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Benedetti F, Silvestri G, Saadat S, Denaro F, Latinovic OS, Davis H, Williams S, Bryant J, Ippodrino R, Rathinam CV, Gallo RC, Zella D. Mycoplasma DnaK increases DNA copy number variants in vivo. Proc Natl Acad Sci U S A 2023; 120:e2219897120. [PMID: 37459550 PMCID: PMC10372619 DOI: 10.1073/pnas.2219897120] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 06/14/2023] [Indexed: 07/20/2023] Open
Abstract
The human microbiota affects critical cellular functions, although the responsible mechanism(s) is still poorly understood. In this regard, we previously showed that Mycoplasma fermentans DnaK, an HSP70 chaperone protein, hampers the activity of important cellular proteins responsible for DNA integrity. Here, we describe a novel DnaK knock-in mouse model generated in our laboratory to study the effect of M. fermentans DnaK expression in vivo. By using an array-based comparative genomic hybridization assay, we demonstrate that exposure to DnaK was associated with a higher number of DNA copy number variants (CNVs) indicative of unbalanced chromosomal alterations, together with reduced fertility and a high rate of fetal abnormalities. Consistent with their implication in genetic disorders, one of these CNVs caused a homozygous Grid2 deletion, resulting in an aberrant ataxic phenotype that recapitulates the extensive biallelic deletion in the Grid2 gene classified in humans as autosomal recessive spinocerebellar ataxia 18. Our data highlight a connection between components of the human urogenital tract microbiota, namely Mycoplasmas, and genetic abnormalities in the form of DNA CNVs, with obvious relevant medical, diagnostic, and therapeutic implications.
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Affiliation(s)
- Francesca Benedetti
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD21201
| | - Giovannino Silvestri
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
- Department of Medicine, School of Medicine, University of Maryland School of Medicine, Baltimore, MD21201
| | - Saman Saadat
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
| | - Frank Denaro
- Department of Biology, Morgan State University, Baltimore, MD21251
| | - Olga S. Latinovic
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD21201
| | - Harry Davis
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
| | - Sumiko Williams
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
| | - Joseph Bryant
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
| | | | - Chozha V. Rathinam
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
- Department of Medicine, School of Medicine, University of Maryland School of Medicine, Baltimore, MD21201
| | - Robert C. Gallo
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
- Department of Medicine, School of Medicine, University of Maryland School of Medicine, Baltimore, MD21201
| | - Davide Zella
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD21201
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2
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Avian A, Clemente N, Mauro E, Isidoro E, Di Napoli M, Dudine S, Del Fabro A, Morini S, Perin T, Giudici F, Cammisuli T, Foschi N, Mocenigo M, Montrone M, Modena C, Polenghi M, Puzzi L, Tomaic V, Valenti G, Sola R, Zanolla S, Vogrig E, Riva E, Angeletti S, Ciccozzi M, Castriciano S, Pachetti M, Petti M, Centonze S, Gerin D, Banks L, Marini B, Canzonieri V, Sopracordevole F, Zanconati F, Ippodrino R. Correction: Clinical validation of full HR-HPV genotyping HPV Selfy assay according to the international guidelines for HPV test requirements for cervical cancer screening on clinician-collected and self-collected samples. J Transl Med 2023; 21:49. [PMID: 36703153 PMCID: PMC9878793 DOI: 10.1186/s12967-023-03882-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Alice Avian
- Ulisse BioMed S.p.A, Area Science Park, SS 14, km 163.5, Trieste, Italy ,grid.438882.d0000 0001 0212 6916Molecular Genetics and Biotechnology PhD Study Programme, University of Nova Gorica, Nova Gorica, Slovenia
| | - Nicolò Clemente
- Ginecologia Oncologica, IRCCS—Centro Di Riferimento Oncologico (CRO) (Istituto Nazionale Tumori—National Cancer Institute), Aviano, Italy
| | - Elisabetta Mauro
- Ulisse BioMed S.p.A, Area Science Park, SS 14, km 163.5, Trieste, Italy
| | - Erica Isidoro
- grid.413694.dAzienda Sanitaria Universitaria Giuliano Isontina UCO/ SC Anatomia e Istologia Patologica, Cattinara Hospital, Trieste, Italy
| | - Michela Di Napoli
- grid.413694.dAzienda Sanitaria Universitaria Giuliano Isontina UCO/ SC Anatomia e Istologia Patologica, Cattinara Hospital, Trieste, Italy
| | - Sandra Dudine
- grid.413694.dAzienda Sanitaria Universitaria Giuliano Isontina UCO/ SC Anatomia e Istologia Patologica, Cattinara Hospital, Trieste, Italy
| | - Anna Del Fabro
- Ginecologia Oncologica, IRCCS—Centro Di Riferimento Oncologico (CRO) (Istituto Nazionale Tumori—National Cancer Institute), Aviano, Italy
