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Manfrini N, Notarbartolo S, Grifantini R, Pesce E. SARS-CoV-2: A Glance at the Innate Immune Response Elicited by Infection and Vaccination. Antibodies (Basel) 2024; 13:13. [PMID: 38390874 PMCID: PMC10885122 DOI: 10.3390/antib13010013] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/13/2024] [Accepted: 02/02/2024] [Indexed: 02/24/2024] Open
Abstract
The COVID-19 pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led to almost seven million deaths worldwide. SARS-CoV-2 causes infection through respiratory transmission and can occur either without any symptoms or with clinical manifestations which can be mild, severe or, in some cases, even fatal. Innate immunity provides the initial defense against the virus by sensing pathogen-associated molecular patterns and triggering signaling pathways that activate the antiviral and inflammatory responses, which limit viral replication and help the identification and removal of infected cells. However, temporally dysregulated and excessive activation of the innate immune response is deleterious for the host and associates with severe COVID-19. In addition to its defensive role, innate immunity is pivotal in priming the adaptive immune response and polarizing its effector function. This capacity is relevant in the context of both SARS-CoV-2 natural infection and COVID-19 vaccination. Here, we provide an overview of the current knowledge of the innate immune responses to SARS-CoV-2 infection and vaccination.
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Affiliation(s)
- Nicola Manfrini
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milan, Italy
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Samuele Notarbartolo
- Infectious Diseases Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Renata Grifantini
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milan, Italy
- CheckmAb Srl, 20122 Milan, Italy
| | - Elisa Pesce
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
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2
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Mancino M, Lai G, De Grossi F, Cuomo A, Manganaro L, Butta GM, Ferrari I, Vicenzi E, Poli G, Pesce E, Oliveto S, Biffo S, Manfrini N. FAM46C Is an Interferon-Stimulated Gene That Inhibits Lentiviral Particle Production by Modulating Autophagy. Microbiol Spectr 2023; 11:e0521122. [PMID: 37358411 PMCID: PMC10434054 DOI: 10.1128/spectrum.05211-22] [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] [Received: 12/22/2022] [Accepted: 06/02/2023] [Indexed: 06/27/2023] Open
Abstract
FAM46C is a multiple myeloma (MM) tumor suppressor whose function is only starting to be elucidated. We recently showed that in MM cells FAM46C triggers apoptosis by inhibiting autophagy and altering intracellular trafficking and protein secretion. To date, both a physiological characterization of FAM46C role and an assessment of FAM46C-induced phenotypes outside of MM are lacking. Preliminary reports suggested an involvement of FAM46C with regulation of viral replication, but this was never confirmed. Here, we show that FAM46C is an interferon-stimulated gene and that the expression of wild-type FAM46C in HEK-293T cells, but not of its most frequently found mutant variants, inhibits the production of both HIV-1-derived and HIV-1 lentiviruses. We demonstrate that this effect does not require transcriptional regulation and does not depend on inhibition of either global or virus-specific translation but rather mostly relies on FAM46C-induced deregulation of autophagy, a pathway that we show to be required for efficient lentiviral particle production. These studies not only provide new insights on the physiological role of the FAM46C protein but also could help in implementing more efficient antiviral strategies on one side and lentiviral particle production approaches on the other. IMPORTANCE FAM46C role has been thoroughly investigated in MM, but studies characterizing its role outside of the tumoral environment are still lacking. Despite the success of antiretroviral therapy in suppressing HIV load to undetectable levels, there is currently no HIV cure, and treatment is lifelong. Indeed, HIV continues to be a major global public health issue. Here, we show that FAM46C expression in HEK-293T cells inhibits the production of both HIV and HIV-derived lentiviruses. We also demonstrate that such inhibitory effect relies, at least in part, on the well-established regulatory role that FAM46C exerts on autophagy. Deciphering the molecular mechanism underlying this regulation will not only facilitate the understanding of FAM46C physiological role but also give new insights on the interplay between HIV and the cellular environment.
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Affiliation(s)
- Marilena Mancino
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Giancarlo Lai
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | | | - Alessandro Cuomo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Lara Manganaro
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Giacomo M. Butta
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Ivan Ferrari
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Elisa Vicenzi
- Viral Pathogenesis and Biosafety Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Guido Poli
- Viral Pathogenesis and Biosafety Unit, San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University School of Medicine, Milan, Italy
| | - Elisa Pesce
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Stefania Oliveto
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
| | - Stefano Biffo
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
| | - Nicola Manfrini
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
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Kiratzis M, Lai G, Calamita P, Mancino M, Iriti M, Manfrini N, Gallo S. RACK1 release from the Ribosome Couples Translational Regulation with Starving Signaling and Possibly Depends on Phosphorylation of Key Serine and Threonine Residues. Cell Mol Biol (Noisy-le-grand) 2023; 69:7-12. [PMID: 37213164 DOI: 10.14715/cmb/2022.69.1.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Indexed: 05/23/2023]
Abstract
The balance between protein anabolism and catabolism sets the foundations on which cells build their homeostasis. RACK1 is a ribosome-associated scaffold protein involved in signal transduction. On the ribosome, RACK1 enhances specific translation. Conversely, upon growth factor/nutrient starvation, RACK1 is present in a ribosome-free form and inhibits protein synthesis. However, the precise role of RACK1 when not bound to the ribosome still requires elucidation. Here, we show that extra-ribosomal RACK1 increases LC3-II accumulation, thereby mimicking an autophagy-like phenotype. Next, based on the ribosome-bound structure of RACK1, we suggest a possible mechanism for RACK1 release from the ribosome which relies on phosphorylation of precise amino acid residues, namely Thr39, Ser63, Thr86, Ser276, Thr277, Ser278, Ser279. Specifically, by performing an unbiased in silico screening using phospho-kinase prediction tools, we propose that, upon starving, AMPK1/2, ULK1/2 and PKR are the strongest candidate protein kinases to phosphorylate RACK1. This may be relevant in the context of caloric restriction and cancer therapy, where repressing translation of specific mRNAs would open important therapeutic avenues. Overall, our work provides novel insight into RACK1 function(s) by connecting its ribosomal and extra-ribosomal activities with translation and signaling.
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Affiliation(s)
- Maria Kiratzis
- Molecular Histology and Cell Growth Unit, National Institute of Molecular Genetics "Fondazione Romeo e Enrica Invernizzi" - INGM, Milan, Italy.
| | - Giancarlo Lai
- Department of Biosciences, University of Milan, Milan, Italy.
| | - Piera Calamita
- Molecular Histology and Cell Growth Unit, National Institute of Molecular Genetics "Fondazione Romeo e Enrica Invernizzi" - INGM, Milan, Italy.
| | - Marilena Mancino
- Molecular Histology and Cell Growth Unit, National Institute of Molecular Genetics "Fondazione Romeo e Enrica Invernizzi" - INGM, Milan, Italy.
| | - Marcello Iriti
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy.
| | - Nicola Manfrini
- Molecular Histology and Cell Growth Unit, National Institute of Molecular Genetics "Fondazione Romeo e Enrica Invernizzi" - INGM, Milan, Italy.
| | - Simone Gallo
- Molecular Histology and Cell Growth Unit, National Institute of Molecular Genetics "Fondazione Romeo e Enrica Invernizzi" - INGM, Milan, Italy.
