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Giambruno R, Zacco E, Ugolini C, Vandelli A, Mulroney L, D’Onghia M, Giuliani B, Criscuolo E, Castelli M, Clementi N, Clementi M, Mancini N, Bonaldi T, Gustincich S, Leonardi T, Tartaglia GG, Nicassio F. Unveiling the role of PUS7-mediated pseudouridylation in host protein interactions specific for the SARS-CoV-2 RNA genome. Mol Ther Nucleic Acids 2023; 34:102052. [PMID: 38028201 PMCID: PMC10630655 DOI: 10.1016/j.omtn.2023.102052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/05/2023] [Indexed: 12/01/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a positive single-stranded RNA virus, engages in complex interactions with host cell proteins throughout its life cycle. While these interactions enable the host to recognize and inhibit viral replication, they also facilitate essential viral processes such as transcription, translation, and replication. Many aspects of these virus-host interactions remain poorly understood. Here, we employed the catRAPID algorithm and utilized the RNA-protein interaction detection coupled with mass spectrometry technology to predict and validate the host proteins that specifically bind to the highly structured 5' and 3' terminal regions of the SARS-CoV-2 RNA. Among the interactions identified, we prioritized pseudouridine synthase PUS7, which binds to both ends of the viral RNA. Using nanopore direct RNA sequencing, we discovered that the viral RNA undergoes extensive post-transcriptional modifications. Modified consensus regions for PUS7 were identified at both terminal regions of the SARS-CoV-2 RNA, including one in the viral transcription regulatory sequence leader. Collectively, our findings offer insights into host protein interactions with the SARS-CoV-2 UTRs and highlight the likely significance of pseudouridine synthases and other post-transcriptional modifications in the viral life cycle. This new knowledge enhances our understanding of virus-host dynamics and could inform the development of targeted therapeutic strategies.
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Affiliation(s)
- Roberto Giambruno
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
- Institute of Biomedical Technologies, National Research Council, 20090 Segrate, Italy
| | - Elsa Zacco
- Central RNA and RNA Systems Biology Labs, Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
| | - Camilla Ugolini
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
- Department of Oncology and Hematology-Oncology, University of Milan, 20122 Milano, Italy
| | - Andrea Vandelli
- Central RNA and RNA Systems Biology Labs, Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Logan Mulroney
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire CB10 1SD, UK
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Monterotondo, RM 00015, Italy
| | - Manfredi D’Onghia
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
| | - Bianca Giuliani
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
| | - Elena Criscuolo
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Matteo Castelli
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Nicola Clementi
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, Italy
- Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Massimo Clementi
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, Italy
- Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Nicasio Mancini
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, Italy
- Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milano, Italy
- Department of Oncology and Hematology-Oncology, University of Milan, 20122 Milano, Italy
| | - Stefano Gustincich
- Central RNA and RNA Systems Biology Labs, Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
| | - Tommaso Leonardi
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
| | - Gian Gaetano Tartaglia
- Central RNA and RNA Systems Biology Labs, Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
- Catalan Institution for Research and Advanced Studies, ICREA, 08010 Barcelona, Spain
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
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2
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Vainieri M, Vandelli A, Benvenuti SC, Bertarelli G. Tracking the digital health gap in elderly: A study in Italian remote areas. Health Policy 2023; 133:104842. [PMID: 37247605 DOI: 10.1016/j.healthpol.2023.104842] [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] [Received: 12/06/2022] [Revised: 03/29/2023] [Accepted: 05/24/2023] [Indexed: 05/31/2023]
Abstract
The Covid-19 pandemic has provided a major innovative thrust to public services regarding their digitization to continue providing an effective response to the population's needs and to reduce management costs. However, there has been a partial lack of those welfare policies that can provide an adequate response to the elderly segment of the population, which is most affected by the introduction of new technologies into the public sphere. This study analyses the digital gap in health in the elderly living in remote areas of Italy and investigates the use of digital devices for health purposes. It compares the use of digital solutions for health with people's common digital competencies and their willingness to use them. A descriptive analysis of the sample was constructed to verify the different responses of the elderly by age, gender, educational qualification, and geographic area. Furthermore, regression analyses have been conducted to test whether there is any dependent effect among the elderly's characteristics or geographic areas. The results highlight the existence of a potential digital health gap among the elderly in remote areas of Italy both due to infrastructural issues and the lack of digital skills. The latter are positively correlated with educational qualification, such that it is also possible to highlight differences between age groups analysed and shape future welfare policies to reduce digital inequality.
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Affiliation(s)
- Milena Vainieri
- Management and Healthcare Laboratory, Institute of Management, Sant'Anna School of Advanced Studies of Pisa, Pisa, Italy
| | - Andrea Vandelli
- Management and Healthcare Laboratory, Institute of Management, Sant'Anna School of Advanced Studies of Pisa, Pisa, Italy.
| | | | - Gaia Bertarelli
- Department of Economics, Ca' Foscari University of Venice, Venice, Italy
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3
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Vandelli A, Arnal Segura M, Monti M, Fiorentino J, Broglia L, Colantoni A, Sanchez de Groot N, Torrent Burgas M, Armaos A, Tartaglia GG. The PRALINE database: protein and Rna humAn singLe nucleotIde variaNts in condEnsates. Bioinformatics 2023; 39:6967034. [PMID: 36592044 PMCID: PMC9825767 DOI: 10.1093/bioinformatics/btac847] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 11/16/2022] [Accepted: 12/30/2022] [Indexed: 01/03/2023] Open
Abstract
SUMMARY Biological condensates are membraneless organelles with different material properties. Proteins and RNAs are the main components, but most of their interactions are still unknown. Here, we introduce PRALINE, a database for the interrogation of proteins and RNAs contained in stress granules, processing bodies and other assemblies including droplets and amyloids. PRALINE provides information about the predicted and experimentally validated protein-protein, protein-RNA and RNA-RNA interactions. For proteins, it reports the liquid-liquid phase separation and liquid-solid phase separation propensities. For RNAs, it provides information on predicted secondary structure content. PRALINE shows detailed information on human single-nucleotide variants, their clinical significance and presence in protein and RNA binding sites, and how they can affect condensates' physical properties. AVAILABILITY AND IMPLEMENTATION PRALINE is freely accessible on the web at http://praline.tartaglialab.com.
