1
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Neeb A, Figueiredo I, Bogdan D, Cato L, Stober J, Jiménez-Vacas JM, Gourain V, Lee II, Seeger R, Muhle-Goll C, Gurel B, Welti J, Nava Rodrigues D, Rekowski J, Qiu X, Jiang Y, Di Micco P, Mateos B, Bielskutė S, Riisnaes R, Ferreira A, Miranda S, Crespo M, Buroni L, Ning J, Carreira S, Bräse S, Jung N, Gräßle S, Swain A, Salvatella X, Plymate SR, Al-Lazikani B, Long HW, Yuan W, Brown M, Cato ACB, de Bono JS, Sharp A. Thio-2 inhibits key signaling pathways required for the development and progression of castration resistant prostate cancer. Mol Cancer Ther 2024:734951. [PMID: 38412481 DOI: 10.1158/1535-7163.mct-23-0354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/26/2023] [Accepted: 02/22/2024] [Indexed: 02/29/2024]
Abstract
Therapies that abrogate persistent androgen receptor (AR) signaling in castration resistant prostate cancer (CRPC) remain an unmet clinical need. The N-terminal domain (NTD) of the AR that drives transcriptional activity in CRPC remains a challenging therapeutic target. Herein we demonstrate that BAG-1 mRNA is highly expressed and associates with signaling pathways, including AR signaling, that are implicated in the development and progression of CRPC. In addition, interrogation of geometric and physiochemical properties of the BAG domain of BAG-1 isoforms identifies it to be a tractable but challenging drug target. Furthermore, through BAG-1 isoform mouse knockout studies we confirm that BAG-1 isoforms regulate hormone physiology and that therapies targeting the BAG domain will be associated with limited 'on-target' toxicity. Importantly, the postulated inhibitor of BAG-1 isoforms, Thio-2, suppressed AR signaling and other important pathways implicated in the development and progression of CRPC to reduce the growth of treatment resistant prostate cancer cell lines and patient derived models. However, the mechanism by which Thio-2 elicits the observed phenotype needs further elucidation since the genomic abrogation of BAG-1 isoforms was unable to recapitulate the Thio-2 mediated phenotype. Overall, these data support the interrogation of related compounds with improved drug-like properties as a novel therapeutic approach in CRPC, and further highlight the clinical potential of treatments that block persistent AR signaling which are currently undergoing clinical evaluation in CRPC.
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Affiliation(s)
- Antje Neeb
- Institute of Cancer Research, Surrey, United Kingdom
| | - Ines Figueiredo
- Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Denisa Bogdan
- Institute of Cancer Research, London, United Kingdom
| | - Laura Cato
- Dana-Farber Cancer Institute, Boston, MA, United States
| | | | | | | | - Irene I Lee
- AbbVie (United States), North Chicago, IL, United States
| | | | | | - Bora Gurel
- Institute of Cancer Research, London, United Kingdom
| | | | | | - Jan Rekowski
- Institute of Cancer Research, London, United Kingdom
| | - Xintao Qiu
- Dana-Farber Cancer Institute, Boston, MA, United States
| | - Yija Jiang
- Dana-Farber Cancer Institute, United States
| | | | - Borja Mateos
- Institute of Biomedical Research of Barcelona, Spain
| | | | - Ruth Riisnaes
- Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Ana Ferreira
- Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Susana Miranda
- Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Mateus Crespo
- Institute of Cancer Research, Sutton, United Kingdom
| | | | - Jian Ning
- Institute of Cancer Research, London, United Kingdom
| | | | - Stefan Bräse
- KIT Campus South, Institute of Organic Chemistry, Karlsruhe, Germany
| | - Nicole Jung
- Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Simone Gräßle
- Karlsruhe Institute of Technology (KIT), Karlsruhe, Eggenstein-Leopoldshafen, Germany
| | - Amanda Swain
- Institute of Cancer Research, London, United Kingdom
| | | | | | | | - Henry W Long
- Dana-Farber Cancer Institute, Boston, MA, United States
| | - Wei Yuan
- Institute of Cancer Research, Sutton, United Kingdom
| | - Myles Brown
- Dana-Farber Cancer Institute, Boston, MA, United States
| | - Andrew C B Cato
- Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | | | - Adam Sharp
- Institute of Cancer Research, Sutton, Surrey, United Kingdom
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2
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Bruscalupi G, Di Micco P, Failla CM, Pascarella G, Morea V, Saliola M, De Paolis A, Venditti S, Mauro ML. Arabidopsis thaliana sirtuins control proliferation and glutamate dehydrogenase activity. Plant Physiol Biochem 2023; 194:236-245. [PMID: 36436414 DOI: 10.1016/j.plaphy.2022.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 11/04/2022] [Accepted: 11/06/2022] [Indexed: 06/16/2023]
Abstract
Sirtuins are part of a gene family of NAD-dependent deacylases that act on histone and non-histone proteins and control a variety of activities in all living organisms. Their roles are mainly related to energy metabolism and include lifetime regulation, DNA repair, stress resistance, and proliferation. A large amount of knowledge concerning animal sirtuins is available, but data about their plant counterparts are scarce. Plants possess few sirtuins that have, like in animals, a recognized role in stress defense and metabolism regulation. However, engagement in proliferation control, which has been demonstrated for mammalian sirtuins, has not been reported for plant sirtuins so far. In this work, srt1 and srt2 Arabidopsis mutant seedlings have been used to evaluate in vivo the role of sirtuins in cell proliferation and regulation of glutamate dehydrogenase, an enzyme demonstrated to be involved in the control of cell cycle in SIRT4-defective human cells. Moreover, bioinformatic analyses have been performed to elucidate sequence, structure, and function relationships between Arabidopsis sirtuins and between each of them and the closest mammalian homolog. We found that cell proliferation and GDH activity are higher in mutant seedlings, suggesting that both sirtuins exert a physiological inhibitory role in these processes. In addition, mutant seedlings show plant growth and root system improvement, in line with metabolic data. Our data also indicate that utilization of an easy to manipulate organism, such as Arabidopsis plant, can help to shed light on the molecular mechanisms underlying the function of genes present in interkingdom species.
