Virology, Drug Discovery, Immunology and Microbiology, Molecular Biology
29
Scopus Publications
Scopus Publications
In vitro Control of RNA Virus Infections by M1-Polarized Human Monocyte-Derived Macrophages New Microbiologica, 2025
Quantitative characterisation of extracellular vesicles designed to decoy or compete with SARS-CoV-2 reveals differential mode of action across variants of concern and highlights the diversity of Omicron Melanie Schürz, Isabel Pagani, Eva Klinglmayr, Heloisa Melo Benirschke, Martin Mayora Neto, Luis J. V. Galietta, Arianna Venturini, Nicoletta Pedemonte, Valeria Capurro, Sandra Laner-Plamberger, Christoph Grabmer, Essi Emminger, Martin Wolf, Marianne Steiner, Cyrus Kohlmetz, Niklas Mayr, Liliia Paniushkina, Katharina Schallmoser, Dirk Strunk, Hans Brandstetter, Martin Hintersteiner, Nigel Temperton, Elisa Vicenzi, Nicole Meisner-Kober Cell Communication and Signaling, 2025 BACKGROUND: The converging biology between enveloped viruses and extracellular vesicles (EVs) has raised interest in the application of engineered EVs as antiviral therapeutics. Following the recent COVID-19 pandemic, EVs engineered with either the ACE2-receptor or Spike-protein have been proposed as strategy to either decoy SARS-CoV-2, or to compete with its cell entry. For generic use as a platform for future pandemic preparedness, a systematic and quantitative comparison of both strategies is required to assess their limitations and benefits across different variants of concern. METHODS: Here we generated EVs decorated with either the ACE2-receptor or the Spike-protein of (Wuhan)-SARS-CoV-2 and used single vesicle imaging for in-depth quantitative characterisation. These vesicles were then systematically tested for anti-viral activity across SARS-CoV-2 variants of concern using both, pseudotype and live virus cellular infection models including primary human bronchial and nasal explants. RESULTS: Spike-protein EVs or ACE2-EVs recovered from transiently transfected HEK293T cells comprised only a small fraction of the EV secretome (5% or 20%, respectively) and were primarily derived from the plasma membrane rather than multivesicular bodies. Redirecting intracellular trafficking of the Spike protein by mutating its transmembrane or subcellular localisation domains did not increase the yields of Spike-EVs. Both types of vesicles inhibited SARS-CoV-2 (D614G) in a dose dependent manner with kinetics and immunohistochemistry consistent with an inhibition at the initial cell entry stage. ACE2-EVs were more potent than Spike-EVs and at least 500-1000 times more potent than soluble antibodies in a pseudotype model. Surprisingly, ACE2-EVs switched from an inhibitory to an enhancer activity for the Omicron BA.1 variant whereas Spike-EVs retained their activity across all variants of concern. CONCLUSIONS: While our data show that both types of engineered EVs potently inhibit SARS-CoV, the decoy versus competition strategy may result in diverging outcomes when considering viral evolution into new variants of concern. While Spike-EVs retain their competition for receptor binding even against higher affinity viral Spike mutations, the formation of complexes between ACE2-EVs and the virus may not only result in inhibition by decoy. As EVs are actively internalised by cells themselves, they may shuttle the virus into cells, resulting in a productive alternative cell entry route for variants such as Omicron, that diverge from strict plasma membrane protease cleavage to the use of endosomal proteases for release of their genome.