| | - Stefano Morini
- Ginecologia Oncologica, IRCCS—Centro Di Riferimento Oncologico (CRO) (Istituto Nazionale Tumori—National Cancer Institute), Aviano, Italy
| | - Tiziana Perin
- Ginecologia Oncologica, IRCCS—Centro Di Riferimento Oncologico (CRO) (Istituto Nazionale Tumori—National Cancer Institute), Aviano, Italy
| | - Fabiola Giudici
- grid.5133.40000 0001 1941 4308Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Tamara Cammisuli
- grid.418321.d0000 0004 1757 9741Anatomia Patologica, IRCCS—CRO (Istituto Nazionale Tumori - National Cancer Institute), Aviano, Italy
| | - Nicola Foschi
- Ulisse BioMed S.p.A, Area Science Park, SS 14, km 163.5, Trieste, Italy
| | - Marco Mocenigo
- Ulisse BioMed S.p.A, Area Science Park, SS 14, km 163.5, Trieste, Italy ,grid.438882.d0000 0001 0212 6916Molecular Genetics and Biotechnology PhD Study Programme, University of Nova Gorica, Nova Gorica, Slovenia
| | - Michele Montrone
- Ulisse BioMed S.p.A, Area Science Park, SS 14, km 163.5, Trieste, Italy
| | - Chiara Modena
- Ulisse BioMed S.p.A, Area Science Park, SS 14, km 163.5, Trieste, Italy
| | - Martina Polenghi
- Ulisse BioMed S.p.A, Area Science Park, SS 14, km 163.5, Trieste, Italy
| | - Luca Puzzi
- Ulisse BioMed S.p.A, Area Science Park, SS 14, km 163.5, Trieste, Italy
| | - Vjekoslav Tomaic
- grid.4905.80000 0004 0635 7705Institut Ruđer Bošković, Zagreb, Croatia
| | - Giulio Valenti
- Ulisse BioMed S.p.A, Area Science Park, SS 14, km 163.5, Trieste, Italy
| | - Riccardo Sola
- Ulisse BioMed S.p.A, Area Science Park, SS 14, km 163.5, Trieste, Italy
| | - Shivani Zanolla
- Ulisse BioMed S.p.A, Area Science Park, SS 14, km 163.5, Trieste, Italy
| | - Enea Vogrig
- Ulisse BioMed S.p.A, Area Science Park, SS 14, km 163.5, Trieste, Italy
| | - Elisabetta Riva
- grid.488514.40000000417684285Policlinico Universitario Campus Biomedico, Rome, Italy
| | - Silvia Angeletti
- grid.488514.40000000417684285Policlinico Universitario Campus Biomedico, Rome, Italy
| | - Massimo Ciccozzi
- grid.488514.40000000417684285Policlinico Universitario Campus Biomedico, Rome, Italy
| | | | - Maria Pachetti
- Ulisse BioMed S.p.A, Area Science Park, SS 14, km 163.5, Trieste, Italy ,grid.418712.90000 0004 1760 7415Institute of Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Matteo Petti
- Ulisse BioMed S.p.A, Area Science Park, SS 14, km 163.5, Trieste, Italy
| | - Sandro Centonze
- Clinical Research Unit, Azienda Sanitaria Universitaria Giuliano Isontina, Trieste, Italy
| | - Daniela Gerin
- Cervical Cancer Screening Coordination Unit, Azienda Sanitaria Universitaria Giuliano Isontina, Trieste, Italy
| | - Lawrence Banks
- grid.425196.d0000 0004 1759 4810International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Bruna Marini
- Ulisse BioMed S.p.A, Area Science Park, SS 14, km 163.5, Trieste, Italy
| | - Vincenzo Canzonieri
- grid.5133.40000 0001 1941 4308Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy ,grid.418321.d0000 0004 1757 9741Anatomia Patologica, IRCCS—CRO (Istituto Nazionale Tumori - National Cancer Institute), Aviano, Italy
| | - Francesco Sopracordevole
- Ginecologia Oncologica, IRCCS—Centro Di Riferimento Oncologico (CRO) (Istituto Nazionale Tumori—National Cancer Institute), Aviano, Italy
| | - Fabrizio Zanconati
- grid.413694.dAzienda Sanitaria Universitaria Giuliano Isontina UCO/ SC Anatomia e Istologia Patologica, Cattinara Hospital, Trieste, Italy ,grid.5133.40000 0001 1941 4308Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Rudy Ippodrino
- Ulisse BioMed S.p.A, Area Science Park, SS 14, km 163.5, Trieste, Italy
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3
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Rossetti M, Merlo R, Bagheri N, Moscone D, Valenti A, Saha A, Arantes PR, Ippodrino R, Ricci F, Treglia I, Delibato E, van der Oost J, Palermo G, Perugino G, Porchetta A. Enhancement of CRISPR/Cas12a trans-cleavage activity using hairpin DNA reporters. Nucleic Acids Res 2022; 50:8377-8391. [PMID: 35822842 PMCID: PMC9371913 DOI: 10.1093/nar/gkac578] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 12/24/2022] Open
Abstract
The RNA programmed non-specific (trans) nuclease activity of CRISPR-Cas Type V and VI systems has opened a new era in the field of nucleic acid-based detection. Here, we report on the enhancement of trans-cleavage activity of Cas12a enzymes using hairpin DNA sequences as FRET-based reporters. We discover faster rate of trans-cleavage activity of Cas12a due to its improved affinity (Km) for hairpin DNA structures, and provide mechanistic insights of our findings through Molecular Dynamics simulations. Using hairpin DNA probes we significantly enhance FRET-based signal transduction compared to the widely used linear single stranded DNA reporters. Our signal transduction enables faster detection of clinically relevant double stranded DNA targets with improved sensitivity and specificity either in the presence or in the absence of an upstream pre-amplification step.