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4
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Miluzio A, Cuomo A, Cordiglieri C, Donnici L, Pesce E, Bombaci M, Conti M, Fasciani A, Terracciano L, Manganaro L, Toccafondi M, Scagliola A, Oliveto S, Ricciardi S, Grifantini R, De Francesco R, Abrignani S, Manfrini N, Biffo S. Mapping of functional SARS-CoV-2 receptors in human lungs establishes differences in variant binding and SLC1A5 as a viral entry modulator of hACE2. EBioMedicine 2022; 87:104390. [PMID: 36584595 PMCID: PMC9795807 DOI: 10.1016/j.ebiom.2022.104390] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The COVID-19 pandemic is an infectious disease caused by SARS-CoV-2. The first step of SARS-CoV-2 infection is the recognition of angiotensin-converting enzyme 2 (ACE2) receptors by the receptor-binding domain (RBD) of the viral Spike (S) glycoprotein. Although the molecular and structural bases of the SARS-CoV-2-RBD/hACE2 interaction have been thoroughly investigated in vitro, the relationship between hACE2 expression and in vivo infection is less understood. METHODS Here, we developed an efficient SARS-CoV-2-RBD binding assay suitable for super resolution microscopy and simultaneous hACE2 immunodetection and mapped the correlation between hACE2 receptor abundance and SARS-CoV-2-RBD binding, both in vitro and in human lung biopsies. Next, we explored the specific proteome of SARS-CoV-2-RBD/hACE2 through a comparative mass spectrometry approach. FINDINGS We found that only a minority of hACE2 positive spots are actually SARS-CoV-2-RBD binding sites, and that the relationship between SARS-CoV-2-RBD binding and hACE2 presence is variable, suggesting the existence of additional factors. Indeed, we found several interactors that are involved in receptor localization and viral entry and characterized one of them: SLC1A5, an amino acid transporter. High-resolution receptor-binding studies showed that co-expression of membrane-bound SLC1A5 with hACE2 predicted SARS-CoV-2 binding and entry better than hACE2 expression alone. SLC1A5 depletion reduces SARS-CoV-2 binding and entry. Notably, the Omicron variant is more efficient in binding hACE2 sites, but equally sensitive to SLC1A5 downregulation. INTERPRETATION We propose a method for mapping functional SARS-CoV-2 receptors in vivo. We confirm the existence of hACE2 co-factors that may contribute to differential sensitivity of cells to infection. FUNDING This work was supported by an unrestricted grant from "Fondazione Romeo ed Enrica Invernizzi" to Stefano Biffo and by AIRC under MFAG 2021 - ID. 26178 project - P.I. Manfrini Nicola.
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Affiliation(s)
- Annarita Miluzio
- National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", INGM, 20122, Milan, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Chiara Cordiglieri
- National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", INGM, 20122, Milan, Italy
| | - Lorena Donnici
- National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", INGM, 20122, Milan, Italy
| | - Elisa Pesce
- National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", INGM, 20122, Milan, Italy
| | - Mauro Bombaci
- National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", INGM, 20122, Milan, Italy
| | - Matteo Conti
- National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", INGM, 20122, Milan, Italy
| | - Alessandra Fasciani
- National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", INGM, 20122, Milan, Italy
| | - Luigi Terracciano
- Institute of Pathology, University Hospital Basel, 4031, Basel, Switzerland
| | - Lara Manganaro
- National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", INGM, 20122, Milan, Italy
| | - Mirco Toccafondi
- National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", INGM, 20122, Milan, Italy
| | - Alessandra Scagliola
- National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", INGM, 20122, Milan, Italy
| | - Stefania Oliveto
- National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", INGM, 20122, Milan, Italy
| | - Sara Ricciardi
- National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", INGM, 20122, Milan, Italy,Department of Biosciences, University of Milan, 20133, Milan, Italy
| | - Renata Grifantini
- National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", INGM, 20122, Milan, Italy
| | - Raffaele De Francesco
- National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", INGM, 20122, Milan, Italy,Department of Pharmacological and Biomolecular Sciences, University of Milan, 20133, Milan, Italy
| | - Sergio Abrignani
- National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", INGM, 20122, Milan, Italy,Department of Clinical Sciences and Community Health, University of Milan, 20122, Milan, Italy
| | - Nicola Manfrini
- National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", INGM, 20122, Milan, Italy,Department of Biosciences, University of Milan, 20133, Milan, Italy,Corresponding author. National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", INGM, 20122, Milan, Italy.
| | - Stefano Biffo
- National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", INGM, 20122, Milan, Italy,Department of Biosciences, University of Milan, 20133, Milan, Italy,Corresponding author. National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", INGM, 20122, Milan, Italy.
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5
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Scagliola A, Miluzio A, Mori G, Ricciardi S, Oliveto S, Manfrini N, Biffo S. Inhibition of eIF6 Activity Reduces Hepatocellular Carcinoma Growth: An In Vivo and In Vitro Study. Int J Mol Sci 2022; 23:ijms23147720. [PMID: 35887068 PMCID: PMC9319760 DOI: 10.3390/ijms23147720] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/07/2022] [Accepted: 07/09/2022] [Indexed: 02/06/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is characterized by the accumulation of lipids in the liver. Given the high prevalence of NAFLD, its evolution to nonalcoholic steatohepatitis (NASH) and hepatocellular carcinoma (HCC) is of global concern. Therapies for managing NASH-driven HCC can benefit from targeting factors that play a continuous role in NAFLD evolution to HCC. Recent work has shown that postprandial liver translation exacerbates lipid accumulation through the activity of a translation factor, eukaryotic initiation factor 6 (eIF6). Here, we test the effect of eIF6 inhibition on the progression of HCC. Mice heterozygous for eIF6 express half the level of eIF6 compared to wt mice and are resistant to the formation of HCC nodules upon exposure to a high fat/high sugar diet combined with liver damage. Histology showed that nodules in eIF6 het mice were smaller with reduced proliferation compared to wt nodules. By using an in vitro model of human HCC, we confirm that eIF6 depletion reduces the growth of HCC spheroids. We also tested three pharmacological inhibitors of eIF6 activity—eIFsixty-1, eIFsixty-4, and eIFsixty-6—and all three reduced eIF6 binding to 60S ribosomes and limited the growth of HCC spheroids. Thus, inhibition of eIF6 activity is feasible and limits HCC formation.
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Affiliation(s)
- Alessandra Scagliola
- National Institute of Molecular Genetics, Fondazione Romeo ed Enrica Invernizzi, Via Sforza 35, 20122 Milan, Italy; (A.S.); (A.M.); (G.M.); (S.R.); (S.O.); (N.M.)
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Annarita Miluzio
- National Institute of Molecular Genetics, Fondazione Romeo ed Enrica Invernizzi, Via Sforza 35, 20122 Milan, Italy; (A.S.); (A.M.); (G.M.); (S.R.); (S.O.); (N.M.)
| | - Giada Mori
- National Institute of Molecular Genetics, Fondazione Romeo ed Enrica Invernizzi, Via Sforza 35, 20122 Milan, Italy; (A.S.); (A.M.); (G.M.); (S.R.); (S.O.); (N.M.)
| | - Sara Ricciardi
- National Institute of Molecular Genetics, Fondazione Romeo ed Enrica Invernizzi, Via Sforza 35, 20122 Milan, Italy; (A.S.); (A.M.); (G.M.); (S.R.); (S.O.); (N.M.)
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Stefania Oliveto
- National Institute of Molecular Genetics, Fondazione Romeo ed Enrica Invernizzi, Via Sforza 35, 20122 Milan, Italy; (A.S.); (A.M.); (G.M.); (S.R.); (S.O.); (N.M.)
