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Puccio S, Grillo G, Consiglio A, Soluri MF, Sblattero D, Cotella D, Santoro C, Liuni S, Bellis GD, Lugli E, Peano C, Licciulli F. InteractomeSeq: a web server for the identification and profiling of domains and epitopes from phage display and next generation sequencing data. Nucleic Acids Res 2020; 48:W200-W207. [PMID: 32402076 PMCID: PMC7319578 DOI: 10.1093/nar/gkaa363] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/16/2020] [Accepted: 05/05/2020] [Indexed: 01/03/2023] Open
Abstract
High-Throughput Sequencing technologies are transforming many research fields, including the analysis of phage display libraries. The phage display technology coupled with deep sequencing was introduced more than a decade ago and holds the potential to circumvent the traditional laborious picking and testing of individual phage rescued clones. However, from a bioinformatics point of view, the analysis of this kind of data was always performed by adapting tools designed for other purposes, thus not considering the noise background typical of the 'interactome sequencing' approach and the heterogeneity of the data. InteractomeSeq is a web server allowing data analysis of protein domains ('domainome') or epitopes ('epitome') from either Eukaryotic or Prokaryotic genomic phage libraries generated and selected by following an Interactome sequencing approach. InteractomeSeq allows users to upload raw sequencing data and to obtain an accurate characterization of domainome/epitome profiles after setting the parameters required to tune the analysis. The release of this tool is relevant for the scientific and clinical community, because InteractomeSeq will fill an existing gap in the field of large-scale biomarkers profiling, reverse vaccinology, and structural/functional studies, thus contributing essential information for gene annotation or antigen identification. InteractomeSeq is freely available at https://InteractomeSeq.ba.itb.cnr.it/.
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Affiliation(s)
- Simone Puccio
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, IRCCS, Rozzano (Milan), 20089, Italy
| | - Giorgio Grillo
- Institute for Biomedical Technologies, National Research Council, Bari 70100, Italy
| | - Arianna Consiglio
- Institute for Biomedical Technologies, National Research Council, Bari 70100, Italy
| | - Maria Felicia Soluri
- Department of Health Sciences & Center for TranslationalResearch on Autoimmune and Allergic Disease (CAAD), Università del Piemonte Orientale, Novara 28100, Italy
| | - Daniele Sblattero
- Department of Life Sciences, University of Trieste, Trieste 34100, Italy
| | - Diego Cotella
- Department of Health Sciences & Center for TranslationalResearch on Autoimmune and Allergic Disease (CAAD), Università del Piemonte Orientale, Novara 28100, Italy
| | - Claudio Santoro
- Department of Health Sciences & Center for TranslationalResearch on Autoimmune and Allergic Disease (CAAD), Università del Piemonte Orientale, Novara 28100, Italy
| | - Sabino Liuni
- Institute for Biomedical Technologies, National Research Council, Bari 70100, Italy
| | - Gianluca De Bellis
- Institute for Biomedical Technologies, National Research Council, Segrate (Milan) 20090, Italy
| | - Enrico Lugli
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, IRCCS, Rozzano (Milan), 20089, Italy.,Humanitas Flow Cytometry Core, Humanitas Clinical and Research Center, IRCCS, Rozzano (Milan) 20089, Italy
| | - Clelia Peano
- Institute of Genetic and Biomedical Research, UoS Milan, National Research Council, Rozzano (Milan) 20089, Italy.,Genomic Unit, Humanitas Clinical and Research Center, IRCCS,Rozzano (Milan) 20089, Italy
| | - Flavio Licciulli
- Institute for Biomedical Technologies, National Research Council, Bari 70100, Italy
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Soluri MF, Puccio S, Caredda G, Edomi P, D’Elios MM, Cianchi F, Troilo A, Santoro C, Sblattero D, Peano C. Defining the Helicobacter pylori Disease-Specific Antigenic Repertoire. Front Microbiol 2020; 11:1551. [PMID: 32849324 PMCID: PMC7396715 DOI: 10.3389/fmicb.2020.01551] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 06/16/2020] [Indexed: 12/19/2022] Open
Abstract
The analysis of the interaction between Helicobacter pylori (HP) and the host in vivo is an extremely informative way to enlighten the molecular mechanisms behind the persistency/latency of the bacterium as well as in the progression of the infection. An important source of information is represented by circulating antibodies targeting the bacteria that define a specific "disease signature" with prospective diagnostic implications. The diagnosis of some of the HP induced diseases such as gastric cancer (GC), MALT lymphoma (MALT), and autoimmune gastritis (AIG) is not easy because patients do not show symptoms of illness in early-onset stages, at the same time they progress rapidly. The possibility of identifying markers able to provide an early diagnosis would be extremely beneficial since a late diagnosis results in a delay in undergoing active therapy and reduces the survival rate of patients. With the aim to identify the HP antigens recognized during the host immune-response to the infection and possibly disease progression, we applied a discovery-driven approach, that combines "phage display" and deep sequencing. The procedure is based on the selection of ORF phage libraries, specifically generated from the pathogen's genome, with sera antibodies from patients with different HP-related diseases. To this end two phage display libraries have been constructed starting from genomic DNA from the reference HP 26695 and the pathogenic HP B128 strains; libraries were filtered for ORFs by using an ORF selection vector developed by our group (Di Niro et al., 2005; Soluri et al., 2018), selected with antibodies from patients affected by GC, MALT, and AIG and putative HP antigens/epitopes were identified after Sequencing and ranking. The results show that individual selection significantly reduced the library diversity and comparison of individual ranks for each condition allowed us to highlight a pattern of putative antigens specific for the different pathological outcomes or common for all of them. Within the putative antigens enriched after selection, we have validated protein CagY/Cag7 by ELISA assay as a marker of HP infection and progression. Overall, we have defined HP antigenic repertoire and identified a panel of putative specific antigens/epitopes for three different HP infection pathological outcomes that could be validated in the next future.
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Affiliation(s)
- Maria Felicia Soluri
- Department of Health Sciences & IRCAD, Università del Piemonte Orientale, Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Disease, Università del Piemonte Orientale, Novara, Italy
| | - Simone Puccio
- Laboratory of Translational Immunology, IRCCS, Humanitas Clinical and Research Center, Rozzano, Italy
| | - Giada Caredda
- Department of Excellence in Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Paolo Edomi
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Mario Milco D’Elios
- Department of Experimental and Clinical Medicine, School of Human Health Sciences, University of Florence, Florence, Italy
| | - Fabio Cianchi
- Department of Experimental and Clinical Medicine, School of Human Health Sciences, University of Florence, Florence, Italy
| | - Arianna Troilo
- Department of Experimental and Clinical Medicine, School of Human Health Sciences, University of Florence, Florence, Italy
| | - Claudio Santoro
- Department of Health Sciences & IRCAD, Università del Piemonte Orientale, Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Disease, Università del Piemonte Orientale, Novara, Italy
| | | | - Clelia Peano
- Institute of Genetic and Biomedical Research, UoS Milan, National Research Council, Milan, Italy
- Genomic Unit, IRCCS, Humanitas Clinical and Research Center, Milan, Italy
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