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Affiliation(s)
- Giovannella Bruscalupi
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Piazzale A. Moro 5, 00185, Rome, Italy.
| | - Patrizio Di Micco
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Piazzale A. Moro 5, 00185, Rome, Italy.
| | - Cristina Maria Failla
- IDI-IRCCS, Laboratory of Experimental Immunology, Via dei Monti di Creta 104, 00167, Rome, Italy.
| | - Gianmarco Pascarella
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Piazzale A. Moro 5, 00185, Rome, Italy; National Research Council of Italy, Institute of Molecular Biology and Pathology, Sapienza University of Rome, Piazzale A. Moro 5, 00185, Rome, Italy.
| | - Veronica Morea
- National Research Council of Italy, Institute of Molecular Biology and Pathology, Sapienza University of Rome, Piazzale A. Moro 5, 00185, Rome, Italy.
| | - Michele Saliola
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Piazzale A. Moro 5, 00185, Rome, Italy.
| | - Angelo De Paolis
- Institute of Sciences of Food Production (ISPA-CNR), Via Monteroni, Lecce, 73100, Italy.
| | - Sabrina Venditti
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Piazzale A. Moro 5, 00185, Rome, Italy.
| | - Maria Luisa Mauro
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Piazzale A. Moro 5, 00185, Rome, Italy.
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3
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Colotti G, Failla CM, Lacal PM, Ungarelli M, Ruffini F, Di Micco P, Orecchia A, Morea V. Neuropilin-1 is required for endothelial cell adhesion to soluble vascular endothelial growth factor receptor 1. FEBS J 2021; 289:183-198. [PMID: 34252269 PMCID: PMC9290910 DOI: 10.1111/febs.16119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 05/27/2021] [Accepted: 07/12/2021] [Indexed: 12/22/2022]
Abstract
Neuropilin‐1 (NRP‐1) is a semaphorin receptor involved in neuron guidance, and a co‐receptor for selected isoforms of the vascular endothelial growth factor (VEGF) family. NRP‐1 binding to several VEGF‐A isoforms promotes growth factor interaction with VEGF receptor (VEGFR)‐2, increasing receptor phosphorylation. Additionally, NRP‐1 directly interacts with VEGFR‐1, but this interaction competes with NRP‐1 binding to VEGF‐A165 and does not enhance VEGFR‐1 activation. In this work, we investigated in detail the role of NRP‐1 interaction with the soluble isoform of VEGFR‐1 (sVEGFR‐1) in angiogenesis. sVEGFR‐1 acts both as a decoy receptor for VEGFs and as an extracellular matrix protein directly binding to α5β1 integrin on endothelial cells. By combining cell adhesion assays and surface plasmon resonance experiments on purified proteins, we found that sVEGFR‐1/NRP‐1 interaction is required both for α5β1 integrin binding to sVEGFR‐1 and for endothelial cell adhesion to a sVEGFR‐1‐containing matrix. We also found that a previously reported anti‐angiogenic peptide (Flt2‐11), which maps in the second VEGFR‐1 Ig‐like domain, specifically binds NRP‐1 and inhibits NRP‐1/sVEGFR‐1 interaction, a process that likely contributes to its anti‐angiogenic activity. In view of potential translational applications, we developed a five‐residue‐long peptide, derived from Flt2‐11, which has the same ability as the parent Flt2‐11 peptide to inhibit cell adhesion to, and migration towards, sVEGFR‐1. Therefore, the Flt2‐5 peptide represents a potential anti‐angiogenic compound per se, as well as an attractive lead for the development of novel angiogenesis inhibitors acting with a different mechanism with respect to currently used therapeutics, which interfere with VEGF‐A165 binding.
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Affiliation(s)
- Gianni Colotti
- Institute of Molecular Biology and Pathology (IBPM) of the National Research Council (CNR), Rome, Italy
| | | | | | | | | | - Patrizio Di Micco
- Department of Biochemical Sciences 'A. Rossi Fanelli', Sapienza' University of Rome, Italy
| | - Angela Orecchia
- Laboratory of Molecular and Cell Biology, IDI-IRCCS, Rome, Italy
| | - Veronica Morea
- Institute of Molecular Biology and Pathology (IBPM) of the National Research Council (CNR), Rome, Italy
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4
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Paschalis A, Welti J, Neeb AJ, Yuan W, Figueiredo I, Pereira R, Ferreira A, Riisnaes R, Rodrigues DN, Jiménez-Vacas JM, Kim S, Uo T, Micco PD, Tumber A, Islam MS, Moesser MA, Abboud M, Kawamura A, Gurel B, Christova R, Gil VS, Buroni L, Crespo M, Miranda S, Lambros MB, Carreira S, Tunariu N, Alimonti A, Al-Lazikani B, Schofield CJ, Plymate SR, Sharp A, de Bono JS. JMJD6 Is a Druggable Oxygenase That Regulates AR-V7 Expression in Prostate Cancer. Cancer Res 2021; 81:1087-1100. [PMID: 33822745 PMCID: PMC8025710 DOI: 10.1158/0008-5472.can-20-1807] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/07/2020] [Accepted: 12/02/2020] [Indexed: 11/16/2022]
Abstract
Endocrine resistance (EnR) in advanced prostate cancer is fatal. EnR can be mediated by androgen receptor (AR) splice variants, with AR splice variant 7 (AR-V7) arguably the most clinically important variant. In this study, we determined proteins key to generating AR-V7, validated our findings using clinical samples, and studied splicing regulatory mechanisms in prostate cancer models. Triangulation studies identified JMJD6 as a key regulator of AR-V7, as evidenced by its upregulation with in vitro EnR, its downregulation alongside AR-V7 by bromodomain inhibition, and its identification as a top hit of a targeted siRNA screen of spliceosome-related genes. JMJD6 protein levels increased (P < 0.001) with castration resistance and were associated with higher AR-V7 levels and shorter survival (P = 0.048). JMJD6 knockdown reduced prostate cancer cell growth, AR-V7 levels, and recruitment of U2AF65 to AR pre-mRNA. Mutagenesis studies suggested that JMJD6 activity is key to the generation of AR-V7, with the catalytic machinery residing within a druggable pocket. Taken together, these data highlight the relationship between JMJD6 and AR-V7 in advanced prostate cancer and support further evaluation of JMJD6 as a therapeutic target in this disease. SIGNIFICANCE: This study identifies JMJD6 as being critical for the generation of AR-V7 in prostate cancer, where it may serve as a tractable target for therapeutic intervention.
