstract The vault nanoparticle is a eukaryotic ribonucleoprotein complex consisting of 78 individual 97 kDa-“major vault protein” (MVP) molecules that form two symmetrical, cup-shaped, hollow halves. It has a huge size (72.5 × 41 × 41 nm) and an internal cavity, wherein the vault poly(ADP-ribose) polymerase (vPARP), telomerase-associated protein-1 (TEP1), and some small untranslated RNAs are accommodated. Plenty of literature reports on the biological role(s) of this nanocomplex, as well as its involvement in diseases, mostly oncological ones. Nevertheless, much has still to be understood as to how vault participates in normal and pathological mechanisms. In this comprehensive review, current understanding of its biological roles is discussed. By different mechanisms, vault’s individual components are involved in major cellular phenomena, which result in protection against cellular stresses, such as DNA-damaging agents, irradiation, hypoxia, hyperosmotic, and oxidative conditions. These diverse cellular functions are accomplished by different mechanisms, mainly gene expression reprogramming, activation of proliferative/prosurvival signaling pathways, export from the nucleus of DNA-damaging drugs, and import of specific proteins. The cellular functions of this nanocomplex may also result in the onset of pathological conditions, mainly (but not exclusively) tumor proliferation and multidrug resistance. The current understanding of its biological roles in physiological and pathological processes should also provide new hints to extend the scope of its exploitation as a nanocarrier for drug delivery.
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25
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Challa S, Stokes MS, Kraus WL. MARTs and MARylation in the Cytosol: Biological Functions, Mechanisms of Action, and Therapeutic Potential. Cells 2021; 10:313. [PMID: 33546365 PMCID: PMC7913519 DOI: 10.3390/cells10020313] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 01/30/2021] [Accepted: 02/01/2021] [Indexed: 12/13/2022] Open
Abstract
Mono(ADP-ribosyl)ation (MARylation) is a regulatory post-translational modification of proteins that controls their functions through a variety of mechanisms. MARylation is catalyzed by mono(ADP-ribosyl) transferase (MART) enzymes, a subclass of the poly(ADP-ribosyl) polymerase (PARP) family of enzymes. Although the role of PARPs and poly(ADP-ribosyl)ation (PARylation) in cellular pathways, such as DNA repair and transcription, is well studied, the role of MARylation and MARTs (i.e., the PARP 'monoenzymes') are not well understood. Moreover, compared to PARPs, the development of MART-targeted therapeutics is in its infancy. Recent studies are beginning to shed light on the structural features, catalytic targets, and biological functions of MARTs. The development of new technologies to study MARTs have uncovered essential roles for these enzymes in the regulation of cellular processes, such as RNA metabolism, cellular transport, focal adhesion, and stress responses. These insights have increased our understanding of the biological functions of MARTs in cancers, neuronal development, and immune responses. Furthermore, several novel inhibitors of MARTs have been developed and are nearing clinical utility. In this review, we summarize the biological functions and molecular mechanisms of MARTs and MARylation, as well as recent advances in technology that have enabled detection and inhibition of their activity. We emphasize PARP-7, which is at the forefront of the MART subfamily with respect to understanding its biological roles and the development of therapeutically useful inhibitors. Collectively, the available studies reveal a growing understanding of the biochemistry, chemical biology, physiology, and pathology of MARTs.
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Affiliation(s)
- Sridevi Challa
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - MiKayla S. Stokes
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Program in Genetics, Development, and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - W. Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Program in Genetics, Development, and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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26
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Palavalli Parsons LH, Challa S, Gibson BA, Nandu T, Stokes MS, Huang D, Lea JS, Kraus WL. Identification of PARP-7 substrates reveals a role for MARylation in microtubule control in ovarian cancer cells. eLife 2021; 10:60481. [PMID: 33475085 PMCID: PMC7884071 DOI: 10.7554/elife.60481] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 01/20/2021] [Indexed: 12/22/2022] Open
Abstract
PARP-7 (TiPARP) is a mono(ADP-ribosyl) transferase whose protein substrates and biological activities are poorly understood. We observed that PARP7 mRNA levels are lower in ovarian cancer patient samples compared to non-cancerous tissue, but PARP-7 protein nonetheless contributes to several cancer-related biological endpoints in ovarian cancer cells (e.g. growth, migration). Global gene expression analyses in ovarian cancer cells subjected to PARP-7 depletion indicate biological roles for PARP-7 in cell-cell adhesion and gene regulation. To identify the MARylated substrates of PARP-7 in ovarian cancer cells, we developed an NAD+ analog-sensitive approach, which we coupled with mass spectrometry to identify the PARP-7 ADP-ribosylated proteome in ovarian cancer cells, including cell-cell adhesion and cytoskeletal proteins. Specifically, we found that PARP-7 MARylates α-tubulin to promote microtubule instability, which may regulate ovarian cancer cell growth and motility. In sum, we identified an extensive PARP-7 ADP-ribosylated proteome with important roles in cancer-related cellular phenotypes.
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Affiliation(s)
- Lavanya H Palavalli Parsons
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, United States.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, United States.,Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Sridevi Challa
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, United States.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Bryan A Gibson
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, United States.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Tulip Nandu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, United States.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, United States
| | - MiKayla S Stokes
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, United States.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Dan Huang
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, United States.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Cardiology, Clinical Center for Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jayanthi S Lea
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, United States
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, United States.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, United States
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27
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Lal S, Snape TJ. A therapeutic update on PARP inhibitors: implications in the treatment of glioma. Drug Discov Today 2020; 26:532-541. [PMID: 33157194 DOI: 10.1016/j.drudis.2020.10.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/07/2020] [Accepted: 10/29/2020] [Indexed: 01/01/2023]
Abstract
Central nervous system (CNS) cancers are among the most aggressive and devastating. Further, due to unavailability of neuro-oncologists and neurosurgeons, the specialized treatment options of CNS cancers are still not completely available in most parts of the world. Among various strategies of inducing death in cancer cells, inhibition of poly(ADP-ribose) polymerase (PARP) has emerged as a beneficial therapy when combined with other anticancer agents. In this review, we provide a detailed therapeutic update of PARP inhibitors that have shown clinical activity against glioma.