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Affiliation(s)
- Andrea Vandelli
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Barcelona 08193, Spain,Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Magdalena Arnal Segura
- Center for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Genova 16152, Italy,Department of Biology and Biotechnologies, University Sapienza Rome, Roma 00185, Italy
| | - Michele Monti
- Center for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Genova 16152, Italy
| | - Jonathan Fiorentino
- Center for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Genova 16152, Italy
| | - Laura Broglia
- Center for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Genova 16152, Italy
| | - Alessio Colantoni
- Department of Biology and Biotechnologies, University Sapienza Rome, Roma 00185, Italy
| | - Natalia Sanchez de Groot
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Barcelona 08193, Spain
| | - Marc Torrent Burgas
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Barcelona 08193, Spain
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4
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Delli Ponti R, Broglia L, Vandelli A, Armaos A, Torrent Burgas M, Sanchez de Groot N, Tartaglia GG. A high-throughput approach to predict A-to-I effects on RNA structure indicates a change of double-stranded content in non-coding RNAs. IUBMB Life 2022; 75:411-426. [PMID: 36057100 DOI: 10.1002/iub.2673] [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] [Received: 05/31/2022] [Accepted: 08/21/2022] [Indexed: 11/09/2022]
Abstract
RNA molecules undergo a number of chemical modifications whose effects can alter their structure and molecular interactions. Previous studies have shown that RNA editing can impact the formation of ribonucleoprotein complexes and influence the assembly of membrane-less organelles such as stress-granules. For instance, N6-methyladenosine (m6A) enhances SG formation and N1-methyladenosine (m1A) prevents their transition to solid-like aggregates. Yet, very little is known about adenosine to inosine (A-to-I) modification that is very abundant in human cells and not only impacts mRNAs but also non-coding RNAs. Here, we built the CROSSalive predictor of A-to-I effects on RNA structure based on high-throughput in-cell experiments. Our method shows an accuracy of 90% in predicting the single and double-stranded content of transcripts and identifies a general enrichment of double-stranded regions caused by A-to-I in long intergenic non-coding RNAs (lincRNAs). For the individual cases of NEAT1, NORAD and XIST, we investigated the relationship between A-to-I editing and interactions with RNA-binding proteins using available CLIP data and catRAPID predictions. We found that A-to-I editing is linked to alteration of interaction sites with proteins involved in phase-separation, which suggests that RNP assembly can be influenced by A-to-I. CROSSalive is available at http://service.tartaglialab.com/new_submission/crossalive. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Riccardo Delli Ponti
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, Singapore
| | - Laura Broglia
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Genoa, Italy
| | - Andrea Vandelli
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Alexandros Armaos
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Genoa, Italy
| | - Marc Torrent Burgas
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Natalia Sanchez de Groot
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Gian Gaetano Tartaglia
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Genoa, Italy.,Department of Biology 'Charles Darwin', Sapienza University of Rome, P.le A. Moro 5, Rome, Italy
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Abstract
Identifying human proteins that interact with SARS-CoV-2 genome is important to understand its replication and to identify therapeutic strategies. Recent studies have unveiled protein interactions of SARS-COV-2 in different cell lines and through a number of high-throughput approaches. Here, we carried out a comparative analysis of four experimental and one computational studies to characterize the interactions of SARS-CoV-2 genomic RNA. Although hundreds of interactors have been identified, only twenty-one appear in all the experiments and show a strong propensity to bind. This set of interactors includes stress granule forming proteins, pre-mRNA regulators and elements involved in the replication process. Our calculations indicate that DDX3X and several editases bind the 5′ end of SARS-CoV-2, a regulatory region previously reported to attract a large number of proteins. The small overlap among experimental datasets suggests that SARS-CoV-2 genome establishes stable interactions only with few interactors, while many proteins bind less tightly. In analogy to what has been previously reported for Xist non-coding RNA, we propose a mechanism of phase separation through which SARS-CoV-2 progressively sequesters human proteins hijacking the host immune response.
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Affiliation(s)
- Andrea Vandelli
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Giovanni Vocino
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Gian Gaetano Tartaglia
- Center for Human Technologies, Istituto Italiano di Tecnologia, Genova, Italy
- Department of Biology ‘Charles Darwin’, Sapienza University of Rome, Rome, Italy
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- *Correspondence: Gian Gaetano Tartaglia,
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6
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Vandelli A, Cid Samper F, Torrent Burgas M, Sanchez de Groot N, Tartaglia GG. The Interplay Between Disordered Regions in RNAs and Proteins Modulates Interactions Within Stress Granules and Processing Bodies. J Mol Biol 2021; 434:167159. [PMID: 34274326 DOI: 10.1016/j.jmb.2021.167159] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/30/2021] [Accepted: 07/09/2021] [Indexed: 01/23/2023]
Abstract
Condensation, or liquid-like phase separation, is a phenomenon indispensable for the spatiotemporal regulation of molecules within the cell. Recent studies indicate that the composition and molecular organization of phase-separated organelles such as Stress Granules (SGs) and Processing Bodies (PBs) are highly variable and dynamic. A dense contact network involving both RNAs and proteins controls the formation of SGs and PBs and an intricate molecular architecture, at present poorly understood, guarantees that these assemblies sense and adapt to different stresses and environmental changes. Here, we investigated the physico-chemical properties of SGs and PBs components and studied the architecture of their interaction networks. We found that proteins and RNAs establishing the largest amount of contacts in SGs and PBs have distinct properties and intrinsic disorder is enriched in all protein-RNA, protein-protein and RNA-RNA interaction networks. The increase of disorder in proteins is accompanied by an enrichment in single-stranded regions of RNA binding partners. Our results suggest that SGs and PBs quickly assemble and disassemble through dynamic contacts modulated by unfolded domains of their components.
