1
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Garcia-Calvo E, García-García A, Rodríguez S, Martín R, García T. Unraveling the Properties of Phage Display Fab Libraries and Their Use in the Selection of Gliadin-Specific Probes by Applying High-Throughput Nanopore Sequencing. Viruses 2024; 16:686. [PMID: 38793567 PMCID: PMC11126117 DOI: 10.3390/v16050686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/19/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
Directed evolution is a pivotal strategy for new antibody discovery, which allowed the generation of high-affinity Fabs against gliadin from two antibody libraries in our previous studies. One of the libraries was exclusively derived from celiac patients' mRNA (immune library) while the other was obtained through a protein engineering approach (semi-immune library). Recent advances in high-throughput DNA sequencing techniques are revolutionizing research across genomics, epigenomics, and transcriptomics. In the present work, an Oxford Nanopore in-lab sequencing device was used to comprehensively characterize the composition of the constructed libraries, both at the beginning and throughout the phage-mediated selection processes against gliadin. A customized analysis pipeline was used to select high-quality reads, annotate chain distribution, perform sequence analysis, and conduct statistical comparisons between the different selection rounds. Some immunological attributes of the most representative phage variants after the selection process were also determined. Sequencing results revealed the successful transfer of the celiac immune response features to the immune library and the antibodies derived from it, suggesting the crucial role of these features in guiding the selection of high-affinity recombinant Fabs against gliadin. In summary, high-throughput DNA sequencing has improved our understanding of the selection processes aimed at generating molecular binders against gliadin.
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Affiliation(s)
| | - Aina García-García
- Department of Nutrition and Food Sciences, School of Veterinary Sciences, Universidad Complutense de Madrid, 28040 Madrid, Spain; (E.G.-C.); (S.R.); (R.M.); (T.G.)
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2
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Gandini A, Gededzha MP, De Maayer T, Barrow P, Mayne E. Diagnosing coeliac disease: A literature review. Hum Immunol 2021; 82:930-936. [PMID: 34462157 DOI: 10.1016/j.humimm.2021.07.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/14/2021] [Accepted: 07/30/2021] [Indexed: 12/14/2022]
Abstract
Coeliac disease (CD) is an autoimmune gastroenteropathy triggered by gliadin and gliadin-tissue transglutaminase (tTG) complexes. CD is one of the few autoimmune diseases with an accurate, non-invasive serological test. Anti-endomysial, anti-tTG and anti-deaminated gliadin peptides (DGP) antibodies are currently used for serological tests with tTG ELISAs being the superior test. Duodenal biopsy, although invasive, is the gold standard for CD diagnosis. HLA genotyping and flow cytometry can also be used as supplementary tests. The incidence of CD is rising globally although the reasons for this remain unclear. In addition, the true incidence of coeliac disease in African populations remains unknown although recent work suggests that South African populations express the alleles associated with this disease. This review examines the pathogenesis and diagnosis of coeliac disease and considers novel and innovative biomarkers in its diagnosis specifically in an African population.
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Affiliation(s)
- Anastasia Gandini
- University of Witwatersrand, South Africa; National Health Laboratory Service, South Africa; Department of Immunology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Maemu P Gededzha
- University of Witwatersrand, South Africa; National Health Laboratory Service, South Africa; Department of Immunology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tim De Maayer
- University of Witwatersrand, South Africa; Rahima Moosa Mother and Child Hospital, South Africa
| | - Peter Barrow
- University of Witwatersrand, South Africa; Wits University Donald Gordon Medical Centre, South Africa
| | - Elizabeth Mayne
- University of Witwatersrand, South Africa; National Health Laboratory Service, South Africa; Department of Immunology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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3
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Li S, Song G, Bai Y, Song N, Zhao J, Liu J, Hu C. Applications of Protein Microarrays in Biomarker Discovery for Autoimmune Diseases. Front Immunol 2021; 12:645632. [PMID: 34012435 PMCID: PMC8126629 DOI: 10.3389/fimmu.2021.645632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/13/2021] [Indexed: 01/18/2023] Open
Abstract
Dysregulated autoantibodies and cytokines were deemed to provide important cues for potential illnesses, such as various carcinomas and autoimmune diseases. Increasing biotechnological approaches have been applied to screen and identify the specific alterations of these biomolecules as distinctive biomarkers in diseases, especially autoimmune diseases. As a versatile and robust platform, protein microarray technology allows researchers to easily profile dysregulated autoantibodies and cytokines associated with autoimmune diseases using various biological specimens, mainly serum samples. Here, we summarize the applications of protein microarrays in biomarker discovery for autoimmune diseases. In addition, the key issues in the process of using this approach are presented for improving future studies.