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Nicola Manfrini
- National Institute of Molecular Genetics, Fondazione Romeo ed Enrica Invernizzi, Via Sforza 35, 20122 Milan, Italy; (A.S.); (A.M.); (G.M.); (S.R.); (S.O.); (N.M.)
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Stefano Biffo
- National Institute of Molecular Genetics, Fondazione Romeo ed Enrica Invernizzi, Via Sforza 35, 20122 Milan, Italy; (A.S.); (A.M.); (G.M.); (S.R.); (S.O.); (N.M.)
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
- Correspondence:
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6
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Pesce E, Manfrini N, Cordiglieri C, Santi S, Bandera A, Gobbini A, Gruarin P, Favalli A, Bombaci M, Cuomo A, Collino F, Cricrì G, Ungaro R, Lombardi A, Mangioni D, Muscatello A, Aliberti S, Blasi F, Gori A, Abrignani S, De Francesco R, Biffo S, Grifantini R. Exosomes Recovered From the Plasma of COVID-19 Patients Expose SARS-CoV-2 Spike-Derived Fragments and Contribute to the Adaptive Immune Response. Front Immunol 2022; 12:785941. [PMID: 35111156 PMCID: PMC8801440 DOI: 10.3389/fimmu.2021.785941] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/16/2021] [Indexed: 12/12/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is an infectious disease caused by beta-coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that has rapidly spread across the globe starting from February 2020. It is well established that during viral infection, extracellular vesicles become delivery/presenting vectors of viral material. However, studies regarding extracellular vesicle function in COVID-19 pathology are still scanty. Here, we performed a comparative study on exosomes recovered from the plasma of either MILD or SEVERE COVID-19 patients. We show that although both types of vesicles efficiently display SARS-CoV-2 spike-derived peptides and carry immunomodulatory molecules, only those of MILD patients are capable of efficiently regulating antigen-specific CD4+ T-cell responses. Accordingly, by mass spectrometry, we show that the proteome of exosomes of MILD patients correlates with a proper functioning of the immune system, while that of SEVERE patients is associated with increased and chronic inflammation. Overall, we show that exosomes recovered from the plasma of COVID-19 patients possess SARS-CoV-2-derived protein material, have an active role in enhancing the immune response, and possess a cargo that reflects the pathological state of patients in the acute phase of the disease.
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Affiliation(s)
- Elisa Pesce
- Istituto Nazionale Genetica Molecolare (INGM), Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan, Italy
| | - Nicola Manfrini
- Istituto Nazionale Genetica Molecolare (INGM), Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan, Italy
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Chiara Cordiglieri
- Istituto Nazionale Genetica Molecolare (INGM), Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan, Italy
| | - Spartaco Santi
- Unit of Bologna, Consiglio Nazionale delle Ricerche (CNR) Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, Bologna, Italy
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Alessandra Bandera
- Infectious Diseases Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
- Centre for Multidisciplinary Research in Health Science (MACH), Università degli Studi di Milano, Milan, Italy
| | - Andrea Gobbini
- Istituto Nazionale Genetica Molecolare (INGM), Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan, Italy
| | - Paola Gruarin
- Istituto Nazionale Genetica Molecolare (INGM), Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan, Italy
| | - Andrea Favalli
- Istituto Nazionale Genetica Molecolare (INGM), Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan, Italy
| | - Mauro Bombaci
- Istituto Nazionale Genetica Molecolare (INGM), Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, Istituto Europeo di Oncologia (IEO), European Institute of Oncology Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Federica Collino
- Laboratory of Translational Research in Paediatric Nephro-Urology, Fondazione Ca’ Granda IRCCS Ospedale Maggiore Policlinico, Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milano, Milan, Italy
| | - Giulia Cricrì
- Laboratory of Translational Research in Paediatric Nephro-Urology, Fondazione Ca’ Granda IRCCS Ospedale Maggiore Policlinico, Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milano, Milan, Italy
| | - Riccardo Ungaro
- Infectious Diseases Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Andrea Lombardi
- Infectious Diseases Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Davide Mangioni
- Infectious Diseases Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Antonio Muscatello
- Infectious Diseases Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefano Aliberti
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
- Respiratory Unit and Cystic Fibrosis Adult Center, Respiratory Unit and Cystic Fibrosis Adult Center, Milan, Italy
| | - Francesco Blasi
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
- Respiratory Unit and Cystic Fibrosis Adult Center, Respiratory Unit and Cystic Fibrosis Adult Center, Milan, Italy
| | - Andrea Gori
- Infectious Diseases Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
- Centre for Multidisciplinary Research in Health Science (MACH), Università degli Studi di Milano, Milan, Italy
| | - Sergio Abrignani
- Istituto Nazionale Genetica Molecolare (INGM), Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan, Italy
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Raffaele De Francesco
- Istituto Nazionale Genetica Molecolare (INGM), Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan, Italy
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Stefano Biffo
- Istituto Nazionale Genetica Molecolare (INGM), Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan, Italy
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Renata Grifantini
- Istituto Nazionale Genetica Molecolare (INGM), Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan, Italy
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7
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Scagliola A, Miluzio A, Ventura G, Oliveto S, Cordiglieri C, Manfrini N, Cirino D, Ricciardi S, Valenti L, Baselli G, D'Ambrosio R, Maggioni M, Brina D, Bresciani A, Biffo S. Targeting of eIF6-driven translation induces a metabolic rewiring that reduces NAFLD and the consequent evolution to hepatocellular carcinoma. Nat Commun 2021; 12:4878. [PMID: 34385447 PMCID: PMC8361022 DOI: 10.1038/s41467-021-25195-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 07/08/2020] [Accepted: 07/24/2021] [Indexed: 12/30/2022] Open
Abstract
A postprandial increase of translation mediated by eukaryotic Initiation Factor 6 (eIF6) occurs in the liver. Its contribution to steatosis and disease is unknown. In this study we address whether eIF6-driven translation contributes to disease progression. eIF6 levels increase throughout the progression from Non-Alcoholic Fatty Liver Disease (NAFLD) to hepatocellular carcinoma. Reduction of eIF6 levels protects the liver from disease progression. eIF6 depletion blunts lipid accumulation, increases fatty acid oxidation (FAO) and reduces oncogenic transformation in vitro. In addition, eIF6 depletion delays the progression from NAFLD to hepatocellular carcinoma, in vivo. Mechanistically, eIF6 depletion reduces the translation of transcription factor C/EBPβ, leading to a drop in biomarkers associated with NAFLD progression to hepatocellular carcinoma and preserves mitochondrial respiration due to the maintenance of an alternative mTORC1-eIF4F translational branch that increases the expression of transcription factor YY1. We provide proof-of-concept that in vitro pharmacological inhibition of eIF6 activity recapitulates the protective effects of eIF6 depletion. We hypothesize the existence of a targetable, evolutionarily conserved translation circuit optimized for lipid accumulation and tumor progression.
