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Ugalde-Triviño L, Molina-Jiménez F, H-Vázquez J, Relaño-Rupérez C, Arias-González L, Casabona S, Pérez-Fernández MT, Martín-Domínguez V, Fernández-Pacheco J, Lucendo AJ, Bernardo D, Santander C, Majano P. Circulating immunome fingerprint in eosinophilic esophagitis is associated with clinical response to proton pump inhibitor treatment. Front Immunol 2024; 15:1374611. [PMID: 38646544 PMCID: PMC11026586 DOI: 10.3389/fimmu.2024.1374611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/25/2024] [Indexed: 04/23/2024] Open
Abstract
Objectives The aim of the study was to characterize the circulating immunome of patients with EoE before and after proton pump inhibitor (PPI) treatment in order to identify potential non-invasive biomarkers of treatment response. Methods PBMCs from 19 healthy controls and 24 EoE patients were studied using a 39-plex spectral cytometry panel. The plasmacytoid dendritic cell (pDC) population was differentially characterized by spectral cytometry analysis and immunofluorescence assays in esophageal biopsies from 7 healthy controls and 13 EoE patients. Results Interestingly, EoE patients at baseline had lower levels of circulating pDC compared with controls. Before treatment, patients with EoE who responded to PPI therapy had higher levels of circulating pDC and classical monocytes, compared with non-responders. Moreover, following PPI therapy pDC levels were increased in all EoE patients, while normal levels were only restored in PPI-responding patients. Finally, circulating pDC levels inversely correlated with peak eosinophil count and pDC count in esophageal biopsies. The number of tissue pDCs significantly increased during active EoE, being even higher in non-responder patients when compared to responder patients pre-PPI. pDC levels decreased after PPI intake, being further restored almost to control levels in responder patients post-PPI. Conclusions We hereby describe a unique immune fingerprint of EoE patients at diagnosis. Moreover, circulating pDC may be also used as a novel non-invasive biomarker to predict subsequent response to PPI treatment.
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Affiliation(s)
- Lola Ugalde-Triviño
- Molecular Biology Unit, Hospital Universitario de la Princesa, Madrid, Spain
- Department of Molecular Biology, Instituto de Investigación Sanitaria Hospital Universitario de La Princesa (IIS-Princesa), Madrid, Spain
| | - Francisca Molina-Jiménez
- Molecular Biology Unit, Hospital Universitario de la Princesa, Madrid, Spain
- Department of Molecular Biology, Instituto de Investigación Sanitaria Hospital Universitario de La Princesa (IIS-Princesa), Madrid, Spain
| | - Juan H-Vázquez
- Mucosal Immunology Lab, Unit of Excellence Institute of Biomedicine and Molecular Genetics (IBGM), University of Valladolid and CSIC, Valladolid, Spain
| | - Carlos Relaño-Rupérez
- Molecular Biology Unit, Hospital Universitario de la Princesa, Madrid, Spain
- Department of Molecular Biology, Instituto de Investigación Sanitaria Hospital Universitario de La Princesa (IIS-Princesa), Madrid, Spain
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Laura Arias-González
- Department of Molecular Biology, Instituto de Investigación Sanitaria Hospital Universitario de La Princesa (IIS-Princesa), Madrid, Spain
- Department of Gastroenterology, Hospital General de Tomelloso, Tomelloso, Ciudad Real, Spain
- Instituto de Investigación Sanitaria de Castilla-La Mancha (IDISCAM), Toledo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Sergio Casabona
- Department of Molecular Biology, Instituto de Investigación Sanitaria Hospital Universitario de La Princesa (IIS-Princesa), Madrid, Spain
- Department of Gastroenterology, Hospital Universitario de La Princesa, Madrid, Spain
| | - María Teresa Pérez-Fernández
- Department of Molecular Biology, Instituto de Investigación Sanitaria Hospital Universitario de La Princesa (IIS-Princesa), Madrid, Spain
- Department of Gastroenterology, Hospital Universitario de La Princesa, Madrid, Spain
| | - Verónica Martín-Domínguez
- Department of Molecular Biology, Instituto de Investigación Sanitaria Hospital Universitario de La Princesa (IIS-Princesa), Madrid, Spain
- Department of Gastroenterology, Hospital Universitario de La Princesa, Madrid, Spain
| | - Jennifer Fernández-Pacheco
- Department of Molecular Biology, Instituto de Investigación Sanitaria Hospital Universitario de La Princesa (IIS-Princesa), Madrid, Spain
- Department of Gastroenterology, Hospital Universitario de La Princesa, Madrid, Spain
| | - Alfredo J. Lucendo
- Department of Molecular Biology, Instituto de Investigación Sanitaria Hospital Universitario de La Princesa (IIS-Princesa), Madrid, Spain
- Department of Gastroenterology, Hospital General de Tomelloso, Tomelloso, Ciudad Real, Spain
- Instituto de Investigación Sanitaria de Castilla-La Mancha (IDISCAM), Toledo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - David Bernardo
- Mucosal Immunology Lab, Unit of Excellence Institute of Biomedicine and Molecular Genetics (IBGM), University of Valladolid and CSIC, Valladolid, Spain
- Centro de Investigaciones Biomedicas en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Cecilio Santander