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Affiliation(s)
- Samridhi Lal
- Amity Institute of Pharmacy, Amity University, Gurugram, 122413, Haryana, India.
| | - Timothy J Snape
- Leicester School of Pharmacy, De Montfort University, Leicester, LE1 9BH, UK
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28
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Whole genome sequencing of colorectal neuroendocrine tumors and in-depth mutational analyses. Med Oncol 2020; 37:56. [PMID: 32424617 DOI: 10.1007/s12032-020-01356-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 02/28/2020] [Indexed: 02/03/2023]
Abstract
Colorectal neuroendocrine tumors (NETs) are rare neoplasms and studies on colorectal NETs are relatively few compared to other tumors. To better understand the pathogenesis of this tumor, we performed whole-genome sequencing and follow-up verification using Sanger sequencing of the colorectal NETs and paired para-tumor tissue. We analyzed the features of the gene mutation spectrum and mutation signature patterns, and analyzed the four pathways that were altered by gene mutation in pancreatic neuroendocrine tumors, including DNA damage and repair, chromatin remodeling, telomere maintenance and mTOR signaling activation. We found that PARP4 which is related to the DNA damage and repair pathway; TSC2, which is related to the mTOR signaling activation pathway; and SLX1A, which is related to telomere maintenance, were mutated in colorectal NETs. Our data analyzed characteristics of gene mutation in colorectal NETs at the whole-genome level, and may help to better understand the pathogenesis of colorectal NETs and may be helpful for potential tumor therapy in the future.
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29
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Xie H, Wang W, Xia B, Jin W, Lou G. Therapeutic applications of PARP inhibitors in ovarian cancer. Biomed Pharmacother 2020; 127:110204. [PMID: 32422564 DOI: 10.1016/j.biopha.2020.110204] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/24/2020] [Accepted: 04/28/2020] [Indexed: 12/21/2022] Open
Abstract
Ovarian cancer is the most lethal gynecologic malignancy with a high recurrence rate. Poly(ADP-ribose) polymerase inhibitors (PARPi) are one of the most active new therapies for treatment of ovarian cancer. These treatment modalities are based on the mechanisms of "synthetic lethal" and "PARP trapping", especially for patients with homologous recombination deficiencies, and they demonstrate a high survival advantage. However, resistance to PARPi is an emerging problem. Identifying potential biomarkers to monitor the resistance and developing drug combination strategies are effective ways to address PARPi resistance. This review introduces the mechanisms of anticancer activity of PARPi and the developmental history in clinical research. Moreover, this paper systematically analyzes the functions of PARP family proteins. Additionally, this work highlights the treatment prospects of the combination of immunotherapy and PARPi in ovarian cancer. Finally, we propose several novel technologies to overcome the limitations of current preclinical studies and utilize them to select potential targets for combined drug therapy and identify biomarkers of PARPi resistance in ovarian cancer.
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Affiliation(s)
- Hongyu Xie
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, PR China
| | - Wenjie Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin 150086, PR China
| | - Bairong Xia
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, PR China
| | - Weilin Jin
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, Key Lab. for Thin Film and Microfabrication Technology of Ministry of Education, School of Electronic Information and Electronic Engineering, Shanghai Jiao Tong University, Shanghai 200240, PR China.
| | - Ge Lou
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, PR China.
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30
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Bioengineered recombinant vault nanoparticles coupled with NY-ESO-1 glioma-associated antigens induce maturation of native dendritic cells. J Neurooncol 2020; 148:1-7. [DOI: 10.1007/s11060-020-03472-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 03/23/2020] [Indexed: 11/27/2022]
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31
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Modification of PARP4, XRCC3, and RAD51 Gene Polymorphisms on the Relation between Bisphenol A Exposure and Liver Abnormality. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17082794. [PMID: 32316696 PMCID: PMC7216258 DOI: 10.3390/ijerph17082794] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/13/2020] [Accepted: 04/16/2020] [Indexed: 12/18/2022]
Abstract
Repair genes may play critical roles in the relationships between environmental exposure and health outcomes. However, no evidence is available about the effect of repair gene polymorphisms on the relationship between bisphenol A (BPA) exposure and liver abnormality. Therefore, we evaluated the effect of nine genotyped polymorphisms in three repair genes, poly(ADP-ribose) polymerase family member 4 (PARP4), X-ray repair cross complementing 3 (XRCC3), and RAD51 recombinase (RAD51), on the relationship between BPA exposure and liver abnormality using repeated measures data for an elderly population. A significant association between BPA levels and liver abnormality was found only in elders with the PARP4 G-C-G haplotype, XRCC3 G-A-G haplotype, or RAD51 T-A-A haplotype (odds ratio (OR) = 2.16 and p = 0.0014 for PARP4; OR = 1.57 and p = 0.0249 for XRCC3; OR = 1.43 and p = 0.0422 for RAD51). Particularly, PARP4 and XRCC3 showed significant interactions with BPA exposure in relation to liver abnormality (p < 0.05 for both genes). These results indicate that PARP4, XRCC3, and RAD51 gene polymorphisms have modification effects on the relationship between BPA exposure and liver abnormality.