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Affiliation(s)
- Alessandra Scagliola
- Istituto Nazionale di Genetica Molecolare, INGM, "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Annarita Miluzio
- Istituto Nazionale di Genetica Molecolare, INGM, "Romeo ed Enrica Invernizzi", Milan, Italy
| | | | - Stefania Oliveto
- Istituto Nazionale di Genetica Molecolare, INGM, "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Chiara Cordiglieri
- Istituto Nazionale di Genetica Molecolare, INGM, "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Nicola Manfrini
- Istituto Nazionale di Genetica Molecolare, INGM, "Romeo ed Enrica Invernizzi", Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
| | - Delia Cirino
- Department of Biosciences, University of Milan, Milan, Italy
| | - Sara Ricciardi
- Istituto Nazionale di Genetica Molecolare, INGM, "Romeo ed Enrica Invernizzi", Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
| | - Luca Valenti
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
- Translational Medicine, Department of Transfusion Medicine and Hematology, Fondazione IRCCS Ca' Granda Ospedale Policlinico, Milan, Italy
| | - Guido Baselli
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Roberta D'Ambrosio
- Department of Hepatology, Fondazione IRCCS Ca' Granda Granda Ospedale Policlinico, Milan, Italy
| | - Marco Maggioni
- Department of Pathology, Fondazione IRCCS Ca' Granda Ospedale Policlinico, Milan, Italy
| | - Daniela Brina
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Alberto Bresciani
- Department of Translational and Discovery Research, IRBM S.p.A., Pomezia (Roma), Italy
| | - Stefano Biffo
- Istituto Nazionale di Genetica Molecolare, INGM, "Romeo ed Enrica Invernizzi", Milan, Italy.
- Department of Biosciences, University of Milan, Milan, Italy.
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8
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Manfrini N, Mancino M, Miluzio A, Oliveto S, Balestra M, Calamita P, Alfieri R, Rossi RL, Sassoè-Pognetto M, Salio C, Cuomo A, Bonaldi T, Manfredi M, Marengo E, Ranzato E, Martinotti S, Cittaro D, Tonon G, Biffo S. FAM46C and FNDC3A Are Multiple Myeloma Tumor Suppressors That Act in Concert to Impair Clearing of Protein Aggregates and Autophagy. Cancer Res 2020; 80:4693-4706. [PMID: 32963011 DOI: 10.1158/0008-5472.can-20-1357] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/15/2020] [Accepted: 09/18/2020] [Indexed: 11/16/2022]
Abstract
Multiple myeloma is a plasma cell neoplasm characterized by the production of unfolded immunoglobulins, which cause endoplasmic reticulum (ER) stress and sensitivity to proteasome inhibition. The genomic landscape of multiple myeloma is characterized by the loss of several genes rarely mutated in other cancers that may underline specific weaknesses of multiple myeloma cells. One of these is FAM46C that is lost in more than 10% of patients with multiple myeloma. We show here that FAM46C is part of a new complex containing the ER-associated protein FNDC3A, which regulates trafficking and secretion and, by impairing autophagy, exacerbates proteostatic stress. Reconstitution of FAM46C in multiple myeloma cells that had lost it induced apoptosis and ER stress. Apoptosis was preceded by an increase of intracellular aggregates, which was not linked to increased translation of IgG mRNA, but rather to impairment of autophagy. Biochemical analysis showed that FAM46C requires interaction with ER bound protein FNDC3A to reside in the cytoplasmic side of the ER. FNDC3A was lost in some multiple myeloma cell lines. Importantly, depletion of FNDC3A increased the fitness of FAM46C-expressing cells and expression of FNDC3A in cells that had lost it recapitulated the effects of FAM46C, inducing aggregates and apoptosis. FAM46C and FNDC3A formed a complex that modulates secretion routes, increasing lysosome exocytosis. The cellular landscape generated by FAM46C/FNDC3A expression predicted sensitivity to sphingosine kinase inhibition. These results suggest that multiple myeloma cells remodel their trafficking machinery to cope with ER stress. SIGNIFICANCE: This study identifies a new multiple myeloma-specific tumor suppressor complex that regulates autophagy and unconventional secretion, highlighting the sensitivity of multiple myeloma cells to the accumulation of protein aggregates.
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Affiliation(s)
- Nicola Manfrini
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi," Milan, Italy.,Department of Biological Sciences, University of Milan, Milan, Italy
| | - Marilena Mancino
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi," Milan, Italy.,Department of Clinical Sciences and Community, University of Milan, Milan, Italy
| | - Annarita Miluzio
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi," Milan, Italy
| | - Stefania Oliveto
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi," Milan, Italy.,Department of Biological Sciences, University of Milan, Milan, Italy
| | - Matteo Balestra
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi," Milan, Italy
| | - Piera Calamita
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi," Milan, Italy.,Department of Biological Sciences, University of Milan, Milan, Italy
| | - Roberta Alfieri
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi," Milan, Italy
| | - Riccardo L Rossi
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi," Milan, Italy
| | - Marco Sassoè-Pognetto
- Department of Neuroscience "Rita Levi Montalcini," University of Turin, Torino, Italy
| | - Chiara Salio
- Department of Veterinary Sciences, University of Turin, Grugliasco, Torino, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Marcello Manfredi
- Center for Translational Research on Autoimmune and Allergic Diseases, University of Piemonte Orientale, Novara, Italy.,ISALIT, Novara, Italy.,Department of Translation Medicine, University of Piemonte Orientale, Novara, Italy
| | - Emilio Marengo
- Center for Translational Research on Autoimmune and Allergic Diseases, University of Piemonte Orientale, Novara, Italy.,ISALIT, Novara, Italy.,Department of Sciences and Technological Innovation, University of Piemonte Orientale, Alessandria, Italy
| | - Elia Ranzato
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Alessandria, Italy
| | - Simona Martinotti
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Alessandria, Italy
| | - Davide Cittaro
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giovanni Tonon
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy.,Functional Genomics of Cancer Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Stefano Biffo
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi," Milan, Italy. .,Department of Biological Sciences, University of Milan, Milan, Italy
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9
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Manfrini N, Ricciardi S, Alfieri R, Ventura G, Calamita P, Favalli A, Biffo S. Ribosome profiling unveils translational regulation of metabolic enzymes in primary CD4 + Th1 cells. Dev Comp Immunol 2020; 109:103697. [PMID: 32330465 DOI: 10.1016/j.dci.2020.103697] [Citation(s) in RCA: 8] [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: 01/29/2020] [Revised: 04/06/2020] [Accepted: 04/06/2020] [Indexed: 05/22/2023]
Abstract
The transition from a naïve to an effector T cell is an essential event that requires metabolic reprogramming. We have recently demonstrated that the rapid metabolic changes that occur following stimulation of naïve T cells require the translation of preexisting mRNAs. Here, we provide evidence that translation regulates the metabolic asset of effector T cells. By performing ribosome profiling in human CD4+ Th1 cells, we show that the metabolism of glucose, fatty acids and pentose phosphates is regulated at the translational level. In Th1 cells, each pathway has at least one enzyme regulated at the translational level and selected enzymes have high translational efficiencies. mRNA expression does not predict protein expression. For instance, PKM2 mRNA is equally present in naïve T and Th1 cells, but the protein is abundant only in Th1. 5'-untranslated regions (UTRs) may partly account for this regulation. Overall we suggest that immunometabolism is controlled by translation.
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Affiliation(s)
- Nicola Manfrini
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", Milano, Italy; Department of Biological Sciences, University of Milan, Milan, Italy
| | - Sara Ricciardi
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", Milano, Italy; Department of Biological Sciences, University of Milan, Milan, Italy
| | - Roberta Alfieri
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", Milano, Italy
| | - Gabriele Ventura
- Department of Biological Sciences, University of Milan, Milan, Italy
| | - Piera Calamita
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", Milano, Italy; Department of Biological Sciences, University of Milan, Milan, Italy
| | - Andrea Favalli
- Department of Biological Sciences, University of Milan, Milan, Italy
| | - Stefano Biffo
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", Milano, Italy; Department of Biological Sciences, University of Milan, Milan, Italy.