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Affiliation(s)
- Alec Paschalis
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Jonathan Welti
- The Institute of Cancer Research, London, United Kingdom
| | - Antje J Neeb
- The Institute of Cancer Research, London, United Kingdom
| | - Wei Yuan
- The Institute of Cancer Research, London, United Kingdom
| | | | - Rita Pereira
- The Institute of Cancer Research, London, United Kingdom
| | - Ana Ferreira
- The Institute of Cancer Research, London, United Kingdom
| | - Ruth Riisnaes
- The Institute of Cancer Research, London, United Kingdom
| | | | - Juan M Jiménez-Vacas
- Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), Cordoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Cordoba, Cordoba, Spain
- Hospital Universitario Reina Sofía (HURS), Cordoba, Spain
| | - Soojin Kim
- Department of Medicine, University of Washington School of Medicine and VAPSHCS-GRECC, Seattle, Washington
| | - Takuma Uo
- Department of Medicine, University of Washington School of Medicine and VAPSHCS-GRECC, Seattle, Washington
| | | | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Md Saiful Islam
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Marc A Moesser
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Martine Abboud
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Bora Gurel
- The Institute of Cancer Research, London, United Kingdom
| | | | - Veronica S Gil
- The Institute of Cancer Research, London, United Kingdom
| | - Lorenzo Buroni
- The Institute of Cancer Research, London, United Kingdom
| | - Mateus Crespo
- The Institute of Cancer Research, London, United Kingdom
| | - Susana Miranda
- The Institute of Cancer Research, London, United Kingdom
| | | | | | - Nina Tunariu
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | | | | | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Stephen R Plymate
- Department of Medicine, University of Washington School of Medicine and VAPSHCS-GRECC, Seattle, Washington
| | - Adam Sharp
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Johann S de Bono
- The Institute of Cancer Research, London, United Kingdom.
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
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5
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Spitaleri A, Zia SR, Di Micco P, Al-Lazikani B, Soler MA, Rocchia W. Tuning Local Hydration Enables a Deeper Understanding of Protein-Ligand Binding: The PP1-Src Kinase Case. J Phys Chem Lett 2021; 12:49-58. [PMID: 33300337 PMCID: PMC7812613 DOI: 10.1021/acs.jpclett.0c03075] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/03/2020] [Indexed: 05/13/2023]
Abstract
Water plays a key role in biomolecular recognition and binding. Despite the development of several computational and experimental approaches, it is still challenging to comprehensively characterize water-mediated effects on the binding process. Here, we investigate how water affects the binding of Src kinase to one of its inhibitors, PP1. Src kinase is a target for treating several diseases, including cancer. We use biased molecular dynamics simulations, where the hydration of predetermined regions is tuned at will. This computational technique efficiently accelerates the SRC-PP1 binding simulation and allows us to identify several key and yet unexplored aspects of the solvent's role. This study provides a further perspective on the binding phenomenon, which may advance the current drug design approaches for the development of new kinase inhibitors.
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Affiliation(s)
- Andrea Spitaleri
- CONCEPT
Lab, Istituto Italiano di Tecnologia, via Morego 30, Genoa I-16163, Italy
- Center
for Omics Sciences, Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Syeda R. Zia
- CONCEPT
Lab, Istituto Italiano di Tecnologia, via Morego 30, Genoa I-16163, Italy
- Dr.
Panjwani Center for Molecular Medicine and Drug Research, International
Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Patrizio Di Micco
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Bissan Al-Lazikani
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Miguel A. Soler
- CONCEPT
Lab, Istituto Italiano di Tecnologia, via Morego 30, Genoa I-16163, Italy
| | - Walter Rocchia
- CONCEPT
Lab, Istituto Italiano di Tecnologia, via Morego 30, Genoa I-16163, Italy
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6
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Varadi M, Berrisford J, Deshpande M, Nair SS, Gutmanas A, Armstrong D, Pravda L, Al-Lazikani B, Anyango S, Barton GJ, Berka K, Blundell T, Borkakoti N, Dana J, Das S, Dey S, Micco PD, Fraternali F, Gibson T, Helmer-Citterich M, Hoksza D, Huang LC, Jain R, Jubb H, Kannas C, Kannan N, Koca J, Krivak R, Kumar M, Levy ED, Madeira F, Madhusudhan MS, Martell HJ, MacGowan S, McGreig JE, Mir S, Mukhopadhyay A, Parca L, Paysan-Lafosse T, Radusky L, Ribeiro A, Serrano L, Sillitoe I, Singh G, Skoda P, Svobodova R, Tyzack J, Valencia A, Fernandez EV, Vranken W, Wass M, Thornton J, Sternberg M, Orengo C, Velankar S. PDBe-KB: a community-driven resource for structural and functional annotations. Nucleic Acids Res 2020; 48:D344-D353. [PMID: 31584092 PMCID: PMC6943075 DOI: 10.1093/nar/gkz853] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/11/2019] [Accepted: 10/01/2019] [Indexed: 11/23/2022] Open
Abstract
The Protein Data Bank in Europe-Knowledge Base (PDBe-KB, https://pdbe-kb.org) is a community-driven, collaborative resource for literature-derived, manually curated and computationally predicted structural and functional annotations of macromolecular structure data, contained in the Protein Data Bank (PDB). The goal of PDBe-KB is two-fold: (i) to increase the visibility and reduce the fragmentation of annotations contributed by specialist data resources, and to make these data more findable, accessible, interoperable and reusable (FAIR) and (ii) to place macromolecular structure data in their biological context, thus facilitating their use by the broader scientific community in fundamental and applied research. Here, we describe the guidelines of this collaborative effort, the current status of contributed data, and the PDBe-KB infrastructure, which includes the data exchange format, the deposition system for added value annotations, the distributable database containing the assembled data, and programmatic access endpoints. We also describe a series of novel web-pages-the PDBe-KB aggregated views of structure data-which combine information on macromolecular structures from many PDB entries. We have recently released the first set of pages in this series, which provide an overview of available structural and functional information for a protein of interest, referenced by a UniProtKB accession.