- Department of Molecular Biology, Instituto de Investigación Sanitaria Hospital Universitario de La Princesa (IIS-Princesa), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
- Department of Gastroenterology, Hospital Universitario de La Princesa, Madrid, Spain
| | - Pedro Majano
- Molecular Biology Unit, Hospital Universitario de la Princesa, Madrid, Spain
- Department of Molecular Biology, Instituto de Investigación Sanitaria Hospital Universitario de La Princesa (IIS-Princesa), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
- Department of Cellular Biology, Faculty of Biology, Universidad Complutense de Madrid, Madrid, Spain
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Koenig MR, Vazquez J, Leyva Jaimes FB, Mitzey AM, Stanic AK, Golos TG. Decidual leukocytes respond to African lineage Zika virus infection with mild anti-inflammatory changes during acute infection in rhesus macaques. Front Immunol 2024; 15:1363169. [PMID: 38515747 PMCID: PMC10954895 DOI: 10.3389/fimmu.2024.1363169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/23/2024] [Indexed: 03/23/2024] Open
Abstract
Zika virus (ZIKV) can be vertically transmitted during pregnancy resulting in a range of adverse pregnancy outcomes. The decidua is commonly found to be infected by ZIKV, yet the acute immune response to infection remains understudied in vivo. We hypothesized that in vivo African-lineage ZIKV infection induces a pro-inflammatory response in the decidua. To test this hypothesis, we evaluated the decidua in pregnant rhesus macaques within the first two weeks following infection with an African-lineage ZIKV and compared our findings to gestationally aged-matched controls. Decidual leukocytes were phenotypically evaluated using spectral flow cytometry, and cytokines and chemokines were measured in tissue homogenates from the decidua, placenta, and fetal membranes. The results of this study did not support our hypothesis. Although ZIKV RNA was detected in the decidual tissue samples from all ZIKV infected dams, phenotypic changes in decidual leukocytes and differences in cytokine profiles suggest that the decidua undergoes mild anti-inflammatory changes in response to that infection. Our findings emphasize the immunological state of the gravid uterus as a relatively immune privileged site that prioritizes tolerance of the fetus over mounting a pro-inflammatory response to clear infection.
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Affiliation(s)
- Michelle R. Koenig
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Jessica Vazquez
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, United States
| | - Fernanda B. Leyva Jaimes
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, United States
| | - Ann M. Mitzey
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Aleksandar K. Stanic
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, United States
| | - Thaddeus G. Golos
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI, United States
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, United States
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States
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Luo T, Patel JG, Zhang X, McBride JW. Antibody reactive immunomes of Ehrlichia chaffeensis and E. canis are diverse and defined by conformational antigenic determinants. Front Cell Infect Microbiol 2024; 13:1321291. [PMID: 38264730 PMCID: PMC10803646 DOI: 10.3389/fcimb.2023.1321291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/19/2023] [Indexed: 01/25/2024] Open
Abstract
For decades, the defined antibody reactive proteins of Ehrlichia chaffeensis and E. canis were limited to a small group with linear antibody epitopes. Recently, our laboratory has utilized an immunomics-based approach to rapidly screen and identify undefined Ehrlichia chaffeensis and E. canis antigenic proteins and antibody epitopes. In this study, we analyzed the remaining portion (~50%) of the E. chaffeensis and E. canis proteomes (n = 444 and n = 405 proteins, respectively), that were not examined in previous studies, to define the complete immunomes of these important pathogens. Almost half of the E. chaffeensis proteins screened (196/444) reacted with antibodies in convalescent HME patient sera, while only 43 E. canis proteins reacted with CME dog sera. New major immunoreactive proteins were identified in E. chaffeensis (n = 7) and E. canis (n = 1), increasing the total number of E. chaffeensis (n = 14) and E. canis proteins (n = 18) that exhibited antibody reactivity comparable to well-defined major antigenic proteins (TRP120 and TRP19). All of the E. chaffeensis but only some E. canis major immunoreactive proteins contained major conformation-dependent antibody epitopes. The E. chaffeensis immunoreactive proteins were generally small (< 250 amino acids; ~27kDa) and the E. canis proteins were slightly larger (> 320 amino acids; ~35 kDa). The majority of these new Ehrlichia major immunoreactive proteins were predicted to be type I secreted effectors, some of which contained transmembrane domains. Characterization of the immunomes of E. chaffeensis and E. canis and understanding the host specific Ehrlichia immune responses will facilitate identification of protective antigens and define the biophysical epitope characteristics vital to effective vaccine development for the ehrlichioses.