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10
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Pesce E, Miluzio A, Turcano L, Minici C, Cirino D, Calamita P, Manfrini N, Oliveto S, Ricciardi S, Grifantini R, Degano M, Bresciani A, Biffo S. Discovery and Preliminary Characterization of Translational Modulators that Impair the Binding of eIF6 to 60S Ribosomal Subunits. Cells 2020; 9:cells9010172. [PMID: 31936702 PMCID: PMC7017188 DOI: 10.3390/cells9010172] [Citation(s) in RCA: 8] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic initiation factor 6 (eIF6) is necessary for the nucleolar biogenesis of 60S ribosomes. However, most of eIF6 resides in the cytoplasm, where it acts as an initiation factor. eIF6 is necessary for maximal protein synthesis downstream of growth factor stimulation. eIF6 is an antiassociation factor that binds 60S subunits, in turn preventing premature 40S joining and thus the formation of inactive 80S subunits. It is widely thought that eIF6 antiassociation activity is critical for its function. Here, we exploited and improved our assay for eIF6 binding to ribosomes (iRIA) in order to screen for modulators of eIF6 binding to the 60S. Three compounds, eIFsixty-1 (clofazimine), eIFsixty-4, and eIFsixty-6 were identified and characterized. All three inhibit the binding of eIF6 to the 60S in the micromolar range. eIFsixty-4 robustly inhibits cell growth, whereas eIFsixty-1 and eIFsixty-6 might have dose- and cell-specific effects. Puromycin labeling shows that eIF6ixty-4 is a strong global translational inhibitor, whereas the other two are mild modulators. Polysome profiling and RT-qPCR show that all three inhibitors reduce the specific translation of well-known eIF6 targets. In contrast, none of them affect the nucleolar localization of eIF6. These data provide proof of principle that the generation of eIF6 translational modulators is feasible.
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Affiliation(s)
- Elisa Pesce
- National Institute of Molecular Genetics, “Fondazione Romeo ed Enrica Invernizzi”, INGM, Via Francesco Sforza 35, 20122 Milan, Italy; (E.P.); (A.M.); (D.C.); (P.C.); (N.M.); (S.O.); (S.R.); (R.G.)
| | - Annarita Miluzio
- National Institute of Molecular Genetics, “Fondazione Romeo ed Enrica Invernizzi”, INGM, Via Francesco Sforza 35, 20122 Milan, Italy; (E.P.); (A.M.); (D.C.); (P.C.); (N.M.); (S.O.); (S.R.); (R.G.)
| | - Lorenzo Turcano
- Department of Translational and Discovery Research, IRBM S.p.A., Via Pontina km 30, 600, 00071 Pomezia (Roma), Italy;
| | - Claudia Minici
- Biocrystallography Unit, Dept. of Immunology, Transplantation and Infectious Diseases, IRCCS Scientific Institute San Raffaele, Via Olgettina 58, 20132 Milan, Italy; (C.M.); (M.D.)
| | - Delia Cirino
- National Institute of Molecular Genetics, “Fondazione Romeo ed Enrica Invernizzi”, INGM, Via Francesco Sforza 35, 20122 Milan, Italy; (E.P.); (A.M.); (D.C.); (P.C.); (N.M.); (S.O.); (S.R.); (R.G.)
- DBS, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Piera Calamita
- National Institute of Molecular Genetics, “Fondazione Romeo ed Enrica Invernizzi”, INGM, Via Francesco Sforza 35, 20122 Milan, Italy; (E.P.); (A.M.); (D.C.); (P.C.); (N.M.); (S.O.); (S.R.); (R.G.)
- DBS, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Nicola Manfrini
- National Institute of Molecular Genetics, “Fondazione Romeo ed Enrica Invernizzi”, INGM, Via Francesco Sforza 35, 20122 Milan, Italy; (E.P.); (A.M.); (D.C.); (P.C.); (N.M.); (S.O.); (S.R.); (R.G.)
- DBS, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Stefania Oliveto
- National Institute of Molecular Genetics, “Fondazione Romeo ed Enrica Invernizzi”, INGM, Via Francesco Sforza 35, 20122 Milan, Italy; (E.P.); (A.M.); (D.C.); (P.C.); (N.M.); (S.O.); (S.R.); (R.G.)
- DBS, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Sara Ricciardi
- National Institute of Molecular Genetics, “Fondazione Romeo ed Enrica Invernizzi”, INGM, Via Francesco Sforza 35, 20122 Milan, Italy; (E.P.); (A.M.); (D.C.); (P.C.); (N.M.); (S.O.); (S.R.); (R.G.)
- DBS, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Renata Grifantini
- National Institute of Molecular Genetics, “Fondazione Romeo ed Enrica Invernizzi”, INGM, Via Francesco Sforza 35, 20122 Milan, Italy; (E.P.); (A.M.); (D.C.); (P.C.); (N.M.); (S.O.); (S.R.); (R.G.)
| | - Massimo Degano
- Biocrystallography Unit, Dept. of Immunology, Transplantation and Infectious Diseases, IRCCS Scientific Institute San Raffaele, Via Olgettina 58, 20132 Milan, Italy; (C.M.); (M.D.)
| | - Alberto Bresciani
- Department of Translational and Discovery Research, IRBM S.p.A., Via Pontina km 30, 600, 00071 Pomezia (Roma), Italy;
- Correspondence: (A.B.); (S.B.)
| | - Stefano Biffo
- National Institute of Molecular Genetics, “Fondazione Romeo ed Enrica Invernizzi”, INGM, Via Francesco Sforza 35, 20122 Milan, Italy; (E.P.); (A.M.); (D.C.); (P.C.); (N.M.); (S.O.); (S.R.); (R.G.)
- DBS, University of Milan, Via Celoria 26, 20133 Milan, Italy
- Correspondence: (A.B.); (S.B.)
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11
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Romano N, Veronese M, Manfrini N, Zolla L, Ceci M. Ribosomal RACK1 promotes proliferation of neuroblastoma cells independently of global translation upregulation. Cell Signal 2019; 53:102-110. [DOI: 10.1016/j.cellsig.2018.09.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 09/26/2018] [Accepted: 09/26/2018] [Indexed: 02/04/2023]
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12
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Ricciardi S, Manfrini N, Alfieri R, Calamita P, Crosti MC, Gallo S, Müller R, Pagani M, Abrignani S, Biffo S. The Translational Machinery of Human CD4 + T Cells Is Poised for Activation and Controls the Switch from Quiescence to Metabolic Remodeling. Cell Metab 2018; 28:961. [PMID: 30517897 PMCID: PMC6288181 DOI: 10.1016/j.cmet.2018.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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13
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Ricciardi S, Manfrini N, Alfieri R, Calamita P, Crosti MC, Gallo S, Müller R, Pagani M, Abrignani S, Biffo S. The Translational Machinery of Human CD4 + T Cells Is Poised for Activation and Controls the Switch from Quiescence to Metabolic Remodeling. Cell Metab 2018; 28:895-906.e5. [PMID: 30197303 PMCID: PMC6773601 DOI: 10.1016/j.cmet.2018.08.009] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/24/2018] [Accepted: 08/07/2018] [Indexed: 12/13/2022]
Abstract
Naive T cells respond to T cell receptor (TCR) activation by leaving quiescence, remodeling metabolism, initiating expansion, and differentiating toward effector T cells. The molecular mechanisms coordinating the naive to effector transition are central to the functioning of the immune system, but remain elusive. Here, we discover that T cells fulfill this transitional process through translational control. Naive cells accumulate untranslated mRNAs encoding for glycolysis and fatty acid synthesis factors and possess a translational machinery poised for immediate protein synthesis. Upon TCR engagement, activation of the translational machinery leads to synthesis of GLUT1 protein to drive glucose entry. Subsequently, translation of ACC1 mRNA completes metabolic reprogramming toward an effector phenotype. Notably, inhibition of the eIF4F complex abrogates lymphocyte metabolic activation and differentiation, suggesting ACC1 to be a key regulatory node. Thus, our results demonstrate that translation is a direct mediator of T cell metabolism and indicate translation factors as targets for novel immunotherapeutic approaches.