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32
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Wang W, Xiong L, Wang P, Wang F, Ma Q. Major vault protein plays important roles in viral infection. IUBMB Life 2020; 72:624-631. [PMID: 31769934 PMCID: PMC7165711 DOI: 10.1002/iub.2200] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 10/30/2019] [Indexed: 12/12/2022]
Abstract
Viral replication and related protein expression inside the host cells, and host antiviral immune responses can lead to the occurrence of diverse diseases. With the outbreak of viral infection, a large number of newly diagnosed and died patients infected with various viruses are still reported every year. Viral infection has already been one of the major global public health issues and lead to huge economic and social burdens. Studying of viral pathogenesis is a very important way to find methods for prevention, diagnosis, and cure of viral infection; more evidence has confirmed that major vault protein (MVP) is closely associated with viral infection and pathogenesis, and this review is intended to provide a broad relationship between viruses and MVP to stimulate the interest of related researchers.
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Affiliation(s)
- Wei Wang
- Department of Clinical Laboratory, Puai Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Liang Xiong
- Department of Clinical Laboratory, Liyuan Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Pengyun Wang
- Department of Clinical Laboratory, Liyuan Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Fubing Wang
- Department of Laboratory MedicineZhongnan Hospital of Wuhan UniversityWuhanChina
| | - Qingfeng Ma
- Department of Clinical Laboratory, Liyuan Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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33
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Ünlü A, Dinç B. Investigation of the three-dimensional structure and interaction mechanism of poly (ADP-ribose) polymerase 4. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1726208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Ayhan Ünlü
- Department of Biophysics, Medical Faculty, Trakya University, Edirne, Turkey
| | - Bircan Dinç
- Department of Biophysics, Medical Faculty, Bahçeşehir University, İstanbul, Turkey
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34
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Kolev NG, Rajan KS, Tycowski KT, Toh JY, Shi H, Lei Y, Michaeli S, Tschudi C. The vault RNA of Trypanosoma brucei plays a role in the production of trans-spliced mRNA. J Biol Chem 2019; 294:15559-15574. [PMID: 31439669 DOI: 10.1074/jbc.ra119.008580] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 08/07/2019] [Indexed: 11/06/2022] Open
Abstract
The vault ribonucleoprotein (RNP), comprising vault RNA (vtRNA) and telomerase-associated protein 1 (TEP1), is found in many eukaryotes. However, previous studies of vtRNAs, for example in mammalian cells, have failed to reach a definitive conclusion about their function. vtRNAs are related to Y RNAs, which are complexed with Ro protein and influence Ro's function in noncoding RNA (ncRNA) quality control and processing. In Trypanosoma brucei, the small noncoding TBsRNA-10 was first described in a survey of the ncRNA repertoire in this organism. Here, we report that TBsRNA-10 in T. brucei is a vtRNA, based on its association with TEP1 and sequence similarity to those of other known and predicted vtRNAs. We observed that like vtRNAs in other species, TBsRNA-10 is transcribed by RNA polymerase III, which in trypanosomes also generates the spliceosomal U-rich small nuclear RNAs. In T. brucei, spliced leader (SL)-mediated trans-splicing of pre-mRNAs is an obligatory step in gene expression, and we found here that T. brucei's vtRNA is highly enriched in a non-nucleolar locus in the cell nucleus implicated in SL RNP biogenesis. Using a newly developed permeabilized cell system for the bloodstream form of T. brucei, we show that down-regulated vtRNA levels impair trans-spliced mRNA production, consistent with a role of vtRNA in trypanosome mRNA metabolism. Our results suggest a common theme for the functions of vtRNAs and Y RNAs. We conclude that by complexing with their protein-binding partners TEP1 and Ro, respectively, these two RNA species modulate the metabolism of various RNA classes.
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Affiliation(s)
- Nikolay G Kolev
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut 06536
| | - K Shanmugha Rajan
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Kazimierz T Tycowski
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06536
| | - Justin Y Toh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut 06536
| | - Huafang Shi
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut 06536
| | - Yuling Lei
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut 06536
| | - Shulamit Michaeli
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Christian Tschudi
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut 06536
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35
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Gottlieb CD, Thompson ACS, Ordureau A, Harper JW, Kopito RR. Acute unfolding of a single protein immediately stimulates recruitment of ubiquitin protein ligase E3C (UBE3C) to 26S proteasomes. J Biol Chem 2019; 294:16511-16524. [PMID: 31375563 DOI: 10.1074/jbc.ra119.009654] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/16/2019] [Indexed: 01/26/2023] Open
Abstract
The intracellular accumulation of aggregated misfolded proteins is a cytopathological hallmark of neurodegenerative diseases. However, the functional relationship between protein misfolding or aggregation and the cellular proteostasis network that monitors and maintains proteome health is poorly understood. Previous studies have associated translational suppression and transcriptional remodeling with the appearance of protein aggregates, but whether these responses are induced by aggregates or their misfolded monomeric or oligomeric precursors remains unclear. Because aggregation in cells is rapid, nonlinear, and asynchronous, it has not been possible to deconvolve these kinetically linked processes to determine the earliest cellular responses to misfolded proteins. Upon removal of the synthetic, biologically inert ligand shield-1 (S1), AgDD, an engineered variant FK506-binding protein (FKBP1A), rapidly (t ½ ∼5 min) unfolds and self-associates, forming detergent-insoluble, microscopic cytoplasmic aggregates. Using global diglycine-capture (K-GG) proteomics, we found here that this solubility transition is associated with immediate increases in ubiquitylation of AgDD itself, along with that of endogenous proteins that are components of the ribosome and the 26S proteasome. We also found that the earliest cellular responses to acute S1 removal include recruitment of ubiquitin protein ligase E3C (UBE3C) to the 26S proteasome and ubiquitylation of two key proteasomal ubiquitin receptors, 26S proteasome regulatory subunit RPN10 (RPN10) and Rpn13 homolog (RPN13 or ADRM1). We conclude that these proteasomal responses are due to AgDD protein misfolding and not to the presence of detergent-insoluble aggregates.
