1
|
Frasson I, Diamante L, Zangrossi M, Carbognin E, Dalla Pietà A, Penna A, Rosato A, Verin R, Torrigiani F, Salata C, Dizanzo MP, Vaccaro L, Cacchiarelli D, Richter SN, Montagner M, Martello G. Identification of druggable host dependency factors shared by multiple SARS-CoV-2 variants of concern. J Mol Cell Biol 2024:mjae004. [PMID: 38305139 DOI: 10.1093/jmcb/mjae004] [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: 02/03/2024] Open
Abstract
The high mutation rate of SARS-CoV-2 leads to the emergence of multiple variants, some of which are resistant to vaccines and drugs targeting viral elements. Targeting host dependency factors, e.g. cellular proteins required for viral replication, would help prevent resistance. However, it remains unclear whether different SARS-CoV-2 variants induce conserved cellular responses and exploit the same core host factors. To this end, we compared three variants of concern and found that the host transcriptional response was conserved, differing only in kinetics and magnitude. Through CRISPR screening, we identified host genes required for infection by each variant. Most of the genes were shared by multiple variants. We validated our hits with small molecules and repurposed Food and Drug Administration-approved drugs. All the drugs were highly active against all the variants tested, including new variants that emerged during the study (Delta and Omicron). Mechanistically, we identified reactive oxygen species production as a key step in early virus replication. Antioxidants such as N-acetyl cysteine (NAC) were effective against all the variants in both human lung cells and a humanised mouse model. Our study supports the use of available antioxidant drugs, such as NAC, as a general and effective anti-COVID-19 approach.
Collapse
Affiliation(s)
- Ilaria Frasson
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
| | - Linda Diamante
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
- Department of Biology, Armenise/Harvard Pluripotent Stem Cell Biology Laboratory, University of Padua, Padua 35131, Italy
| | - Manuela Zangrossi
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
| | - Elena Carbognin
- Department of Biology, Armenise/Harvard Pluripotent Stem Cell Biology Laboratory, University of Padua, Padua 35131, Italy
| | - Anna Dalla Pietà
- Department. of Surgery, Oncology and Gastroenterology, University of Padua, Padua 35128, Italy
| | - Alessandro Penna
- Department. of Surgery, Oncology and Gastroenterology, University of Padua, Padua 35128, Italy
| | - Antonio Rosato
- Department. of Surgery, Oncology and Gastroenterology, University of Padua, Padua 35128, Italy
- Veneto Institute of Oncology IOV-IRCCS, Padua 35128, Italy
| | - Ranieri Verin
- Department of Comparative Biomedicine and Food Science, University of Padua, Padua 35020, Italy
| | - Filippo Torrigiani
- Department of Comparative Biomedicine and Food Science, University of Padua, Padua 35020, Italy
| | - Cristiano Salata
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
| | | | - Lorenzo Vaccaro
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli 80078, Italy
- Department of Translational Medicine, Federico II University, Naples 80138, Italy
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli 80078, Italy
- Department of Translational Medicine, Federico II University, Naples 80138, Italy
- School for Advanced Studies, Genomics and Experimental Medicine Program, University of Naples "Federico II", Naples 80138, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
- Microbiology and Virology Unit, Padua University Hospital, Padua 35128, Italy
| | - Marco Montagner
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
| | - Graziano Martello
- Department of Biology, Armenise/Harvard Pluripotent Stem Cell Biology Laboratory, University of Padua, Padua 35131, Italy
| |
Collapse
|
2
|
Dinarello A, Betto RM, Diamante L, Tesoriere A, Ghirardo R, Cioccarelli C, Meneghetti G, Peron M, Laquatra C, Tiso N, Martello G, Argenton F. STAT3 and HIF1α cooperatively mediate the transcriptional and physiological responses to hypoxia. Cell Death Discov 2023; 9:226. [PMID: 37407568 DOI: 10.1038/s41420-023-01507-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/04/2023] [Accepted: 06/20/2023] [Indexed: 07/07/2023] Open
Abstract
STAT3 and HIF1α are two fundamental transcription factors involved in many merging processes, like angiogenesis, metabolism, and cell differentiation. Notably, under pathological conditions, the two factors have been shown to interact genetically, but both the molecular mechanisms underlying such interactions and their relevance under physiological conditions remain unclear. In mouse embryonic stem cells (ESCs) we manage to determine the specific subset of hypoxia-induced genes that need STAT3 to be properly transcribed and, among them, fundamental genes like Vegfa, Hk1, Hk2, Pfkp and Hilpda are worth mentioning. Unexpectedly, we also demonstrated that the absence of STAT3 does not affect the expression of Hif1α mRNA nor the stabilization of HIF1α protein, but the STAT3-driven regulation of the hypoxia-dependent subset of gene could rely on the physical interaction between STAT3 and HIF1α. To further elucidate the physiological roles of this STAT3 non-canonical nuclear activity, we used a CRISPR/Cas9 zebrafish stat3 knock-out line. Notably, hypoxia-related fluorescence of the hypoxia zebrafish reporter line (HRE:mCherry) cannot be induced when Stat3 is not active and, while Stat3 Y705 phosphorylation seems to have a pivotal role in this process, S727 does not affect the Stat3-dependent hypoxia response. Hypoxia is fundamental for vascularization, angiogenesis and immune cells mobilization; all processes that, surprisingly, cannot be induced by low oxygen levels when Stat3 is genetically ablated. All in all, here we report the specific STAT3/HIF1α-dependent subset of genes in vitro and, for the first time with an in vivo model, we determined some of the physiological roles of STAT3-hypoxia crosstalk.