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Affiliation(s)
- Sara Ricciardi
- INGM, National Institute of Molecular Genetics, "Romeo ed Enrica Invernizzi", Via Francesco Sforza 35, Milan 20122, Italy; Bioscience Department, Università degli Studi di Milano, Milan, Italy
| | - Nicola Manfrini
- INGM, National Institute of Molecular Genetics, "Romeo ed Enrica Invernizzi", Via Francesco Sforza 35, Milan 20122, Italy
| | - Roberta Alfieri
- INGM, National Institute of Molecular Genetics, "Romeo ed Enrica Invernizzi", Via Francesco Sforza 35, Milan 20122, Italy
| | - Piera Calamita
- INGM, National Institute of Molecular Genetics, "Romeo ed Enrica Invernizzi", Via Francesco Sforza 35, Milan 20122, Italy; Bioscience Department, Università degli Studi di Milano, Milan, Italy
| | - Maria Cristina Crosti
- INGM, National Institute of Molecular Genetics, "Romeo ed Enrica Invernizzi", Via Francesco Sforza 35, Milan 20122, Italy
| | - Simone Gallo
- INGM, National Institute of Molecular Genetics, "Romeo ed Enrica Invernizzi", Via Francesco Sforza 35, Milan 20122, Italy
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research and Department of Pharmacy, Saarland University Campus, Building C2.3, Saarbrücken 66123, Germany
| | - Massimiliano Pagani
- INGM, National Institute of Molecular Genetics, "Romeo ed Enrica Invernizzi", Via Francesco Sforza 35, Milan 20122, Italy; Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Sergio Abrignani
- INGM, National Institute of Molecular Genetics, "Romeo ed Enrica Invernizzi", Via Francesco Sforza 35, Milan 20122, Italy; Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Stefano Biffo
- INGM, National Institute of Molecular Genetics, "Romeo ed Enrica Invernizzi", Via Francesco Sforza 35, Milan 20122, Italy; Bioscience Department, Università degli Studi di Milano, Milan, Italy.
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14
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Manfrini N, Ricciardi S, Miluzio A, Fedeli M, Scagliola A, Gallo S, Brina D, Adler T, Busch DH, Gailus-Durner V, Fuchs H, Hrabě de Angelis M, Biffo S. High levels of eukaryotic Initiation Factor 6 (eIF6) are required for immune system homeostasis and for steering the glycolytic flux of TCR-stimulated CD4 + T cells in both mice and humans. Dev Comp Immunol 2017; 77:69-76. [PMID: 28743432 DOI: 10.1016/j.dci.2017.07.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 05/14/2017] [Revised: 07/21/2017] [Accepted: 07/21/2017] [Indexed: 06/07/2023]
Abstract
Eukaryotic Initiation Factor 6 (eIF6) is required for 60S ribosomal subunit biogenesis and efficient initiation of translation. Intriguingly, in both mice and humans, endogenous levels of eIF6 are detrimental as they act as tumor and obesity facilitators, raising the question on the evolutionary pressure that maintains high eIF6 levels. Here we show that, in mice and humans, high levels of eIF6 are required for proper immune functions. First, eIF6 heterozygous (het) mice show an increased mortality during viral infection and a reduction of peripheral blood CD4+ Effector Memory T cells. In human CD4+ T cells, eIF6 levels rapidly increase upon T-cell receptor activation and drive the glycolytic switch and the acquisition of effector functions. Importantly, in CD4+ T cells, eIF6 levels control interferon-γ (IFN-γ) secretion without affecting proliferation. In conclusion, the immune system has a high evolutionary pressure for the maintenance of a dynamic and powerful regulation of the translational machinery.
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Affiliation(s)
- Nicola Manfrini
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi" - INGM, Via F. Sforza 35, 20122 Milan, Italy.
| | - Sara Ricciardi
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi" - INGM, Via F. Sforza 35, 20122 Milan, Italy
| | - Annarita Miluzio
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi" - INGM, Via F. Sforza 35, 20122 Milan, Italy
| | - Maya Fedeli
- Experimental Immunology Unit, Division of Immunology, Transplantation and Infectious Diseases, DIBIT, H. San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Alessandra Scagliola
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi" - INGM, Via F. Sforza 35, 20122 Milan, Italy; Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Simone Gallo
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi" - INGM, Via F. Sforza 35, 20122 Milan, Italy; Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Daniela Brina
- Molecular Oncology Group, Institute of Oncology Research (IOR), Oncology Institute of Southern Switzerland (IOSI), Via Mirasole 22A, Bellinzona, Switzerland
| | - Thure Adler
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Trogerstrasse 30, 81675 Munich, Germany
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany; German Center for Diabetes Research, 85764 Neuherberg, Germany
| | - Stefano Biffo
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi" - INGM, Via F. Sforza 35, 20122 Milan, Italy; Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy.
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15
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Biffo S, Manfrini N, Ricciardi S. Crosstalks between translation and metabolism in cancer. Curr Opin Genet Dev 2017; 48:75-81. [PMID: 29153483 DOI: 10.1016/j.gde.2017.10.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/23/2017] [Accepted: 10/24/2017] [Indexed: 12/26/2022]
Abstract
Albeit cancer patients' heterogeneity, all tumor cells have alterations of both metabolism and translation. The simplest explanation for this common feature is that several oncogenes coordinate a translational and metabolic reprogramming that is necessary for tumor cells to thrive. Overall, at least three oncogenic pathways, namely c-Myc, RAS and PI3K-mTOR, are known to affect both translation and metabolism by stimulating glycolysis and protein synthesis. The crosstalk between metabolite production and the translational machinery is, instead, less understood. What is known is that, on one side, translation initiation factors, such as eIF4E and eIF6, drive tumor growth and regulate metabolism through selective translation of nucleotide biosynthesis, glycolysis and fatty acid synthesis rate-limiting mRNAs, and on the other, that nutrient levels regulate the translational machinery by inducing full activity of translation factors. Therefore, translation and metabolism offer several therapeutic targets to be fully exploited in future studies.
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Affiliation(s)
- Stefano Biffo
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi", INGM, 20122 Milano, Italy; Department of Biosciences, University of Milano, 20133 Milano, Italy.
| | - Nicola Manfrini
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi", INGM, 20122 Milano, Italy
| | - Sara Ricciardi
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi", INGM, 20122 Milano, Italy
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Manfrini N, Ricciardi S, Miluzio A, Fedeli M, Scagliola A, Gallo S, Adler T, Busch DH, Gailus-Durner V, Fuchs H, de Angelis MH, Biffo S. Data on the effects of eIF6 downmodulation on the proportions of innate and adaptive immune system cell subpopulations and on thymocyte maturation. Data Brief 2017; 14:653-658. [PMID: 28924581 PMCID: PMC5591389 DOI: 10.1016/j.dib.2017.08.023] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 08/02/2017] [Accepted: 08/24/2017] [Indexed: 11/28/2022] Open
Abstract
The data described in this article are related to “High levels of eukaryotic Initiation Factor 6 (eIF6) are required for immune system homeostasis and for steering the glycolytic flux of TCR-stimulated CD4+ T cells in both mice and humans” (Manfrini et al., in press) [1]. eIF6 is a translation initiation factor required for ribosomal biogenesis (Sanvito et al., 1999) [2] and for proper translational initiation (Gallo and Manfrini, 2015; Miluzio et al., 2016) [3], [4] whose protein abundance requires tight regulation. Here we analyze by flow cytometry the effects of eIF6 depletion on proportions of specific innate and adaptive immune system subpopulations and on thymocyte maturation in mice.