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Affiliation(s)
- Siting Li
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China.,Department of Rheumatology, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
| | - Guang Song
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Yina Bai
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China.,Department of Rheumatology, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
| | - Ning Song
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China.,Department of Rheumatology, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
| | - Jiuliang Zhao
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China.,Department of Rheumatology, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
| | - Jian Liu
- Department of Rheumatology, Aerospace Center Hospital, Aerospace, Clinical Medical College, Peking University, Beijing, China
| | - Chaojun Hu
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China.,Department of Rheumatology, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
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4
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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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5
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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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6
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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.
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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
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7
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Gao M, Lian H, Yu L, Gong M, Ma L, Zhou Y, Yu M, Yan X. Rolling circle amplification integrated with suspension bead array for ultrasensitive multiplex immunodetection of tumor markers. Anal Chim Acta 2019; 1048:75-84. [DOI: 10.1016/j.aca.2018.10.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/28/2018] [Accepted: 10/02/2018] [Indexed: 12/14/2022]
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Abstract
The display of antibodies on the surface of Saccharomyces cerevisiae cells enables the high-throughput and precise selection of specific binders for the target antigen. The recent implementation of next-generation sequencing (NGS) to antibody display screening provides a complete picture of the entire selected polyclonal population. As such, NGS overcomes the limitations of random clones screening, but it comes with two main limitations: (1) depending upon the platform, the sequencing is usually restricted to the variable heavy chain domain complementary determining region 3 (HCDR3), or VH gene, and does not provide additional information on the rest of the antibody gene, including the VL; and (2) the sequence-identified clones are not physically available for validation. Here, we describe a rapid and effective protocol based on an inverse-PCR method to recover specific antibody clones based on their HCDR3 sequence from a yeast display selection output.
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9
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Soluri MF, Puccio S, Caredda G, Grillo G, Licciulli VF, Consiglio A, Edomi P, Santoro C, Sblattero D, Peano C. Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing. J Vis Exp 2018. [PMID: 30346377 DOI: 10.3791/56981] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Folding reporters are proteins with easily identifiable phenotypes, such as antibiotic resistance, whose folding and function is compromised when fused to poorly folding proteins or random open reading frames. We have developed a strategy where, by using TEM-1 β-lactamase (the enzyme conferring ampicillin resistance) on a genomic scale, we can select collections of correctly folded protein domains from the coding portion of the DNA of any intronless genome. The protein fragments obtained by this approach, the so called "domainome", will be well expressed and soluble, making them suitable for structural/functional studies. By cloning and displaying the "domainome" directly in a phage display system, we have showed that it is possible to select specific protein domains with the desired binding properties (e.g., to other proteins or to antibodies), thus providing essential experimental information for gene annotation or antigen identification. The identification of the most enriched clones in a selected polyclonal population can be achieved by using novel next-generation sequencing technologies (NGS). For these reasons, we introduce deep sequencing analysis of the library itself and the selection outputs to provide complete information on diversity, abundance and precise mapping of each of the selected fragment. The protocols presented here show the key steps for library construction, characterization, and validation.