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Affiliation(s)
| | - Mihaly Varadi
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - John Berrisford
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Mandar Deshpande
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Sreenath S Nair
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Aleksandras Gutmanas
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - David Armstrong
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Lukas Pravda
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Bissan Al-Lazikani
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Stephen Anyango
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | | | - Karel Berka
- Department of Physical Chemistry, Palacky University, Olomouc
| | | | - Neera Borkakoti
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Jose Dana
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Sayoni Das
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | | | - Patrizio Di Micco
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Franca Fraternali
- Randall Centre for Cell & Molecular Biophysics, King's College London, London, UK
| | - Toby Gibson
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Manuela Helmer-Citterich
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica snc, 00133 Rome, Italy
| | - David Hoksza
- Charles University, Prague, Czech Republic
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Liang-Chin Huang
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Rishabh Jain
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Christos Kannas
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Jaroslav Koca
- CEITEC, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Brno, Czech Republic
| | | | - Manjeet Kumar
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - F Madeira
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - M S Madhusudhan
- Indian Institute of Science Education and Research, Pune 411008, India
| | | | | | | | - Saqib Mir
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Abhik Mukhopadhyay
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Luca Parca
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica snc, 00133 Rome, Italy
| | - Typhaine Paysan-Lafosse
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | | | - Antonio Ribeiro
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Ian Sillitoe
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Gulzar Singh
- Indian Institute of Science Education and Research, Pune 411008, India
| | - Petr Skoda
- Charles University, Prague, Czech Republic
| | - Radka Svobodova
- CEITEC, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Brno, Czech Republic
| | - Jonathan Tyzack
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | | | - Eloy Villasclaras Fernandez
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Wim Vranken
- Vrije Universiteit Brussel, Brussels, Belgium
| | - Mark Wass
- University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Janet Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | | | - Christine Orengo
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Sameer Velankar
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
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7
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Kinnersley B, Sud A, Coker EA, Tym JE, Di Micco P, Al-Lazikani B, Houlston RS. Leveraging Human Genetics to Guide Cancer Drug Development. JCO Clin Cancer Inform 2018; 2:1-11. [PMID: 30652614 PMCID: PMC6874034 DOI: 10.1200/cci.18.00077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
PURPOSE The high attrition rate of cancer drug development programs is a barrier to realizing the promise of precision oncology. We have examined whether the genetic insights from genome-wide association studies of cancer can guide drug development and repurposing in oncology. MATERIALS AND METHODS Across 37 cancers, we identified 955 genetic risk variants from the National Human Genome Research Institute-European Bioinformatics Institute genome-wide association study catalog. We linked these variants to target genes using strategies that were based on linkage disequilibrium, DNA three-dimensional structure, and integration of predicted gene function and expression. With the use of the Informa Pharmaprojects database, we identified genes that are targets of unique drugs and assessed the level of enrichment that would be afforded by incorporation of genetic information in preclinical and phase II studies. For targets not under development, we implemented machine learning approaches to assess druggability. RESULTS For all preclinical targets incorporating genetic information, a 2.00-fold enrichment of a drug being successfully approved could be achieved (95% CI, 1.14- to 3.48-fold; P = .02). For phase II targets, a 2.75-fold enrichment could be achieved (95% CI, 1.42- to 5.35-fold; P < .001). Application of genetic information suggests potential repurposing of 15 approved nononcology drugs. CONCLUSION The findings illustrate the value of using insights from the genetics of inherited cancer susceptibility discovery projects as part of a data-driven strategy to inform drug discovery. Support for cancer germline genetic information for prospective targets is available online from the Institute of Cancer Research.
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Affiliation(s)
- Ben Kinnersley
- All authors: The Institute of Cancer Research, London, United Kingdom
| | - Amit Sud
- All authors: The Institute of Cancer Research, London, United Kingdom
| | | | - Joseph E. Tym
- All authors: The Institute of Cancer Research, London, United Kingdom
| | - Patrizio Di Micco
- All authors: The Institute of Cancer Research, London, United Kingdom
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Coker EA, Kinnersley B, Sud A, Micco PD, Al-Lazikani B, Houlston R. Abstract 776: Utilising genetic susceptibility and big data to inform novel cancer therapies. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Despite a move towards personalised medicine, attrition rates for new cancer drugs remain unacceptably high. The pharmaceutical industry has also shown a preference for well-studied targets and pathways, as evidenced by ‘me too' drugs. Together with the challenge of inadequate pre-clinical models, this indicates a need for novel, evidence-based therapeutic targets. Genome-wide association studies (GWAS) have identified over 450 robust genetic variants associated with increased cancer risk. Genes implicated through GWAS are often mutated somatically and therefore represent attractive therapeutic targets. Examples include the target of venetoclax in chronic lymphocytic leukaemia, BCL2.
We exploit this principle more generally by integrating genetic associations for common cancers with drug target data and druggability using the canSAR drug discovery knowledgebase (https://cansar.icr.ac.uk). By harnessing the power of Big Data we aim to both identify opportunities for repurposing of existing drugs, and prioritise novel targets for cancer drug discovery.
We mined the NHGRI-EBI Catalog of published GWAS for all cancer risk SNPs. We annotated candidate target genes through overlapping topologically associating domains (TADs), a more sensitive technique than previously published methods using linkage disequilibrium. We used canSAR to identify target genes for which there is no FDA-approved small molecule drug, and the resource Probe Miner to identify targets for which high-quality chemical probes exist. We also utilised canSAR's machine learning algorithms to assess the druggability of target genes by structure-, ligand-, precedence- and network-based approaches.
We additionally analysed results from cancer drug databases to ascertain whether there is an enrichment of ‘drug target-indication pairs' at successive stages of the drug development pathway for which supporting evidence from GWAS exists: this indicates potential ‘stumbling blocks' that may present a risk for future drug development projects.
7 257 protein-coding genes mapped within TADs overlapping cancer risk SNPs. Of these, 98 were pre-existing targets for which there is an FDA-approved small molecule drug. For the remaining 7 159 genes we performed multi-faceted druggability analyses incorporating assessments of the 3D structure of the target and any protein complexes it exists in, chemical properties of known ligands of the target, and the target's position and role within the human interactome. We comprehensively rank our target-indication pairings by criteria including novelty relative to existing targets and predicted attrition risk.
Mapping approved drug targets back to cancer GWAS signals enables identification of both novel drug targets and patient populations. Collectively our findings show the value of investigating germline cancer genetics as part of interdisciplinary, data-driven approaches to inform drug discovery.
Citation Format: Elizabeth A. Coker, Ben Kinnersley, Amit Sud, Patrizio Di Micco, Bissan Al-Lazikani, Richard Houlston. Utilising genetic susceptibility and big data to inform novel cancer therapies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 776.
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Affiliation(s)
| | | | - Amit Sud
- Inst. of Cancer Research, London, United Kingdom
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Falvo E, Malagrinò F, Arcovito A, Fazi F, Colotti G, Tremante E, Di Micco P, Braca A, Opri R, Giuffrè A, Fracasso G, Ceci P. The presence of glutamate residues on the PAS sequence of the stimuli-sensitive nano-ferritin improves in vivo biodistribution and mitoxantrone encapsulation homogeneity. J Control Release 2018; 275:177-185. [PMID: 29474961 DOI: 10.1016/j.jconrel.2018.02.025] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/14/2018] [Accepted: 02/16/2018] [Indexed: 12/18/2022]
Abstract
A genetically engineered human ferritin heavy chain (HFt)-based construct has been recently shown by our group to efficiently entrap and deliver doxorubicin to cancer cells. This construct, named HFt-MP-PAS, contained a tumor-selective sequence (MP) responsive to proteolytic cleavage by tumor proteases (MMPs), located between each HFt subunit and an outer shielding polypeptide sequence rich in proline (P), serine (S) and alanine (A) residues (PAS). HFt-MP-PAS displayed excellent therapeutic efficacy in xenogenic pancreatic and head and neck cancer models in vivo, leading to a significant increase in overall animal survivals. Here we report a new construct obtained by the genetic insertion of two glutamate residues in the PAS sequence of HFt-MP-PAS. Such new construct, named HFt-MP-PASE, is characterized by improved performances as drug biodistribution in a xenogenic pancreatic cancer model in vivo. Moreover, HFt-MP-PASE efficiently encapsulates the anti-cancer drug mitoxantrone (MIT), and the resulting MIT-loaded nanoparticles proved to be more soluble and monodispersed than the HFt-MP-PAS counterparts. Importantly, in vitro MIT-loaded HFt-MP-PASE kills several cancer cell lines of different origin (colon, breast, sarcoma and pancreas) at least as efficiently as the free drug. Finally, our MIT loaded protein nanocages allowed in vivo an impressive incrementing of the drug accumulation in the tumor with respect to the free drug.