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Affiliation(s)
- Tian Luo
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
| | - Jignesh G. Patel
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
| | - Xiaofeng Zhang
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
| | - Jere W. McBride
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, United States
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, United States
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, United States
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Berkis U, Svirskis S, Krumina A, Gravelsina S, Vilmane A, Araja D, Nora-Krukle Z, Murovska M. Exploring the joint potential of inflammation, immunity, and receptor-based biomarkers for evaluating ME/CFS progression. Front Immunol 2023; 14:1294758. [PMID: 38187396 PMCID: PMC10771384 DOI: 10.3389/fimmu.2023.1294758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
Background Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating chronic condition with no identified diagnostic biomarkers to date. Its prevalence is as high as 0.89% according to metastudies, with a quarter of patients bed- or home-bound, which presents a serious public health challenge. Investigations into the inflammation-immunity axis is encouraged by links to outbreaks and disease waves. Recently, the research of our group revealed that antibodies to beta2-adrenergic (anti-β2AdR) and muscarinic acetylcholine (anti-M4) receptors demonstrate sensitivity to the progression of ME/CFS. The purpose of this study is to investigate the joint potential of inflammatome-characterized by interferon (IFN)-γ, tumor necrosis factor (TNF)-α, interleukin (IL)-2, IL-21, Il-23, IL-6, IL-17A, Activin-B, immunome (IgG1, IgG2, IgG3, IgG4, IgM, and IgA), and receptor-based biomarkers (anti-M3, anti-M4, and anti-β2AdR)-for evaluating ME/CFS progression, and to identify an optimal selection for future validation in prospective clinical studies. Methods A dataset was used originating from 188 individuals, namely, 54 healthy controls, 30 patients with a "mild" condition, 73 patients with a "moderate" condition, and 31 patients with a "severe" condition, clinically assessed by Fukuda/CDC 1994 and international consensus criteria. Inflammatome, immunome, and receptor-based biomarkers were determined in blood plasma via ELISA and multiplex methods. Statistical analysis was done via correlation analysis, principal component analysis, linear discriminant analysis, and random forest classification; inter-group differences were tested via nonparametric Kruskal-Wallis H test followed by the two-stage linear step-up procedure of Benjamini, Krieger, and Yekutieli, and via Mann-Whitney U test. Results The association between inflammatome and immunome markers is broader and stronger (coupling) in the severe group. Principal component factoring separates components associated with inflammatome, immunome, and receptor biomarkers. Random forest modeling demonstrates an excellent accuracy of over 90% for splitting healthy/with condition groups, and 45% for splitting healthy/severity groups. Classifiers with the highest potential are anti-β2AdR, anti-M4, IgG4, IL-2, and IL-6. Discussion The association between inflammatome and immunome markers is a candidate for controlled clinical study of ME/CFS progression markers that could be used for treatment individualization. Thus, the coupling effects between inflammation and immunity are potentially beneficial for the identification of prognostic factors in the context of ME/CFS progression mechanism studies.
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Affiliation(s)
- Uldis Berkis
- Development and Project Department, Riga Stradins University, Riga, Latvia
| | - Simons Svirskis
- Institute of Microbiology and Virology, Riga Stradins University, Riga, Latvia
| | - Angelika Krumina
- Department of Infectology, Riga Stradins University, Riga, Latvia
| | - Sabine Gravelsina
- Institute of Microbiology and Virology, Riga Stradins University, Riga, Latvia
| | - Anda Vilmane
- Institute of Microbiology and Virology, Riga Stradins University, Riga, Latvia
| | - Diana Araja
- Institute of Microbiology and Virology, Riga Stradins University, Riga, Latvia
| | - Zaiga Nora-Krukle
- Institute of Microbiology and Virology, Riga Stradins University, Riga, Latvia
| | - Modra Murovska
- Institute of Microbiology and Virology, Riga Stradins University, Riga, Latvia
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Lingasamy P, Modhukur V, Mändar R, Salumets A. Exploring Immunome and Microbiome Interplay in Reproductive Health: Current Knowledge, Challenges, and Novel Diagnostic Tools. Semin Reprod Med 2023; 41:172-189. [PMID: 38262441 PMCID: PMC10846929 DOI: 10.1055/s-0043-1778017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
The dynamic interplay between the immunome and microbiome in reproductive health is a complex and rapidly advancing research field, holding tremendously vast possibilities for the development of reproductive medicine. This immunome-microbiome relationship influences the innate and adaptive immune responses, thereby affecting the onset and progression of reproductive disorders. However, the mechanisms governing these interactions remain elusive and require innovative approaches to gather more understanding. This comprehensive review examines the current knowledge on reproductive microbiomes across various parts of female reproductive tract, with special consideration of bidirectional interactions between microbiomes and the immune system. Additionally, it explores innate and adaptive immunity, focusing on immunoglobulin (Ig) A and IgM antibodies, their regulation, self-antigen tolerance mechanisms, and their roles in immune homeostasis. This review also highlights ongoing technological innovations in microbiota research, emphasizing the need for standardized detection and analysis methods. For instance, we evaluate the clinical utility of innovative technologies such as Phage ImmunoPrecipitation Sequencing (PhIP-Seq) and Microbial Flow Cytometry coupled to Next-Generation Sequencing (mFLOW-Seq). Despite ongoing advancements, we emphasize the need for further exploration in this field, as a deeper understanding of immunome-microbiome interactions holds promise for innovative diagnostic and therapeutic strategies for reproductive health, like infertility treatment and management of pregnancy.