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Affiliation(s)
- Maria Felicia Soluri
- Department of Health Sciences, Università del Piemonte Orientale & IRCAD, Novara, Italy
| | - Simone Puccio
- Institute of Biomedical Technologies, National Research Council, Segrate, Milan, Italy
| | - Giada Caredda
- Institute of Biomedical Technologies, National Research Council, Segrate, Milan, Italy
| | - Giorgio Grillo
- Institute of Biomedical Technologies, National Research Council, Bari, Italy
| | | | - Arianna Consiglio
- Institute of Biomedical Technologies, National Research Council, Bari, Italy
| | - Paolo Edomi
- Department of Life Sciences, University of Trieste, Italy
| | - Claudio Santoro
- Department of Health Sciences, Università del Piemonte Orientale & IRCAD, Novara, Italy
| | | | - Clelia Peano
- Institute of Genetic and Biomedical Research, National Research Council, Rozzano, Milan, Italy; Humanitas Clinical and Research Center, Rozzano, Milan, Italy;
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10
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Svedberg G, Jeong Y, Na H, Jang J, Nilsson P, Kwon S, Gantelius J, Svahn HA. Towards encoded particles for highly multiplexed colorimetric point of care autoantibody detection. LAB ON A CHIP 2017; 17:549-556. [PMID: 28102419 DOI: 10.1039/c6lc01358a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Highly multiplexed point of care tests could improve diagnostic accuracy and differential diagnostic capacity in for instance emergency medicine and low resource environments. Available technology platforms for POC biomarker detection are typically simplex or low-plexed, whereas common lab-based microarray systems allow for the simultaneous detection of thousands of DNA or protein biomarkers. In this study, we demonstrate a novel suspension particle array platform that utilizes 900 μm bricks for POC amenable colorimetric biomarker detection with an encoding capacity of over two million. Due to the mm-scale size, both the lithographic codes and colorimetric signals of individual particles can be visualized using a consumer grade office flatbed scanner, with a potential for simultaneous imaging of around 19 000 particles per scan. The analytical sensitivity of the assay was determined to be 4 ng ml-1 using an antibody model system. As a proof of concept, autoantibodies toward anoctamin 2 were detected in order to discriminate between multiple sclerosis plasma samples and healthy controls with p < 0.0001 and an inter-assay % CV of 9.44%.
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Affiliation(s)
- Gustav Svedberg
- Division of Proteomics and Nanobiotechnology, Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-17165 Stockholm, Sweden.
| | - Yunjin Jeong
- Department of Electrical and Computer Science, Seoul National University, Daehak-dong, Gwanak-gu, Seoul 151-742, Republic of Korea. and Institutes of Entrepreneurial BioConvergence, Seoul National University, Daehak-dong, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Hunjong Na
- Department of Electrical and Computer Science, Seoul National University, Daehak-dong, Gwanak-gu, Seoul 151-742, Republic of Korea. and QuantaMatrix Inc. 105, B1, Center for medical innovation, Seoul National University Hospital, Daehak-ro, Jongno-gu, Seoul, Republic of Korea
| | - Jisung Jang
- QuantaMatrix Inc. 105, B1, Center for medical innovation, Seoul National University Hospital, Daehak-ro, Jongno-gu, Seoul, Republic of Korea
| | - Peter Nilsson
- Affinity Proteomics, Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-17165 Stockholm, Sweden
| | - Sunghoon Kwon
- Department of Electrical and Computer Science, Seoul National University, Daehak-dong, Gwanak-gu, Seoul 151-742, Republic of Korea. and Institutes of Entrepreneurial BioConvergence, Seoul National University, Daehak-dong, Gwanak-gu, Seoul 151-742, Republic of Korea and QuantaMatrix Inc. 105, B1, Center for medical innovation, Seoul National University Hospital, Daehak-ro, Jongno-gu, Seoul, Republic of Korea
| | - Jesper Gantelius
- Division of Proteomics and Nanobiotechnology, Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-17165 Stockholm, Sweden.
| | - Helene Andersson Svahn
- Division of Proteomics and Nanobiotechnology, Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-17165 Stockholm, Sweden.