Distinct Responses of Cystic Fibrosis Epithelial Cells to SARS-CoV-2 and Influenza A Virus Isabel Pagani, Arianna Venturini, Valeria Capurro, Alessandro Nonis, Silvia Ghezzi, Mariateresa Lena, Beatriz Alcalá-Franco, Fabrizio Gianferro, Daniela Guidone, Carla Colombo, Nicoletta Pedemonte, Alessandra Bragonzi, Cristina Cigana, Luis J. V. Galietta, Elisa Vicenzi American Journal of Respiratory Cell and Molecular Biology, 2025 The coronavirus disease (COVID-19) pandemic has underscored the impact of viral infections on individuals with cystic fibrosis (CF). Initial observations suggested lower COVID-19 rates among CF populations; however, subsequent clinical data have presented a more complex scenario. This study aimed to investigate how bronchial epithelial cells from individuals with and without CF, including various CFTR (CF transmembrane conductance regulator) mutations, respond to in vitro infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and SARS-CoV. Comparisons with the influenza A virus (IAV) were included based on evidence that patients with CF experience heightened morbidity from IAV infection. Our findings showed that CF epithelial cells exhibited reduced replication of SARS-CoV-2, regardless of the type of CFTR mutation or SARS-CoV-2 variant, as well as the original 2003 SARS-CoV. In contrast, these cells displayed more efficient IAV replication than non-CF cells. Interestingly, the reduced susceptibility to SARS-CoV-2 in CF was not linked to the expression of ACE2 (angiotensin-converting enzyme 2) receptor or to CFTR dysfunction, as pharmacological treatments to restore CFTR function did not normalize the viral response. Both SARS-CoV-2 infection and CFTR function influenced the concentrations of certain cytokines and chemokines, although these effects were not correlated. Overall, this study reveals a unique viral response in CF epithelial cells, characterized by reduced replication for some viruses like SARS-CoV-2, while showing increased susceptibility to others, such as IAV. This research offers a new perspective on CF and viral interactions, emphasizing the need for further investigation into the mechanisms underlying these differences.
Restriction of Zika Virus Replication in Human Monocyte-Derived Macrophages by Pro-Inflammatory (M1) Polarization Isabel Pagani, Silvia Ghezzi, Giulia Aimola, Paola Podini, Francesca Genova, Elisa Vicenzi, Guido Poli International Journal of Molecular Sciences, 2025 Zika virus (ZIKV), a member of the Flaviviridae family, is primarily transmitted through mosquito bites, but can also spread via sexual contact and from mother to fetus. While often asymptomatic, ZIKV can lead to severe neurological conditions, including microcephaly in fetuses and Guillain–Barré Syndrome in adults. ZIKV can infect placental macrophages and fetal microglia in vivo as well as human monocytes and monocyte-derived macrophages (MDMs) in vitro. Here, we observed that both human monocytes, and MDM particularly, supported ZIKV replication without evident cytopathicity, with virions accumulating in cytoplasmic vacuoles. We also investigated whether the cytokine-induced polarization of MDMs into M1 or M2 cells affected ZIKV replication. The stimulation of MDMs with pro-inflammatory cytokines (interferon-γ and tumor necrosis factor-α) polarized MDMs into M1 cells, significantly reducing ZIKV replication, akin to previous observations with a human immunodeficiency virus type-1 infection. In contrast, M2 polarization, induced by interleukin-4, did not affect ZIKV replication in MDMs. M1 polarization selectively reduced the expression of MERTK, a TAM family putative entry receptor, and increased the expression of several interferon-stimulated genes (ISGs) previously associated with the containment of ZIKV infection; of interest, ZIKV infection transiently boosted the expression of some ISGs in M1-MDMs. These findings suggest a dual mechanism of ZIKV restriction in M1-MDMs and highlight potential antiviral strategies targeting innate immune responses.
Evolution of SARS-CoV-2 spike trimers towards optimized heparan sulfate cross-linking and inter-chain mobility Jurij Froese, Marco Mandalari, Monica Civera, Stefano Elli, Isabel Pagani, Elisa Vicenzi, Itzel Garcia-Monge, Daniele Di Iorio, Saskia Frank, Antonella Bisio, Dominik Lenhart, Rudolf Gruber, Edwin A. Yates, Ralf P. Richter, Marco Guerrini, Seraphine V. Wegner, Kay Grobe Scientific Reports, 2024 The heparan sulfate (HS)-rich extracellular matrix (ECM) serves as an initial interaction site for the homotrimeric spike (S) protein of SARS-CoV-2 to facilitate subsequent docking to angiotensin-converting enzyme 2 (ACE2) receptors and cellular infection. More recent variants, notably Omicron, have evolved by swapping several amino acids to positively charged residues to enhance the interaction of the S-protein trimer with the negatively charged HS. However, these enhanced interactions may reduce Omicron’s ability to move through the HS-rich ECM to effectively find ACE2 receptors and infect cells, raising the question of how to mechanistically explain HS-associated viral movement. In this work, we show that Omicron S proteins have evolved to balance HS interaction stability and dynamics, resulting in enhanced mobility on an HS-functionalized artificial matrix. This property is achieved by the ability of Omicron S-proteins to cross-link at least two HS chains, allowing direct S-protein switching between chains as a prerequisite for cell surface mobility. Optimized HS interactions can be targeted pharmaceutically, as an HS mimetic significantly suppressed surface binding and cellular infection specifically of the Omicron variant. These findings suggest a robust way to interfere with SARS-CoV-2 Omicron infection and potentially future variants.