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Affiliation(s)
- Marianna Rossetti
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
| | - Rosa Merlo
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Neda Bagheri
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
| | - Danila Moscone
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
| | - Anna Valenti
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Aakash Saha
- Department of Bioengineering and Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA 52512 USA
| | - Pablo R Arantes
- Department of Bioengineering and Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA 52512 USA
| | - Rudy Ippodrino
- Ulisse BioMed S.r.l. Area Science Park, 34149 Trieste, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
| | - Ida Treglia
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, Italy
| | - Elisabetta Delibato
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, Italy
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA 52512 USA
| | - Giuseppe Perugino
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy.,Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte Sant'Angelo, Ed. 7, Via Cintia 26, 80126 Naples, Italy
| | - Alessandro Porchetta
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
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4
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Avian A, Clemente N, Mauro E, Isidoro E, Di Napoli M, Dudine S, Del Fabro A, Morini S, Perin T, Giudici F, Cammisuli T, Foschi N, Mocenigo M, Montrone M, Modena C, Polenghi M, Puzzi L, Tomaic V, Valenti G, Sola R, Zanolla S, Vogrig E, Riva E, Angeletti S, Ciccozzi M, Castriciano S, Pachetti M, Petti M, Centonze S, Gerin D, Banks L, Marini B, Canzonieri V, Sopracordevole F, Zanconati F, Ippodrino R. Clinical validation of full HR-HPV genotyping HPV Selfy assay according to the international guidelines for HPV test requirements for cervical cancer screening on clinician-collected and self-collected samples. J Transl Med 2022; 20:231. [PMID: 35581584 PMCID: PMC9115952 DOI: 10.1186/s12967-022-03383-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 02/25/2022] [Accepted: 04/07/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND According to international guidelines, Human Papillomavirus (HPV) DNA tests represent a valid alternative to Pap Test for primary cervical cancer screening, provided that they guarantee balanced clinical sensitivity and specificity for cervical intraepithelial neoplasia grade 2 or more (CIN2+) lesions. The study aimed to assess whether HPV Selfy (Ulisse BioMed - Trieste, Italy), a full-genotyping HPV DNA test that detects and differentiates 14 high-risk HPV (HR-HPV) types, meets the criteria for primary cervical cancer screening described in the international guidelines, on clinician-collected as well as on self-collected samples. METHODS For each participant woman, consecutively referring to Azienda Sanitaria Universitaria Giuliano Isontina (Trieste, Italy) and CRO-National Cancer Institute (Aviano, Italy) for the cervical cancer screening program, the following samples were tested: (a) a clinician-collected cervical specimen, analyzed with the reference test (Hybrid Capture®2 test, HC2) and HPV Selfy; and (b) a self-collected vaginal sample, analyzed with HPV Selfy. Enrolled women were also asked to fulfill a questionnaire about self-sampling acceptability. As required by guidelines, a non-inferiority test was conducted to compare the clinical performance of the test under evaluation with its reference test. RESULTS HPV Selfy clinical sensitivity and specificity resulted non-inferior to those of HC2. By analysis of a total of 889 cervical liquid-based cytology samples from a screening population, of which 98 were from women with CIN2+, HPV Selfy showed relative sensitivity and specificity for CIN2+ of 0.98 and 1.00 respectively (non-inferiority score test: P = 0.01747 and P = 0.00414, respectively); the test reached adequate intra- and inter-laboratory reproducibility. Moreover, we demonstrated that the performance of HPV Selfy on self-collected vaginal samples was non-inferior to the performance obtained on clinician-collected cervical specimen (0.92 relative sensitivity and 0.97 relative specificity). Finally, through HPV Selfy genotyping, we were able to describe HPV types prevalence in the study population. CONCLUSIONS HPV Selfy fulfills all the requirements of the international Meijer's guidelines and has been clinically validated for primary cervical cancer screening purposes. Moreover, HPV Selfy has also been validated for self-sampling according to VALHUDES guidelines. Therefore, at date, HPV Selfy is the only full-genotyping test validated both for screening purposes and for self-sampling. Trial registration ASUGI Trieste n. 16008/2018; CRO Aviano n.17149/2018.
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Affiliation(s)
- Alice Avian
- Ulisse BioMed S.P.a, Area Science Park, SS 14, km 163.5, Trieste, Italy ,grid.438882.d0000 0001 0212 6916Molecular Genetics and Biotechnology PhD Study Programme, University of Nova Gorica, Nova Gorica, Slovenia
| | - Nicolò Clemente
- grid.418321.d0000 0004 1757 9741Ginecologia Oncologica, IRCCS - Centro Di Riferimento Oncologico (CRO) (Istituto Nazionale Tumori – National Cancer Institute), Aviano, Italy
| | - Elisabetta Mauro
- Ulisse BioMed S.P.a, Area Science Park, SS 14, km 163.5, Trieste, Italy
| | - Erica Isidoro
- grid.413694.dAzienda Sanitaria Universitaria Giuliano Isontina UCO/SC Anatomia e Istologia Patologica, Cattinara Hospital, Trieste, Italy
| | - Michela Di Napoli
- grid.413694.dAzienda Sanitaria Universitaria Giuliano Isontina UCO/SC Anatomia e Istologia Patologica, Cattinara Hospital, Trieste, Italy
| | - Sandra Dudine
- grid.413694.dAzienda Sanitaria Universitaria Giuliano Isontina UCO/SC Anatomia e Istologia Patologica, Cattinara Hospital, Trieste, Italy
| | - Anna Del Fabro
- grid.418321.d0000 0004 1757 9741Ginecologia Oncologica, IRCCS - Centro Di Riferimento Oncologico (CRO) (Istituto Nazionale Tumori – National Cancer Institute), Aviano, Italy
| | - Stefano Morini
- grid.418321.d0000 0004 1757 9741Ginecologia Oncologica, IRCCS - Centro Di Riferimento Oncologico (CRO) (Istituto Nazionale Tumori – National Cancer Institute), Aviano, Italy
| | - Tiziana Perin
