1
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Latini S, Venafra V, Massacci G, Bica V, Graziosi S, Pugliese GM, Iannuccelli M, Frioni F, Minnella G, Marra JD, Chiusolo P, Pepe G, Helmer Citterich M, Mougiakakos D, Böttcher M, Fischer T, Perfetto L, Sacco F. Unveiling the signaling network of FLT3-ITD AML improves drug sensitivity prediction. eLife 2024; 12:RP90532. [PMID: 38564252 PMCID: PMC10987088 DOI: 10.7554/elife.90532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Indexed: 04/04/2024] Open
Abstract
Currently, the identification of patient-specific therapies in cancer is mainly informed by personalized genomic analysis. In the setting of acute myeloid leukemia (AML), patient-drug treatment matching fails in a subset of patients harboring atypical internal tandem duplications (ITDs) in the tyrosine kinase domain of the FLT3 gene. To address this unmet medical need, here we develop a systems-based strategy that integrates multiparametric analysis of crucial signaling pathways, and patient-specific genomic and transcriptomic data with a prior knowledge signaling network using a Boolean-based formalism. By this approach, we derive personalized predictive models describing the signaling landscape of AML FLT3-ITD positive cell lines and patients. These models enable us to derive mechanistic insight into drug resistance mechanisms and suggest novel opportunities for combinatorial treatments. Interestingly, our analysis reveals that the JNK kinase pathway plays a crucial role in the tyrosine kinase inhibitor response of FLT3-ITD cells through cell cycle regulation. Finally, our work shows that patient-specific logic models have the potential to inform precision medicine approaches.
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Affiliation(s)
- Sara Latini
- Cellular and Molecular Biology, Department of Biology, University of Rome Tor VergataRomeItaly
| | - Veronica Venafra
- Cellular and Molecular Biology, Department of Biology, University of Rome Tor VergataRomeItaly
| | | | - Valeria Bica
- Cellular and Molecular Biology, Department of Biology, University of Rome Tor VergataRomeItaly
| | - Simone Graziosi
- Cellular and Molecular Biology, Department of Biology, University of Rome Tor VergataRomeItaly
| | | | | | - Filippo Frioni
- Sezione di Ematologia, Dipartimento di Scienze Radiologiche ed Ematologiche, Università Cattolica del Sacro CuoreRomeItaly
| | - Gessica Minnella
- Dipartimento di Diagnostica per Immagini, Radioterapia Oncologica ed Ematologia, Fondazione Policlinico A. Gemelli IRCCSRomeItaly
| | - John Donald Marra
- Sezione di Ematologia, Dipartimento di Scienze Radiologiche ed Ematologiche, Università Cattolica del Sacro CuoreRomeItaly
| | - Patrizia Chiusolo
- Sezione di Ematologia, Dipartimento di Scienze Radiologiche ed Ematologiche, Università Cattolica del Sacro CuoreRomeItaly
| | - Gerardo Pepe
- Department of Biology, University of Rome Tor VergataRomeItaly
| | | | - Dimitros Mougiakakos
- Health Campus for Inflammation, Immunity and Infection (GCI3), Otto-von-Guericke University of MagdeburgMagdeburgGermany
- Department of Hematology and Oncology, Otto-von-Guericke University of MagdeburgMagdeburgGermany
| | - Martin Böttcher
- Health Campus for Inflammation, Immunity and Infection (GCI3), Otto-von-Guericke University of MagdeburgMagdeburgGermany
- Department of Hematology and Oncology, Otto-von-Guericke University of MagdeburgMagdeburgGermany
| | - Thomas Fischer
- Health Campus for Inflammation, Immunity and Infection (GCI3), Otto-von-Guericke University of MagdeburgMagdeburgGermany
- Institute of Molecular and Clinical Immunology, Otto-von-Guericke University of MagdeburgMagdeburgGermany
| | - Livia Perfetto
- Department of Biology, University of Rome Tor VergataRomeItaly
- Department of Biology, Fondazione Human TechnopoleMilanItaly
| | - Francesca Sacco
- Department of Biology, University of Rome Tor VergataRomeItaly
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
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Blandino F, Malacaria E, Figlioli C, Noto A, Pugliese GM, Franchitto A, Pichierri P. Phosphorylation status of MUS81 is a modifier of Olaparib sensitivity in BRCA2-deficient cells. Nucleic Acids Res 2023:7186995. [PMID: 37254810 PMCID: PMC10359636 DOI: 10.1093/nar/gkad470] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 05/05/2023] [Accepted: 05/15/2023] [Indexed: 06/01/2023] Open