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Affiliation(s)
- Elisabetta Falvo
- Institute of Molecular Biology and Pathology, CNR - National Research Council of Italy, 00185 Rome, Italy
| | - Francesca Malagrinò
- Institute of Molecular Biology and Pathology, CNR - National Research Council of Italy, 00185 Rome, Italy; Department of Biochemical Sciences "A. Rossi-Fanelli", "Sapienza" University, 00185 Rome, Italy
| | - Alessandro Arcovito
- Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, 00168 Rome, Italy
| | - Francesco Fazi
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical Embryology, "Sapienza" University, 00161 Rome, Italy
| | - Gianni Colotti
- Institute of Molecular Biology and Pathology, CNR - National Research Council of Italy, 00185 Rome, Italy
| | - Elisa Tremante
- Oncogenomics and Epigenetics, Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Patrizio Di Micco
- Department of Biochemical Sciences "A. Rossi-Fanelli", "Sapienza" University, 00185 Rome, Italy
| | - Aldo Braca
- BSP Pharmaceuticals, 04013 Latina, Italy
| | - Roberta Opri
- Department of Medicine, University of Verona, 37134 Verona, Italy
| | - Alessandro Giuffrè
- Institute of Molecular Biology and Pathology, CNR - National Research Council of Italy, 00185 Rome, Italy
| | - Giulio Fracasso
- Department of Medicine, University of Verona, 37134 Verona, Italy.
| | - Pierpaolo Ceci
- Institute of Molecular Biology and Pathology, CNR - National Research Council of Italy, 00185 Rome, Italy.
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Coker EA, Di Micco P, Tym JE, Mitsopoulos C, Komianou A, Antolin AA, Al-Lazikani B. Abstract B096: canSAR, a cancer research and drug discovery knowledgebase. Mol Cancer Ther 2018. [DOI: 10.1158/1535-7163.targ-17-b096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
canSAR (http://cansar.icr.ac.uk) is a freely available, multidisciplinary, cancer-focused knowledgebase developed to bring together information from genomic, transcriptomic, protein, pathway, chemical, pharmacologic, and 3D structural data. canSAR provides a powerful, uniqu,e and user-friendly portal to enable translational research and to help generate and test hypotheses and support scientific decision-making in drug discovery both before and after target selection. With its three alternative approaches to examine druggability, canSAR represents the most comprehensive public druggability assessment resource. canSAR provides 3D-structure-based druggability assessment for more than 3,100,000 cavities on more than 391,000 protein chains; ligand-based druggability assessment for 8,197 human proteins; and, more recently, protein network-based druggability results for 13,345 human proteins. Together these provide a powerful enabler for target selection and validation for drug discovery. Druggability assessments are presented alongside data from resources including 224,000 clinical trials from ClinicalTrials.gov, drug indications from Cancer.gov, target gene expression from TCGA for cell lines, and patient samples to provide a detailed picture of the target’s biologic context. Recent updates to canSAR include integration of ChEMBL 23 and additional curation of a protein-protein interaction network of 13,500 nodes. canSAR is currently used by more than 65,000 users annually from both academia and industry, and we will illustrate how canSAR can empower decision making in translational drug discovery.
Citation Format: Elizabeth A. Coker, Patrizio Di Micco, Joesph E. Tym, Costas Mitsopoulos, Angeliki Komianou, Albert A. Antolin, Bissan Al-Lazikani. canSAR, a cancer research and drug discovery knowledgebase [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr B096.
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Perli E, Fiorillo A, Giordano C, Pisano A, Montanari A, Grazioli P, Campese AF, Di Micco P, Tuppen HA, Genovese I, Poser E, Preziuso C, Taylor RW, Morea V, Colotti G, d'Amati G. Short peptides from leucyl-tRNA synthetase rescue disease-causing mitochondrial tRNA point mutations. Hum Mol Genet 2015; 25:903-15. [PMID: 26721932 PMCID: PMC4754043 DOI: 10.1093/hmg/ddv619] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 12/18/2015] [Indexed: 01/11/2023] Open
Abstract
Mutations in mitochondrial (mt) genes coding for mt-tRNAs are responsible for a range of syndromes, for which no effective treatment is available. We recently showed that the carboxy-terminal domain (Cterm) of human mt-leucyl tRNA synthetase rescues the pathologic phenotype associated either with the m.3243A>G mutation in mt-tRNALeu(UUR) or with mutations in the mt-tRNAIle, both of which are aminoacylated by Class I mt-aminoacyl-tRNA synthetases (mt-aaRSs). Here we show, by using the human transmitochondrial cybrid model, that the Cterm is also able to improve the phenotype caused by the m.8344A>G mutation in mt-tRNALys, aminoacylated by a Class II aaRS. Importantly, we demonstrate that the same rescuing ability is retained by two Cterm-derived short peptides, β30_31 and β32_33, which are effective towards both the m.8344A>G and the m.3243A>G mutations. Furthermore, we provide in vitro evidence that these peptides bind with high affinity wild-type and mutant human mt-tRNALeu(UUR) and mt-tRNALys, and stabilize mutant mt-tRNALeu(UUR). In conclusion, we demonstrate that small Cterm-derived peptides can be effective tools to rescue cellular defects caused by mutations in a wide range of mt-tRNAs.