Collapse
Affiliation(s)
| | | | - Linda Diamante
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | | | | | | | | | - Claudio Laquatra
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Natascia Tiso
- Department of Biology, University of Padova, Padova, Italy
| | | | | |
Collapse
|
3
|
Ferlazzo GM, Gambetta AM, Amato S, Cannizzaro N, Angiolillo S, Arboit M, Diamante L, Carbognin E, Romani P, La Torre F, Galimberti E, Pflug F, Luoni M, Giannelli S, Pepe G, Capocci L, Di Pardo A, Vanzani P, Zennaro L, Broccoli V, Leeb M, Moro E, Maglione V, Martello G. Genome-wide screening in pluripotent cells identifies Mtf1 as a suppressor of mutant huntingtin toxicity. Nat Commun 2023; 14:3962. [PMID: 37407555 DOI: 10.1038/s41467-023-39552-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/19/2023] [Indexed: 07/07/2023] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by CAG-repeat expansions in the huntingtin (HTT) gene. The resulting mutant HTT (mHTT) protein induces toxicity and cell death via multiple mechanisms and no effective therapy is available. Here, we employ a genome-wide screening in pluripotent mouse embryonic stem cells (ESCs) to identify suppressors of mHTT toxicity. Among the identified suppressors, linked to HD-associated processes, we focus on Metal response element binding transcription factor 1 (Mtf1). Forced expression of Mtf1 counteracts cell death and oxidative stress caused by mHTT in mouse ESCs and in human neuronal precursor cells. In zebrafish, Mtf1 reduces malformations and apoptosis induced by mHTT. In R6/2 mice, Mtf1 ablates motor defects and reduces mHTT aggregates and oxidative stress. Our screening strategy enables a quick in vitro identification of promising suppressor genes and their validation in vivo, and it can be applied to other monogenic diseases.
Collapse
Affiliation(s)
- Giorgia Maria Ferlazzo
- Department of Molecular Medicine, Medical School, University of Padua, 35131, Padua, Italy
- Aptuit (Verona) S.r.l., an Evotec Company, Campus Levi-Montalcini, 37135, Verona, Italy
| | - Anna Maria Gambetta
- Department of Molecular Medicine, Medical School, University of Padua, 35131, Padua, Italy
- Department of Biology, University of Padova, Via U. Bassi 58B, 35131, Padua, Italy
| | - Sonia Amato
- Department of Biology, University of Padova, Via U. Bassi 58B, 35131, Padua, Italy
- Department of Neuroscience, University of Padova, Via Belzoni, 160, 35131, Padua, Italy
| | - Noemi Cannizzaro
- Department of Molecular Medicine, Medical School, University of Padua, 35131, Padua, Italy
| | - Silvia Angiolillo
- Department of Molecular Medicine, Medical School, University of Padua, 35131, Padua, Italy
| | - Mattia Arboit
- Department of Molecular Medicine, Medical School, University of Padua, 35131, Padua, Italy
| | - Linda Diamante
- Department of Biology, University of Padova, Via U. Bassi 58B, 35131, Padua, Italy
| | - Elena Carbognin
- Department of Biology, University of Padova, Via U. Bassi 58B, 35131, Padua, Italy
| | - Patrizia Romani
- Department of Molecular Medicine, Medical School, University of Padua, 35131, Padua, Italy
| | - Federico La Torre
- Department of Biology, University of Padova, Via U. Bassi 58B, 35131, Padua, Italy
| | - Elena Galimberti
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Dr Bohr Gasse 9, 1030, Vienna, Austria
| | - Florian Pflug
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Dr Bohr Gasse 9, 1030, Vienna, Austria
| | - Mirko Luoni
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Serena Giannelli
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
| | | | | | | | - Paola Vanzani
- Department of Molecular Medicine, Medical School, University of Padua, 35131, Padua, Italy
| | - Lucio Zennaro
- Department of Molecular Medicine, Medical School, University of Padua, 35131, Padua, Italy
| | - Vania Broccoli
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
- CNR Institute of Neuroscience, 20854, Vedrano al Lambro, Italy
| | - Martin Leeb
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Dr Bohr Gasse 9, 1030, Vienna, Austria
| | - Enrico Moro
- Department of Molecular Medicine, Medical School, University of Padua, 35131, Padua, Italy
| | | | - Graziano Martello
- Department of Biology, University of Padova, Via U. Bassi 58B, 35131, Padua, Italy.