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Affiliation(s)
- Andrea Vandelli
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain
| | - Fernando Cid Samper
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain
| | - Marc Torrent Burgas
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Natalia Sanchez de Groot
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain.
| | - Gian Gaetano Tartaglia
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain; Center for Human Technologies, Istituto Italiano di Tecnologia, 16152 Genova, Italy; Department of Biology 'Charles Darwin', Sapienza University of Rome, 00185 Rome, Italy; Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
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7
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Battistelli C, Garbo S, Riccioni V, Montaldo C, Santangelo L, Vandelli A, Strippoli R, Tartaglia GG, Tripodi M, Cicchini C. Design and Functional Validation of a Mutant Variant of the LncRNA HOTAIR to Counteract Snail Function in Epithelial-to-Mesenchymal Transition. Cancer Res 2021; 81:103-113. [PMID: 33158813 PMCID: PMC7611326 DOI: 10.1158/0008-5472.can-20-1764] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/05/2020] [Accepted: 11/03/2020] [Indexed: 12/18/2022]
Abstract
HOTAIR is a lncRNA overexpressed in several epithelial cancers and strongly correlated with invasion. This lncRNA was proven a pivotal element of the epithelial-to-mesenchymal transition (EMT), a transdifferentiation process triggering metastasis. Snail, master inducer of EMT, requires HOTAIR to recruit EZH2 on specific epithelial target genes (i.e., HNF4α, E-cadherin, and HNF1α) and cause their repression. Here, we designed a HOTAIR deletion mutant form, named HOTAIR-sbid, including the putative Snail-binding domain but depleted of the EZH2-binding domain. HOTAIR-sbid acted as a dominant negative of the endogenous HOTAIR. In both murine and human tumor cells, HOTAIR-sbid impaired the ability of HOTAIR to bind Snail and, in turn, trigger H3K27me3/EZH2-mediated repression of Snail epithelial target genes. Notably, HOTAIR-sbid expression was proven to reduce cellular motility, invasiveness, anchorage-independent growth, and responsiveness to TGFβ-induced EMT. These data provide evidence on a lncRNA-based strategy to effectively impair the function of a master EMT-transcriptional factor. SIGNIFICANCE: This study defines an innovative RNA-based strategy to interfere with a pivotal function of the tumor-related lncRNA HOTAIR, comprising a dominant negative mutant that was computationally designed and that impairs epithelial-to-mesenchymal transition.
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Affiliation(s)
- Cecilia Battistelli
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome, Italy.
| | - Sabrina Garbo
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome, Italy
| | - Veronica Riccioni
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome, Italy
| | - Claudia Montaldo
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - Laura Santangelo
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - Andrea Vandelli
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology and Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Department of Biochemistry and Molecular Biology, Systems Biology of Infection Lab, Universitat Autònoma de Barcelona, Spain
| | - Raffaele Strippoli
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome, Italy
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - Gian Gaetano Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology and Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genoa, Italy
- Department of Biology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Marco Tripodi
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome, Italy.
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - Carla Cicchini
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome, Italy
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8
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Vandelli A, Monti M, Milanetti E, Armaos A, Rupert J, Zacco E, Bechara E, Delli Ponti R, Tartaglia GG. Structural analysis of SARS-CoV-2 genome and predictions of the human interactome. Nucleic Acids Res 2020. [PMID: 33068416 DOI: 10.1101/2020.03.28.013789] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023] Open
Abstract
Specific elements of viral genomes regulate interactions within host cells. Here, we calculated the secondary structure content of >2000 coronaviruses and computed >100 000 human protein interactions with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The genomic regions display different degrees of conservation. SARS-CoV-2 domain encompassing nucleotides 22 500-23 000 is conserved both at the sequence and structural level. The regions upstream and downstream, however, vary significantly. This part of the viral sequence codes for the Spike S protein that interacts with the human receptor angiotensin-converting enzyme 2 (ACE2). Thus, variability of Spike S is connected to different levels of viral entry in human cells within the population. Our predictions indicate that the 5' end of SARS-CoV-2 is highly structured and interacts with several human proteins. The binding proteins are involved in viral RNA processing, include double-stranded RNA specific editases and ATP-dependent RNA-helicases and have strong propensity to form stress granules and phase-separated assemblies. We propose that these proteins, also implicated in viral infections such as HIV, are selectively recruited by SARS-CoV-2 genome to alter transcriptional and post-transcriptional regulation of host cells and to promote viral replication.
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Affiliation(s)
- Andrea Vandelli
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Michele Monti
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
| | - Edoardo Milanetti
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Alexandros Armaos
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
| | - Jakob Rupert
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
- Department of Biology 'Charles Darwin', Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
| | - Elsa Zacco
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
| | - Elias Bechara
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
| | - Riccardo Delli Ponti
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Gian Gaetano Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
- Department of Biology 'Charles Darwin', Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), 23 Passeig Lluis Companys, 08010 Barcelona, Spain
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9
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Vandelli A, Monti M, Milanetti E, Armaos A, Rupert J, Zacco E, Bechara E, Delli Ponti R, Tartaglia G. Structural analysis of SARS-CoV-2 genome and predictions of the human interactome. Nucleic Acids Res 2020; 48:11270-11283. [PMID: 33068416 PMCID: PMC7672441 DOI: 10.1093/nar/gkaa864] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [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: 08/19/2020] [Revised: 09/15/2020] [Accepted: 09/25/2020] [Indexed: 12/17/2022] Open
Abstract
Specific elements of viral genomes regulate interactions within host cells. Here, we calculated the secondary structure content of >2000 coronaviruses and computed >100 000 human protein interactions with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The genomic regions display different degrees of conservation. SARS-CoV-2 domain encompassing nucleotides 22 500-23 000 is conserved both at the sequence and structural level. The regions upstream and downstream, however, vary significantly. This part of the viral sequence codes for the Spike S protein that interacts with the human receptor angiotensin-converting enzyme 2 (ACE2). Thus, variability of Spike S is connected to different levels of viral entry in human cells within the population. Our predictions indicate that the 5' end of SARS-CoV-2 is highly structured and interacts with several human proteins. The binding proteins are involved in viral RNA processing, include double-stranded RNA specific editases and ATP-dependent RNA-helicases and have strong propensity to form stress granules and phase-separated assemblies. We propose that these proteins, also implicated in viral infections such as HIV, are selectively recruited by SARS-CoV-2 genome to alter transcriptional and post-transcriptional regulation of host cells and to promote viral replication.
