1
|
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.
Collapse
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
| |
Collapse
|
2
|
Antony F, Deantonio C, Cotella D, Soluri MF, Tarasiuk O, Raspagliesi F, Adorni F, Piazza S, Ciani Y, Santoro C, Macor P, Mezzanzanica D, Sblattero D. High-throughput assessment of the antibody profile in ovarian cancer ascitic fluids. Oncoimmunology 2019; 8:e1614856. [PMID: 31428516 DOI: 10.1080/2162402x.2019.1614856] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 04/25/2019] [Accepted: 04/27/2019] [Indexed: 12/31/2022] Open
Abstract
The identification of effective biomarkers for early diagnosis, prognosis, and response to treatments remains a challenge in ovarian cancer (OC) research. Here, we present an unbiased high-throughput approach to profile ascitic fluid autoantibodies in order to obtain a tumor-specific antigen signature in OC. We first reported the reactivity of immunoglobulins (Igs) purified from OC patient ascites towards two different OC cell lines. Using a discovery set of Igs, we selected tumor-specific antigens from a phage display cDNA library. After biopanning, 700 proteins were expressed as fusion protein and used in protein array to enable large-scale immunoscreening with independent sets of cancer and noncancerous control. Finally, the selected antigens were validated by ELISA. The initial screening identified eight antigenic clones: CREB3, MRPL46, EXOSC10, BCOR, HMGN2, HIP1R, OLFM4, and KIAA1755. These antigens were all validated by ELISA in a study involving ascitic Igs from 153 patients (69 with OC, 34 with other cancers and 50 without cancer), with CREB3 showing the highest sensitivity (86.95%) and specificity (98%). Notably, we were able to identify an association between the tumor-associated (TA) antibody response and the response to a first-line tumor treatment (platinum-based chemotherapy). A stronger association was found by combining three antigens (BCOR, CREB3, and MRLP46) as a single antibody signature. Measurement of an ascitic fluid antibody response to multiple TA antigens may aid in the identification of new prognostic signatures in OC patients and shift attention to new potentially relevant targets.
Collapse
Affiliation(s)
- Frank Antony
- Department of Health Sciences, and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), Università del Piemonte Orientale, Novara, Italy
| | - Cecilia Deantonio
- Department of Health Sciences, and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), Università del Piemonte Orientale, Novara, Italy
| | - Diego Cotella
- Department of Health Sciences, and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), Università del Piemonte Orientale, Novara, Italy
| | - Maria Felicia Soluri
- Department of Health Sciences, and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), Università del Piemonte Orientale, Novara, Italy
| | - Olga Tarasiuk
- Department of Health Sciences, and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), Università del Piemonte Orientale, Novara, Italy
| | | | - Fulvio Adorni
- Epidemiology Unit, Institute of Biomedical Technologies, National Research Council, Milan, Italy
| | - Silvano Piazza
- Bioinformatics and Functional Genomics Unit, Laboratorio Nazionale del Consorzio Interuniversitario per le Biotecnologie (LNCIB), Area Science Park Trieste, Italy
| | - Yari Ciani
- Bioinformatics and Functional Genomics Unit, Laboratorio Nazionale del Consorzio Interuniversitario per le Biotecnologie (LNCIB), Area Science Park Trieste, Italy
| | - Claudio Santoro
- Department of Health Sciences, and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), Università del Piemonte Orientale, Novara, Italy
| | - Paolo Macor
- Department of Life Science, University of Trieste, Trieste, Italy
| | - Delia Mezzanzanica
- Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | |
Collapse
|
3
|
Deantonio C, Sedini V, Cesaro P, Quasso F, Cotella D, Persichetti F, Santoro C, Sblattero D. An Air-Well sparging minifermenter system for high-throughput protein production. Microb Cell Fact 2014; 13:132. [PMID: 25218288 PMCID: PMC4172861 DOI: 10.1186/s12934-014-0132-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 08/27/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Over the last few years High-Throughput Protein Production (HTPP) has played a crucial role for functional proteomics. High-quality, high yield and fast recombinant protein production are critical for new HTPP technologies. Escherichia coli is usually the expression system of choice in protein production thanks to its fast growth, ease of handling and high yields of protein produced. Even though shake-flask cultures are widely used, there is an increasing need for easy to handle, lab scale, high throughput systems. RESULTS In this article we described a novel minifermenter system suitable for HTPP. The Air-Well minifermenter system is made by a homogeneous air sparging device that includes an air diffusion system, and a stainless steel 96 needle plate integrated with a 96 deep well plate where cultures take place. This system provides aeration to achieve higher optical density growth compared to classical shaking growth without the decrease in pH value and bacterial viability. Moreover the yield of recombinant protein is up to 3-fold higher with a considerable improvement in the amount of full length proteins. CONCLUSIONS High throughput production of hundreds of proteins in parallel can be obtained sparging air in a continuous and controlled manner. The system used is modular and can be easily modified and scaled up to meet the demands for HTPP.