Abstract
The MUS81 complex is crucial for preserving genome stability through resolution of branched DNA intermediates in mitosis and also for the processing of deprotected replication forks in BRCA2-deficient cells. Because of the existence of two different MUS81 complexes in mammalian cells that act in M- or S-phase, whether and how the PARPi sensitivity of BRCA2-deficient cells is affected by loss of MUS81 function is unclear. Here, using a mutant of MUS81 that impairs its function in M-phase, we show that viability of BRCA2-deficient cells but not their PARPi sensitivity requires a fully-functional MUS81 complex in mitosis. In contrast, expression of a constitutively-active MUS81 is sufficient to confer PARPi resistance. From a mechanistic point of view, our data indicate that deregulated action of the mitotic active form of MUS81 in S-phase leads to the cleavage of stalled replication forks before their reversal, bypassing fork deprotection, and engaging a Polθ-dependent DSBs repair. Collectively, our findings describe a novel mechanism leading to PARPi resistance that involves unscheduled MUS81-dependent cleavage of intact, unreversed replication forks. Since this cleavage occurs mimicking the phosphorylated status of S87 of MUS81, our data suggest that hyperphosphorylation of this residue in S-phase might represent a novel biomarker to identify resistance to PARPi.
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Affiliation(s)
- Francesca Blandino
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Eva Malacaria
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Carolina Figlioli
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Alessandro Noto
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
- Istituto Nazionale Biostrutture e Biosistemi - Roma Area Research Unit - Via delle Medaglie d'Oro 305, 00136 Rome, Italy
| | - Giusj Monia Pugliese
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Annapaola Franchitto
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Pietro Pichierri
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
- Istituto Nazionale Biostrutture e Biosistemi - Roma Area Research Unit - Via delle Medaglie d'Oro 305, 00136 Rome, Italy
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3
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Pugliese GM, Venafra V, Bica V, Massacci G, Latini S, Graziosi S, Fischer T, Mougiakakos D, Boettcher M, Perfetto L, Sacco F. Impact of FLT3-ITD location on cytarabine sensitivity in AML: a network-based approach. Leukemia 2023; 37:1151-1155. [PMID: 36966261 PMCID: PMC10169656 DOI: 10.1038/s41375-023-01881-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/08/2023] [Accepted: 03/16/2023] [Indexed: 03/27/2023]
Affiliation(s)
- Giusj Monia Pugliese
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Veronica Venafra
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Valeria Bica
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Giorgia Massacci
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Sara Latini
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Simone Graziosi
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Thomas Fischer
- Institute of Molecular and Clinical Immunology, University of Magdeburg, Magdeburg, Germany
- Health Campus for Inflammation, Immunity and Infection (GCI3), University of Magdeburg, Magdeburg, Germany
| | - Dimitrios Mougiakakos
- Health Campus for Inflammation, Immunity and Infection (GCI3), University of Magdeburg, Magdeburg, Germany
- Department of Hematology and Oncology, University of Magdeburg, Magdeburg, Germany
| | - Martin Boettcher
- Health Campus for Inflammation, Immunity and Infection (GCI3), University of Magdeburg, Magdeburg, Germany
- Department of Hematology and Oncology, University of Magdeburg, Magdeburg, Germany
| | - Livia Perfetto
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
- Department of Biology, Fondazione Human Technopole, Via Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Francesca Sacco
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy.
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, Pozzuoli, 80078, Italy.