- grid.418321.d0000 0004 1757 9741Ginecologia Oncologica, IRCCS - Centro Di Riferimento Oncologico (CRO) (Istituto Nazionale Tumori – National Cancer Institute), Aviano, Italy
| | - Fabiola Giudici
- grid.5133.40000 0001 1941 4308Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Tamara Cammisuli
- grid.418321.d0000 0004 1757 9741Anatomia Patologica, IRCCS – CRO (Istituto Nazionale Tumori - National Cancer Institute), Aviano, Italy
| | - Nicola Foschi
- Ulisse BioMed S.P.a, Area Science Park, SS 14, km 163.5, Trieste, Italy
| | - Marco Mocenigo
- Ulisse BioMed S.P.a, Area Science Park, SS 14, km 163.5, Trieste, Italy ,grid.438882.d0000 0001 0212 6916Molecular Genetics and Biotechnology PhD Study Programme, University of Nova Gorica, Nova Gorica, Slovenia
| | - Michele Montrone
- Ulisse BioMed S.P.a, Area Science Park, SS 14, km 163.5, Trieste, Italy
| | - Chiara Modena
- Ulisse BioMed S.P.a, Area Science Park, SS 14, km 163.5, Trieste, Italy
| | - Martina Polenghi
- Ulisse BioMed S.P.a, Area Science Park, SS 14, km 163.5, Trieste, Italy
| | - Luca Puzzi
- Ulisse BioMed S.P.a, Area Science Park, SS 14, km 163.5, Trieste, Italy
| | - Vjekoslav Tomaic
- grid.4905.80000 0004 0635 7705Institut Ruđer Bošković, Zagreb, Croatia
| | - Giulio Valenti
- Ulisse BioMed S.P.a, Area Science Park, SS 14, km 163.5, Trieste, Italy
| | - Riccardo Sola
- Ulisse BioMed S.P.a, Area Science Park, SS 14, km 163.5, Trieste, Italy
| | - Shivani Zanolla
- Ulisse BioMed S.P.a, Area Science Park, SS 14, km 163.5, Trieste, Italy
| | - Enea Vogrig
- Ulisse BioMed S.P.a, Area Science Park, SS 14, km 163.5, Trieste, Italy
| | - Elisabetta Riva
- grid.488514.40000000417684285Policlinico Universitario Campus Biomedico, Rome, Italy
| | - Silvia Angeletti
- grid.488514.40000000417684285Policlinico Universitario Campus Biomedico, Rome, Italy
| | - Massimo Ciccozzi
- grid.488514.40000000417684285Policlinico Universitario Campus Biomedico, Rome, Italy
| | | | - Maria Pachetti
- Ulisse BioMed S.P.a, Area Science Park, SS 14, km 163.5, Trieste, Italy ,grid.418712.90000 0004 1760 7415Institute of Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Matteo Petti
- Ulisse BioMed S.P.a, Area Science Park, SS 14, km 163.5, Trieste, Italy
| | - Sandro Centonze
- Clinical Research Unit, Azienda Sanitaria Universitaria Giuliano Isontina, Trieste, Italy
| | - Daniela Gerin
- Cervical Cancer Screening Coordination Unit, Azienda Sanitaria Universitaria Giuliano Isontina, Trieste, Italy
| | - Lawrence Banks
- grid.425196.d0000 0004 1759 4810International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Bruna Marini
- Ulisse BioMed S.P.a, Area Science Park, SS 14, km 163.5, Trieste, Italy
| | - Vincenzo Canzonieri
- grid.5133.40000 0001 1941 4308Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy ,grid.418321.d0000 0004 1757 9741Anatomia Patologica, IRCCS – CRO (Istituto Nazionale Tumori - National Cancer Institute), Aviano, Italy
| | - Francesco Sopracordevole
- grid.418321.d0000 0004 1757 9741Ginecologia Oncologica, IRCCS - Centro Di Riferimento Oncologico (CRO) (Istituto Nazionale Tumori – National Cancer Institute), Aviano, Italy
| | - Fabrizio Zanconati
- grid.413694.dAzienda Sanitaria Universitaria Giuliano Isontina UCO/SC Anatomia e Istologia Patologica, Cattinara Hospital, Trieste, Italy ,grid.5133.40000 0001 1941 4308Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Rudy Ippodrino
- Ulisse BioMed S.P.a, Area Science Park, SS 14, km 163.5, Trieste, Italy
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5
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Zerbato V, Sanson G, De Luca M, Di Bella S, di Masi A, Caironi P, Marini B, Ippodrino R, Luzzati R. The Impact of Serum Albumin Levels on COVID-19 Mortality. Infect Dis Rep 2022; 14:278-286. [PMID: 35645213 PMCID: PMC9149867 DOI: 10.3390/idr14030034] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 04/07/2022] [Accepted: 04/14/2022] [Indexed: 12/22/2022] Open
Abstract
Low serum albumin (SA) correlates with mortality in critically ill patients, including those with COVID-19. We aimed to identify SA thresholds to predict the risk of longer hospital stay, severe respiratory failure, and death in hospitalized adult patients with COVID-19 pneumonia. A prospective longitudinal study was conducted at the Infectious Diseases Unit of Trieste University Hospital (Italy) between March 2020 and June 2021. The evaluated outcomes were: (1) need of invasive mechanical ventilation (IMV); (2) length of hospital stay (LOS); and (3) 90-day mortality rate. We enrolled 864 patients. Hypoalbuminemia (<3.5 g/dL) was detected in 586 patients (67.8%). SA on admission was significantly lower in patients who underwent IMV (2.9 vs. 3.4 g/dL; p < 0.001). The optimal SA cutoff predicting the need of IMV was 3.17 g/dL (AUC 0.688; 95% CI: 0.618−0.759; p < 0.001) and this threshold appeared as an independent risk factor for the risk of IMV in multivariate Cox regression analysis. The median LOS was 12 days and a higher SA was predictive for a shorter LOS (p < 0.001). The overall 90-day mortality rate was 15%. SA was significantly lower in patients who died within 90 days from hospital admission (3.1 g/dL; IQR 2.8−3.4; p < 0.001) as compared to those who survived (3.4 g/dL; IQR 3.1−3.7). The optimal SA threshold predicting high risk of 90-day mortality was 3.23 g/dL (AUC 0.678; 95% CI: 0.629−0.734; p < 0.001). In a multivariate Cox regression analysis, SA of <3.23 g/dL appeared to be an independent risk factor for 90-day mortality. Our results suggest that low SA on admission may identify patients with COVID-19 pneumonia at higher risk of severe respiratory failure, death, and longer LOS. Clinicians could consider 3.2 g/dL as a prognostic threshold for both IMV and mortality in hospitalized COVID-19 patients.
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Affiliation(s)
- Verena Zerbato
- Infectious Diseases Unit, Trieste University Hospital (ASUGI), 34125 Trieste, Italy;
| | - Gianfranco Sanson
- Clinical Department of Medical, Surgical and Health Sciences, Trieste University, 34149 Trieste, Italy; (G.S.); (R.L.)
| | - Marina De Luca
- Operative Unit of Medicina Clinica, Trieste University Hospital (ASUGI), 34125 Trieste, Italy;
| | - Stefano Di Bella
- Clinical Department of Medical, Surgical and Health Sciences, Trieste University, 34149 Trieste, Italy; (G.S.); (R.L.)