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Affiliation(s)
- Colin D Gottlieb
- Department of Biology, Stanford University, Stanford, California 94305
| | | | - Alban Ordureau
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, Massachusetts 02115
| | - J Wade Harper
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, Massachusetts 02115
| | - Ron R Kopito
- Department of Biology, Stanford University, Stanford, California 94305
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36
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Fulcher JA, Tamshen K, Wollenberg AL, Kickhoefer VA, Mrazek J, Elliott J, Ibarrondo FJ, Anton PA, Rome LH, Maynard HD, Deming T, Yang OO. Human Vault Nanoparticle Targeted Delivery of Antiretroviral Drugs to Inhibit Human Immunodeficiency Virus Type 1 Infection. Bioconjug Chem 2019; 30:2216-2227. [PMID: 31265254 DOI: 10.1021/acs.bioconjchem.9b00451] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
"Vaults" are ubiquitously expressed endogenous ribonucleoprotein nanoparticles with potential utility for targeted drug delivery. Here, we show that recombinant human vault nanoparticles are readily engulfed by certain key human peripheral blood mononuclear cells (PBMC), predominately dendritic cells, monocytes/macrophages, and activated T cells. As these cell types are the primary targets for human immunodeficiency virus type 1 (HIV-1) infection, we examined the utility of recombinant human vaults for targeted delivery of antiretroviral drugs. We chemically modified three different antiretroviral drugs, zidovudine, tenofovir, and elvitegravir, for direct conjugation to vaults. Tested in infection assays, drug-conjugated vaults inhibited HIV-1 infection of PBMC with equivalent activity to free drugs, indicating vault delivery and drug release in the cytoplasm of HIV-1-susceptible cells. The ability to deliver functional drugs via vault nanoparticle conjugates suggests their potential utility for targeted drug delivery against HIV-1.
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Affiliation(s)
- Jennifer A Fulcher
- Division of Infectious Diseases, Department of Medicine , David Geffen School of Medicine at UCLA , Los Angeles , California , United States
| | - Kyle Tamshen
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California , United States
| | - Alexander L Wollenberg
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California , United States
| | - Valerie A Kickhoefer
- Department of Biological Chemistry , David Geffen School of Medicine at UCLA , Los Angeles , California , United States
| | - Jan Mrazek
- Division of Infectious Diseases, Department of Medicine , David Geffen School of Medicine at UCLA , Los Angeles , California , United States
| | - Julie Elliott
- Vatche and Tamar Manoukian Division of Digestive Diseases , David Geffen School of Medicine at UCLA , Los Angeles , California , United States
| | - F Javier Ibarrondo
- Division of Infectious Diseases, Department of Medicine , David Geffen School of Medicine at UCLA , Los Angeles , California , United States
| | - Peter A Anton
- Vatche and Tamar Manoukian Division of Digestive Diseases , David Geffen School of Medicine at UCLA , Los Angeles , California , United States.,AIDS Healthcare Foundation , Los Angeles , California , United States
| | - Leonard H Rome
- Department of Biological Chemistry , David Geffen School of Medicine at UCLA , Los Angeles , California , United States.,California NanoSystems Institute , University of California , Los Angeles , California , United States
| | - Heather D Maynard
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California , United States.,California NanoSystems Institute , University of California , Los Angeles , California , United States.,Department of Bioengineering , University of California , Los Angeles , California , United States
| | - Timothy Deming
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California , United States.,California NanoSystems Institute , University of California , Los Angeles , California , United States.,Department of Bioengineering , University of California , Los Angeles , California , United States
| | - Otto O Yang
- Division of Infectious Diseases, Department of Medicine , David Geffen School of Medicine at UCLA , Los Angeles , California , United States.,AIDS Healthcare Foundation , Los Angeles , California , United States
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37
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Muñoz-Juan A, Carreño A, Mendoza R, Corchero JL. Latest Advances in the Development of Eukaryotic Vaults as Targeted Drug Delivery Systems. Pharmaceutics 2019; 11:E300. [PMID: 31261673 PMCID: PMC6680493 DOI: 10.3390/pharmaceutics11070300] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/21/2019] [Accepted: 06/26/2019] [Indexed: 12/04/2022] Open
Abstract
The use of smart drug delivery systems (DDSs) is one of the most promising approaches to overcome some of the drawbacks of drug-based therapies, such as improper biodistribution and lack of specific targeting. Some of the most attractive candidates as DDSs are naturally occurring, self-assembling protein nanoparticles, such as viruses, virus-like particles, ferritin cages, bacterial microcompartments, or eukaryotic vaults. Vaults are large ribonucleoprotein nanoparticles present in almost all eukaryotic cells. Expression in different cell factories of recombinant versions of the "major vault protein" (MVP) results in the production of recombinant vaults indistinguishable from native counterparts. Such recombinant vaults can encapsulate virtually any cargo protein, and they can be specifically targeted by engineering the C-terminus of MVP monomer. These properties, together with nanometric size, a lumen large enough to accommodate cargo molecules, biodegradability, biocompatibility and no immunogenicity, has raised the interest in vaults as smart DDSs. In this work we provide an overview of eukaryotic vaults as a new, self-assembling protein-based DDS, focusing in the latest advances in the production and purification of this platform, its application in nanomedicine, and the current preclinical and clinical assays going on based on this nanovehicle.
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Affiliation(s)
- Amanda Muñoz-Juan
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Aida Carreño
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Rosa Mendoza
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain
| | - José L Corchero
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain.