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Affiliation(s)
- Elena Perli
- Department of Radiology, Oncology and Pathology
| | | | | | | | - Arianna Montanari
- Department of Biology and Biotechnologies 'Charles Darwin' and Pasteur Institute-Cenci Bolognetti Foundation, Rome 00161, Italy
| | - Paola Grazioli
- Department of Molecular Medicine, Sapienza University of Rome, Rome 00161, Italy
| | - Antonio F Campese
- Department of Molecular Medicine, Sapienza University of Rome, Rome 00161, Italy
| | | | - Helen A Tuppen
- Wellcome Trust Center for Mitochondrial Research, Institute for Ageing and Health, Newcastle University, Newcastle upon Tyne NE1 7RU, UK and
| | | | - Elena Poser
- Department of Biochemical Sciences "A. Rossi Fanelli"
| | | | - Robert W Taylor
- Wellcome Trust Center for Mitochondrial Research, Institute for Ageing and Health, Newcastle University, Newcastle upon Tyne NE1 7RU, UK and
| | - Veronica Morea
- National Research Council of Italy, Institute of Molecular Biology and Pathology, Rome 00185, Italy
| | - Gianni Colotti
- National Research Council of Italy, Institute of Molecular Biology and Pathology, Rome 00185, Italy
| | - Giulia d'Amati
- Department of Radiology, Oncology and Pathology, Pasteur Institute-Cenci Bolognetti Foundation, Rome 00161, Italy,
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Abstract
We have recently characterized the degradation profiles of 2 human IgG1 monoclonal antibodies, the tumor-targeting mAb H10 and the anti-HIV mAb 2G12. Both mAbs were produced in plants either as stable transgenics or using a transient expression system based on leaf agroinfiltration. The purified antibodies were separated by 1DE and protein bands were characterized by N-terminal sequencing. The proteolytic cleavage sites identified in the heavy chain (HC) of both antibodies were localized in 3 inter-domain regions, suggesting that the number of proteolytic cleavage events taking place in plants is limited. One of the cleavage sites, close to the hinge region, was common to both antibodies.
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Affiliation(s)
- Marcello Donini
- a Laboratory of Biotechnology; ENEA Research Center Casaccia ; Rome , Italy
| | - Raffaele Lombardi
- a Laboratory of Biotechnology; ENEA Research Center Casaccia ; Rome , Italy
| | - Chiara Lonoce
- a Laboratory of Biotechnology; ENEA Research Center Casaccia ; Rome , Italy
| | - Mariasole Di Carli
- a Laboratory of Biotechnology; ENEA Research Center Casaccia ; Rome , Italy
| | - Carla Marusic
- a Laboratory of Biotechnology; ENEA Research Center Casaccia ; Rome , Italy
| | - Veronica Morea
- b National Research Council; Institute of Molecular Biology and Pathology ; Rome , Italy
| | - Patrizio Di Micco
- c Department of Radiology, Oncology and Pathology ; Sapienza University of Rome ; Rome , Italy
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Hehle VK, Lombardi R, van Dolleweerd CJ, Paul MJ, Di Micco P, Morea V, Benvenuto E, Donini M, Ma JKC. Site-specific proteolytic degradation of IgG monoclonal antibodies expressed in tobacco plants. Plant Biotechnol J 2015; 13:235-45. [PMID: 25283551 DOI: 10.1111/pbi.12266] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 08/11/2014] [Accepted: 08/16/2014] [Indexed: 05/25/2023]
Abstract
Plants are promising hosts for the production of monoclonal antibodies (mAbs). However, proteolytic degradation of antibodies produced both in stable transgenic plants and using transient expression systems is still a major issue for efficient high-yield recombinant protein accumulation. In this work, we have performed a detailed study of the degradation profiles of two human IgG1 mAbs produced in plants: an anti-HIV mAb 2G12 and a tumour-targeting mAb H10. Even though they use different light chains (κ and λ, respectively), the fragmentation pattern of both antibodies was similar. The majority of Ig fragments result from proteolytic degradation, but there are only a limited number of plant proteolytic cleavage events in the immunoglobulin light and heavy chains. All of the cleavage sites identified were in the proximity of interdomain regions and occurred at each interdomain site, with the exception of the VL /CL interface in mAb H10 λ light chain. Cleavage site sequences were analysed, and residue patterns characteristic of proteolytic enzymes substrates were identified. The results of this work help to define common degradation events in plant-produced mAbs and raise the possibility of predicting antibody degradation patterns 'a priori' and designing novel stabilization strategies by site-specific mutagenesis.
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Affiliation(s)
- Verena K Hehle
- Molecular Immunology Unit, Division of Clinical Sciences, St. George's University of London, London, UK
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Di Micco P, Fazzi D'Orsi M, Morea V, Frontali L, Francisci S, Montanari A. The yeast model suggests the use of short peptides derived from mt LeuRS for the therapy of diseases due to mutations in several mt tRNAs. Biochim Biophys Acta 2014; 1843:3065-74. [PMID: 25261707 DOI: 10.1016/j.bbamcr.2014.09.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/09/2014] [Accepted: 09/11/2014] [Indexed: 01/23/2023]
Abstract
We have previously established a yeast model of mitochondrial (mt) diseases. We showed that defective respiratory phenotypes due to point-mutations in mt tRNA(Leu(UUR)), tRNA(Ile) and tRNA(Val) could be relieved by overexpression of both cognate and non-cognate nuclearly encoded mt aminoacyl-tRNA synthetases (aaRS) LeuRS, IleRS and ValRS. More recently, we showed that the isolated carboxy-terminal domain (Cterm) of yeast mt LeuRS, and even short peptides derived from the human Cterm, have the same suppressing abilities as the whole enzymes. In this work, we extend these results by investigating the activity of a number of mt aaRS from either class I or II towards a panel of mt tRNAs. The Cterm of both human and yeast mt LeuRS has the same spectrum of activity as mt aaRS belonging to class I and subclass a, which is the most extensive among the whole enzymes. Yeast Cterm is demonstrated to be endowed with mt targeting activity. Importantly, peptide fragments β30_31 and β32_33, derived from the human Cterm, have even higher efficiency as well as wider spectrum of activity, thus opening new avenues for therapeutic intervention. Bind-shifting experiments show that the β30_31 peptide directly interacts with human mt tRNA(Leu(UUR)) and tRNA(Ile), suggesting that the rescuing activity of isolated peptide fragments is mediated by a chaperone-like mechanism. Wide-range suppression appears to be idiosyncratic of LeuRS and its fragments, since it is not shared by Cterminal regions derived from human mt IleRS or ValRS, which are expected to have very different structures and interactions with tRNAs.
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Affiliation(s)
- Patrizio Di Micco
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Mario Fazzi D'Orsi
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Veronica Morea
- National Research Council of Italy (CNR) - Institute of Biology, Molecular Medicine and Nanobiotechnology (IBMN), Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Laura Frontali
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy; Pasteur Institute - Cenci Bolognetti Foundation, Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Silvia Francisci
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy; Pasteur Institute - Cenci Bolognetti Foundation, Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Arianna Montanari
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy.