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Affiliation(s)
- Andrea Vandelli
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Michele Monti
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
| | - Edoardo Milanetti
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Alexandros Armaos
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
| | - Jakob Rupert
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
- Department of Biology ‘Charles Darwin’, Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
| | - Elsa Zacco
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
| | - Elias Bechara
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
| | - Riccardo Delli Ponti
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Gian Gaetano Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
- Department of Biology ‘Charles Darwin’, Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), 23 Passeig Lluis Companys, 08010 Barcelona, Spain
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Vecchi G, Sormanni P, Mannini B, Vandelli A, Tartaglia GG, Dobson CM, Hartl FU, Vendruscolo M. Proteome-wide observation of the phenomenon of life on the edge of solubility. Proc Natl Acad Sci U S A 2020; 117:1015-1020. [PMID: 31892536 PMCID: PMC6969518 DOI: 10.1073/pnas.1910444117] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [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] [Indexed: 12/28/2022] Open
Abstract
To function effectively proteins must avoid aberrant aggregation, and hence they are expected to be expressed at concentrations safely below their solubility limits. By analyzing proteome-wide mass spectrometry data of Caenorhabditis elegans, however, we show that the levels of about three-quarters of the nearly 4,000 proteins analyzed in adult animals are close to their intrinsic solubility limits, indeed exceeding them by about 10% on average. We next asked how aging and functional self-assembly influence these solubility limits. We found that despite the fact that the total quantity of proteins within the cellular environment remains approximately constant during aging, protein aggregation sharply increases between days 6 and 12 of adulthood, after the worms have reproduced, as individual proteins lose their stoichiometric balances and the cellular machinery that maintains solubility undergoes functional decline. These findings reveal that these proteins are highly prone to undergoing concentration-dependent phase separation, which on aging is rationalized in a decrease of their effective solubilities, in particular for proteins associated with translation, growth, reproduction, and the chaperone system.
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Affiliation(s)
- Giulia Vecchi
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom
| | - Benedetta Mannini
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom
| | - Andrea Vandelli
- Gene Function and Evolution, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
| | - Gian Gaetano Tartaglia
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, 16163 Genoa, Italy
- CRG, BIST, 08003 Barcelona, Spain
- Institucio Catalana de Recerca i Estudis Avancats (ICREA), 08010 Barcelona, Spain
- Department of Biology "Charles Darwin," Sapienza University of Rome, 00185 Rome, Italy
| | - Christopher M Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom;
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Ponti RD, Armaos A, Vandelli A, Tartaglia GG. CROSSalive: a web server for predicting the in vivo structure of RNA molecules. Bioinformatics 2019; 36:940-941. [PMID: 31504168 PMCID: PMC9883674 DOI: 10.1093/bioinformatics/btz666] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 05/24/2019] [Revised: 05/24/2019] [Accepted: 08/26/2019] [Indexed: 02/02/2023] Open
Abstract
MOTIVATION RNA structure is difficult to predict in vivo due to interactions with enzymes and other molecules. Here we introduce CROSSalive, an algorithm to predict the single- and double-stranded regions of RNAs in vivo using predictions of protein interactions. RESULTS Trained on icSHAPE data in presence (m6a+) and absence of N6 methyladenosine modification (m6a-), CROSSalive achieves cross-validation accuracies between 0.70 and 0.88 in identifying high-confidence single- and double-stranded regions. The algorithm was applied to the long non-coding RNA Xist (17 900 nt, not present in the training) and shows an Area under the ROC curve of 0.83 in predicting structured regions. AVAILABILITY AND IMPLEMENTATION CROSSalive webserver is freely accessible at http://service.tartaglialab.com/new_submission/crossalive. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Riccardo Delli Ponti
- Gene Function and Evolution, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain,Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Alexandros Armaos
- Gene Function and Evolution, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain,Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Andrea Vandelli
- Gene Function and Evolution, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain,Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
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Fabbri A, Servadei F, Marchesini G, Stein SC, Vandelli A. Observational approach to subjects with mild-to-moderate head injury and initial non-neurosurgical lesions. J Neurol Neurosurg Psychiatry 2008; 79:1180-5. [PMID: 18356255 DOI: 10.1136/jnnp.2007.135178] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND The model of care for patients with mild-to-moderate head injury and CT-detected lesions that do not require an immediate intervention is a matter of debate. This study compared the effects on outcome of a model based either on observation in a neurosurgical unit (NSU) or in a peripheral hospital (PH), making use of neurosurgical expertise via a teleradiology system. PATIENTS AND METHODS The investigation reviewed the data that was prospectively collected in 865 cases with mild-to-moderate head injury and positive CT scan, not needing immediate neurosurgical evacuation. Outcome was determined at 6 months. The predictive value of location of observation on outcome was evaluated by logistic regression, after adjustment for the propensity score to the type of observation (calculated on main entry variables). FINDINGS 700 subjects had a mild head injury, 105 had a moderate injury with GCS 13-11 and 60 with Glasgow Coma Scale (GCS) 10-9. Only 152/865 subjects (17.6%) were admitted to a NSU. During observation, neurosurgery was necessary in 117 cases (13.5%), 74/152 (48.7%) NSU-observed patients and 43/713 (6.0%; p<0.001) PH-observed cases. The outcome was unfavourable in 18% of the NSU cases versus 10% of the PH cases (p = 0.143). After correction for propensity, no significant differences were found between models of observation (NSU vs. PH; odds ratio, 0.92; 95% confidence interval, 0.49 to 1.75). INTERPRETATION A model of care based on observation in PH with neurosurgical consult by teleradiology system, repeat CT scanning and transfer time 30-60 min to a NSU is not detrimental for subjects with initial non-neurosurgical lesions after mild-to-moderate head injury.