A novel STING variant triggers endothelial toxicity and SAVI disease Erika Valeri, Sara Breggion, Federica Barzaghi, Monah Abou Alezz, Giovanni Crivicich, Isabel Pagani, Federico Forneris, Claudia Sartirana, Matteo Costantini, Stefania Costi, Achille Marino, Eleonora Chiarotto, Davide Colavito, Rolando Cimaz, Ivan Merelli, Elisa Vicenzi, Alessandro Aiuti, Anna Kajaste-Rudnitski Journal of Experimental Medicine, 2024 Gain-of-function mutations in STING cause STING-associated vasculopathy with onset in infancy (SAVI) characterized by early-onset systemic inflammation, skin vasculopathy, and interstitial lung disease. Here, we report and characterize a novel STING variant (F269S) identified in a SAVI patient. Single-cell transcriptomics of patient bone marrow revealed spontaneous activation of interferon (IFN) and inflammatory pathways across cell types and a striking prevalence of circulating naïve T cells was observed. Inducible STING F269S expression conferred enhanced signaling through ligand-independent translocation of the protein to the Golgi, protecting cells from viral infections but preventing their efficient immune priming. Additionally, endothelial cell activation was promoted and further exacerbated by cytokine secretion by SAVI immune cells, resulting in inflammation and endothelial damage. Our findings identify STING F269S mutation as a novel pathogenic variant causing SAVI, highlight the importance of the crosstalk between endothelial and immune cells in the context of lung disease, and contribute to a better understanding of how aberrant STING activation can cause pathology.
RAGE engagement by SARS-CoV-2 enables monocyte infection and underlies COVID-19 severity Roberta Angioni, Matteo Bonfanti, Nicolò Caporale, Ricardo Sánchez-Rodríguez, Fabio Munari, Aurora Savino, Sebastiano Pasqualato, Damiano Buratto, Isabel Pagani, Nicole Bertoldi, Carlo Zanon, Paolo Ferrari, Eugenia Ricciardelli, Cristina Putaggio, Silvia Ghezzi, Francesco Elli, Luca Rotta, Alessandro Scardua, Janine Weber, Valentina Cecatiello, Francesco Iorio, Francesco Zonta, Anna Maria Cattelan, Elisa Vicenzi, Alessandro Vannini, Barbara Molon, Carlo Emanuele Villa, Antonella Viola, Giuseppe Testa Cell Reports Medicine, 2023 The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has fueled the COVID-19 pandemic with its enduring medical and socioeconomic challenges because of subsequent waves and long-term consequences of great concern. Here, we chart the molecular basis of COVID-19 pathogenesis by analyzing patients' immune responses at single-cell resolution across disease course and severity. This approach confirms cell subpopulation-specific dysregulation in COVID-19 across disease course and severity and identifies a severity-associated activation of the receptor for advanced glycation endproducts (RAGE) pathway in monocytes. In vitro THP1-based experiments indicate that monocytes bind the SARS-CoV-2 S1-receptor binding domain (RBD) via RAGE, pointing to RAGE-Spike interaction enabling monocyte infection. Thus, our results demonstrate that RAGE is a functional receptor of SARS-CoV-2 contributing to COVID-19 severity.