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11
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Patrucco L, Peano C, Chiesa A, Guida F, Luisi I, Boria I, Mignone F, De Bellis G, Zucchelli S, Gustincich S, Santoro C, Sblattero D, Cotella D. Identification of novel proteins binding the AU-rich element of α-prothymosin mRNA through the selection of open reading frames (RIDome). RNA Biol 2016; 12:1289-300. [PMID: 26512911 DOI: 10.1080/15476286.2015.1107702] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
We describe here a platform for high-throughput protein expression and interaction analysis aimed at identifying the RNA-interacting domainome. This approach combines the selection of a phage library displaying "filtered" open reading frames with next-generation DNA sequencing. The method was validated using an RNA bait corresponding to the AU-rich element of α-prothymosin, an RNA motif that promotes mRNA stability and translation through its interaction with the RNA-binding protein ELAVL1. With this strategy, we not only confirmed known RNA-binding proteins that specifically interact with the target RNA (such as ELAVL1/HuR and RBM38) but also identified proteins not previously known to be ARE-binding (R3HDM2 and RALY). We propose this technology as a novel approach for studying the RNA-binding proteome.
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Affiliation(s)
- Laura Patrucco
- a Department of Health Sciences and Interdisciplinary Research Center on Autoimmune Diseases (IRCAD) ; Università del Piemonte Orientale ; Novara , Italy
| | - Clelia Peano
- b Institute of Biomedical Technologies; National Research Council (ITB CNR) ; Milan , Italy
| | - Andrea Chiesa
- a Department of Health Sciences and Interdisciplinary Research Center on Autoimmune Diseases (IRCAD) ; Università del Piemonte Orientale ; Novara , Italy
| | - Filomena Guida
- c Department of Life Sciences ; University of Trieste ; Italy
| | - Imma Luisi
- c Department of Life Sciences ; University of Trieste ; Italy
| | - Ilenia Boria
- d Department of Chemistry ; University of Milan ; Italy
| | - Flavio Mignone
- e Department of Sciences and Innovation ; Università del Piemonte Orientale ; Alessandria , Italy
| | - Gianluca De Bellis
- b Institute of Biomedical Technologies; National Research Council (ITB CNR) ; Milan , Italy
| | - Silvia Zucchelli
- a Department of Health Sciences and Interdisciplinary Research Center on Autoimmune Diseases (IRCAD) ; Università del Piemonte Orientale ; Novara , Italy.,f Area of Neuroscience; SISSA ; Trieste , Italy
| | | | - Claudio Santoro
- a Department of Health Sciences and Interdisciplinary Research Center on Autoimmune Diseases (IRCAD) ; Università del Piemonte Orientale ; Novara , Italy
| | - Daniele Sblattero
- a Department of Health Sciences and Interdisciplinary Research Center on Autoimmune Diseases (IRCAD) ; Università del Piemonte Orientale ; Novara , Italy.,c Department of Life Sciences ; University of Trieste ; Italy
| | - Diego Cotella
- a Department of Health Sciences and Interdisciplinary Research Center on Autoimmune Diseases (IRCAD) ; Università del Piemonte Orientale ; Novara , Italy
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12
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Abstract
Autoantibodies are a key component for the diagnosis, prognosis and monitoring of various diseases. In order to discover novel autoantibody targets, highly multiplexed assays based on antigen arrays hold a great potential and provide possibilities to analyze hundreds of body fluid samples for their reactivity pattern against thousands of antigens in parallel. Here, we provide an overview of the available technologies for producing antigen arrays, highlight some of the technical and methodological considerations and discuss their applications as discovery tools. Together with recent studies utilizing antigen arrays, we give an overview on how the different types of antigen arrays have and will continue to deliver novel insights into autoimmune diseases among several others.