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Perli E, Giordano C, Pisano A, Montanari A, Campese AF, Reyes A, Ghezzi D, Nasca A, Tuppen HA, Orlandi M, Di Micco P, Poser E, Taylor RW, Colotti G, Francisci S, Morea V, Frontali L, Zeviani M, d'Amati G. The isolated carboxy-terminal domain of human mitochondrial leucyl-tRNA synthetase rescues the pathological phenotype of mitochondrial tRNA mutations in human cells. EMBO Mol Med 2014; 6:169-82. [PMID: 24413190 PMCID: PMC3927953 DOI: 10.1002/emmm.201303198] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 09/16/2013] [Accepted: 10/17/2013] [Indexed: 11/16/2022] Open
Abstract
Mitochondrial (mt) diseases are multisystem disorders due to mutations in nuclear or mtDNA genes. Among the latter, more than 50% are located in transfer RNA (tRNA) genes and are responsible for a wide range of syndromes, for which no effective treatment is available at present. We show that three human mt aminoacyl-tRNA syntethases, namely leucyl-, valyl-, and isoleucyl-tRNA synthetase are able to improve both viability and bioenergetic proficiency of human transmitochondrial cybrid cells carrying pathogenic mutations in the mt-tRNA(Ile) gene. Importantly, we further demonstrate that the carboxy-terminal domain of human mt leucyl-tRNA synthetase is both necessary and sufficient to improve the pathologic phenotype associated either with these "mild" mutations or with the "severe" m.3243A>G mutation in the mt-tRNA(L)(eu(UUR)) gene. Furthermore, we provide evidence that this small, non-catalytic domain is able to directly and specifically interact in vitro with human mt-tRNA(Leu(UUR)) with high affinity and stability and, with lower affinity, with mt-tRNA(Ile). Taken together, our results sustain the hypothesis that the carboxy-terminal domain of human mt leucyl-tRNA synthetase can be used to correct mt dysfunctions caused by mt-tRNA mutations.
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Affiliation(s)
- Elena Perli
- Department of Radiology, Oncology and Pathology, Sapienza University of RomeRome, Italy
- Pasteur Institute-Cenci Bolognetti FoundationRome, Italy
| | - Carla Giordano
- Department of Radiology, Oncology and Pathology, Sapienza University of RomeRome, Italy
| | - Annalinda Pisano
- Department of Radiology, Oncology and Pathology, Sapienza University of RomeRome, Italy
- Department of Internal Medicine and Medical Specialties, Sapienza University of RomeRome, Italy
| | - Arianna Montanari
- Department of Radiology, Oncology and Pathology, Sapienza University of RomeRome, Italy
- Pasteur Institute-Cenci Bolognetti FoundationRome, Italy
- Department of Biology and Biotechnologies ‘Charles Darwin’, Sapienza University of RomeRome, Italy
| | - Antonio F Campese
- Department of Molecular Medicine, Sapienza University of RomeRome, Italy
| | | | - Daniele Ghezzi
- Unit of Molecular Neurogenetics, The Foundation “Carlo Besta” Institute of Neurology IRCCSMilan, Italy
| | - Alessia Nasca
- Unit of Molecular Neurogenetics, The Foundation “Carlo Besta” Institute of Neurology IRCCSMilan, Italy
| | - Helen A Tuppen
- Wellcome Trust Center for Mitochondrial Research, Institute for Ageing and Health, Newcastle UniversityNewcastle upon Tyne, UK
| | - Maurizia Orlandi
- Department of Radiology, Oncology and Pathology, Sapienza University of RomeRome, Italy
- Department of Molecular Medicine, Sapienza University of RomeRome, Italy
| | - Patrizio Di Micco
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of RomeRome, Italy
| | - Elena Poser
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of RomeRome, Italy
| | - Robert W Taylor
- Wellcome Trust Center for Mitochondrial Research, Institute for Ageing and Health, Newcastle UniversityNewcastle upon Tyne, UK
| | - Gianni Colotti
- National Research Council of Italy, Institute of Molecular Biology and PathologyRome, Italy
| | - Silvia Francisci
- Pasteur Institute-Cenci Bolognetti FoundationRome, Italy
- Department of Biology and Biotechnologies ‘Charles Darwin’, Sapienza University of RomeRome, Italy
| | - Veronica Morea
- National Research Council of Italy, Institute of Molecular Biology and PathologyRome, Italy
| | - Laura Frontali
- Pasteur Institute-Cenci Bolognetti FoundationRome, Italy
- Department of Biology and Biotechnologies ‘Charles Darwin’, Sapienza University of RomeRome, Italy
| | | | - Giulia d'Amati
- Department of Radiology, Oncology and Pathology, Sapienza University of RomeRome, Italy
- Pasteur Institute-Cenci Bolognetti FoundationRome, Italy
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Saccoccia F, Di Micco P, Boumis G, Brunori M, Koutris I, Miele AE, Morea V, Sriratana P, Williams DL, Bellelli A, Angelucci F. Moonlighting by different stressors: crystal structure of the chaperone species of a 2-Cys peroxiredoxin. Structure 2012; 20:429-39. [PMID: 22405002 DOI: 10.1016/j.str.2012.01.004] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 12/02/2011] [Accepted: 01/03/2012] [Indexed: 11/29/2022]
Abstract
2-Cys peroxiredoxins (Prxs) play two different roles depending on the physiological status of the cell. They are thioredoxin-dependent peroxidases under low oxidative stress and ATP-independent chaperones upon exposure to high peroxide concentrations. These alternative functions have been associated with changes in the oligomerization state from low-(LMW) to high-molecular-weight (HMW) species. Here we present the structures of Schistosoma mansoni PrxI in both states: the LMW decamer and the HMW 20-mer formed by two stacked decamers. The latter is the structure of a 2-Cys Prx chaperonic form. Comparison of the structures sheds light on the mechanism by which chemical stressors, such as high H(2)O(2) concentration and acidic pH, are sensed and translated into a functional switch in this protein family. We also propose a model to account for the in vivo formation of long filaments of stacked Prx rings.