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
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38
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Abstract
ADP-ribosylation (ADPr) is an ancient reversible modification of cellular macromolecules controlling major biological processes as diverse as DNA damage repair, transcriptional regulation, intracellular transport, immune and stress responses, cell survival and proliferation. Furthermore, enzymatic reactions of ADPr are central in the pathogenesis of many human diseases, including infectious conditions. By providing a review of ADPr signalling in bacterial systems, we highlight the relevance of this chemical modification in the pathogenesis of human diseases depending on host-pathogen interactions. The post-antibiotic era has raised the need to find alternative approaches to antibiotic administration, as major pathogens becoming resistant to antibiotics. An in-depth understanding of ADPr reactions provides the rationale for designing novel antimicrobial strategies for treatment of infectious diseases. In addition, the understanding of mechanisms of ADPr by bacterial virulence factors offers important hints to improve our knowledge on cellular processes regulated by eukaryotic homologous enzymes, which are often involved in the pathogenesis of human diseases.
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39
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Cirello V, Colombo C, Pogliaghi G, Proverbio MC, Rossi S, Mussani E, Tosi D, Bulfamante G, Bonoldi E, Gherardi G, Persani L, Fugazzola L. Genetic variants of PARP4 gene and PARP4P2 pseudogene in patients with multiple primary tumors including thyroid cancer. Mutat Res 2019; 816-818:111672. [PMID: 31203137 DOI: 10.1016/j.mrfmmm.2019.111672] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/29/2019] [Indexed: 12/22/2022]
Abstract
Recently, the PARP4 gene has been identified as a possible susceptibility gene of primary thyroid and breast cancers. We analyzed PARP4 in 53 patients with multiple primary cancers including a thyroid cancer (TC), in 74 patients with TC alone, and in 88 healthy donors. Two PARP4 intronic variants within the IVS29 (c.3543 + 44T > C) and the IVS22 (c.2758 + 9G > A) were found only in the two patient groups. Moreover, we found a rare variant (r.522C > A) within a PARP4 pseudogene (PARP4P2) in one patient with four primary tumors, and with a familial cancer history. PARP4 mRNA was absent in all primary tumors and matched normal tissues, whereas the pseudogene variant transcript was always expressed. Consistently, immunostaining for PARP4 protein was negative at nuclear level in all tissues, thus suggesting that PARP4P2 pseudogene variant could alter its regulatory role on PARP4, inducing the down-regulation of PARP4 expression at both tumor and normal tissues level. In conclusion, germline intronic PARP4 variants could be a risk factor for the development of TC, and PARP4P2 pseudogene variations associated with PARP4 down-regulation may confer susceptibility to develop multiple metachronous cancers.
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Affiliation(s)
- Valentina Cirello
- IRCCS Istituto Auxologico Italiano, Department of Endocrine and Metabolic Diseases, Milan, Italy
| | - Carla Colombo
- IRCCS Istituto Auxologico Italiano, Department of Endocrine and Metabolic Diseases, Milan, Italy
| | - Gabriele Pogliaghi
- IRCCS Istituto Auxologico Italiano, Department of Endocrine and Metabolic Diseases, Milan, Italy
| | - Maria Carla Proverbio
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Stefania Rossi
- ASST Fatebenefratelli Sacco, UOC Anatomia Patologica Fatenefratelli, Milan, Italy
| | - Elena Mussani
- ASST Fatebenefratelli Sacco, UOC Anatomia Patologica Fatenefratelli, Milan, Italy
| | - Delfina Tosi
- Unit of Pathology, ASST Santi Paolo e Carlo, Milan, Italy; Department of Health Sciences, Università degli Studi di Milano, Mila, Italy
| | - Gaetano Bulfamante
- Unit of Pathology, ASST Santi Paolo e Carlo, Milan, Italy; Department of Health Sciences, Università degli Studi di Milano, Mila, Italy
| | | | - Giorgio Gherardi
- ASST Fatebenefratelli Sacco, UOC Anatomia Patologica Fatenefratelli, Milan, Italy
| | - Luca Persani
- IRCCS Istituto Auxologico Italiano, Department of Endocrine and Metabolic Diseases, Milan, Italy; Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Laura Fugazzola
- IRCCS Istituto Auxologico Italiano, Department of Endocrine and Metabolic Diseases, Milan, Italy; Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.
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40
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Prawira A, Munusamy P, Yuan J, Chan CHT, Koh GL, Shuen TWH, Hu J, Yap YS, Tan MH, Ang P, Lee ASG. Assessment of PARP4 as a candidate breast cancer susceptibility gene. Breast Cancer Res Treat 2019; 177:145-153. [PMID: 31119570 DOI: 10.1007/s10549-019-05286-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 05/17/2019] [Indexed: 10/26/2022]
Abstract
PURPOSE PARP4 has been proposed as a candidate breast cancer susceptibility gene. However, its function and involvement in breast carcinogenesis is unclear. We sought to determine the variant frequency of PARP4 in BRCA-negative women referred for genetic testing from Singapore and to perform functional analyses of PARP4. METHODS Next-generation sequencing of PARP4 was conducted for 198 BRCA-negative cases from Singapore. Three independent case-control association analyses of PARP4 were performed for (1) our Singaporean cohort, (2) three dbGaP datasets, and (3) cases from TCGA, with controls from the Exome Aggregation Consortium (ExAC). PARP4 knockout cells were generated utilizing the CRISPR-Cas9 approach in MDA-MB-231 (breast cancer) and MCF10A (normal breast) cell lines, and colony formation, cell proliferation, and migration assays carried out. RESULTS Candidate variants in PARP4 were identified in 5.5% (11/198) of our Singapore cohort. Case-control association studies for our cases and the dbGaP datasets showed no significant association. However, a significant association was observed for PARP4 variants when comparing 988 breast cancer cases from the TCGA provisional data and 53,105 controls from ExAC (ALL) (OR 0.249, 95% CI 0.139-0.414, P = 2.86 × 10-11). PARP4 knockout did not affect the clonogenicity, proliferation rate, and migration of normal breast cells, but appeared to decrease the proliferation rate and clonogenicity of breast cancer cells. CONCLUSIONS Taken together, our results do not support that PARP4 functions as a cancer susceptibility gene. This study highlights the importance of performing functional analyses for candidate cancer predisposition genes.