- Correspondence:
| | | | - Pietro Caironi
- Department of Anaesthesia and Critical Care, AOU S. Luigi Gonzaga, Department of Oncology, University of Turin, 10043 Turin, Italy;
| | - Bruna Marini
- Ulisse BioMed Labs, Area Science Park, SS 14, km 163.5, 34149 Trieste, Italy; (B.M.); (R.I.)
| | - Rudy Ippodrino
- Ulisse BioMed Labs, Area Science Park, SS 14, km 163.5, 34149 Trieste, Italy; (B.M.); (R.I.)
| | - Roberto Luzzati
- Clinical Department of Medical, Surgical and Health Sciences, Trieste University, 34149 Trieste, Italy; (G.S.); (R.L.)
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6
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Di Bella S, Luzzati R, Principe L, Zerbato V, Meroni E, Giuffrè M, Crocè LS, Merlo M, Perotto M, Dolso E, Maurel C, Lovecchio A, Dal Bo E, Lagatolla C, Marini B, Ippodrino R, Sanson G. Aspirin and Infection: A Narrative Review. Biomedicines 2022; 10:biomedicines10020263. [PMID: 35203473 PMCID: PMC8868581 DOI: 10.3390/biomedicines10020263] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 12/27/2021] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 02/01/2023] Open
Abstract
Acetylsalicylic acid (ASA) is one of the most commonly used drugs in the world. It derives from the extract of white willow bark, whose therapeutic potential was known in Egypt since 1534 BC. ASA’s pharmacological effects are historically considered secondary to its anti-inflammatory, platelet-inhibiting properties; however, human studies demonstrating a pro-inflammatory effect of ASA exist. It is likely that we are aware of only part of ASA’s mechanisms of action; moreover, the clinical effect is largely dependent on dosages. During the past few decades, evidence of the anti-infective properties of ASA has emerged. We performed a review of such research in order to provide a comprehensive overview of ASA and viral, bacterial, fungal and parasitic infections, as well as ASA’s antibiofilm properties.
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Affiliation(s)
- Stefano Di Bella
- Clinical Department of Medical, Surgical and Health Sciences, University of Trieste, 34127 Trieste, Italy; (S.D.B.); (R.L.); (L.S.C.); (M.M.); (M.P.); (G.S.)
| | - Roberto Luzzati
- Clinical Department of Medical, Surgical and Health Sciences, University of Trieste, 34127 Trieste, Italy; (S.D.B.); (R.L.); (L.S.C.); (M.M.); (M.P.); (G.S.)
| | - Luigi Principe
- Clinical Pathology and Microbiology Unit, “S. Giovanni di Dio” Hospital, 88900 Crotone, Italy;
| | - Verena Zerbato
- Infectious Diseases Unit, Trieste University Hospital, 34149 Trieste, Italy; (V.Z.); (E.D.); (C.M.); (A.L.)
| | - Elisa Meroni
- Clinical Microbiology and Virology Unit, “A. Manzoni” Hospital, 23900 Lecco, Italy;
| | - Mauro Giuffrè
- Clinical Department of Medical, Surgical and Health Sciences, University of Trieste, 34127 Trieste, Italy; (S.D.B.); (R.L.); (L.S.C.); (M.M.); (M.P.); (G.S.)
- Correspondence: ; Tel.: +39-040-3994-305
| | - Lory Saveria Crocè
- Clinical Department of Medical, Surgical and Health Sciences, University of Trieste, 34127 Trieste, Italy; (S.D.B.); (R.L.); (L.S.C.); (M.M.); (M.P.); (G.S.)
| | - Marco Merlo
- Clinical Department of Medical, Surgical and Health Sciences, University of Trieste, 34127 Trieste, Italy; (S.D.B.); (R.L.); (L.S.C.); (M.M.); (M.P.); (G.S.)
| | - Maria Perotto
- Clinical Department of Medical, Surgical and Health Sciences, University of Trieste, 34127 Trieste, Italy; (S.D.B.); (R.L.); (L.S.C.); (M.M.); (M.P.); (G.S.)
| | - Elisabetta Dolso
- Infectious Diseases Unit, Trieste University Hospital, 34149 Trieste, Italy; (V.Z.); (E.D.); (C.M.); (A.L.)
| | - Cristina Maurel
- Infectious Diseases Unit, Trieste University Hospital, 34149 Trieste, Italy; (V.Z.); (E.D.); (C.M.); (A.L.)
| | - Antonio Lovecchio
- Infectious Diseases Unit, Trieste University Hospital, 34149 Trieste, Italy; (V.Z.); (E.D.); (C.M.); (A.L.)
| | - Eugenia Dal Bo
- Cardiothoracic-Vascular Department, Azienda Sanitaria Universitaria Integrata, Cattinara University Hospital, 34149 Trieste, Italy;
| | - Cristina Lagatolla
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy;
| | - Bruna Marini
- Ulisse BioMed Labs, Area Science Park, 34149 Trieste, Italy; (B.M.); (R.I.)
| | - Rudy Ippodrino
- Ulisse BioMed Labs, Area Science Park, 34149 Trieste, Italy; (B.M.); (R.I.)
| | - Gianfranco Sanson
- Clinical Department of Medical, Surgical and Health Sciences, University of Trieste, 34127 Trieste, Italy; (S.D.B.); (R.L.); (L.S.C.); (M.M.); (M.P.); (G.S.)
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Mocenigo M, Porchetta A, Rossetti M, Brass E, Tonini L, Puzzi L, Tagliabue E, Triulzi T, Marini B, Ricci F, Ippodrino R. Rapid, Cost-Effective Peptide/Nucleic Acid-Based Platform for Therapeutic Antibody Monitoring in Clinical Samples. ACS Sens 2020; 5:3109-3115. [PMID: 32909731 DOI: 10.1021/acssensors.0c01046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We demonstrate here a homogeneous assay, named NanoHybrid, for monoclonal antibody quantification directly in serum samples in a single-step format. NanoHybrid is composed of both synthetic peptide nucleic acids (PNAs) and nucleic acid strands conjugated to recognition elements and optical labels and is designed to allow fast fluorescence quantification of a therapeutic antibody. More specifically, we have characterized our analytical assay for the detection of trastuzumab (Herceptin), a monoclonal antibody (mAb) drug used for breast cancer treatment and for tumors overexpressing the HER2/neu protein. We show here that NanoHybrid is capable of performing fast drug quantification directly in blood serum. The results obtained with a pool of samples from breast cancer patients under trastuzumab treatment are compared with CE-IVD ELISA (enzyme-linked immunosorbent assay) showing a good agreement (Cohen's K = 0.729). Due to the modular nature of the NanoHybrid platform, this technology can be programmed to potentially detect and quantify any antibody for which a high-affinity recognition element has been characterized. We envision the application of NanoHybrid in a point-of-care (POC) drug monitoring system based on disposable kits for therapeutic drug management.