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Affiliation(s)
- Nicola Manfrini
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi" - INGM, via F. Sforza 35, 20122 Milan, Italy
| | - Sara Ricciardi
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi" - INGM, via F. Sforza 35, 20122 Milan, Italy
| | - Annarita Miluzio
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi" - INGM, via F. Sforza 35, 20122 Milan, Italy
| | - Maya Fedeli
- Experimental Immunology Unit, Division of Immunology, Transplantation and Infectious Diseases, DIBIT, H. San Raffaele Scientific Institute, via Olgettina 58, 20132 Milan, Italy
| | - Alessandra Scagliola
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi" - INGM, via F. Sforza 35, 20122 Milan, Italy.,Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Simone Gallo
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi" - INGM, via F. Sforza 35, 20122 Milan, Italy.,Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Thure Adler
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Trogerstrasse 30, 81675 Munich, Germany
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany.,Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany.,German Center for Diabetes Research, 85764 Neuherberg, Germany
| | - Stefano Biffo
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi" - INGM, via F. Sforza 35, 20122 Milan, Italy.,Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
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Oliveto S, Mancino M, Manfrini N, Biffo S. Role of microRNAs in translation regulation and cancer. World J Biol Chem 2017; 8:45-56. [PMID: 28289518 PMCID: PMC5329714 DOI: 10.4331/wjbc.v8.i1.45] [Citation(s) in RCA: 276] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/20/2016] [Accepted: 01/18/2017] [Indexed: 02/05/2023] Open
Abstract
MicroRNAs (miRNAs) are pervasively expressed and regulate most biological functions. They function by modulating transcriptional and translational programs and therefore they orchestrate both physiological and pathological processes, such as development, cell differentiation, proliferation, apoptosis and tumor growth. miRNAs work as small guide molecules in RNA silencing, by negatively regulating the expression of several genes both at mRNA and protein level, by degrading their mRNA target and/or by silencing translation. One of the most recent advances in the field is the comprehension of their role in oncogenesis. The number of miRNA genes is increasing and an alteration in the level of miRNAs is involved in the initiation, progression and metastases formation of several tumors. Some tumor types show a distinct miRNA signature that distinguishes them from normal tissues and from other cancer types. Genetic and biochemical evidence supports the essential role of miRNAs in tumor development. Although the abnormal expression of miRNAs in cancer cells is a widely accepted phenomenon, the cause of this dysregulation is still unknown. Here, we discuss the biogenesis of miRNAs, focusing on the mechanisms by which they regulate protein synthesis. In addition we debate on their role in cancer, highlighting their potential to become therapeutic targets.
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Gallo S, Manfrini N. Working hard at the nexus between cell signaling and the ribosomal machinery: An insight into the roles of RACK1 in translational regulation. ACTA ACUST UNITED AC 2015; 3:e1120382. [PMID: 26824030 DOI: 10.1080/21690731.2015.1120382] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [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: 08/20/2015] [Revised: 10/19/2015] [Accepted: 11/09/2015] [Indexed: 02/08/2023]
Abstract
RACK1 is a ribosome-associated protein which functions as a receptor for activated PKCs. It also acts as a scaffold for many other proteins involved in diverse signaling pathways, e.g. Src, JNK, PDE4D and FAK signaling. With such a broad interactome, RACK1 has been suggested to function as a linker between cell signaling and the translation machinery. Accordingly, RACK1 modulates translation at different levels in several model organisms. For instance, it regulates ribosome stalling and mRNA quality control in yeasts and promotes translation efficiency downstream of specific cellular stimuli in mammals. However, the molecular mechanism by which RACK1 exerts these roles is widely uncharacterized. Moreover, the full list of ribosome-recruited RACK1 interactors still needs characterization. Here we discuss in vivo and in vitro findings to better delineate the roles of RACK1 in regulating ribosome function and translation.
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Affiliation(s)
- Simone Gallo
- Molecular Histology and Cell Growth Unit; National Institute of Molecular Genetics - INGM "Romeo and Enrica Invernizzi" ; Milan, Italy
| | - Nicola Manfrini
- Molecular Histology and Cell Growth Unit; National Institute of Molecular Genetics - INGM "Romeo and Enrica Invernizzi" ; Milan, Italy
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Manfrini N, Clerici M, Wery M, Colombo CV, Descrimes M, Morillon A, d'Adda di Fagagna F, Longhese MP. Resection is responsible for loss of transcription around a double-strand break in Saccharomyces cerevisiae. eLife 2015; 4. [PMID: 26231041 PMCID: PMC4541074 DOI: 10.7554/elife.08942] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [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: 05/22/2015] [Accepted: 07/30/2015] [Indexed: 11/13/2022] Open
Abstract
Emerging evidence indicate that the mammalian checkpoint kinase ATM induces transcriptional silencing in cis to DNA double-strand breaks (DSBs) through a poorly understood mechanism. Here we show that in Saccharomyces cerevisiae a single DSB causes transcriptional inhibition of proximal genes independently of Tel1/ATM and Mec1/ATR. Since the DSB ends undergo nucleolytic degradation (resection) of their 5'-ending strands, we investigated the contribution of resection in this DSB-induced transcriptional inhibition. We discovered that resection-defective mutants fail to stop transcription around a DSB, and the extent of this failure correlates with the severity of the resection defect. Furthermore, Rad9 and generation of γH2A reduce this DSB-induced transcriptional inhibition by counteracting DSB resection. Therefore, the conversion of the DSB ends from double-stranded to single-stranded DNA, which is necessary to initiate DSB repair by homologous recombination, is responsible for loss of transcription around a DSB in S. cerevisiae.
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Affiliation(s)
- Nicola Manfrini
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Michela Clerici
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Maxime Wery
- Institut Curie, Dynamics of Genetic Information: Fundamental Basis and Cancer, Université Pierre et Marie Curie, Paris, France
| | | | - Marc Descrimes
- Institut Curie, Dynamics of Genetic Information: Fundamental Basis and Cancer, Université Pierre et Marie Curie, Paris, France
| | - Antonin Morillon
- Institut Curie, Dynamics of Genetic Information: Fundamental Basis and Cancer, Université Pierre et Marie Curie, Paris, France
| | | | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
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Manfrini N, Trovesi C, Wery M, Martina M, Cesena D, Descrimes M, Morillon A, d'Adda di Fagagna F, Longhese MP. RNA-processing proteins regulate Mec1/ATR activation by promoting generation of RPA-coated ssDNA. EMBO Rep 2014; 16:221-31. [PMID: 25527408 DOI: 10.15252/embr.201439458] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Eukaryotic cells respond to DNA double-strand breaks (DSBs) by activating a checkpoint that depends on the protein kinases Tel1/ATM and Mec1/ATR. Mec1/ATR is activated by RPA-coated single-stranded DNA (ssDNA), which arises upon nucleolytic degradation (resection) of the DSB. Emerging evidences indicate that RNA-processing factors play critical, yet poorly understood, roles in genomic stability. Here, we provide evidence that the Saccharomyces cerevisiae RNA decay factors Xrn1, Rrp6 and Trf4 regulate Mec1/ATR activation by promoting generation of RPA-coated ssDNA. The lack of Xrn1 inhibits ssDNA generation at the DSB by preventing the loading of the MRX complex. By contrast, DSB resection is not affected in the absence of Rrp6 or Trf4, but their lack impairs the recruitment of RPA, and therefore of Mec1, to the DSB. Rrp6 and Trf4 inactivation affects neither Rad51/Rad52 association nor DSB repair by homologous recombination (HR), suggesting that full Mec1 activation requires higher amount of RPA-coated ssDNA than HR-mediated repair. Noteworthy, deep transcriptome analyses do not identify common misregulated gene expression that could explain the observed phenotypes. Our results provide a novel link between RNA processing and genome stability.