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4
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Tomassucci G, Tortora L, Pugliese GM, Stramaglia F, Simonelli L, Marini C, Terashima K, Wakita T, Ayukawa S, Yokoya T, Kudo K, Nohara M, Mizokawa T, Saini NL. Temperature dependent local inhomogeneity and magnetic moments of (Li 1-xFe x)OHFeSe superconductors. Phys Chem Chem Phys 2023; 25:6684-6692. [PMID: 36806473 DOI: 10.1039/d3cp00004d] [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: 02/05/2023]
Abstract
We have combined the extended X-ray absorption fine structure (EXAFS) and X-ray emission spectroscopy (XES) to investigate the local structure and the local iron magnetic moments of (Li1-xFex)OHFeSe (x∼0.2) superconductors. The local structure, studied by Fe K-edge EXAFS measurements, is found to be inhomogeneous that is characterized by different Fe-Se bond lengths. The inhomogeneous phase exhibits a peculiar temperature dependence with lattice anomalies in the local structural parameters at the critical temperature Tc (36 K) and at the spin density wave (SDW) transition temperature TN (130 K). Fe Kβ XES shows iron to be in a low spin state with the local Fe magnetic moment evolving anomalously as a function of temperature. Apart from a quantitative measurement of the local structure of (Li1-xFex)OHFeSe, providing direct evidence of nanoscale inhomogeneity, the results provide further evidence of the vital role that the coupled electronic, lattice and magnetic degrees of freedom play in the iron-based superconductors.
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Affiliation(s)
- G Tomassucci
- Dipartimento di Fisica, Universitá di Roma "La Sapienza" - P. le Aldo Moro 2, 00185 Roma, Italy.
| | - L Tortora
- Dipartimento di Fisica, Universitá di Roma "La Sapienza" - P. le Aldo Moro 2, 00185 Roma, Italy.
| | - G M Pugliese
- Dipartimento di Fisica, Universitá di Roma "La Sapienza" - P. le Aldo Moro 2, 00185 Roma, Italy.
| | - F Stramaglia
- Dipartimento di Fisica, Universitá di Roma "La Sapienza" - P. le Aldo Moro 2, 00185 Roma, Italy. .,Microscopy and Magnetism Group, Swiss Light Source, Paul Scherrer Institut, Villigen, Switzerland
| | - L Simonelli
- CELLS - ALBA Synchrotron Radiation Facility, Carrer de la Llum 2-26, 08290, Cerdanyola del Valles, Barcelona, Spain
| | - C Marini
- CELLS - ALBA Synchrotron Radiation Facility, Carrer de la Llum 2-26, 08290, Cerdanyola del Valles, Barcelona, Spain
| | - K Terashima
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama 700-8530, Japan.,National Institute for Materials Science, Sengen 1-2-1, Tsukuba, Ibaraki 305-0047, Japan
| | - T Wakita
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama 700-8530, Japan
| | - S Ayukawa
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama 700-8530, Japan
| | - T Yokoya
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama 700-8530, Japan
| | - K Kudo
- Department of Physics, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - M Nohara
- Department of Quantum Matter, Hiroshima University, Hiroshima 739-8530, Japan
| | - T Mizokawa
- Department of Applied Physics, Waseda University, Tokyo 169-8555, Japan
| | - N L Saini
- Dipartimento di Fisica, Universitá di Roma "La Sapienza" - P. le Aldo Moro 2, 00185 Roma, Italy.
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5
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Pugliese GM, Latini S, Massacci G, Perfetto L, Sacco F. Combining Mass Spectrometry-Based Phosphoproteomics with a Network-Based Approach to Reveal FLT3-Dependent Mechanisms of Chemoresistance. Proteomes 2021; 9:19. [PMID: 33925552 PMCID: PMC8167576 DOI: 10.3390/proteomes9020019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/22/2021] [Accepted: 04/24/2021] [Indexed: 12/19/2022] Open
Abstract
FLT3 mutations are the most frequently identified genetic alterations in acute myeloid leukemia (AML) and are associated with poor clinical outcome, relapse and chemotherapeutic resistance. Elucidating the molecular mechanisms underlying FLT3-dependent pathogenesis and drug resistance is a crucial goal of biomedical research. Given the complexity and intricacy of protein signaling networks, deciphering the molecular basis of FLT3-driven drug resistance requires a systems approach. Here we discuss how the recent advances in mass spectrometry (MS)-based (phospho) proteomics and multiparametric analysis accompanied by emerging computational approaches offer a platform to obtain and systematically analyze cell-specific signaling networks and to identify new potential therapeutic targets.