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Affiliation(s)
| | - Vijayachitra Modhukur
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Reet Mändar
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
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Nath AN, Retnakumar RJ, Francis A, Chhetri P, Thapa N, Chattopadhyay S. Peptic Ulcer and Gastric Cancer: Is It All in the Complex Host-Microbiome Interplay That Is Encoded in the Genomes of "Us" and "Them"? Front Microbiol 2022; 13:835313. [PMID: 35547123 PMCID: PMC9083406 DOI: 10.3389/fmicb.2022.835313] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
It is increasingly being recognized that severe gastroduodenal diseases such as peptic ulcer and gastric cancer are not just the outcomes of Helicobacter pylori infection in the stomach. Rather, both diseases develop and progress due to the perfect storms created by a combination of multiple factors such as the expression of different H. pylori virulence proteins, consequent human immune responses, and dysbiosis in gastrointestinal microbiomes. In this mini review, we have discussed how the genomes of H. pylori and other gastrointestinal microbes as well as the genomes of different human populations encode complex and variable virulome–immunome interplay, which influences gastroduodenal health. The heterogeneities that are encrypted in the genomes of different human populations and in the genomes of their respective resident microbes partly explain the inconsistencies in clinical outcomes among the H. pylori-infected people.
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Affiliation(s)
- Angitha N Nath
- Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
| | - R J Retnakumar
- Rajiv Gandhi Centre for Biotechnology, Trivandrum, India.,Manipal Academy of Higher Education, Manipal, India
| | - Ashik Francis
- Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
| | - Prakash Chhetri
- Department of Zoology, Biotech Hub, Nar Bahadur Bhandari Degree College, Tadong, India
| | - Namrata Thapa
- Department of Zoology, Biotech Hub, Nar Bahadur Bhandari Degree College, Tadong, India
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Devaprasad A, Radstake TRDJ, Pandit A. Integration of Immunome With Disease-Gene Network Reveals Common Cellular Mechanisms Between IMIDs and Drug Repurposing Strategies. Front Immunol 2021; 12:669400. [PMID: 34108969 PMCID: PMC8181425 DOI: 10.3389/fimmu.2021.669400] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/04/2021] [Indexed: 01/25/2023] Open
Abstract
Objective Development and progression of immune-mediated inflammatory diseases (IMIDs) involve intricate dysregulation of the disease-associated genes (DAGs) and their expressing immune cells. Identifying the crucial disease-associated cells (DACs) in IMIDs has been challenging due to the underlying complex molecular mechanism. Methods Using transcriptome profiles of 40 different immune cells, unsupervised machine learning, and disease-gene networks, we constructed the Disease-gene IMmune cell Expression (DIME) network and identified top DACs and DAGs of 12 phenotypically different IMIDs. We compared the DIME networks of IMIDs to identify common pathways between them. We used the common pathways and publicly available drug-gene network to identify promising drug repurposing targets. Results We found CD4+Treg, CD4+Th1, and NK cells as top DACs in inflammatory arthritis such as ankylosing spondylitis (AS), psoriatic arthritis, and rheumatoid arthritis (RA); neutrophils, granulocytes, and BDCA1+CD14+ cells in systemic lupus erythematosus and systemic scleroderma; ILC2, CD4+Th1, CD4+Treg, and NK cells in the inflammatory bowel diseases (IBDs). We identified lymphoid cells (CD4+Th1, CD4+Treg, and NK) and their associated pathways to be important in HLA-B27 type diseases (psoriasis, AS, and IBDs) and in primary-joint-inflammation-based inflammatory arthritis (AS and RA). Based on the common cellular mechanisms, we identified lifitegrast as a potential drug repurposing candidate for Crohn's disease and other IMIDs. Conclusions Existing methods are inadequate in capturing the intricate involvement of the crucial genes and cell types essential to IMIDs. Our approach identified the key DACs, DAGs, common mechanisms between IMIDs, and proposed potential drug repurposing targets using the DIME network. To extend our method to other diseases, we built the DIME tool (https://bitbucket.org/systemsimmunology/dime/) to help scientists uncover the etiology of complex and rare diseases to further drug development by better-determining drug targets, thereby mitigating the risk of failure in late clinical development.