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Affiliation(s)
- Nicola Manfrini
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Camilla Trovesi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Maxime Wery
- Institut Curie, CNRS UMR3244 Université Pierre et Marie Curie, Paris Cedex 05, France
| | - Marina Martina
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Daniele Cesena
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Marc Descrimes
- Institut Curie, CNRS UMR3244 Université Pierre et Marie Curie, Paris Cedex 05, France
| | - Antonin Morillon
- Institut Curie, CNRS UMR3244 Université Pierre et Marie Curie, Paris Cedex 05, France
| | - Fabrizio d'Adda di Fagagna
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Milan, Italy Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
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Trovesi C, Manfrini N, Falcettoni M, Longhese MP. Regulation of the DNA damage response by cyclin-dependent kinases. J Mol Biol 2013; 425:4756-66. [PMID: 23603016 DOI: 10.1016/j.jmb.2013.04.013] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [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: 12/27/2012] [Revised: 04/09/2013] [Accepted: 04/15/2013] [Indexed: 12/13/2022]
Abstract
The eukaryotic cell cycle comprises a series of events, whose ordering and correct progression depends on the oscillating activity of cyclin-dependent kinases (Cdks), which safeguard timely duplication and segregation of the genome. Cell division is intimately connected to an evolutionarily conserved DNA damage response (DDR), which involves DNA repair pathways that reverse DNA lesions, as well as checkpoint pathways that inhibit cell cycle progression while repair occurs. There is increasing evidence that Cdks are involved in the DDR, in particular in DNA repair by homologous recombination and in activation of the checkpoint response. However, Cdks have to be carefully regulated, because even an excess of their activity can affect genome stability. In this review, we consider the physiological role of Cdks in the DDR.
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Affiliation(s)
- Camilla Trovesi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
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Bonetti D, Clerici M, Manfrini N, Lucchini G, Longhese MP. The MRX complex plays multiple functions in resection of Yku- and Rif2-protected DNA ends. PLoS One 2010; 5:e14142. [PMID: 21152442 PMCID: PMC2994746 DOI: 10.1371/journal.pone.0014142] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 11/09/2010] [Indexed: 02/06/2023] Open
Abstract
The ends of both double-strand breaks (DSBs) and telomeres undergo tightly regulated 5′ to 3′ resection. Resection of DNA ends, which is specifically inhibited during the G1 cell cycle phase, requires the MRX complex, Sae2, Sgs1 and Exo1. Moreover, it is negatively regulated by the non-homologous end-joining component Yku and the telomeric protein Rif2. Here, we investigate the nuclease activities that are inhibited at DNA ends by Rif2 and Yku in G1 versus G2 by using an inducible short telomere assay. We show that, in the absence of the protective function of Rif2, resection in G1 depends primarily on MRX nuclease activity and Sae2, whereas Exo1 and Sgs1 bypass the requirement of MRX nuclease activity only if Yku is absent. In contrast, Yku-mediated inhibition is relieved in G2, where resection depends on Mre11 nuclease activity, Exo1 and, to a minor extent, Sgs1. Furthermore, Exo1 compensates for a defective MRX nuclease activity more efficiently in the absence than in the presence of Rif2, suggesting that Rif2 inhibits not only MRX but also Exo1. Notably, the presence of MRX, but not its nuclease activity, is required and sufficient to override Yku-mediated inhibition of Exo1 in G2, whereas it is required but not sufficient in G1. Finally, the integrity of MRX is also necessary to promote Exo1- and Sgs1-dependent resection, possibly by facilitating Exo1 and Sgs1 recruitment to DNA ends. Thus, resection of DNA ends that are protected by Yku and Rif2 involves multiple functions of the MRX complex that do not necessarily require its nuclease activity.
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Affiliation(s)
- Diego Bonetti
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
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Longhese MP, Bonetti D, Manfrini N, Clerici M. Mechanisms and regulation of DNA end resection. EMBO J 2010; 29:2864-74. [PMID: 20647996 DOI: 10.1038/emboj.2010.165] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Accepted: 06/28/2010] [Indexed: 02/07/2023] Open
Abstract
DNA double-strand breaks (DSBs) are highly hazardous for genome integrity, because failure to repair these lesions can lead to genomic instability. DSBs can arise accidentally at unpredictable locations into the genome, but they are also normal intermediates in meiotic recombination. Moreover, the natural ends of linear chromosomes resemble DSBs. Although intrachromosomal DNA breaks are potent stimulators of the DNA damage response, the natural ends of linear chromosomes are packaged into protective structures called telomeres that suppress DNA repair/recombination activities. Although DSBs and telomeres are functionally different, they both undergo 5'-3' nucleolytic degradation of DNA ends, a process known as resection. The resulting 3'-single-stranded DNA overhangs enable repair of DSBs by homologous recombination (HR), whereas they allow the action of telomerase at telomeres. The molecular activities required for DSB and telomere end resection are similar, indicating that the initial steps of HR and telomerase-mediated elongation are related. Resection of both DSBs and telomeres must be tightly regulated in time and space to ensure genome stability and cell survival.
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Affiliation(s)
- Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza, Milan, Italy.
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Manfrini N, Guerini I, Citterio A, Lucchini G, Longhese MP. Processing of meiotic DNA double strand breaks requires cyclin-dependent kinase and multiple nucleases. J Biol Chem 2010; 285:11628-37. [PMID: 20150422 DOI: 10.1074/jbc.m110.104083] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Meiotic recombination requires the formation of programmed Spo11-dependent DNA double strand breaks (DSBs). In Saccharomyces cerevisiae, the Sae2 protein and the Mre11-Rad50-Xrs2 complex are necessary to remove the covalently attached Spo11 protein from the DNA ends, which are then resected by so far unknown nucleases. Here, we demonstrate that phosphorylation of Sae2 Ser-267 by cyclin-dependent kinase 1 (Cdk1) is required to initiate meiotic DSB resection by allowing Spo11 removal from DSB ends. This finding suggests that Cdk1 activity is required for the processing of Spo11-induced DSBs, thus providing a mechanism for coordinating DSB resection with progression through meiotic prophase. Furthermore, the helicase Sgs1 and the nucleases Exo1 and Dna2 participate in lengthening the 5'-3' resection tracts during meiosis by controlling a step subsequent to Spo11 removal.
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Affiliation(s)
- Nicola Manfrini
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
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Longhese MP, Bonetti D, Guerini I, Manfrini N, Clerici M. DNA double-strand breaks in meiosis: Checking their formation, processing and repair. DNA Repair (Amst) 2009; 8:1127-38. [DOI: 10.1016/j.dnarep.2009.04.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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