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Affiliation(s)
- Giusj Monia Pugliese
- Department of Biology, University of Rome Tor Vergata, Via delle Ricerca Scientifica 1, 00133 Rome, Italy; (G.M.P.); (S.L.); (G.M.)
| | - Sara Latini
- Department of Biology, University of Rome Tor Vergata, Via delle Ricerca Scientifica 1, 00133 Rome, Italy; (G.M.P.); (S.L.); (G.M.)
| | - Giorgia Massacci
- Department of Biology, University of Rome Tor Vergata, Via delle Ricerca Scientifica 1, 00133 Rome, Italy; (G.M.P.); (S.L.); (G.M.)
| | - Livia Perfetto
- Fondazione Human Technopole, Department of Biology, Via Cristina Belgioioso 171, 20157 Milan, Italy;
| | - Francesca Sacco
- Department of Biology, University of Rome Tor Vergata, Via delle Ricerca Scientifica 1, 00133 Rome, Italy; (G.M.P.); (S.L.); (G.M.)
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6
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Perfetto L, Micarelli E, Iannuccelli M, Lo Surdo P, Giuliani G, Latini S, Pugliese GM, Massacci G, Vumbaca S, Riccio F, Fuoco C, Paoluzi S, Castagnoli L, Cesareni G, Licata L, Sacco F. A Resource for the Network Representation of Cell Perturbations Caused by SARS-CoV-2 Infection. Genes (Basel) 2021; 12:450. [PMID: 33809949 PMCID: PMC8004236 DOI: 10.3390/genes12030450] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 03/01/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 02/06/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has caused more than 2.3 million casualties worldwide and the lack of effective treatments is a major health concern. The development of targeted drugs is held back due to a limited understanding of the molecular mechanisms underlying the perturbation of cell physiology observed after viral infection. Recently, several approaches, aimed at identifying cellular proteins that may contribute to COVID-19 pathology, have been reported. Albeit valuable, this information offers limited mechanistic insight as these efforts have produced long lists of cellular proteins, the majority of which are not annotated to any cellular pathway. We have embarked in a project aimed at bridging this mechanistic gap by developing a new bioinformatic approach to estimate the functional distance between a subset of proteins and a list of pathways. A comprehensive literature search allowed us to annotate, in the SIGNOR 2.0 resource, causal information underlying the main molecular mechanisms through which severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and related coronaviruses affect the host-cell physiology. Next, we developed a new strategy that enabled us to link SARS-CoV-2 interacting proteins to cellular phenotypes via paths of causal relationships. Remarkably, the extensive information about inhibitors of signaling proteins annotated in SIGNOR 2.0 makes it possible to formulate new potential therapeutic strategies. The proposed approach, which is generally applicable, generated a literature-based causal network that can be used as a framework to formulate informed mechanistic hypotheses on COVID-19 etiology and pathology.
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Affiliation(s)
- Livia Perfetto
- Fondazione Human Technopole, Department of Biology, Via Cristina Belgioioso, 171, 20157 Milan, Italy; (L.P.); (P.L.S.)
| | - Elisa Micarelli
- Department of Biology, University of Rome Tor Vergata, Via delle Ricerca Scientifica 1, 00133 Rome, Italy; (E.M.); (M.I.); (G.G.); (S.L.); (G.M.P.); (G.M.); (S.V.); (F.R.); (C.F.); (S.P.); (L.C.); (G.C.); (L.L.)
| | - Marta Iannuccelli
- Department of Biology, University of Rome Tor Vergata, Via delle Ricerca Scientifica 1, 00133 Rome, Italy; (E.M.); (M.I.); (G.G.); (S.L.); (G.M.P.); (G.M.); (S.V.); (F.R.); (C.F.); (S.P.); (L.C.); (G.C.); (L.L.)
| | - Prisca Lo Surdo
- Fondazione Human Technopole, Department of Biology, Via Cristina Belgioioso, 171, 20157 Milan, Italy; (L.P.); (P.L.S.)
| | - Giulio Giuliani
- Department of Biology, University of Rome Tor Vergata, Via delle Ricerca Scientifica 1, 00133 Rome, Italy; (E.M.); (M.I.); (G.G.); (S.L.); (G.M.P.); (G.M.); (S.V.); (F.R.); (C.F.); (S.P.); (L.C.); (G.C.); (L.L.)
| | - Sara Latini
- Department of Biology, University of Rome Tor Vergata, Via delle Ricerca Scientifica 1, 00133 Rome, Italy; (E.M.); (M.I.); (G.G.); (S.L.); (G.M.P.); (G.M.); (S.V.); (F.R.); (C.F.); (S.P.); (L.C.); (G.C.); (L.L.)