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Basu A, Woods-Burnham L, Ortiz G, Rios-Colon L, Figueroa J, Albesa R, Andrade LE, Mahler M, Casiano CA. Specificity of antinuclear autoantibodies recognizing the dense fine speckled nuclear pattern: Preferential targeting of DFS70/LEDGFp75 over its interacting partner MeCP2. Clin Immunol 2015; 161:241-50. [PMID: 26235378 PMCID: PMC4712632 DOI: 10.1016/j.clim.2015.07.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 07/28/2015] [Accepted: 07/29/2015] [Indexed: 11/26/2022]
Abstract
Human antinuclear autoantibodies (ANAs) targeting the dense fine speckled (DFS) nuclear protein DFS70, commonly known as lens epithelium derived growth factor p75 (LEDGFp75), present a clinical puzzle since their significance remains elusive. While their frequencies are low in ANA-positive autoimmune rheumatic diseases, they are relatively elevated in clinical laboratory referrals, diverse inflammatory conditions, and 'apparently' healthy individuals. We reported previously that DFS70/LEDGFp75 is an autoantigen in prostate cancer that closely interacts with another 70kD DFS nuclear protein, methyl CpG binding protein 2 (MeCP2). This led us to investigate if anti-DFS sera exclusively target DFS70/LEDGFp75 or also recognize MeCP2. Using several complementary autoantibody detection platforms and cellular/molecular approaches we evaluated 65 human sera producing anti-DFS autoantibodies. Our results show that these antibodies are highly specific for DFS70/LEDGFp75 and do not target MeCP2. Establishing the specificity of anti-DFS autoantibodies has implications for increasing our understanding of their biological significance and clinical utility.
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Affiliation(s)
- Anamika Basu
- Center for Health Disparities and Molecular Medicine, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Leanne Woods-Burnham
- Center for Health Disparities and Molecular Medicine, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Greisha Ortiz
- Center for Health Disparities and Molecular Medicine, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Leslimar Rios-Colon
- Center for Health Disparities and Molecular Medicine, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Johnny Figueroa
- Center for Health Disparities and Molecular Medicine, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Roger Albesa
- Department of Research, Inova Diagnostics, Inc., San Diego, CA, USA
| | - Luis E Andrade
- Rheumatology Division, Universidade Federal de Sao Paulo, Immunology Division, Fleury Medicine and Health Laboratories, Sao Paulo, Brazil
| | - Michael Mahler
- Department of Research, Inova Diagnostics, Inc., San Diego, CA, USA
| | - Carlos A Casiano
- Center for Health Disparities and Molecular Medicine, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA, USA; Department of Medicine, Division of Rheumatology, Loma Linda University School of Medicine, Loma Linda, CA, USA.
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14
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Fredolini C, Byström S, Pin E, Edfors F, Tamburro D, Iglesias MJ, Häggmark A, Hong MG, Uhlen M, Nilsson P, Schwenk JM. Immunocapture strategies in translational proteomics. Expert Rev Proteomics 2015; 13:83-98. [PMID: 26558424 PMCID: PMC4732419 DOI: 10.1586/14789450.2016.1111141] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Aiming at clinical studies of human diseases, antibody-assisted assays have been applied to biomarker discovery and toward a streamlined translation from patient profiling to assays supporting personalized treatments. In recent years, integrated strategies to couple and combine antibodies with mass spectrometry-based proteomic efforts have emerged, allowing for novel possibilities in basic and clinical research. Described in this review are some of the field's current and emerging immunocapture approaches from an affinity proteomics perspective. Discussed are some of their advantages, pitfalls and opportunities for the next phase in clinical and translational proteomics.