Collapse
|
4
|
D'Angelo S, Mignone F, Deantonio C, Di Niro R, Bordoni R, Marzari R, De Bellis G, Not T, Ferrara F, Bradbury A, Santoro C, Sblattero D. Profiling celiac disease antibody repertoire. Clin Immunol 2013; 148:99-109. [DOI: 10.1016/j.clim.2013.04.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 04/09/2013] [Accepted: 04/10/2013] [Indexed: 02/07/2023]
|
5
|
Luisi I, Pavan S, Fontanive G, Tossi A, Benedetti F, Savoini A, Maurizio E, Sgarra R, Sblattero D, Berti F. An albumin-derived peptide scaffold capable of binding and catalysis. PLoS One 2013; 8:e56469. [PMID: 23451052 PMCID: PMC3579865 DOI: 10.1371/journal.pone.0056469] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 01/09/2013] [Indexed: 11/18/2022] Open
Abstract
We have identified a 101-amino-acid polypeptide derived from the sequence of the IIA binding site of human albumin. The polypeptide contains residues that make contact with IIA ligands in the parent protein, and eight cysteine residues to form disulfide bridges, that stabilize the polypeptide structure. Seventy-four amino acids are located in six α-helical regions, while the remaining thirty-seven amino acids form six connecting coil/loop regions. A soluble GST fusion protein was expressed in E. coli in yields as high as 4 mg/l. This protein retains the IIA fragment's capacity to bind typical ligands such as warfarin and efavirenz and other albumin's functional properties such as aldolase activity and the ability to direct the stereochemical outcome of a diketone reduction. This newly cloned polypeptide thus represents a valuable starting point for the construction of libraries of binders and catalysts with improved proficiency.
Collapse
Affiliation(s)
- Immacolata Luisi
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Trieste, Italy
- Dipartimento di Scienze della Vita, Università di Trieste, Trieste, Italy
| | - Silvia Pavan
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Trieste, Italy
| | - Giampaolo Fontanive
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Trieste, Italy
| | - Alessandro Tossi
- Dipartimento di Scienze della Vita, Università di Trieste, Trieste, Italy
| | - Fabio Benedetti
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Trieste, Italy
| | | | - Elisa Maurizio
- Dipartimento di Scienze della Vita, Università di Trieste, Trieste, Italy
| | - Riccardo Sgarra
- Dipartimento di Scienze della Vita, Università di Trieste, Trieste, Italy
| | - Daniele Sblattero
- Dipartimento di Scienze della Salute, Università del Piemonte Orientale “Amedeo Avogadro”, Novara, Italy
| | - Federico Berti
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Trieste, Italy
| |
Collapse
|
6
|
Naimuddin M, Kubo T. Display of disulfide-rich proteins by complementary DNA display and disulfide shuffling assisted by protein disulfide isomerase. Anal Biochem 2011; 419:33-9. [PMID: 21867670 DOI: 10.1016/j.ab.2011.07.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2011] [Revised: 07/07/2011] [Accepted: 07/27/2011] [Indexed: 10/17/2022]
Abstract
We report an efficient system to produce and display properly folded disulfide-rich proteins facilitated by coupled complementary DNA (cDNA) display and protein disulfide isomerase-assisted folding. The results show that a neurotoxin protein containing four disulfide linkages can be displayed in the folded state. Furthermore, it can be refolded on a solid support that binds efficiently to its natural acetylcholine receptor. Probing the efficiency of the display proteins prepared by these methods provided up to 8-fold higher enrichment by the selective enrichment method compared with cDNA display alone, more than 10-fold higher binding to its receptor by the binding assays, and more than 10-fold higher affinities by affinity measurements. Cotranslational folding was found to have better efficiency than posttranslational refolding between the two investigated methods. We discuss the utilities of efficient display of such proteins in the preparation of superior quality proteins and protein libraries for directed evolution leading to ligand discovery.
Collapse
Affiliation(s)
- Mohammed Naimuddin
- Janusys Corporation, Saitama Industrial Technology Center, Skip City, Kawaguchi, Saitama 333-0844, Japan.
| | | |
Collapse
|
7
|
Woo MK, Heo CK, Hwang HM, Ko JH, Yoo HS, Cho EW. Optimization of phage-immobilized ELISA for autoantibody profiling in human sera. Biotechnol Lett 2010; 33:655-61. [DOI: 10.1007/s10529-010-0483-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 11/17/2010] [Indexed: 11/30/2022]
|