| | - Giusj Monia Pugliese
- Department of Biology, University of Rome Tor Vergata, Via delle Ricerca Scientifica 1, 00133 Rome, Italy; (E.M.); (M.I.); (G.G.); (S.L.); (G.M.P.); (G.M.); (S.V.); (F.R.); (C.F.); (S.P.); (L.C.); (G.C.); (L.L.)
| | - Giorgia Massacci
- Department of Biology, University of Rome Tor Vergata, Via delle Ricerca Scientifica 1, 00133 Rome, Italy; (E.M.); (M.I.); (G.G.); (S.L.); (G.M.P.); (G.M.); (S.V.); (F.R.); (C.F.); (S.P.); (L.C.); (G.C.); (L.L.)
| | - Simone Vumbaca
- Department of Biology, University of Rome Tor Vergata, Via delle Ricerca Scientifica 1, 00133 Rome, Italy; (E.M.); (M.I.); (G.G.); (S.L.); (G.M.P.); (G.M.); (S.V.); (F.R.); (C.F.); (S.P.); (L.C.); (G.C.); (L.L.)
| | - Federica Riccio
- Department of Biology, University of Rome Tor Vergata, Via delle Ricerca Scientifica 1, 00133 Rome, Italy; (E.M.); (M.I.); (G.G.); (S.L.); (G.M.P.); (G.M.); (S.V.); (F.R.); (C.F.); (S.P.); (L.C.); (G.C.); (L.L.)
| | - Claudia Fuoco
- Department of Biology, University of Rome Tor Vergata, Via delle Ricerca Scientifica 1, 00133 Rome, Italy; (E.M.); (M.I.); (G.G.); (S.L.); (G.M.P.); (G.M.); (S.V.); (F.R.); (C.F.); (S.P.); (L.C.); (G.C.); (L.L.)
| | - Serena Paoluzi
- Department of Biology, University of Rome Tor Vergata, Via delle Ricerca Scientifica 1, 00133 Rome, Italy; (E.M.); (M.I.); (G.G.); (S.L.); (G.M.P.); (G.M.); (S.V.); (F.R.); (C.F.); (S.P.); (L.C.); (G.C.); (L.L.)
| | - Luisa Castagnoli
- Department of Biology, University of Rome Tor Vergata, Via delle Ricerca Scientifica 1, 00133 Rome, Italy; (E.M.); (M.I.); (G.G.); (S.L.); (G.M.P.); (G.M.); (S.V.); (F.R.); (C.F.); (S.P.); (L.C.); (G.C.); (L.L.)
| | - Gianni Cesareni
- Department of Biology, University of Rome Tor Vergata, Via delle Ricerca Scientifica 1, 00133 Rome, Italy; (E.M.); (M.I.); (G.G.); (S.L.); (G.M.P.); (G.M.); (S.V.); (F.R.); (C.F.); (S.P.); (L.C.); (G.C.); (L.L.)
| | - Luana Licata
- Department of Biology, University of Rome Tor Vergata, Via delle Ricerca Scientifica 1, 00133 Rome, Italy; (E.M.); (M.I.); (G.G.); (S.L.); (G.M.P.); (G.M.); (S.V.); (F.R.); (C.F.); (S.P.); (L.C.); (G.C.); (L.L.)
| | - Francesca Sacco
- Department of Biology, University of Rome Tor Vergata, Via delle Ricerca Scientifica 1, 00133 Rome, Italy; (E.M.); (M.I.); (G.G.); (S.L.); (G.M.P.); (G.M.); (S.V.); (F.R.); (C.F.); (S.P.); (L.C.); (G.C.); (L.L.)
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7
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Pugliese GM, Paris E, Capone FG, Stramaglia F, Wakita T, Terashima K, Yokoya T, Mizokawa T, Mizuguchi Y, Saini NL. The local structure of self-doped BiS 2-based layered systems as a function of temperature. Phys Chem Chem Phys 2020; 22:22217-22225. [PMID: 32996510 DOI: 10.1039/d0cp03974h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have studied the local structure of layered Eu(La,Ce)FBiS2 compounds by Bi L3-edge extended X-ray absorption fine structure (EXAFS) measurements as a function of temperature. We find that the BiS2 sub-lattice is largely distorted in EuFBiS2, characterized by two different in-plane Bi-S1 distances. The distortion is marginally affected by partial substitutions of Ce (Eu0.5Ce0.5FBiS2) and La (Eu0.5La0.5FBiS2). The temperature dependence of the local structure distortion reveals an indication of possible charge density wave like instability in the pristine self-doped EuFBiS2 and Ce substituted Eu0.5Ce0.5FBiS2 while it is suppressed in La substituted Eu0.5La0.5FBiS2. In compounds with higher superconducting transition temperature, the axial Bi-S2 bond distance is elongated and the related bond stiffness decreased, suggesting some important role of this in the charge transfer mechanism for self-doping in the active BiS2-layer. In-plane Bi-S1 distances are generally softer than the axial Bi-S2 distance and they suffer further softening by the substitutions. The results are discussed in relation to an important role of the Bi defect chemistry driven asymmetric local environment in the physical properties of these materials.