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Affiliation(s)
- Abhinandan Devaprasad
- Division Internal Medicine and Dermatology, University Medical Center Utrecht, Utrecht, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Timothy R. D. J. Radstake
- Division Internal Medicine and Dermatology, University Medical Center Utrecht, Utrecht, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Aridaman Pandit
- Division Internal Medicine and Dermatology, University Medical Center Utrecht, Utrecht, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
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8
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Haynes WA, Kamath K, Waitz R, Daugherty PS, Shon JC. Protein-Based Immunome Wide Association Studies (PIWAS) for the Discovery of Significant Disease-Associated Antigens. Front Immunol 2021; 12:625311. [PMID: 33986742 PMCID: PMC8110919 DOI: 10.3389/fimmu.2021.625311] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 04/07/2021] [Indexed: 12/17/2022] Open
Abstract
Identification of the antigens associated with antibodies is vital to understanding immune responses in the context of infection, autoimmunity, and cancer. Discovering antigens at a proteome scale could enable broader identification of antigens that are responsible for generating an immune response or driving a disease state. Although targeted tests for known antigens can be straightforward, discovering antigens at a proteome scale using protein and peptide arrays is time consuming and expensive. We leverage Serum Epitope Repertoire Analysis (SERA), an assay based on a random bacterial display peptide library coupled with next generation sequencing (NGS), to power the development of Protein-based Immunome Wide Association Study (PIWAS). PIWAS uses proteome-based signals to discover candidate antibody-antigen epitopes that are significantly elevated in a subset of cases compared to controls. After demonstrating statistical power relative to the magnitude and prevalence of effect in synthetic data, we apply PIWAS to systemic lupus erythematosus (SLE, n=31) and observe known autoantigens, Smith and Ribosomal protein P, within the 22 highest scoring candidate protein antigens across the entire human proteome. We validate the magnitude and location of the SLE specific signal against the Smith family of proteins using a cohort of patients who are positive by predicate anti-Sm tests. To test the generalizability of the method in an additional autoimmune disease, we identified and validated autoantigenic signals to SSB, CENPA, and keratin proteins in a cohort of individuals with Sjogren’s syndrome (n=91). Collectively, these results suggest that PIWAS provides a powerful new tool to discover disease-associated serological antigens within any known proteome.
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Affiliation(s)
| | - Kathy Kamath
- Serimmune, Inc., Santa Barbara, CA, United States
| | | | | | - John C Shon
- Serimmune, Inc., Santa Barbara, CA, United States
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Abstract
It is increasingly clear that an extraordinarily diverse range of clinically important conditions—including infections, vaccinations, autoimmune diseases, transplants, transfusion reactions, aging, and cancers—leave telltale signatures in the millions of V(D)J-rearranged antibody and T cell receptor [TR per the Human Genome Organization (HUGO) nomenclature but more commonly known as TCR] genes collectively expressed by a person’s B cells (antibodies) and T cells. We refer to these as the immunome. Because of its diversity and complexity, the immunome provides singular opportunities for advancing personalized medicine by serving as the substrate for a highly multiplexed, near-universal blood test. Here we discuss some of these opportunities, the current state of immunome-based diagnostics, and highlight some of the challenges involved. We conclude with a call to clinicians, researchers, and others to join efforts with the Adaptive Immune Receptor Repertoire Community (AIRR-C) to realize the diagnostic potential of the immunome.
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Affiliation(s)
- Ramy A Arnaout
- Department of Pathology and Division of Clinical Informatics, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, United States.,Department of Pathology, Harvard Medical School, Boston, MA, United States
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Nicholas Schwab
- Department of Neurology and Institute of Translational Neurology, University of Muenster, Muenster, Germany
| | - Florian Rubelt
- Roche Sequencing Solutions, Pleasanton, CA, United States
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10
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Gkouskou K, Vlastos I, Karkalousos P, Chaniotis D, Sanoudou D, Eliopoulos AG. The "Virtual Digital Twins" Concept in Precision Nutrition. Adv Nutr 2020; 11:1405-1413. [PMID: 32770212 PMCID: PMC7666894 DOI: 10.1093/advances/nmaa089] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/15/2020] [Accepted: 07/06/2020] [Indexed: 12/13/2022] Open
Abstract
Nutritional and lifestyle changes remain at the core of healthy aging and disease prevention. Accumulating evidence underscores the impact of genetic, metabolic, and host gut microbial factors on individual responses to nutrients, paving the way for the stratification of nutritional guidelines. However, technological advances that incorporate biological, nutritional, lifestyle, and health data at an unprecedented scale and depth conceptualize a future where preventative dietary interventions will exceed stratification and will be highly individualized. We herein discuss how genetic information combined with longitudinal metabolomic, immune, behavioral, and gut microbial parameters, and bioclinical variables could define a digital replica of oneself, a "virtual digital twin," which could serve to guide nutrition in a personalized manner. Such a model may revolutionize the management of obesity and its comorbidities, and provide a pillar for healthy aging.