Heparin Precursors with Reduced Anticoagulant Properties Retain Antiviral and Protective Effects That Potentiate the Efficacy of Sofosbuvir against Zika Virus Infection in Human Neural Progenitor Cells Isabel Pagani, Linda Ottoboni, Paola Panina-Bordignon, Gianvito Martino, Guido Poli, Sarah Taylor, Jeremy E. Turnbull, Edwin Yates, Elisa Vicenzi Pharmaceuticals, 2023 Zika virus (ZIKV) infection during pregnancy can result in severe birth defects, such as microcephaly, as well as a range of other related health complications. Heparin, a clinical-grade anticoagulant, is shown to protect neural progenitor cells from death following ZIKV infection. Although heparin can be safely used during pregnancy, it retains off-target anticoagulant effects if directly employed against ZIKV infection. In this study, we investigated the effects of chemically modified heparin derivatives with reduced anticoagulant activities. These derivatives were used as experimental probes to explore the structure–activity relationships. Precursor fractions of porcine heparin, obtained during the manufacture of conventional pharmaceutical heparin with decreased anticoagulant activities, were also explored. Interestingly, these modified heparin derivatives and precursor fractions not only prevented cell death but also inhibited the ZIKV replication of infected neural progenitor cells grown as neurospheres. These effects were observed regardless of the specific sulfation position or overall charge. Furthermore, the combination of heparin with Sofosbuvir, an antiviral licensed for the treatment of hepatitis C (HCV) that also belongs to the same Flaviviridae family as ZIKV, showed a synergistic effect. This suggested that a combination therapy approach involving heparin precursors and Sofosbuvir could be a potential strategy for the prevention or treatment of ZIKV infections.
Interferon-inducible phospholipids govern IFITM3-dependent endosomal antiviral immunity Giulia Unali, Giovanni Crivicich, Isabel Pagani, Monah Abou‐Alezz, Filippo Folchini, Erika Valeri, Vittoria Matafora, Julie A Reisz, Anna Maria Sole Giordano, Ivan Cuccovillo, Giacomo M Butta, Lorena Donnici, Angelo D'Alessandro, Raffaele De Francesco, Lara Manganaro, Davide Cittaro, Ivan Merelli, Carolina Petrillo, Angela Bachi, Elisa Vicenzi, Anna Kajaste‐Rudnitski EMBO Journal, 2023 The interferon‐induced transmembrane proteins (IFITM) are implicated in several biological processes, including antiviral defense, but their modes of action remain debated. Here, taking advantage of pseudotyped viral entry assays and replicating viruses, we uncover the requirement of host co‐factors for endosomal antiviral inhibition through high‐throughput proteomics and lipidomics in cellular models of IFITM restriction. Unlike plasma membrane (PM)‐localized IFITM restriction that targets infectious SARS‐CoV2 and other PM‐fusing viral envelopes, inhibition of endosomal viral entry depends on lysines within the conserved IFITM intracellular loop. These residues recruit Phosphatidylinositol 3,4,5‐trisphosphate (PIP3) that we show here to be required for endosomal IFITM activity. We identify PIP3 as an interferon‐inducible phospholipid that acts as a rheostat for endosomal antiviral immunity. PIP3 levels correlated with the potency of endosomal IFITM restriction and exogenous PIP3 enhanced inhibition of endocytic viruses, including the recent SARS‐CoV2 Omicron variant. Together, our results identify PIP3 as a critical regulator of endosomal IFITM restriction linking it to the Pi3K/Akt/mTORC pathway and elucidate cell‐compartment‐specific antiviral mechanisms with potential relevance for the development of broadly acting antiviral strategies.
Origin and evolution of SARS-CoV-2 Isabel Pagani, Silvia Ghezzi, Simone Alberti, Guido Poli, Elisa Vicenzi European Physical Journal Plus, 2023 SARS-CoV-2 is a novel coronavirus that emerged in China at the end of 2019 causing the severe disease known as coronavirus disease 2019 (COVID-19). SARS-CoV-2, as to the previously highly pathogenic human coronaviruses named SARS-CoV, the etiological agent of severe acute respiratory syndrome (SARS), has a zoonotic origin, although SARS-CoV-2 precise chain of animal-to-human transmission remains undefined. Unlike the 2002–2003 pandemic caused by SARS-CoV whose extinction from the human population was achieved in eight months, SARS-CoV-2 has been spreading globally in an immunologically naïve population in an unprecedented manner. The efficient infection and replication of SARS-CoV-2 has resulted in the emergence of viral variants that have become predominant posing concerns about their containment as they are more infectious with variable pathogenicity in respect to the original virus. Although vaccine availability is limiting severe disease and death caused by SARS-CoV-2 infection, its extinction is far to be close and predictable. In this regard, the emersion of the Omicron viral variant in November 2021 was characterized by humoral immune escape and it has reinforced the importance of the global monitoring of SARS-CoV-2 evolution. Given the importance of the SARS-CoV-2 zoonotic origin, it will also be crucial to monitor the animal-human interface to be better prepared to cope with future infections of pandemic potential.