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Affiliation(s)
- G M Pugliese
- Dipartimento di Fisica, Universitá di Roma "La Sapienza"- P. le Aldo Moro 2, 00185 Roma, Italy.
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8
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Bellisai C, Sciamanna I, Rovella P, Giovannini D, Baranzini M, Pugliese GM, Zeya Ansari MS, Milite C, Sinibaldi-Vallebona P, Cirilli R, Sbardella G, Pichierri P, Trisciuoglio D, Lavia P, Serafino A, Spadafora C. Reverse transcriptase inhibitors promote the remodelling of nuclear architecture and induce autophagy in prostate cancer cells. Cancer Lett 2020; 478:133-145. [PMID: 32112906 DOI: 10.1016/j.canlet.2020.02.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 12/17/2022]
Abstract
Emerging data indicate that the reverse transcriptase (RT) protein encoded by LINE-1 transposable elements is a promising cancer target. Nonnucleoside RT inhibitors, e.g. efavirenz (EFV) and SPV122.2, reduce proliferation and promote differentiation of cancer cells, concomitant with a global reprogramming of the transcription profile. Both inhibitors have therapeutic anticancer efficacy in animal models. Here we have sought to clarify the mechanisms of RT inhibitors in cancer cells. We report that exposure of PC3 metastatic prostate carcinoma cells to both RT inhibitors results in decreased proliferation, and concomitantly induces genome damage. This is associated with rearrangements of the nuclear architecture, particularly at peripheral chromatin, disruption of the nuclear lamina, and budding of micronuclei. These changes are reversible upon discontinuation of the RT-inhibitory treatment, with reconsititution of the lamina and resumption of the cancer cell original features. The use of pharmacological autophagy inhibitors proves that autophagy is largely responsible for the antiproliferative effect of RT inhibitors. These alterations are not induced in non-cancer cell lines exposed to RT inhibitors. These data provide novel insight in the molecular pathways targeted by RT inhibitors in cancer cells.
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Affiliation(s)
- Cristina Bellisai
- Institute of Translational Pharmacology (IFT), CNR Consiglio Nazionale delle Ricerche, 00133, Rome, Italy; University of Rome "Tor Vergata", 00133, Rome, Italy
| | | | - Paola Rovella
- Institute of Molecular Biology and Pathology (IBPM), CNR Consiglio Nazionale delle Ricerche, c/o Department of Biology and Biotechnology, Sapienza University of Rome, 00185, Rome, Italy
| | - Daniela Giovannini
- Institute of Translational Pharmacology (IFT), CNR Consiglio Nazionale delle Ricerche, 00133, Rome, Italy
| | - Mirko Baranzini
- Institute of Translational Pharmacology (IFT), CNR Consiglio Nazionale delle Ricerche, 00133, Rome, Italy
| | - Giusj Monia Pugliese
- University of Rome "Tor Vergata", 00133, Rome, Italy; Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Mohammad Salik Zeya Ansari
- Institute of Molecular Biology and Pathology (IBPM), CNR Consiglio Nazionale delle Ricerche, c/o Department of Biology and Biotechnology, Sapienza University of Rome, 00185, Rome, Italy
| | - Ciro Milite
- Department of Pharmacy, University of Salerno, 84084, Fisciano, SA, Italy
| | - Paola Sinibaldi-Vallebona
- Institute of Translational Pharmacology (IFT), CNR Consiglio Nazionale delle Ricerche, 00133, Rome, Italy; University of Rome "Tor Vergata", 00133, Rome, Italy
| | | | - Gianluca Sbardella
- Department of Pharmacy, University of Salerno, 84084, Fisciano, SA, Italy
| | | | - Daniela Trisciuoglio
- Institute of Molecular Biology and Pathology (IBPM), CNR Consiglio Nazionale delle Ricerche, c/o Department of Biology and Biotechnology, Sapienza University of Rome, 00185, Rome, Italy
| | - Patrizia Lavia
- Institute of Molecular Biology and Pathology (IBPM), CNR Consiglio Nazionale delle Ricerche, c/o Department of Biology and Biotechnology, Sapienza University of Rome, 00185, Rome, Italy
| | - Annalucia Serafino
- Institute of Translational Pharmacology (IFT), CNR Consiglio Nazionale delle Ricerche, 00133, Rome, Italy
| | - Corrado Spadafora
- Institute of Translational Pharmacology (IFT), CNR Consiglio Nazionale delle Ricerche, 00133, Rome, Italy.