| |
Collapse
|
4
|
Diamante L, Martello G. Metabolic regulation in pluripotent stem cells. Curr Opin Genet Dev 2022; 75:101923. [PMID: 35691147 DOI: 10.1016/j.gde.2022.101923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/28/2022] [Accepted: 05/05/2022] [Indexed: 11/03/2022]
Abstract
Pluripotent stem cells (PSCs) have the capacity to give rise to all cell types of the adult body and to expand rapidly while retaining genome integrity, representing a perfect tool for regenerative medicine. PSCs are obtained from preimplantation embryos as embryonic stem cells (ESCs), or by reprogramming of somatic cells as induced pluripotent stem cells (iPSCs). Understanding the metabolic requirements of PSCs is instrumental for their efficient generation, expansion and differentiation. PSCs reshape their metabolic profile during developmental progression. Fatty acid oxidation is strictly required for energy production in naive PSCs, but becomes dispensable in more advanced, or primed, PSCs. Other metabolites directly affect proliferation, differentiation or the epigenetic profile of PSCs, showing how metabolism plays an instructive role on PSC behaviour. Developmental progression of pluripotent cells can be paused, both in vitro and in vivo, in response to hormonal and metabolic alterations. Such reversible pausing has been recently linked to mammalian target of rapamycin activity, lipid metabolism and mitochondrial activity. Finally, metabolism is not simply regulated by exogenous stimuli or nutrient availability in PSCs, as key pluripotency regulators, such as Oct4, Stat3 and Tfcp2l1, actively shape the metabolic profile of PSCs.
Collapse
Affiliation(s)
- Linda Diamante
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | | |
Collapse
|
5
|
Betto RM, Diamante L, Perrera V, Audano M, Rapelli S, Lauria A, Incarnato D, Arboit M, Pedretti S, Rigoni G, Guerineau V, Touboul D, Stirparo GG, Lohoff T, Boroviak T, Grumati P, Soriano ME, Nichols J, Mitro N, Oliviero S, Martello G. Metabolic control of DNA methylation in naive pluripotent cells. Nat Genet 2021; 53:215-229. [PMID: 33526924 PMCID: PMC7116828 DOI: 10.1038/s41588-020-00770-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 12/17/2020] [Indexed: 12/31/2022]
Abstract
Naive epiblast and embryonic stem cells (ESCs) give rise to all cells of adults. Such developmental plasticity is associated with genome hypomethylation. Here, we show that LIF-Stat3 signaling induces genomic hypomethylation via metabolic reconfiguration. Stat3-/- ESCs show decreased α-ketoglutarate production from glutamine, leading to increased Dnmt3a and Dnmt3b expression and DNA methylation. Notably, genome methylation is dynamically controlled through modulation of α-ketoglutarate availability or Stat3 activation in mitochondria. Alpha-ketoglutarate links metabolism to the epigenome by reducing the expression of Otx2 and its targets Dnmt3a and Dnmt3b. Genetic inactivation of Otx2 or Dnmt3a and Dnmt3b results in genomic hypomethylation even in the absence of active LIF-Stat3. Stat3-/- ESCs show increased methylation at imprinting control regions and altered expression of cognate transcripts. Single-cell analyses of Stat3-/- embryos confirmed the dysregulated expression of Otx2, Dnmt3a and Dnmt3b as well as imprinted genes. Several cancers display Stat3 overactivation and abnormal DNA methylation; therefore, the molecular module that we describe might be exploited under pathological conditions.
Collapse
Affiliation(s)
- Riccardo M Betto
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | - Linda Diamante
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | - Valentina Perrera
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
- Neuroscience Sector, International School for Advanced Studies (SISSA), Trieste, Italy
| | - Matteo Audano
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, Milan, Italy
| | - Stefania Rapelli
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), Candiolo, Italy
| | - Andrea Lauria
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), Candiolo, Italy
| | - Danny Incarnato
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, the Netherlands
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, the Netherlands
| | - Mattia Arboit
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | - Silvia Pedretti
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, Milan, Italy
| | - Giovanni Rigoni
- Department of Biology, University of Padua, Padua, Italy
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Vincent Guerineau
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS, Gif-sur-Yvette, France
| | - David Touboul
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS, Gif-sur-Yvette, France
| | | | - Tim Lohoff
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Thorsten Boroviak
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Paolo Grumati
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | | | - Jennifer Nichols
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Nico Mitro
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, Milan, Italy.
| | - Salvatore Oliviero
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy.
- Italian Institute for Genomic Medicine (IIGM), Candiolo, Italy.
| | - Graziano Martello
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy.
- Department of Biology, University of Padua, Padua, Italy.
| |
Collapse
|