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Affiliation(s)
| | - Ioannis Vlastos
- Department of Biology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Petros Karkalousos
- Department of Biomedical Sciences, University of West Attica, Athens, Greece
| | - Dimitrios Chaniotis
- Department of Biomedical Sciences, University of West Attica, Athens, Greece
| | - Despina Sanoudou
- Clinical Genomics and Pharmacogenomics Unit, 4th Department of Internal Medicine, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece,Center for New Biotechnologies and Precision Medicine, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece,Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
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11
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Paleja B, Low AHL, Kumar P, Saidin S, Lajam A, Nur Hazirah S, Chua C, Li Yun L, Albani S. Systemic Sclerosis Perturbs the Architecture of the Immunome. Front Immunol 2020; 11:1602. [PMID: 32849542 PMCID: PMC7423974 DOI: 10.3389/fimmu.2020.01602] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 06/16/2020] [Indexed: 11/13/2022] Open
Abstract
Systemic sclerosis (SSc) is an autoimmune disease characterized by excessive fibrosis of skin and internal organs, and vascular dysfunction. Association of T and B cell subsets has been reported in SSc; however, there is lack of systematic studies of functional relations between immune cell subsets in this disease. This lack of mechanistic knowledge hampers targeted intervention. In the current study we sought to determine differential immune cell composition and their interactions in peripheral blood of SSc patients. Mononuclear cells from blood of SSc patients (n = 20) and healthy controls (n = 10) were analyzed by mass cytometry using a 36-marker (cell surface and intracellular) panel. Transcriptome analysis (m-RNA sequencing) was performed on sorted T and B cell subsets. Unsupervised clustering analysis revealed significant differences in the frequencies of T and B cell subsets in patients. Correlation network analysis highlighted an overall dysregulated immune architecture coupled with domination of inflammatory senescent T cell modules in SSc patients. Transcriptome analysis of sorted immune cells revealed an activated phenotype of CD4 and mucosal associated invariant T (MAIT) cells in patients, accompanied by increased expression of inhibitory molecules, reminiscent of phenotype exhibited by functionally adapted, exhausted T cells in response to chronic stimulation. Overall, this study provides an in-depth analysis of the systemic immunome in SSc, highlighting the potential pathogenic role of inflammation and chronic stimulation-mediated “functional adaptation” of immune cells.
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Affiliation(s)
- Bhairav Paleja
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Andrea Hsiu Ling Low
- Department of Rheumatology and Immunology, Singapore General Hospital, Singapore, Singapore.,Duke-NUS Medical School, Singapore, Singapore
| | - Pavanish Kumar
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Suzan Saidin
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Ahmad Lajam
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Sharifah Nur Hazirah
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Camillus Chua
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Lai Li Yun
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Salvatore Albani
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, Singapore, Singapore
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12
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Poulsen TBG, Damgaard D, Jørgensen MM, Senolt L, Blackburn JM, Nielsen CH, Stensballe A. Identification of Novel Native Autoantigens in Rheumatoid Arthritis. Biomedicines 2020; 8:biomedicines8060141. [PMID: 32486012 PMCID: PMC7345460 DOI: 10.3390/biomedicines8060141] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 05/27/2020] [Indexed: 12/16/2022] Open
Abstract
The majority of patients diagnosed with rheumatoid arthritis (RA) have developed autoantibodies against neoepitopes in proteins that have undergone post-translational modification, e.g., citrullination or carbamylation. There is growing evidence of their molecular relevance and their potential utility to improve diagnosis, patient stratification, and prognosis for precision medicine. Autoantibodies reacting to native proteins may also have a role in RA pathogenesis, however, their reactivity patterns remain much less studied. We hypothesized that a high-density protein array technology could shed light onto the normal and disease-related autoantibodies produced in healthy and RA patient subgroups. In an exploratory study, we investigated the global reactivity of autoantibodies in plasma pools from 15 anti-cyclic citrullinated peptide (CCP)-positive and 10 anti-CCP-negative RA patients and 10 healthy donors against more than 1600 native and unmodified human proteins using a high-density protein array. A total of 102 proteins recognized by IgG autoantibodies were identified, hereof 86 were recognized by antibodies from CCP-positive RA patients and 76 from anti-CCP-negative RA patients, but not by antibodies from healthy donors. Twenty-four of the identified autoantigens have previously been identified in synovial fluid. Multiple human proteins in their native conformation are recognized by autoantibodies from anti-CCP-positive as well as anti-CCP-negative RA patients.
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Affiliation(s)
- Thomas B. G. Poulsen
- Department of Health Science and Technology, Aalborg University, 9220 Aalborg, Denmark
- Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, 380 Huaibeizhuang, Huairou district, Beijing 100049, China
- Correspondence: (T.B.G.P.); (A.S.); Tel.: +45-2615-9368 (T.B.G.P.); +45-6160-8786 (A.S.)
| | - Dres Damgaard
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark; (D.D.); (C.H.N.)
| | - Malene Møller Jørgensen
- Department of Clinical Immunology, Aalborg University Hospital, 9000 Aalborg, Denmark;
- Department of Clinical Medicine, Aalborg University, 9000 Aalborg, Denmark
| | - Ladislav Senolt
- Institute of Rheumatology and Department of Rheumatology, 1st Faculty of Medicine, Charles University, 121 08 Prague, Czech Republic;
| | - Jonathan M. Blackburn
- Department of Integrative Biomedical Sciences & Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7700, South Africa;
- Sengenics Corporation Pte Ltd., Singapore 409051, Singapore
| | - Claus H. Nielsen
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark; (D.D.); (C.H.N.)
| | - Allan Stensballe
- Department of Health Science and Technology, Aalborg University, 9220 Aalborg, Denmark
- Correspondence: (T.B.G.P.); (A.S.); Tel.: +45-2615-9368 (T.B.G.P.); +45-6160-8786 (A.S.)