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9
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Pugliese GM, Stramaglia F, Goto Y, Terashima K, Simonelli L, Fujiwara H, Puri A, Marini C, Hacisalihoglu MY, d'Acapito F, Yokoya T, Mizokawa T, Mizuguchi Y, Saini NL. Temperature dependent local atomic displacements in NaSn 2As 2 system. J Phys Condens Matter 2019; 31:425402. [PMID: 31226700 DOI: 10.1088/1361-648x/ab2bd4] [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] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
NaSn2As2 is mechanically exfoliable layered van der Waals (vdW) Zintl phase that is getting interesting due to its low thermal conductivity and recently observed superconductivity. Here, we have investigated the temperature dependent local structure of NaSn2As2 by a combined analysis of As K-edge and Sn K-edge extended x-ray absorption fine structure measurements. The system is intrinsically disordered with the interatomic distances largely consistent to those estimated by average structure measurements. The stretching force constants of different bond distances have been determined using temperature dependent mean square relative displacements. The Sn-As distance is the strongest bond in this system, having covalent nature, unlike the weaker interlayer distances which are characterized by vdW type bonding. Among them, As-Na distance is slightly weaker than Sn-Sn(i) below ∼200 K and tends to get stronger above this temperature. The anomalous behavior of As-Na bond suggests that the mechanical exfoliation in this system is likely to be temperature dependent. The anomaly in the interlayer atomic correlations may be due to a charge density wave-like instability around this temperature, indicated by earlier experiments. The local structure and disorder are discussed in relation to the physical properties of NaSn2As2.
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Affiliation(s)
- G M Pugliese
- Dipartimento di Fisica, Università di Roma 'La Sapienza', P. le Aldo Moro 2, 00185 Roma, Italy
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10
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Pugliese GM, Salaris F, Palermo V, Marabitti V, Morina N, Rosa A, Franchitto A, Pichierri P. Inducible SMARCAL1 knockdown in iPSC reveals a link between replication stress and altered expression of master differentiation genes. Dis Model Mech 2019; 12:dmm.039487. [PMID: 31515241 PMCID: PMC6826020 DOI: 10.1242/dmm.039487] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 08/30/2019] [Indexed: 12/15/2022] Open
Abstract
Schimke immuno-osseous dysplasia is an autosomal recessive genetic osteochondrodysplasia characterized by dysmorphism, spondyloepiphyseal dysplasia, nephrotic syndrome and frequently T cell immunodeficiency. Several hypotheses have been proposed to explain the pathophysiology of the disease; however, the mechanism by which SMARCAL1 mutations cause the syndrome is elusive. Here, we generated a conditional SMARCAL1 knockdown model in induced pluripotent stem cells (iPSCs) to mimic conditions associated with the severe form the disease. Using multiple cellular endpoints, we characterized this model for the presence of phenotypes linked to the replication caretaker role of SMARCAL1. Our data show that conditional knockdown of SMARCAL1 in human iPSCs induces replication-dependent and chronic accumulation of DNA damage triggering the DNA damage response. Furthermore, they indicate that accumulation of DNA damage and activation of the DNA damage response correlates with increased levels of R-loops and replication-transcription interference. Finally, we provide evidence that SMARCAL1-deficient iPSCs maintain active DNA damage response beyond differentiation, possibly contributing to the observed altered expression of a subset of germ layer-specific master genes. Confirming the relevance of SMARCAL1 loss for the observed phenotypes, they are prevented or rescued after re-expression of wild-type SMARCAL1 in our iPSC model. In conclusion, our conditional SMARCAL1 knockdown model in iPSCs may represent a powerful model when studying pathogenetic mechanisms of severe Schimke immuno-osseous dysplasia.