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Affiliation(s)
- Fulvio Saccoccia
- Department of Biochemical Sciences, Sapienza University of Rome and Istituto Pasteur-Fondazione Cenci Bolognetti, P.le Aldo Moro 5, 00185 Rome, Italy
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Vannucci L, Falvo E, Fornara M, Di Micco P, Benada O, Krizan J, Svoboda J, Hulikova-Capkova K, Morea V, Boffi A, Ceci P. Selective targeting of melanoma by PEG-masked protein-based multifunctional nanoparticles. Int J Nanomedicine 2012; 7:1489-509. [PMID: 22619508 PMCID: PMC3356193 DOI: 10.2147/ijn.s28242] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background Nanoparticle-based systems are promising for the development of imaging and therapeutic agents. The main advantage of nanoparticles over traditional systems lies in the possibility of loading multiple functionalities onto a single molecule, which are useful for therapeutic and/or diagnostic purposes. These functionalities include targeting moieties which are able to recognize receptors overexpressed by specific cells and tissues. However, targeted delivery of nanoparticles requires an accurate system design. We present here a rationally designed, genetically engineered, and chemically modified protein-based nanoplatform for cell/tissue-specific targeting. Methods Our nanoparticle constructs were based on the heavy chain of the human protein ferritin (HFt), a highly symmetrical assembly of 24 subunits enclosing a hollow cavity. HFt-based nanoparticles were produced using both genetic engineering and chemical functionalization methods to impart several functionalities, ie, the α-melanocyte-stimulating hormone peptide as a melanoma-targeting moiety, stabilizing and HFt-masking polyethylene glycol molecules, rhodamine fluorophores, and magnetic resonance imaging agents. The constructs produced were extensively characterized by a number of physicochemical techniques, and assayed for selective melanoma-targeting in vitro and in vivo. Results Our HFt-based nanoparticle constructs functionalized with the α-melanocyte-stimulating hormone peptide moiety and polyethylene glycol molecules were specifically taken up by melanoma cells but not by other cancer cell types in vitro. Moreover, experiments in melanoma-bearing mice indicate that these constructs have an excellent tumor-targeting profile and a long circulation time in vivo. Conclusion By masking human HFt with polyethylene glycol and targeting it with an α-melanocyte-stimulating hormone peptide, we developed an HFt-based melanoma-targeting nanoplatform for application in melanoma diagnosis and treatment. These results could be of general interest, because the same strategy can be exploited to develop ad hoc nanoplatforms for specific delivery towards any cell/tissue type for which a suitable targeting moiety is available.
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Affiliation(s)
- Luca Vannucci
- Institute of Microbiology, Academy of Sciences of the Czech Republic, VVI, Prague, Czech Republic
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Montanari A, De Luca C, Di Micco P, Morea V, Frontali L, Francisci S. Structural and functional role of bases 32 and 33 in the anticodon loop of yeast mitochondrial tRNAIle. RNA 2011; 17:1983-1996. [PMID: 21914842 PMCID: PMC3198592 DOI: 10.1261/rna.2878711] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 07/20/2011] [Indexed: 05/31/2023]
Abstract
Previous work has demonstrated the usefulness of the yeast model to investigate the molecular mechanisms underlying defects due to base substitutions in mitochondrial tRNA genes, and to identify suppressing molecules endowed with potential clinical relevance. The present paper extends these investigations to two human equivalent yeast mutations located at positions 32 and 33 in the anticodon loop of tRNA(Ile). Notwithstanding the proximity of the two T>C base substitutions, the effects of these mutations have been found to be quite different in yeast, as they are in human. The T32C substitution has a very severe effect in yeast, consisting in a complete inhibition of growth on nonfermentable substrates. Conversely, respiratory defects caused by the T33C mutation could only be observed in a defined genetic context. Analyses of available sequences and selected tRNA three-dimensional structures were performed to provide explanations for the different behavior of these adjacent mutations. Examination of the effects of previously identified suppressors demonstrated that overexpression of the TUF1 gene did not rescue the defective phenotypes determined by either mutation, possibly as a consequence of the lack of interactions between EF-Tu and the tRNA anticodon arm in known structures. On the contrary, both the cognate IleRS and the noncognate LeuRS and ValRS are endowed with suppressing activities toward both mutations. This allows us to extend to the tRNA(Ile) mutants the cross-suppression activity of aminoacyl-tRNA synthetases previously demonstrated for tRNA(Leu) and tRNA(Val) mutants.
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Affiliation(s)
- Arianna Montanari
- Department of Biology and Biotechnology, Pasteur Institute, Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy
| | - Cristina De Luca
- Department of Biology and Biotechnology, Pasteur Institute, Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy
| | - Patrizio Di Micco
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, 00185 Rome, Italy
| | - Veronica Morea
- CNR—National Research Council of Italy, Institute of Molecular Biology and Pathology, 00185 Rome, Italy
| | - Laura Frontali
- Department of Biology and Biotechnology, Pasteur Institute, Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy
| | - Silvia Francisci
- Department of Biology and Biotechnology, Pasteur Institute, Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy
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Perli E, Giordano C, Tuppen HAL, Montopoli M, Montanari A, Orlandi M, Pisano A, Catanzaro D, Caparrotta L, Musumeci B, Autore C, Morea V, Di Micco P, Campese AF, Leopizzi M, Gallo P, Francisci S, Frontali L, Taylor RW, d'Amati G. Isoleucyl-tRNA synthetase levels modulate the penetrance of a homoplasmic m.4277T>C mitochondrial tRNA(Ile) mutation causing hypertrophic cardiomyopathy. Hum Mol Genet 2011; 21:85-100. [PMID: 21945886 DOI: 10.1093/hmg/ddr440] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The genetic and epigenetic factors underlying the variable penetrance of homoplasmic mitochondrial DNA mutations are poorly understood. We investigated a 16-year-old patient with hypertrophic cardiomyopathy harboring a homoplasmic m.4277T>C mutation in the mt-tRNA(Ile) (MTTI) gene. Skeletal muscle showed multiple respiratory chain enzyme abnormalities and a decreased steady-state level of the mutated mt-tRNA(Ile). Transmitochondrial cybrids grown on galactose medium demonstrated a functional effect of this mutation on cell viability, confirming pathogenicity. These findings were reproduced in transmitochondrial cybrids, harboring a previously described homoplasmic m.4300A>G MTTI mutation. The pathogenic role of the m.4277T>C mutation may be ascribed to misfolding of the mt-tRNA molecule, as demonstrated by the altered electrophoretic migration of the mutated mt-tRNA. Indeed, structure and sequence analyses suggest that thymidine at position 4277 of mt-tRNA(Ile) is involved in a conserved tertiary interaction with thymidine at position 4306. Interestingly, the mutation showed variable penetrance within family members, with skeletal muscle from the patient's clinically unaffected mother demonstrating normal muscle respiratory chain activities and steady-state levels of mt-tRNA(Ile), while homoplasmic for the m.4277T>C mutation. Analysis of mitochondrial isoleucyl-tRNA synthetase revealed significantly higher expression levels in skeletal muscle and fibroblasts of the unaffected mother when compared with the proband, while the transient over-expression of the IARS2 gene in patient transmitochondrial cybrids improved cell viability. This is the first observation that constitutively high levels of aminoacyl-tRNA synthetases (aaRSs) in human tissues prevent the phenotypic expression of a homoplasmic mt-tRNA point mutation. These findings extend previous observations on aaRSs therapeutic effects in yeast and human.
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Affiliation(s)
- Elena Perli
- Department of Internal Medicine and Medical Specialities, Sapienza University of Rome, 00161 Roma, Italy
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Micco PD. Superficial vein thrombosis in malignancy: an underestimated problem. Exp Oncol 2008; 30:4-5. [PMID: 18438335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
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