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13
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Takami H, Fukushima S, Aoki K, Satomi K, Narumi K, Hama N, Matsushita Y, Fukuoka K, Yamasaki K, Nakamura T, Mukasa A, Saito N, Suzuki T, Yanagisawa T, Nakamura H, Sugiyama K, Tamura K, Maehara T, Nakada M, Nonaka M, Asai A, Yokogami K, Takeshima H, Iuchi T, Kanemura Y, Kobayashi K, Nagane M, Kurozumi K, Yoshimoto K, Matsuda M, Matsumura A, Hirose Y, Tokuyama T, Kumabe T, Ueki K, Narita Y, Shibui S, Totoki Y, Shibata T, Nakazato Y, Nishikawa R, Matsutani M, Ichimura K. Intratumoural immune cell landscape in germinoma reveals multipotent lineages and exhibits prognostic significance. Neuropathol Appl Neurobiol 2019; 46:111-124. [PMID: 31179566 DOI: 10.1111/nan.12570] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 06/03/2019] [Indexed: 12/13/2022]
Abstract
AIMS Alterations in microenvironments are a hallmark of cancer, and these alterations in germinomas are of particular significance. Germinoma, the most common subtype of central nervous system germ cell tumours, often exhibits massive immune cell infiltration intermingled with tumour cells. The role of these immune cells in germinoma, however, remains unknown. METHODS We investigated the cellular constituents of immune microenvironments and their clinical impacts on prognosis in 100 germinoma cases. RESULTS Patients with germinomas lower in tumour cell content (i.e. higher immune cell infiltration) had a significantly longer progression-free survival time than those with higher tumour cell contents (P = 0.03). Transcriptome analyses and RNA in-situ hybridization indicated that infiltrating immune cells comprised a wide variety of cell types, including lymphocytes and myelocyte-lineage cells. High expression of CD4 was significantly associated with good prognosis, whereas elevated nitric oxide synthase 2 was associated with poor prognosis. PD1 (PDCD1) was expressed by immune cells present in most germinomas (93.8%), and PD-L1 (CD274) expression was found in tumour cells in the majority of germinomas examined (73.5%). CONCLUSIONS The collective data strongly suggest that infiltrating immune cells play an important role in predicting treatment response. Further investigation should lead to additional categorization of germinoma to safely reduce treatment intensity depending on tumour/immune cell balance and to develop possible future immunotherapies.
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Affiliation(s)
- H Takami
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan.,Department of Neurosurgery, Faculty of Medicine, The University of Tokyo Hospital, Tokyo, Japan
| | - S Fukushima
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | - K Aoki
- Division of Gene and Immune Medicine, National Cancer Center Research Institute, Tokyo, Japan
| | - K Satomi
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan.,Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - K Narumi
- Division of Gene and Immune Medicine, National Cancer Center Research Institute, Tokyo, Japan
| | - N Hama
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Y Matsushita
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan.,Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - K Fukuoka
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan.,Division of Pediatric Neuro-Oncology, Saitama Medical University International Medical Center, Saitama, Japan
| | - K Yamasaki
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan.,Department of Pediatrics, Osaka City General Hospital, Osaka, Japan
| | - T Nakamura
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan.,Department of Neurosurgery, Graduate School of Medicine, Yokohama City University, Kanagawa, Japan
| | - A Mukasa
- Department of Neurosurgery, Faculty of Medicine, The University of Tokyo Hospital, Tokyo, Japan.,Department of Neurosurgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - N Saito
- Department of Neurosurgery, Faculty of Medicine, The University of Tokyo Hospital, Tokyo, Japan
| | - T Suzuki
- Department of Neuro-Oncology/Neurosurgery, Saitama Medical University International Medical Center, Saitama, Japan
| | - T Yanagisawa
- Division of Pediatric Neuro-Oncology, Saitama Medical University International Medical Center, Saitama, Japan
| | - H Nakamura
- Department of Neurosurgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan.,Department of Neurosurgery, Kurume University, Fukuoka, Japan
| | - K Sugiyama
- Department of Neurosurgery, Faculty of Medicine, Hiroshima University, Hiroshima, Japan
| | - K Tamura
- Department of Neurosurgery, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - T Maehara
- Department of Neurosurgery, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - M Nakada
- Department of Neurosurgery, Graduate School of Medical Science, Kanazawa University, Ishikawa, Japan
| | - M Nonaka
- Department of Neurosurgery, Kansai Medical University Hospital, Osaka, Japan
| | - A Asai
- Department of Neurosurgery, Kansai Medical University Hospital, Osaka, Japan
| | - K Yokogami
- Department of Neurosurgery, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - H Takeshima
- Department of Neurosurgery, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - T Iuchi
- Department of Neurosurgery, Chiba Cancer Center, Chiba, Japan
| | - Y Kanemura
- Department of Neurosurgery, Osaka National Hospital, National Hospital Organization, Osaka, Japan.,Department of Biomedical Research and Innovation, Institute for Clinical Research, Osaka National Hospital, National Hospital Organization, Osaka, Japan