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Affiliation(s)
- Giusj Monia Pugliese
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Federico Salaris
- Center for Life Nano Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy.,Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Valentina Palermo
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Veronica Marabitti
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Nicolò Morina
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Alessandro Rosa
- Center for Life Nano Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy.,Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Annapaola Franchitto
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Pietro Pichierri
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy .,Istituto Nazionale Biostrutture e Biosistemi, Via delle Medaglie d'Oro, 00136 Rome, Italy
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11
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Palma A, Pugliese GM, Murfuni I, Marabitti V, Malacaria E, Rinalducci S, Minoprio A, Sanchez M, Mazzei F, Zolla L, Franchitto A, Pichierri P. Phosphorylation by CK2 regulates MUS81/EME1 in mitosis and after replication stress. Nucleic Acids Res 2019; 46:5109-5124. [PMID: 29850896 PMCID: PMC6007509 DOI: 10.1093/nar/gky280] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 06/23/2017] [Accepted: 04/04/2018] [Indexed: 12/21/2022] Open
Abstract
The MUS81 complex is crucial for preserving genome stability through the resolution of branched DNA intermediates in mitosis. However, untimely activation of the MUS81 complex in S-phase is dangerous. Little is known about the regulation of the human MUS81 complex and how deregulated activation affects chromosome integrity. Here, we show that the CK2 kinase phosphorylates MUS81 at Serine 87 in late-G2/mitosis, and upon mild replication stress. Phosphorylated MUS81 interacts with SLX4, and this association promotes the function of the MUS81 complex. In line with a role in mitosis, phosphorylation at Serine 87 is suppressed in S-phase and is mainly detected in the MUS81 molecules associated with EME1. Loss of CK2-dependent MUS81 phosphorylation contributes modestly to chromosome integrity, however, expression of the phosphomimic form induces DSBs accumulation in S-phase, because of unscheduled targeting of HJ-like DNA intermediates, and generates a wide chromosome instability phenotype. Collectively, our findings describe a novel regulatory mechanism controlling the MUS81 complex function in human cells. Furthermore, they indicate that, genome stability depends mainly on the ability of cells to counteract targeting of branched intermediates by the MUS81/EME1 complex in S-phase, rather than on a correct MUS81 function in mitosis.
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Affiliation(s)
- Anita Palma
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Giusj Monia Pugliese
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Ivana Murfuni
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Veronica Marabitti
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Eva Malacaria
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Sara Rinalducci
- Proteomics, Metabolomics and Interactomics Lab, Department of Ecology and Biology, Università della Tuscia, Viale dell'Università snc, 01100 Viterbo, Italy
| | - Anna Minoprio
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Massimo Sanchez
- Core Facilities Center - Section of Cytometry, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Filomena Mazzei
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Lello Zolla
- Proteomics, Metabolomics and Interactomics Lab, Department of Ecology and Biology, Università della Tuscia, Viale dell'Università snc, 01100 Viterbo, Italy
| | - Annapaola Franchitto
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Pietro Pichierri
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
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12
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Malacaria E, Pugliese GM, Honda M, Marabitti V, Aiello FA, Spies M, Franchitto A, Pichierri P. Author Correction: Rad52 prevents excessive replication fork reversal and protects from nascent strand degradation. Nat Commun 2019; 10:2023. [PMID: 31043602 PMCID: PMC6494817 DOI: 10.1038/s41467-019-10072-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Affiliation(s)
- Eva Malacaria
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Giusj Monia Pugliese
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Masayoshi Honda
- Department of Biochemistry, Carver College of Medicine, University of Iowa, 51 Newton Road 4-403 Bowen Science Building, Iowa City, IA, 52242, USA
| | - Veronica Marabitti
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Francesca Antonella Aiello
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Maria Spies
- Department of Biochemistry, Carver College of Medicine, University of Iowa, 51 Newton Road 4-403 Bowen Science Building, Iowa City, IA, 52242, USA
| | - Annapaola Franchitto
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Pietro Pichierri
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy. .,Istituto Nazionale Biostrutture e Biosistemi, Viale delle Medaglie d'Oro, 305, 00136, Rome, Italy.
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