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Affiliation(s)
- Marco Mocenigo
- Ulisse BioMed Labs, Area Science Park, SS 14, km 163.5, 34149 Trieste, Italy
- Molecular Genetics and Biotechnology PhD Study Programme, University of Nova Gorica, Vipavska 13, 5000 Nova Gorica, Slovenia
| | - Alessandro Porchetta
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Marianna Rossetti
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Erik Brass
- Ulisse BioMed Labs, Area Science Park, SS 14, km 163.5, 34149 Trieste, Italy
| | - Lucia Tonini
- Ulisse BioMed Labs, Area Science Park, SS 14, km 163.5, 34149 Trieste, Italy
| | - Luca Puzzi
- Ulisse BioMed Labs, Area Science Park, SS 14, km 163.5, 34149 Trieste, Italy
| | - Elda Tagliabue
- Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Tiziana Triulzi
- Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Bruna Marini
- Ulisse BioMed Labs, Area Science Park, SS 14, km 163.5, 34149 Trieste, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Rudy Ippodrino
- Ulisse BioMed Labs, Area Science Park, SS 14, km 163.5, 34149 Trieste, Italy
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Pachetti M, Marini B, Giudici F, Benedetti F, Angeletti S, Ciccozzi M, Masciovecchio C, Ippodrino R, Zella D. Impact of lockdown on Covid-19 case fatality rate and viral mutations spread in 7 countries in Europe and North America. J Transl Med 2020; 18:338. [PMID: 32878627 PMCID: PMC7463225 DOI: 10.1186/s12967-020-02501-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [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: 05/28/2020] [Accepted: 08/25/2020] [Indexed: 01/22/2023] Open
Abstract
Background Severe acute respiratory syndrome CoV-2 (SARS-CoV-2) caused the first coronavirus disease 2019 (COVID-19) outbreak in China and has become a public health emergency of international concern. SARS-CoV-2 outbreak has been declared a pandemic by WHO on March 11th, 2020 and the same month several Countries put in place different lockdown restrictions and testing strategies in order to contain the spread of the virus. Methods The calculation of the Case Fatality Rate of SARS-CoV-2 in the Countries selected was made by using the data available at https://github.com/owid/covi-19-data/tree/master/public/data. Case fatality rate was calculated as the ratio between the death cases due to COVID-19, over the total number of SARS-CoV-2 reported cases 14 days before. Standard Case Fatality Rate values were normalized by the Country-specific ρ factor, i.e. the number of PCR tests/1 million inhabitants over the number of reported cases/1 million inhabitants. Case-fatality rates between Countries were compared using proportion test. Post-hoc analysis in the case of more than two groups was performed using pairwise comparison of proportions and p value was adjusted using Holm method. We also analyzed 487 genomic sequences from the GISAID database derived from patients infected by SARS-CoV-2 from January 2020 to April 2020 in Italy, Spain, Germany, France, Sweden, UK and USA. SARS-CoV-2 reference genome was obtained from the GenBank database (NC_045512.2). Genomes alignment was performed using Muscle and Jalview software. We, then, calculated the Case Fatality Rate of SARS-CoV-2 in the Countries selected. Results In this study we analyse how different lockdown strategies and PCR testing capability adopted by Italy, France, Germany, Spain, Sweden, UK and USA have influenced the Case Fatality Rate and the viral mutations spread. We calculated case fatality rates by dividing the death number of a specific day by the number of patients with confirmed COVID-19 infection observed 14 days before and normalized by a ρ factor which takes into account the diagnostic PCR testing capability of each Country and the number of positive cases detected. We notice the stabilization of a clear pattern of mutations at sites nt241, nt3037, nt14408 and nt23403. A novel nonsynonymous SARS-CoV-2 mutation in the spike protein (nt24368) has been found in genomes sequenced in Sweden, which enacted a soft lockdown strategy. Conclusions Strict lockdown strategies together with a wide diagnostic PCR testing of the population were correlated with a relevant decline of the case fatality rate in different Countries. The emergence of specific patterns of mutations concomitant with the decline in case fatality rate needs further confirmation and their biological significance remains unclear.
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Affiliation(s)
- Maria Pachetti
- Elettra Sincrotrone Trieste-Area Science Park, Trieste, Italy.,Department of Physics, University of Trieste, Via Valerio 2, Trieste, Italy
| | | | - Fabiola Giudici
- Department of Medicine, Surgery and Health Science, University of Trieste, Trieste, Italy
| | - Francesca Benedetti
- Institute of Human Virology, Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, USA
| | - Silvia Angeletti
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
| | - Massimo Ciccozzi
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
| | | | - Rudy Ippodrino
- Department of Medicine, Surgery and Health Science, University of Trieste, Trieste, Italy.
| | - Davide Zella
- Institute of Human Virology, Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, USA. .,Member of the Global Virus Network, Baltimore, USA.