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Affiliation(s)
- Aldo Prawira
- Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre, Singapore, Singapore
| | - Prabhakaran Munusamy
- Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre, Singapore, Singapore
| | - Jimin Yuan
- Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre, Singapore, Singapore
| | - Claire Hian Tzer Chan
- Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre, Singapore, Singapore
| | - Geok Ling Koh
- Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre, Singapore, Singapore
| | | | - Jiancheng Hu
- Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre, Singapore, Singapore.,Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore, Singapore
| | - Yoon Sim Yap
- Department of Medical Oncology, National Cancer Centre, Singapore, Singapore
| | - Min Han Tan
- Department of Medical Oncology, National Cancer Centre, Singapore, Singapore.,Institute of Bioengineering and Nanotechnology, Singapore, Singapore.,Lucence Diagnostics Pte Ltd, Singapore, Singapore
| | - Peter Ang
- Department of Medical Oncology, National Cancer Centre, Singapore, Singapore.,Oncocare Cancer Centre, Gleneagles Medical Centre, Singapore, Singapore
| | - Ann Siew Gek Lee
- Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre, Singapore, Singapore. .,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,Office of Clinical and Academic Faculty Affairs, Duke-NUS Medical School, Singapore, Singapore.
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41
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Grimaldi G, Catara G, Palazzo L, Corteggio A, Valente C, Corda D. PARPs and PAR as novel pharmacological targets for the treatment of stress granule-associated disorders. Biochem Pharmacol 2019; 167:64-75. [PMID: 31102582 DOI: 10.1016/j.bcp.2019.05.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/13/2019] [Indexed: 12/13/2022]
Abstract
Among the post-translational modifications, ADP-ribosylation has been for long time the least integrated in the scheme of the structural protein modifications affecting physiological functions. In spite of the original findings on bacterial-dependent ADP-ribosylation catalysed by toxins such as cholera and pertussis toxin, only with the discovery of the poly-ADP-ribosyl polymerase (PARP) family the field has finally expanded and the role of ADP-ribosylation has been recognised in both physiological and pathological processes, including cancer, infectious and neurodegenerative diseases. This is now a rapidly expanding field of investigation, centred on the role of the different PARPs and their substrates in various diseases, and on the potential of PARP inhibitors as novel pharmacological tools to be employed in relevant pathological context. In this review we analyse the role that members of the PARP family and poly-ADP-ribose (PAR; the product of PARP1 and PARP5a activity) play in the processes following the exposure of cells to different stresses. The cell response that arises following conditions such as heat, osmotic, oxidative stresses or viral infection relies on the formation of stress granules, which are transient cytoplasmic membrane-less structures, that include untranslated mRNA, specific proteins and PAR, this last one serving as the "collector" of all components (that bind to it in a non-covalent manner). The resulting phenotypes are cells in which translation, intracellular transport or pro-apoptotic pathways are reversibly inhibited, for the time the given stress holds. Interestingly, the formation of defective stress granules has been detected in diverse pathological conditions including neurological disorders and cancer. Analysing the molecular details of stress granule formation under these conditions offers a novel view on the pathogenesis of these diseases and, as a consequence, the possibility of identifying novel drug targets for their treatment.
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Affiliation(s)
- Giovanna Grimaldi
- Institute of Protein Biochemistry, National Research Council of Italy, Via Pietro Castellino 111, Naples 80131, Italy.
| | - Giuliana Catara
- Institute of Protein Biochemistry, National Research Council of Italy, Via Pietro Castellino 111, Naples 80131, Italy
| | - Luca Palazzo
- Institute of Protein Biochemistry, National Research Council of Italy, Via Pietro Castellino 111, Naples 80131, Italy
| | - Annunziata Corteggio
- Institute of Protein Biochemistry, National Research Council of Italy, Via Pietro Castellino 111, Naples 80131, Italy
| | - Carmen Valente
- Institute of Protein Biochemistry, National Research Council of Italy, Via Pietro Castellino 111, Naples 80131, Italy
| | - Daniela Corda
- Institute of Protein Biochemistry, National Research Council of Italy, Via Pietro Castellino 111, Naples 80131, Italy.
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42
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Bütepage M, Krieg S, Eckei L, Li J, Rossetti G, Verheugd P, Lüscher B. Assessment of Intracellular Auto-Modification Levels of ARTD10 Using Mono-ADP-Ribose-Specific Macrodomains 2 and 3 of Murine Artd8. Methods Mol Biol 2019; 1813:41-63. [PMID: 30097860 DOI: 10.1007/978-1-4939-8588-3_4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mono-ADP-ribosylation is a posttranslational modification, which is catalyzed in cells by certain members of the ADP-ribosyltransferase diphtheria toxin-like family (ARTD) of ADP-ribosyltransferases (aka PARP enzymes). It involves the transfer of a single residue of ADP-ribose (ADPr) from the cofactor NAD+ onto substrate proteins. Although 12 of the 17 members of the ARTD family have been defined as mono-ARTDs in in vitro assays, relatively little is known about their exact cellular functions. A major challenge is the detection of mono-ADP-ribosylated (MARylated) proteins in cells as no antibodies are available that detect exclusively MARylated proteins. As an alternative to classical antibodies, the MAR-specific binding domains macro2 and macro3 of Artd8 can be utilized alone or in combination, to demonstrate intracellular auto-modification levels of ARTD10 in cells in both co-immunoprecipitation and co-localization experiments. Here we demonstrate that different macrodomain constructs of human ARTD8 and murine Artd8, alone or in combination, exert differences with regard to their interaction with ARTD10 in cells. Precisely, while the macrodomains of murine Artd8 interacted with ARTD10 in cells in a MARylation-dependent manner, the macrodomains of human ARTD8 interacted with ARTD10 independent of its catalytic activity. Moreover, we show that a combination of macro2 and macro3 of murine Artd8 was recruited more efficiently to ARTD10 during co-localization experiments compared to the single domains. Therefore, murine Artd8 macrodomain constructs can serve as a tool to evaluate intracellular ARTD10 auto-modification levels using the described methods, while the human ARTD8 macrodomains are less suited because of ADPr-independent binding to ARTD10. Protocols for co-immunoprecipitation and co-localization experiments are described in detail.