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Affiliation(s)
- A Fabbri
- Dipartimento dell'Emergenza, Presidio Ospedaliero Morgagni-Pierantoni, Azienda Unità Sanitaria Locale di Forlì, Italy.
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Fabbri A, Servadei F, Marchesini G, Stein SC, Vandelli A. Early predictors of unfavourable outcome in subjects with moderate head injury in the emergency department. J Neurol Neurosurg Psychiatry 2008; 79:567-73. [PMID: 17766433 DOI: 10.1136/jnnp.2007.120162] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Subjects with moderate head injury are a particular challenge for the emergency physician. They represent a heterogeneous population of subjects with large variability in injury severity, clinical course and outcome. We aimed to determine the early predictors of outcome of subjects with moderate head injury admitted to an Emergency Department (ED) of a general hospital linked via telemedicine to the Regional Neurosurgical Centre. PATIENTS AND METHODS We reviewed, prospectively, 12,675 subjects attending the ED of a General Hospital between 1999 and 2005 for head injury. A total of 309 cases (2.4%) with an admission Glasgow Coma Scale (GCS) 9-13 were identified as having moderate head injury. The main outcome measure was an unfavourable outcome at 6 months after injury. The predictive value of a model based on main entry variables was evaluated by logistic regression analysis. FINDINGS 64.7% of subjects had a computed tomographic scan that was positive for intracranial injury, 16.5% needed a neurosurgical intervention, 14.6% had an unfavourable outcome at 6 months (death, permanent vegetative state, permanent severe disability). Six variables (basal skull fracture, subarachnoid haemorrhage, coagulopathy, subdural haematoma, modified Marshall category and GCS) predicted an unfavourable outcome at 6 months. This combination of variables predicts the 6-month outcome with high sensitivity (95.6%) and specificity (86.0%). INTERPRETATION A group of selected variables proves highly accurate in the prediction of unfavourable outcome at 6 months, when applied to subjects admitted to an ED of a General Hospital with moderate head injury.
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MESH Headings
- Adolescent
- Adult
- Aged
- Brain Concussion/diagnosis
- Brain Concussion/mortality
- Brain Concussion/surgery
- Brain Damage, Chronic/etiology
- Brain Injuries/diagnosis
- Brain Injuries/mortality
- Brain Injuries/surgery
- Cerebral Hemorrhage, Traumatic/diagnosis
- Cerebral Hemorrhage, Traumatic/mortality
- Cerebral Hemorrhage, Traumatic/surgery
- Child
- Diffuse Axonal Injury/diagnosis
- Diffuse Axonal Injury/mortality
- Diffuse Axonal Injury/surgery
- Disability Evaluation
- Emergency Service, Hospital
- Female
- Follow-Up Studies
- Glasgow Coma Scale
- Hematoma, Epidural, Cranial/diagnosis
- Hematoma, Epidural, Cranial/mortality
- Hematoma, Epidural, Cranial/surgery
- Hospital Mortality
- Humans
- Injury Severity Score
- Italy
- Male
- Middle Aged
- Neurologic Examination
- Persistent Vegetative State/etiology
- Prognosis
- Remote Consultation
- Skull Fracture, Depressed/diagnosis
- Skull Fracture, Depressed/mortality
- Skull Fracture, Depressed/surgery
- Tomography, X-Ray Computed
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Affiliation(s)
- A Fabbri
- Dipartimento dell'Emergenza, Presidio Ospedaliero Morgagni-Pierantoni, Azienda USL Forlì, Via Forlanini 34, I-47100 Forlì, Italy.
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Sartini M, Cremonesi P, Tamagno R, Cristina ML, Orlando P, Vandelli A, Carinci A, Caruso A, Grotti A, Iacovella A, La Brocca A, Mangioncalda A, Longanesi AM, Susi B, Barletta C, Braglia D, Coen D, Tazza D, Gottardi E, Palego E, Urbano E, Bar F, Bussani F, De Giorgi F, Esposito F, Fabi F, Lotti F, Miglio F, Moscariello F, Pertoldi F, Sardella F, Tosato F, Abregal G, Baldi G, Carbone G, Cerqua G, Giagnorio G, Pia G, Piazza G, Tedesco G, Sallustio GF, Morana I, Beringheli L, Jannotti L, Spinsi L, Zulli L, Cavazza M, De Simone M, Galletti M, Gioffrè Florio M, Greco M, Longoni M, Luppi M, Magnani M, Mazzone M, Pastorello M, Pazzaglia M, Ravaglia M, Zammataro M, Zanna M, Bressan MA, Saggese MP, Gentiloni Silveri N, Scopetta N, De Mitri O, Fantin O, Boscolo P, Cancemi P, De Angelis P, Di Pietro P, Mosca P, Pacelli P, Torboli P, Copetti R, Fazio R, Losordo R, Melandri R, Papitto R, Chiaravalle S, Orlando S, Sturlese U, Di Grande A, Narbone G, Zimmermann H, Martinelli L, Clanchini V, Paternosto D, Fiorilli M, Del Prato C, Becheri M, Lanigra M, Guerra G, Sinno C, Soragna A, Ferranio MP, Bua V, Capra R, Lualdi E. Quality in emergency departments: a study on 3,285,440 admissions. J Prev Med Hyg 2007; 48:17-23. [PMID: 17506233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
INTRODUCTION A multi-centre study has been conducted, during 2005, by means of a questionnaire posted on the Italian Society of Emergency Medicine (SIMEU) web page. Our intention was to carry out an organisational and functional analysis of Italian Emergency Departments (ED) in order to pick out some macro-indicators of the activities performed. Participation was good, in that 69 ED (3,285,440 admissions to emergency services) responded to the questionnaire. METHODS The study was based on 18 questions: 3 regarding the personnel of the ED, 2 regarding organisational and functional aspects, 5 on the activity of the ED, 7 on triage and 1 on the assessment of the quality perceived by the users of the ED. RESULTS AND CONCLUSION The replies revealed that 91.30% of the ED were equipped with data-processing software, which, in 96.83% of cases, tracked the entire itinerary of the patient. About 48,000 patients/year used the ED: 76.72% were discharged and 18.31% were hospitalised. Observation Units were active in 81.16% of the ED examined. Triage programmes were in place in 92.75% of ED: in 75.81% of these, triage was performed throughout the entire itinerary of the patient; in 16.13% it was performed only symptom-based, and in 8.06% only on-call. Of the patients arriving at the ED, 24.19% were assigned a non-urgent triage code, 60.01% a urgent code, 14.30% a emergent code and 1.49% a life-threatening code. Waiting times were: 52.39 min for non-urgent patients, 40.26 min for urgent, 12.08 for emergent, and 1.19 for life-threatening patients.