Biobanking for COVID-19 research Patrizia ROVERE-QUERINI, Cristina TRESOLDI, Caterina CONTE, Annalisa RUGGERI, Silvia GHEZZI, Rebecca DE LORENZO, Luigi DI FILIPPO, Nicola FARINA, Giuseppe A. RAMIREZ, Marco RIPA, Nicasio MANCINI, Elisa CANTARELLI, Laura GALLI, Andrea POLI, Francesco DE COBELLI, Chiara BONINI, Angelo A. MANFREDI, Stefano FRANCHINI, Marzia SPESSOT, Michele CARLUCCI, Lorenzo DAGNA, Paolo SCARPELLINI, Alberto AMBROSIO, Davide DI NAPOLI, Emanuele BOSI, Moreno TRESOLDI, Adriano LAZZARIN, Giovanni LANDONI, Gianvito MARTINO, Alberto ZANGRILLO, Guido POLI, Antonella CASTAGNA, Elisa VICENZI, Massimo CLEMENTI, Fabio CICERI, and Panminerva Medica, 2022
Recognition and inhibition of SARS-CoV-2 by humoral innate immunity pattern recognition molecules Matteo Stravalaci, Isabel Pagani, Elvezia Maria Paraboschi, Mattia Pedotti, Andrea Doni, Francesco Scavello, Sarah N. Mapelli, Marina Sironi, Chiara Perucchini, Luca Varani, Milos Matkovic, Andrea Cavalli, Daniela Cesana, Pierangela Gallina, Nicoletta Pedemonte, Valeria Capurro, Nicola Clementi, Nicasio Mancini, Pietro Invernizzi, Rafael Bayarri-Olmos, Peter Garred, Rino Rappuoli, Stefano Duga, Barbara Bottazzi, Mariagrazia Uguccioni, Rosanna Asselta, Elisa Vicenzi, Alberto Mantovani, Cecilia Garlanda Nature Immunology, 2022
The Long and Winding Road towards an HIV Cure New Microbiologica, 2022
The Hyperlipidaemic Drug Fenofibrate Significantly Reduces Infection by SARS-CoV-2 in Cell Culture Models Scott P. Davies, Courtney J. Mycroft-West, Isabel Pagani, Harriet J. Hill, Yen-Hsi Chen, Richard Karlsson, Ieva Bagdonaite, Scott E. Guimond, Zania Stamataki, Marcelo Andrade De Lima, Jeremy E. Turnbull, Zhang Yang, Elisa Vicenzi, Mark A. Skidmore, Farhat L. Khanim, Alan Richardson Frontiers in Pharmacology, 2021
Heparin Inhibits Cellular Invasion by SARS-CoV-2: Structural Dependence of the Interaction of the Spike S1 Receptor-Binding Domain with Heparin Courtney J. Mycroft-West, Dunhao Su, Isabel Pagani, Timothy R. Rudd, Stefano Elli, Neha S. Gandhi, Scott E. Guimond, Gavin J. Miller, Maria C. Z. Meneghetti, Helena B. Nader, Yong Li, Quentin M. Nunes, Patricia Procter, Nicasio Mancini, Massimo Clementi, Antonella Bisio, Nicholas R. Forsyth, Vito Ferro, Jeremy E. Turnbull, Marco Guerrini, David G. Fernig, Elisa Vicenzi, Edwin A. Yates, Marcelo A. Lima, Mark A. Skidmore Thrombosis and Haemostasis, 2020
A Human Bi-specific Antibody against Zika Virus with High Therapeutic Potential Jiaqi Wang, Marco Bardelli, Diego A. Espinosa, Mattia Pedotti, Thiam-Seng Ng, Siro Bianchi, Luca Simonelli, Elisa X.Y. Lim, Mathilde Foglierini, Fabrizia Zatta, Stefano Jaconi, Martina Beltramello, Elisabetta Cameroni, Guntur Fibriansah, Jian Shi, Taylor Barca, Isabel Pagani, Alicia Rubio, Vania Broccoli, Elisa Vicenzi, Victoria Graham, Steven Pullan, Stuart Dowall, Roger Hewson, Simon Jurt, Oliver Zerbe, Karin Stettler, Antonio Lanzavecchia, Federica Sallusto, Andrea Cavalli, Eva Harris, Shee-Mei Lok, Luca Varani, Davide Corti Cell, 2017