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Affiliation(s)
- Mareike Bütepage
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Aachen, Germany.
| | - Sarah Krieg
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Laura Eckei
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Jinyu Li
- College of Chemistry, Fuzhou University, Fuzhou, China
| | - Giulia Rossetti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Jülich, Germany.,Jülich Supercomputing Centre, Jülich, Germany.,Department of Oncology, Hematology and Stem Cell Transplantation, Medical School, RWTH Aachen University, Aachen, Germany
| | - Patricia Verheugd
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Aachen, Germany.
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43
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Palazzo L, Ahel I. PARPs in genome stability and signal transduction: implications for cancer therapy. Biochem Soc Trans 2018; 46:1681-1695. [PMID: 30420415 PMCID: PMC6299239 DOI: 10.1042/bst20180418] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 09/15/2018] [Accepted: 09/21/2018] [Indexed: 01/03/2023]
Abstract
The poly(ADP-ribose) polymerase (PARP) superfamily of enzymes catalyses the ADP-ribosylation (ADPr) of target proteins by using nicotinamide adenine dinucleotide (NAD+) as a donor. ADPr reactions occur either in the form of attachment of a single ADP-ribose nucleotide unit on target proteins or in the form of ADP-ribose chains, with the latter called poly(ADP-ribosyl)ation. PARPs regulate many cellular processes, including the maintenance of genome stability and signal transduction. In this review, we focus on the PARP family members that possess the ability to modify proteins by poly(ADP-ribosyl)ation, namely PARP1, PARP2, Tankyrase-1, and Tankyrase-2. Here, we detail the cellular functions of PARP1 and PARP2 in the regulation of DNA damage response and describe the function of Tankyrases in Wnt-mediated signal transduction. Furthermore, we discuss how the understanding of these pathways has provided some major breakthroughs in the treatment of human cancer.
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Affiliation(s)
- Luca Palazzo
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, U.K.
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44
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Synthesis and assembly of human vault particles in yeast. Biotechnol Bioeng 2018; 115:2941-2950. [DOI: 10.1002/bit.26825] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/04/2018] [Accepted: 08/30/2018] [Indexed: 01/04/2023]
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45
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Galbiati E, Avvakumova S, La Rocca A, Pozzi M, Messali S, Magnaghi P, Colombo M, Prosperi D, Tortora P. A fast and straightforward procedure for vault nanoparticle purification and the characterization of its endocytic uptake. Biochim Biophys Acta Gen Subj 2018; 1862:2254-2260. [PMID: 30036602 DOI: 10.1016/j.bbagen.2018.07.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/12/2018] [Accepted: 07/17/2018] [Indexed: 02/03/2023]
Abstract
BACKGROUND Vaults are eukaryotic ribonucleoprotein particles composed of up 78 copies of the 97 kDa major vault protein that assembles into a barrel-like, "nanocapsule" enclosing poly(ADP-ribose) polymerase, telomerase-associated protein-1 and small untranslated RNAs. Overall, the molecular mass of vault particles amounts to about 13 MDa. Although it has been implicated in several cellular functions, its physiological roles remain poorly understood. Also, the possibility to exploit it as a nanovector for drug delivery is currently being explored in several laboratories. METHODS Using the baculovirus expression system, vaults were expressed and purified by a dialysis step using a 1 MDa molecular weight cutoff membrane and a subsequent size exclusion chromatography. Purity was assessed by SDS-PAGE, transmission electron microscopy and dynamic light scattering. Particle's endocytic uptake was monitored by flow cytometry and confocal microscopy. RESULTS The purification protocol here reported is far simpler and faster than those currently available and lead to the production of authentic vault. We then demonstrated its clathrin-mediated endocytic uptake by normal fibroblast and glioblastoma, but not carcinoma cell lines. In contrast, no significant caveolin-mediated endocytosis was detected. CONCLUSIONS These results provide the first evidence for an intrinsic propensity of the vault complex to undergo endocytic uptake cultured eukaryotic cells. GENERAL SIGNIFICANCE The newly developed purification procedure will greatly facilitate any investigation based on the use of the vault particle as a natural nanocarrier. Its clathrin-mediated endocytic uptake observed in normal and in some tumor cell lines sheds light on its physiological role.
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Affiliation(s)
- Elisabetta Galbiati
- Department of Biotechnologies and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, I-20126 Milano, Italy
| | - Svetlana Avvakumova
- Department of Biotechnologies and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, I-20126 Milano, Italy
| | - Alessandra La Rocca
- Department of Biotechnologies and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, I-20126 Milano, Italy
| | - Maria Pozzi
- Department of Biotechnologies and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, I-20126 Milano, Italy
| | - Silvia Messali
- Oncology, Nerviano Medical Sciences, Viale Pasteur 10, Milano, 20014, Nerviano, Italy
| | - Paola Magnaghi
- Oncology, Nerviano Medical Sciences, Viale Pasteur 10, Milano, 20014, Nerviano, Italy
| | - Miriam Colombo
- Department of Biotechnologies and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, I-20126 Milano, Italy
| | - Davide Prosperi
- Department of Biotechnologies and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, I-20126 Milano, Italy
| | - Paolo Tortora
- Department of Biotechnologies and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, I-20126 Milano, Italy.