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Affiliation(s)
- M Sartini
- Dept. Health Sciences, University of Genoa, Italy.
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Baldi G, Altomonte F, Altomonte M, Ghirarduzzi A, Brusasco C, Parodi RC, Ricciardi A, Remollino V, Spisni V, Saporito A, Caiazza A, Musso G, Cervellin G, Lamberti S, Buzzalino M, De Giorgi F, Del Prato C, Golinelli MP, Gai V, Monsù R, Gioffre' M, Giovanardi D, Cattaneo S, Frumento F, Caporrella A, Re G, De Iaco F, Bologna G, Nocenti F, Lorenzi C, Zoratti R, Sciolla A, Tiscione V, Pastorello M, Vandelli A, Villa A, Zanna M, De Palma A, Iorio A. Intracranial Haemorrhage in Patients on Antithrombotics: Clinical Presentation and Determinants of Outcome in a Prospective Multicentric Study in Italian Emergency Departments. Cerebrovasc Dis 2006; 22:286-93. [PMID: 16847397 DOI: 10.1159/000094604] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2006] [Accepted: 05/22/2006] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Intracranial haemorrhage (ICH) is the type of stroke associated with the highest death rate, and about 30% of ICH occurs in patients on antithrombotic treatment. This study relates clinical presentations and outcome of ICH patients on oral anticoagulant (OA) or antiplatelet (AP) therapy admitted to 33 Italian emergency departments (ED). METHODS Consecutive patients were enrolled after cranial computed tomography (CT). Primary outcome was the Modified Rankin Scale (MRS) score at 3 months of follow-up. Common descriptive statistics were computed after stratification for traumatic or spontaneous ICH and identification of the anatomical location of bleeding. Multivariate logistic regression was used to assess predictors of death. RESULTS We recruited 434 patients on AP therapy and 232 on OA. There were 432 spontaneous and 234 traumatic ICH patients. The proportions of AP and OA patients undergoing neurosurgery were 21.8 and 19.4%, respectively, while < 30% underwent procoagulant medical treatment. At the 3-month follow-up, the case fatality rate was 42.0%, while disability or death (MRS 3-6) was 68.1%. The odds ratio for death in OA versus AP patients was 2.63 (95% CI 1.73-4.00) in the whole population and 2.80 (95% CI 1.77-4.41) in intraparenchymal event patients. Glasgow Coma Scale, age, spontaneous event and anticoagulant use were found to be predictors of death both in traumatic and spontaneous events. CONCLUSION This study confirms the high prevalence of death or disability in OA and AP patients with ICH. As far as the determinants of mortality and disability are concerned, the results of this study might be useful in the clinical management and allocation of resources in the ED setting. The observed low use of procoagulant therapy highlights the need for ED educational programmes to heighten the awareness of available and effective haemostatic treatments.
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Fabbri A, Servadei F, Marchesini G, Morselli-Labate AM, Dente M, Iervese T, Spada M, Vandelli A. Prospective validation of a proposal for diagnosis and management of patients attending the emergency department for mild head injury. J Neurol Neurosurg Psychiatry 2004; 75:410-6. [PMID: 14966157 PMCID: PMC1738984 DOI: 10.1136/jnnp.2003.016113] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND In mild head injury, predictors to select patients for computed tomography (CT) and/or to plan proper management are needed. The strength of evidence of published recommendations is insufficient for current use. We assessed the diagnostic accuracy and the clinical validity of the proposal of the Neurotraumatology Committee of the World Federation of Neurosurgical Societies on mild head injury from an emergency department perspective. METHODS In a three year period, 5578 adolescent and adult subjects were prospectively recruited and managed according to the proposed protocol. Outcome measures were: (a) any post-traumatic lesion; (b) need for neurosurgical intervention; (c) unfavourable outcome (death, permanent vegetative state or severe disability) after six months. The predictive value of a model based on five variables (Glasgow coma score, clinical findings, risk factors, neurological deficits, and skull fracture) was tested by logistic regression analysis. FINDINGS At first CT evaluation 327 patients (5.9%) had intracranial post-traumatic lesions. In 16 cases (0.3%) previously undiagnosed lesions were detected after re-evaluation within seven days. Neurosurgical intervention was needed in 71 patients (1.3%) and an unfavourable outcome occurred in 39 cases (0.7%). The area under the ROC curve of the variables in predicting post-traumatic lesions was 0.906 (0.009) (sensitivity 70.0%, specificity 94.1% at best cut off), neurosurgical intervention was 0.926 (0.016) (sensitivity 81.7%, specificity 94.1%), and unfavourable outcome was 0.953 (0.014) (sensitivity 88.1%, specificity 95.1%). INTERPRETATION The variables prove highly accurate in the prediction of clinically meaningful outcomes, when applied to a consecutive set of patients with mild head injury in the clinical setting of a 1st level emergency department.