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Benedetti F, Pachetti M, Marini B, Ippodrino R, Ciccozzi M, Zella D. SARS-CoV-2: March toward adaptation. J Med Virol 2020; 92:2274-2276. [PMID: 32598499 PMCID: PMC7361333 DOI: 10.1002/jmv.26233] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 06/23/2020] [Accepted: 06/25/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Francesca Benedetti
- Department of Biochemistry and Molecular Biology, School of Medicine, Institute of Human Virology, University of Maryland, Baltimore, Maryland
| | - Maria Pachetti
- Department of Physics, Elettra Sincrotrone Trieste, University of Trieste, Trieste, Italy
| | | | | | - Massimo Ciccozzi
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
| | - Davide Zella
- Department of Biochemistry and Molecular Biology, School of Medicine, Institute of Human Virology, University of Maryland, Baltimore, Maryland.,Global Virus Network, Baltimore, Maryland
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Benedetti F, Pachetti M, Marini B, Ippodrino R, Gallo RC, Ciccozzi M, Zella D. Inverse correlation between average monthly high temperatures and COVID-19-related death rates in different geographical areas. J Transl Med 2020; 18:251. [PMID: 32576227 PMCID: PMC7309213 DOI: 10.1186/s12967-020-02418-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [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: 05/14/2020] [Accepted: 06/15/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND With the aim of providing a dynamic evaluation of the effects of basic environmental parameters on COVID-19-related death rate, we assessed the correlation between average monthly high temperatures and population density, with death/rate (monthly number of deaths/1 M people) for the months of March (start of the analysis and beginning of local epidemic in most of the Western World, except in Italy where it started in February) and April 2020 (continuation of the epidemic). Different geographical areas of the Northern Hemisphere in the United States and in Europe were selected in order to provide a wide range among the different parameters. The death rates were gathered from an available dataset. As a further control, we also included latitude, as a proxy for temperature. METHODS Utilizing a publicly available dataset, we retrieved data for the months of March and April 2020 for 25 areas in Europe and in the US. We computed the monthly number of deaths/1 M people of confirmed COVID-19 cases and calculated the average monthly high temperatures and population density for all these areas. We determined the correlation between number of deaths/1 M people and the average monthly high temperatures, the latitude and the population density. RESULTS We divided our analysis in two parts: analysis of the correlation among the different variables in the month of March and subsequent analysis in the month of April. The differences were then evaluated. In the month of March there was no statistical correlation between average monthly high temperatures of the considered geographical areas and number of deaths/1 M people. However, a statistically significant inverse correlation became significant in the month of April between average monthly high temperatures (p = 0.0043) and latitude (p = 0.0253) with number of deaths/1 M people. We also observed a statistically significant correlation between population density and number of deaths/1 M people both in the month of March (p = 0.0297) and in the month of April (p = 0.0116), when three areas extremely populated (NYC, Los Angeles and Washington DC) were included in the calculation. Once these three areas were removed, the correlation was not statistically significant (p = 0.1695 in the month of March, and p = 0.7076 in the month of April). CONCLUSIONS The number of COVID-19-related deaths/1 M people was essentially the same during the month of March for all the geographical areas considered, indicating essentially that the infection was circulating quite uniformly except for Lombardy, Italy, where it started earlier. Lockdown measures were implemented between the end of March and beginning of April, except for Italy which started March 9th. We observed a strong, statistically significant inverse correlation between average monthly high temperatures with the number of deaths/1 M people. We confirmed the data by analyzing the correlation with the latitude, which can be considered a proxy for high temperature. Previous studies indicated a negative effect of high climate temperatures on Sars-COV-2 spreading. Our data indicate that social distancing measure are more successful in the presence of higher average monthly temperatures in reducing COVID-19-related death rate, and a high level of population density seems to negatively impact the effect of lockdown measures.
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Affiliation(s)
- Francesca Benedetti
- Institute of Human Virology, Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, USA
| | - Maria Pachetti
- Elettra Sincrotrone Trieste - Area Science Park, Trieste, Italy
- Department of Physics, University of Trieste, Via Valerio 2, Trieste, Italy
| | - Bruna Marini
- Ulisse BioMed - Area Science Park, Trieste, Italy
| | | | - Robert C. Gallo
- Institute of Human Virology, Department of Medicine, School of Medicine, University of Maryland, Baltimore, USA
- Global Virus Network, Baltimore, USA
| | - Massimo Ciccozzi
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
| | - Davide Zella
- Institute of Human Virology, Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, USA
- Global Virus Network, Baltimore, USA
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Rossetti M, Brannetti S, Mocenigo M, Marini B, Ippodrino R, Porchetta A. Harnessing Effective Molarity to Design an Electrochemical DNA‐based Platform for Clinically Relevant Antibody Detection. Angew Chem Int Ed Engl 2020; 59:14973-14978. [DOI: 10.1002/anie.202005124] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Marianna Rossetti
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Simone Brannetti
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Marco Mocenigo
- Ulisse BioMed S.r.l. Area Science Park 34149 Trieste Italy
| | - Bruna Marini
- Ulisse BioMed S.r.l. Area Science Park 34149 Trieste Italy
| | - Rudy Ippodrino
- Ulisse BioMed S.r.l. Area Science Park 34149 Trieste Italy
| | - Alessandro Porchetta
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
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12
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Rossetti M, Brannetti S, Mocenigo M, Marini B, Ippodrino R, Porchetta A. Harnessing Effective Molarity to Design an Electrochemical DNA‐based Platform for Clinically Relevant Antibody Detection. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005124] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Marianna Rossetti
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Simone Brannetti
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Marco Mocenigo
- Ulisse BioMed S.r.l. Area Science Park 34149 Trieste Italy
| | - Bruna Marini
- Ulisse BioMed S.r.l. Area Science Park 34149 Trieste Italy
| | - Rudy Ippodrino
- Ulisse BioMed S.r.l. Area Science Park 34149 Trieste Italy
| | - Alessandro Porchetta
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