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46
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Yu R, Zhang Y, Lu Q, Cui L, Wang Y, Wang X, Cheng G, Liu Z, Dai M, Yuan Z. Differentially expressed genes in response to cyadox in swine liver analyzed by DDRT-PCR. Res Vet Sci 2018; 118:72-78. [DOI: 10.1016/j.rvsc.2018.01.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 01/18/2018] [Accepted: 01/18/2018] [Indexed: 11/24/2022]
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47
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Abstract
Nicotinamide adenine dinucleotide (NAD), the cell's hydrogen carrier for redox enzymes, is well known for its role in redox reactions. More recently, it has emerged as a signaling molecule. By modulating NAD+-sensing enzymes, NAD+ controls hundreds of key processes from energy metabolism to cell survival, rising and falling depending on food intake, exercise, and the time of day. NAD+ levels steadily decline with age, resulting in altered metabolism and increased disease susceptibility. Restoration of NAD+ levels in old or diseased animals can promote health and extend lifespan, prompting a search for safe and efficacious NAD-boosting molecules that hold the promise of increasing the body's resilience, not just to one disease, but to many, thereby extending healthy human lifespan.
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Affiliation(s)
- Luis Rajman
- Paul F. Glenn Center for the Biological Mechanisms of Aging, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Karolina Chwalek
- Paul F. Glenn Center for the Biological Mechanisms of Aging, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - David A Sinclair
- Paul F. Glenn Center for the Biological Mechanisms of Aging, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Laboratory for Ageing Research, Department of Pharmacology, School of Medical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia.
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48
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Crawford K, Bonfiglio JJ, Mikoč A, Matic I, Ahel I. Specificity of reversible ADP-ribosylation and regulation of cellular processes. Crit Rev Biochem Mol Biol 2018; 53:64-82. [PMID: 29098880 DOI: 10.1080/10409238.2017.1394265] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 10/12/2017] [Accepted: 10/16/2017] [Indexed: 02/08/2023]
Abstract
Proper and timely regulation of cellular processes is fundamental to the overall health and viability of organisms across all kingdoms of life. Thus, organisms have evolved multiple highly dynamic and complex biochemical signaling cascades in order to adapt and survive diverse challenges. One such method of conferring rapid adaptation is the addition or removal of reversible modifications of different chemical groups onto macromolecules which in turn induce the appropriate downstream outcome. ADP-ribosylation, the addition of ADP-ribose (ADPr) groups, represents one of these highly conserved signaling chemicals. Herein we outline the writers, erasers and readers of ADP-ribosylation and dip into the multitude of cellular processes they have been implicated in. We also review what we currently know on how specificity of activity is ensured for this important modification.
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Affiliation(s)
- Kerryanne Crawford
- a Sir William Dunn School of Pathology , University of Oxford , Oxford , UK
| | | | - Andreja Mikoč
- c Division of Molecular Biology , Ruđer Bošković Institute , Zagreb , Croatia
| | - Ivan Matic
- b Max Planck Institute for Biology of Ageing , Cologne , Germany
| | - Ivan Ahel
- a Sir William Dunn School of Pathology , University of Oxford , Oxford , UK
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49
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Zhen Y, Yu Y. Proteomic Analysis of the Downstream Signaling Network of PARP1. Biochemistry 2018; 57:429-440. [PMID: 29327913 DOI: 10.1021/acs.biochem.7b01022] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Poly-ADP-ribosylation (PARylation) is a protein posttranslational modification (PTM) that is critically involved in many biological processes that are linked to cell stress responses. It is catalyzed by a class of enzymes known as poly-ADP-ribose polymerases (PARPs). In particular, PARP1 is a nuclear protein that is activated upon sensing nicked DNA. Once activated, PARP1 is responsible for the synthesis of a large number of PARylated proteins and initiation of the DNA damage response mechanisms. This observation provided the rationale for developing PARP1 inhibitors for the treatment of human malignancies. Indeed, three PARP1 inhibitors (Olaparib, Rucaparib, and Niraparib) have recently been approved by the Food and Drug Administration for the treatment of ovarian cancer. Moreover, in 2017, both Olaparib and Niraparib have also been approved for the treatment of fallopian tube cancer and primary peritoneal cancer. Despite this very exciting progress in the clinic, the basic signaling mechanism that connects PARP1 to a diverse array of biological processes is still poorly understood. This is, in large part, due to the inherent technical difficulty associated with the analysis of protein PARylation, which is a low-abundance, labile, and heterogeneous PTM. The study of PARylation has been greatly facilitated by the recent advances in mass spectrometry-based proteomic technologies tailored to the analysis of this modification. In this Perspective, we discuss these breakthroughs, including their technical development, and applications that provide a global view of the many biological processes regulated by this important protein modification.
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Affiliation(s)
- Yuanli Zhen
- Department of Biochemistry, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States
| | - Yonghao Yu
- Department of Biochemistry, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States
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50
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Wang M, Abad D, Kickhoefer VA, Rome LH, Mahendra S. Encapsulation of Exogenous Proteins in Vault Nanoparticles. Methods Mol Biol 2018; 1798:25-37. [PMID: 29868949 DOI: 10.1007/978-1-4939-7893-9_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Natural vault nanoparticles are ribonucleoprotein particles with a mass of 13 MDa that have been found in a wide variety of eukaryotes. Empty recombinant vaults are assembled from heterologously expressed Major Vault Protein (MVP), forming the barrel-shaped vault shell. These structures are morphologically indistinguishable from natural vault particles. Here, we describe the packaging and purification of exogenous proteins into these recombinant vault particles by mixing with proteins attached to the INT domain that binds to MVP.
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Affiliation(s)
- Meng Wang
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA, USA
| | - Danny Abad
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA
| | - Valerie A Kickhoefer
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA
| | - Leonard H Rome
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA
| | - Shaily Mahendra
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA, USA.
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