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Affiliation(s)
- Claudia Fredolini
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Sanna Byström
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Elisa Pin
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Fredrik Edfors
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Davide Tamburro
- Department of Oncology-Pathology, Clinical Proteomics Mass Spectrometry, SciLifeLab, Karolinska Institutet, Solna, Sweden
| | - Maria Jesus Iglesias
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Anna Häggmark
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Mun-Gwan Hong
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Mathias Uhlen
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Peter Nilsson
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Jochen M Schwenk
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
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15
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Gourlay LJ, Peano C, Deantonio C, Perletti L, Pietrelli A, Villa R, Matterazzo E, Lassaux P, Santoro C, Puccio S, Sblattero D, Bolognesi M. Selecting soluble/foldable protein domains through single-gene or genomic ORF filtering: structure of the head domain of Burkholderia pseudomallei antigen BPSL2063. ACTA ACUST UNITED AC 2015; 71:2227-35. [PMID: 26527140 DOI: 10.1107/s1399004715015680] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 08/21/2015] [Indexed: 11/10/2022]
Abstract
The 1.8 Å resolution crystal structure of a conserved domain of the potential Burkholderia pseudomallei antigen and trimeric autotransporter BPSL2063 is presented as a structural vaccinology target for melioidosis vaccine development. Since BPSL2063 (1090 amino acids) hosts only one conserved domain, and the expression/purification of the full-length protein proved to be problematic, a domain-filtering library was generated using β-lactamase as a reporter gene to select further BPSL2063 domains. As a result, two domains (D1 and D2) were identified and produced in soluble form in Escherichia coli. Furthermore, as a general tool, a genomic open reading frame-filtering library from the B. pseudomallei genome was also constructed to facilitate the selection of domain boundaries from the entire ORFeome. Such an approach allowed the selection of three potential protein antigens that were also produced in soluble form. The results imply the further development of ORF-filtering methods as a tool in protein-based research to improve the selection and production of soluble proteins or domains for downstream applications such as X-ray crystallography.
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Affiliation(s)
- Louise J Gourlay
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Clelia Peano
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20090 Segrate, Italy
| | - Cecilia Deantonio
- Department of Health Sciences and IRCAD, University of Eastern Piedmont, Via Solaroli 17, 28100 Novara, Italy
| | - Lucia Perletti
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Alessandro Pietrelli
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20090 Segrate, Italy
| | - Riccardo Villa
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Elena Matterazzo
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Patricia Lassaux
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Claudio Santoro
- Department of Health Sciences and IRCAD, University of Eastern Piedmont, Via Solaroli 17, 28100 Novara, Italy
| | - Simone Puccio
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20090 Segrate, Italy
| | - Daniele Sblattero
- Department of Life Sciences, University of Trieste, Via Weiss 2, 34128 Trieste, Italy
| | - Martino Bolognesi
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
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16
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Matochko WL, Derda R. Next-generation sequencing of phage-displayed peptide libraries. Methods Mol Biol 2015; 1248:249-66. [PMID: 25616338 DOI: 10.1007/978-1-4939-2020-4_17] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Genetically encoded peptide libraries enabled the discovery of ligands for clinically relevant targets and functional materials. Next-generation sequencing (NGS) of these libraries improved the selection of ligands by detecting low abundant clones and quantifying changes in copy numbers of clones without many rounds of selection. Although NGS platforms have been widely used in genome assembly, quantification of gene expression (RNA-seq), and metagenomic analyses, few examples in the literature describe sequencing phage libraries. This chapter aims to provide a detailed method for sequencing a Ph.D.-7 phage display library by Ion Torrent. The main techniques covered in this chapter include (1) preparation of a phage library for sequencing, (2) sequencing, and (3) analysis of the sequencing data by a custom Matlab script.