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Affiliation(s)
- A Fabbri
- Dipartimento Emergenza-Urgenza Accettazione, Ospedale GB Morgagni, Azienda Unità Sanitaria Locale di Forlì, Italy.
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Fabbri A, Marchesini G, Morselli-Labate AM, Ruggeri S, Fallani M, Melandri R, Bua V, Pasquale A, Vandelli A. Comprehensive drug screening in decision making of patients attending the emergency department for suspected drug overdose. Emerg Med J 2003; 20:25-8. [PMID: 12533362 PMCID: PMC1725990 DOI: 10.1136/emj.20.1.25] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVES This study aimed to evaluate the usefulness of a comprehensive drug screening method as a first line diagnostic tool on clinical decision making in patients attending an emergency department for suspected drug overdose in terms of agreement between physicians on patients' disposal. METHODS Five emergency physicians retrospectively evaluated the records of 142 adult patients, admitted to the emergency department of a community hospital for suspected drug overdose. They were asked for an expert opinion on patients' disposal at the end of the observation period, based on paired records, with/without the results of a comprehensive drug screening. RESULTS In the absence of the drug screening, a very poor agreement (kappa statistics) was observed between physicians. When the drug screening was available, the interobserver agreement for decision on patients' disposal increased to the fair to good range (global agreement: from 0.238 (0.019) to 0.461 (0.020) (mean(SE)); p<0.001). The agreement also increased when admission to an intensive care unit, to a general ward, and discharge from hospital were separately analysed. The availability of drug screening would have saved 21.7% of hospital admissions and 53.3% of high dependency and/or intensive care unit admissions. CONCLUSION Comprehensive drug screening adds to decision making for patients attending an emergency department for suspected drug overdose, improving agreement among physicians on patients' disposal and potentially saving hospital resources.
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Affiliation(s)
- A Fabbri
- Dipartimento Emergenza-Urgenza Accettazione, Ospedale GB Morgagni, Azienda Unità Sanitaria Locale di Forl, Italy Cattedra di Malattie del Metabolismo, Università degli Studi di Bologna, Italy.
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Fabbri A, Marchesini G, Morselli-Labate AM, Rossi F, Cicognani A, Dente M, Iervese T, Ruggeri S, Mengozzi U, Vandelli A. Positive blood alcohol concentration and road accidents. A prospective study in an Italian emergency department. Emerg Med J 2002; 19:210-4. [PMID: 11971829 PMCID: PMC1725851 DOI: 10.1136/emj.19.3.210] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
STUDY OBJECTIVE To examine if a positive blood alcohol concentration (BAC) at the time of crash (>or=0.50 g/l), independently of any clinical evidence and laboratory results indicating acute alcohol intoxication, is associated with specific features of patients involved, specific types of injury, and characteristics of the accident. METHODS In this prospective cohort study, the BAC was measured in adult patients who had been injured and who were admitted to an Italian emergency department within four hours after a road accident. Altogether 2354 trauma patients were included between January to December 1998 out of 2856 eligible subjects. RESULTS BAC exceeded 0.50 g/l in 425 subjects (18.1%), but was in a toxic range (>1.00 g/l) in only 179 subjects (7.6%). BAC positivity was significantly more common in men, in young subjects, in subjects driving cars or trucks, and in persons involved in a crash during night time and at weekends. It was associated with higher trauma severity, but no differences were found in injury body distribution according to vehicle type. In multivariate logistic regression analysis, the risk of a positive BAC in injured patients at the time of crash was independently associated with night time (odds ratio: 3.48; 95% confidence intervals: 2.46 to 4.91), male sex (3.08 (2.36 to 4.01)), weekend nights (1.21 (1.05 to 1.41)), and age (0.92 (0.86 to 0.99) per decades). CONCLUSION In injured patients after a road accident, a BAC at the time of crash in a non-toxic range (>or=0.50 g/l) is associated with specific characteristics of crash, as well as increased risk of higher trauma severity. More careful monitoring is needed in young men during weekend nights for highest risk of BAC positivity after a road accident.
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Affiliation(s)
- A Fabbri
- Dipartimento Emergenza-Urgenza Accettazione, Ospedale GB Morgagni, Azienda Unità Sanitaria Locale di Forlì, Italy.
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Fabbri A, Marchesini G, Morselli-Labate AM, Rossi F, Cicognani A, Dente M, Iervese T, Ruggeri S, Mengozzi U, Vandelli A. Blood alcohol concentration and management of road trauma patients in the emergency department. J Trauma 2001; 50:521-8. [PMID: 11265033 DOI: 10.1097/00005373-200103000-00018] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The effects of blood alcohol on injury after crash are controversial, and safe limits are not settled. We examined if a positive blood alcohol concentration, even in a nontoxic range, affects management and outcome of injured patients after road crashes. METHODS In this prospective cohort study, we recruited all adult subjects admitted to an emergency department within 4 hours after a road crash. Outcomes were mortality or expected permanent disability, and data related to patients' management. RESULTS Alcohol-positive trauma patients were more frequently critical at admission (odds ratio [OR], 1.89; 95% confidence interval [CI], 1.18-3.02), and had an increased risk of combined mortality or expected permanent disability (OR, 1.67; 95% CI, 1.08-2.58), need for intensive care (OR, 1.87; 95% CI, 1.01-3.46), surgery (OR, 1.91; 95% CI, 1.37-2.66) and blood transfusions (OR, 2.09; 95% CI, 1.20-3.64), and acute medical complications (OR, 1.94; 95% CI, 1.33-2.85). All these events were explained by higher trauma severity. Only the risk of unsuspected injuries, diagnosed only at final evaluation, was independently associated with a positive blood alcohol concentration (OR, 4.98; 95% CI, 3.62-6.87), in addition to trauma severity and preexisting chronic conditions. Blood alcohol measurement significantly improved the accuracy in predicting unsuspected injuries, from 81.3% to 86.2%. CONCLUSION In injured patients after a road crash, a positive blood alcohol concentration increases the chance that the final diagnosis will include more injuries than initially documented. More careful monitoring is needed in alcohol-positive trauma patients, independent of clinical status, injury severity, and overt symptoms of alcohol intoxication.