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Pachetti M, Marini B, Benedetti F, Giudici F, Mauro E, Storici P, Masciovecchio C, Angeletti S, Ciccozzi M, Gallo RC, Zella D, Ippodrino R. Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant. J Transl Med 2020; 18:179. [PMID: 32321524 PMCID: PMC7174922 DOI: 10.1186/s12967-020-02344-6] [Citation(s) in RCA: 576] [Impact Index Per Article: 144.0] [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: 03/31/2020] [Accepted: 04/11/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND SARS-CoV-2 is a RNA coronavirus responsible for the pandemic of the Severe Acute Respiratory Syndrome (COVID-19). RNA viruses are characterized by a high mutation rate, up to a million times higher than that of their hosts. Virus mutagenic capability depends upon several factors, including the fidelity of viral enzymes that replicate nucleic acids, as SARS-CoV-2 RNA dependent RNA polymerase (RdRp). Mutation rate drives viral evolution and genome variability, thereby enabling viruses to escape host immunity and to develop drug resistance. METHODS We analyzed 220 genomic sequences from the GISAID database derived from patients infected by SARS-CoV-2 worldwide from December 2019 to mid-March 2020. SARS-CoV-2 reference genome was obtained from the GenBank database. Genomes alignment was performed using Clustal Omega. Mann-Whitney and Fisher-Exact tests were used to assess statistical significance. RESULTS We characterized 8 novel recurrent mutations of SARS-CoV-2, located at positions 1397, 2891, 14408, 17746, 17857, 18060, 23403 and 28881. Mutations in 2891, 3036, 14408, 23403 and 28881 positions are predominantly observed in Europe, whereas those located at positions 17746, 17857 and 18060 are exclusively present in North America. We noticed for the first time a silent mutation in RdRp gene in England (UK) on February 9th, 2020 while a different mutation in RdRp changing its amino acid composition emerged on February 20th, 2020 in Italy (Lombardy). Viruses with RdRp mutation have a median of 3 point mutations [range: 2-5], otherwise they have a median of 1 mutation [range: 0-3] (p value < 0.001). CONCLUSIONS These findings suggest that the virus is evolving and European, North American and Asian strains might coexist, each of them characterized by a different mutation pattern. The contribution of the mutated RdRp to this phenomenon needs to be investigated. To date, several drugs targeting RdRp enzymes are being employed for SARS-CoV-2 infection treatment. Some of them have a predicted binding moiety in a SARS-CoV-2 RdRp hydrophobic cleft, which is adjacent to the 14408 mutation we identified. Consequently, it is important to study and characterize SARS-CoV-2 RdRp mutation in order to assess possible drug-resistance viral phenotypes. It is also important to recognize whether the presence of some mutations might correlate with different SARS-CoV-2 mortality rates.
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Affiliation(s)
- Maria Pachetti
- Elettra Sincrotrone Trieste - Area Science Park, Trieste, Italy
- Department of Physics, University of Trieste, Via Valerio 2, Trieste, Italy
| | - Bruna Marini
- Ulisse BioMed - Area Science Park, Trieste, Italy
| | - Francesca Benedetti
- Institute of Human Virology, Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, USA
| | - Fabiola Giudici
- Department of Medicine, Surgery and Health Science, University of Trieste, Trieste, Italy
| | | | - Paola Storici
- Elettra Sincrotrone Trieste - Area Science Park, Trieste, Italy
| | | | - Silvia Angeletti
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
| | - Massimo Ciccozzi
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
| | - Robert C Gallo
- Institute of Human Virology, Department of Medicine, School of Medicine, University of Maryland, Baltimore, USA
- Co-founder and International Science Advisor - Global Virus Network, Baltimore, USA
| | - Davide Zella
- Institute of Human Virology, Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, USA.
- Member of the Global Virus Network, Baltimore, USA.
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Rossetti M, Ippodrino R, Marini B, Palleschi G, Porchetta A. Antibody-Mediated Small Molecule Detection Using Programmable DNA-Switches. Anal Chem 2018; 90:8196-8201. [DOI: 10.1021/acs.analchem.8b01584] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Marianna Rossetti
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Rudy Ippodrino
- Ulisse BioMed S.r.l., Area Science Park, 34149 Trieste, Italy
| | - Bruna Marini
- Ulisse BioMed S.r.l., Area Science Park, 34149 Trieste, Italy
| | - Giuseppe Palleschi
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Alessandro Porchetta
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
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15
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Porchetta A, Ippodrino R, Marini B, Caruso A, Caccuri F, Ricci F. Programmable Nucleic Acid Nanoswitches for the Rapid, Single-Step Detection of Antibodies in Bodily Fluids. J Am Chem Soc 2018; 140:947-953. [PMID: 29313682 DOI: 10.1021/jacs.7b09347] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Antibody detection plays a pivotal role in the diagnosis of pathogens and monitoring the success of vaccine immunization. However, current serology techniques require multiple, time-consuming washing and incubation steps, which limit their applicability in point-of-care (POC) diagnostics and high-throughput assays. We developed here a nucleic acid nanoswitch platform able to instantaneously measure immunoglobulins of type G and E (IgG and IgE) levels directly in blood serum and other bodily fluids. The system couples the advantages of target-binding induced colocalization and nucleic acid conformational-change nanoswitches. Due to the modular nature of the recognition platform, the method can potentially be applied to the detection of any antibody for which an antigen can be conjugated to a nucleic acid strand. In this work we show the sensitive, fast and cost-effective detection of four different antibodies and demonstrate the possible use of this approach for the monitoring of antibody levels in HIV+ patients immunized with AT20 therapeutic vaccine.
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Affiliation(s)
- Alessandro Porchetta
- Department of Chemistry, University of Rome , Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Rudy Ippodrino
- Ulisse BioMed S.r.l. , Area Science Park, 34149 Trieste, Italy
| | - Bruna Marini
- Ulisse BioMed S.r.l. , Area Science Park, 34149 Trieste, Italy
| | - Arnaldo Caruso
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia Medical School , Piazzale Spedali Civili 1, 25123 Brescia, Italy
| | - Francesca Caccuri
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia Medical School , Piazzale Spedali Civili 1, 25123 Brescia, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome , Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
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Moro L, Turemis M, Marini B, Ippodrino R, Giardi MT. Better together: Strategies based on magnetic particles and quantum dots for improved biosensing. Biotechnol Adv 2017; 35:51-63. [DOI: 10.1016/j.biotechadv.2016.11.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 09/29/2016] [Accepted: 11/27/2016] [Indexed: 12/14/2022]
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