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Affiliation(s)
- Wadim L Matochko
- Department of Chemistry, Alberta Glycomis Centre, University of Alberta, 11227 Saskatchewan Dr., Edmonton, AB, Canada, T6G 2G2
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Brito MD, Martins Â, Henrique R, Mariz J. Enteropathy-associated T cell lymphoma as a complication of silent celiac disease. Hematol Rep 2014; 6:5612. [PMID: 25568762 PMCID: PMC4274481 DOI: 10.4081/hr.2014.5612] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 11/02/2014] [Accepted: 11/13/2014] [Indexed: 01/16/2023] Open
Abstract
Celiac disease is an autoimmune disorder in which a genetic predisposition and the ingestion of wheat gluten triggers a deleterious immune response. This response is complex and may lead to manifestations other than enteropathyha: hepatitis, dermatitis and neuropathy. There is higher risk for neoplasia. We observed an atypical case, corresponding to a 69-year old female presenting with complicated celiac disease. The patient was referred following the histological examination of an enterectomy specimen, which unexpectedly revealed an enteropathy-associated T cell lymphoma in a background of celiac disease. Patient’s previous medical history comprised several abdominal surgical procedures, without other prior symptoms suggestive of celiac disease. Indeed, the patient was obese and no signs of malabsortion were apparent. This case draws our attention to clinically silent celiac disease, which represents a diagnostic challenge. Thus, this should be kept in mind whenever a patient presents with abdominal relapsing complications, otherwise unexplained.
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Affiliation(s)
| | | | - Rui Henrique
- Department of Pathology, Portuguese Institute of Oncology of Porto , Portugal
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18
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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.
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Abstract
Celiac disease (CD) has a multifactorial etiology with complex genetics and frequently occurs in association with other autoimmune disorders. Even though triggered by a dietary antigen, it shows many autoimmune features, the most peculiar being the presence of high titers of anti-tissue transglutaminase 2 autoantibodies, produced in the small intestinal mucosa since the early stages of the disease. More than 60% of CD-associated susceptibility loci are shared with at least another autoimmune condition, suggesting common pathogenic mechanisms. In particular, recognition of peptides by HLA molecules, posttranslational modifications required for optimal peptide binding and immune mechanisms leading to tissue damage have been found in CD as well as in other autoimmune diseases. This review briefly summarizes the main autoimmune features of CD, underlining the similarities with other autoimmune disorders, in particular with type 1 diabetes mellitus. Furthermore, the role of gluten and microbiome in driving autoimmunity is discussed.
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20
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Cretich M, Damin F, Chiari M. Protein microarray technology: how far off is routine diagnostics? Analyst 2014; 139:528-42. [DOI: 10.1039/c3an01619f] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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21
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Antibody biomarker discovery through in vitro directed evolution of consensus recognition epitopes. Proc Natl Acad Sci U S A 2013; 110:19330-5. [PMID: 24222690 DOI: 10.1073/pnas.1314792110] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
To enable discovery of serum antibodies indicative of disease and simultaneously develop reagents suitable for diagnosis, in vitro directed evolution was applied to identify consensus peptides recognized by patients' serum antibodies. Bacterial cell-displayed peptide libraries were quantitatively screened for binders to serum antibodies from patients with celiac disease (CD), using cell-sorting instrumentation to identify two distinct consensus epitope families specific to CD patients (PEQ and (E)/DxFV(Y)/FQ). Evolution of the (E)/DxFV(Y)/FQ consensus epitope identified a celiac-specific epitope, distinct from the two CD hallmark antigens tissue transglutaminase-2 and deamidated gliadin, exhibiting 71% sensitivity and 99% specificity (n = 231). Expansion of the first-generation PEQ consensus epitope via in vitro evolution yielded octapeptides QPEQAFPE and PFPEQxFP that identified ω- and γ-gliadins, and their deamidated forms, as immunodominant B-cell epitopes in wheat and related cereal proteins. The evolved octapeptides, but not first-generation peptides, discriminated one-way blinded CD and non-CD sera (n = 78) with exceptional accuracy, yielding 100% sensitivity and 98% specificity. Because this method, termed antibody diagnostics via evolution of peptides, does not require prior knowledge of pathobiology, it may be broadly useful for de novo discovery of antibody biomarkers and reagents for their detection.
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