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Affiliation(s)
- A Fabbri
- Dipartimento Emergenza-Urgenza Accettazione, Ospedale G.B. Morgagni, Azienda Unità Sanitaria Locale di Forlì, Italy.
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Vandelli A, Cariani G, Bonora G, Padovani F, Saragoni L, Dell'Amore D. Adenomyoma of the stomach. Report of a case and review of the literature. Surg Endosc 1993; 7:185-7. [PMID: 8503076 DOI: 10.1007/bf00594104] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A case of adenomyoma of the prepyloric antrum and a review of the previous reported in the literature are presented. The tumor is composed of cysts and glandular structures lined by cuboidal-to-columnar epithelium surrounded by hypertrophic smooth muscle bundles. Furthermore, glands resembling Brunner's and/or heterotopic pancreatic tissue are present in some patients. The endoscopic characteristics of the lesion are discussed, as well as the diagnostic and therapeutic approaches.
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Affiliation(s)
- A Vandelli
- Department of Emergency Medicine, University of Bologna, St. Orsola Hospital, Italy
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Vandelli A, Cariani G, Fontana G. Unipolar coagulation in colon angiodysplasia. Surg Endosc 1992; 6:263. [PMID: 1296661 DOI: 10.1007/bf02498819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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24
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Cariani G, Vandelli A, Fontana G, Bonora G, Mazzoleni G. Autoimmune gastritis: is Helicobacter pylori a merely commensal or a pathogenic agent? Dig Dis Sci 1992; 37:1304-5. [PMID: 1499458 DOI: 10.1007/bf01296579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Cariani G, Vandelli A, Santini D, Caselli A, Fontana G. Omeprazole in short-term treatment of Helicobacter pylori positive duodenal ulcer. Ital J Gastroenterol 1991; 23:597-8. [PMID: 1760568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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26
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Cariani G, Vandelli A, Santini D, Aversa GP, Fontana G. Lack of activity of omeprazole against Helicobacter pylori. Am J Gastroenterol 1991; 86:1690. [PMID: 1951259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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28
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Pezzilli R, Broccoli PL, Melandri R, Vandelli A, Re G, Fontana G. Exocrine pancreatic involvement in Wegener's granulomatosis. A case report. Ital J Gastroenterol 1991; 23:258-60. [PMID: 1742517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A rare case of exocrine pancreatic damage in a patient with Wegener's granulomatosis is reported. The pancreatic amino acid consumption test, a new tubeless technique, revealed exocrine pancreatic insufficiency before and after immunosuppressive therapy. The presence of exocrine pancreatic insufficiency in this patient raises the possibility of pancreatic involvement in Wegener's granulomatosis.
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Affiliation(s)
- R Pezzilli
- Servizio di Pronto Soccorso e Medicina d'Urgenza, Ospedale Sant'Orsola, Bologna, Italy
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Maiolo P, Costa PL, Vandelli A, Bocchini R, Della Gaudenza M, Fontana G. [Comparison between the therapeutic efficacy of H2 blockers and somatostatin in hemorrhage of the upper digestive tract]. Recenti Prog Med 1985; 76:79-83. [PMID: 2859643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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31
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Maiolo P, Vandelli A, Costa PL, Silvani G, Melandri M, Fontana G. [Sigmoidoscopy and colonoscopy. Considerations on methodological strategy]. Minerva Dietol Gastroenterol 1982; 28:119-121. [PMID: 7099445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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32
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Vandelli A, Gullini S, Maiolo P, Silvani G, Costa PL, Fontana G. [Clinical, morphological and functional effects of a non-steroid anti-inflammatory drug on the gastric mucosa]. Minerva Dietol Gastroenterol 1981; 27:31-8. [PMID: 6894787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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33
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Costa PL, Vandelli A, Silvani G, Maiolo P, Melandri M, Camporesi C, Fontana G. [Ultrasonography in the diagnosis of cardiac liver]. Recenti Prog Med 1980; 68:491-503. [PMID: 7006003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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34
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Fontana G, Costa PL, Vandelli A, Silvani G, Maiolo P. [Ultrasonography in pancreatic cancer]. Radiol Med 1979; 65:932. [PMID: 554225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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35
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Caletti GC, Vandelli A, Bolondi L, Fontana G, Labò G. Endoscopic retrograde cholangiography (ERC) through artificial endoscopic choledocho-duodenal fistula. Endoscopy 1978; 10:203-6. [PMID: 699889 DOI: 10.1055/s-0028-1098295] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A new endoscopic method for retrograde cholangiography in cases of unsuccessful cannulation of the papilla is described. In 1 patient with obstructive jaundice, severe diabetes and a previous history of biliary pain traditional ERC failed. An endoscopic artificial choledocho-duodenal fistula by means of a diathermic cutter (needle type) was performed at the lower end of the intramural portion of the common bile duct for retrograde cholangiography. X-ray showed an obstruction of the common bile duct due to a carcinoma of the head of the pancreas. Complications did not occur during the procedure and in the post-operative period. It is concluded that the described method may be helpful when traditional selective ERC fails, moreover it may permit an endoscopic choledocho-duodenostomy for choledocholithiasis in cases of unsuccessful endoscopic papillo-sphincterotomy.
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