| | - K Kobayashi
- Department of Neurosurgery, Faculty of Medicine, Kyorin University, Tokyo, Japan
| | - M Nagane
- Department of Neurosurgery, Faculty of Medicine, Kyorin University, Tokyo, Japan
| | - K Kurozumi
- Department of Neurological Surgery, Dentistry, and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama, Japan
| | - K Yoshimoto
- Department of Neurosurgery, Kyusyu University Hospital, Fukuoka, Japan
| | - M Matsuda
- Department of Neurosurgery, University of Tsukuba Hospital, Ibaraki, Japan
| | - A Matsumura
- Department of Neurosurgery, University of Tsukuba Hospital, Ibaraki, Japan
| | - Y Hirose
- Department of Neurosurgery, Fujita Health University Hospital, Aichi, Japan
| | - T Tokuyama
- Department of Neurosurgery, Hamamatsu University Hospital, Shizuoka, Japan
| | - T Kumabe
- Department of Neurosurgery, Kitasato University, Kanagawa, Japan
| | - K Ueki
- Department of Neurosurgery, Dokkyo Medical Univeristy, Tochigi, Japan
| | - Y Narita
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - S Shibui
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Y Totoki
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - T Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Y Nakazato
- Department of Pathology, Hidaka Hospital, Gunma, Japan
| | - R Nishikawa
- Department of Neurosurgery, Graduate School of Medicine, Yokohama City University, Kanagawa, Japan
| | - M Matsutani
- Department of Neurosurgery, Graduate School of Medicine, Yokohama City University, Kanagawa, Japan
| | - K Ichimura
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
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14
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Abstract
The paper discusses the techniques which are currently implemented for vaccine production based on virus-like particles (VLPs). The factors which determine the characteristics of VLP monomers assembly are provided in detail. Analysis of the literature demonstrates that the development of the techniques of VLP production and immobilization of target antigens on their surface have led to the development of universal platforms which make it possible for virtually any known antigen to be exposed on the particle surface in a highly concentrated form. As a result, the focus of attention has shifted from the approaches to VLP production to the development of a precise interface between the organism's immune system and the peptides inducing a strong immune response to pathogens or the organism's own pathological cells. Immunome-specified methods for vaccine design and the prospects of immunoprophylaxis are discussed. Certain examples of vaccines against viral diseases and cancers are considered.
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Affiliation(s)
- B. V. Syomin
- Institute for Statistical Studies and Economics of Knowledge (ISSEK),
National Research University Higher School of Economics, 101000 Moscow, Russia
| | - Y. V. Ilyin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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15
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Abstract
The paper discusses the techniques which are currently implemented for vaccine production based on virus-like particles (VLPs). The factors which determine the characteristics of VLP monomers assembly are provided in detail. Analysis of the literature demonstrates that the development of the techniques of VLP production and immobilization of target antigens on their surface have led to the development of universal platforms which make it possible for virtually any known antigen to be exposed on the particle surface in a highly concentrated form. As a result, the focus of attention has shifted from the approaches to VLP production to the development of a precise interface between the organism's immune system and the peptides inducing a strong immune response to pathogens or the organism's own pathological cells. Immunome-specified methods for vaccine design and the prospects of immunoprophylaxis are discussed. Certain examples of vaccines against viral diseases and cancers are considered.
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Affiliation(s)
- B V Syomin
- Institute for Statistical Studies and Economics of Knowledge (ISSEK), National Research University Higher School of Economics, Moscow, 101000 Russia.,
| | - Y V Ilyin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
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16
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Gyurján I, Rosskopf S, Coronell JAL, Muhr D, Singer C, Weinhäusel A. IgG based immunome analyses of breast cancer patients reveal underlying signaling pathways. Oncotarget 2019; 10:3491-3505. [PMID: 31191821 PMCID: PMC6544406 DOI: 10.18632/oncotarget.26834] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/23/2019] [Indexed: 12/21/2022] Open
Abstract
Background: Breast cancer is the most frequent and one of the most fatal malignancies among women. Within the concept of personalized medicine, molecular characterization of tumors is usually performed by analyzing somatic mutations, RNA gene expression signatures or the proteome by mass-spectrometry. Alternatively, the immunological fingerprint of the patients can be analyzed by protein microarrays, which is able to provide another layer of molecular pathological information without invasive intervention. Results: We have investigated the immune signature of breast cancer patients and compared them with healthy controls, using protein microarray-based IgG profiling. The identified differentially reactive antigens (n=517) were further evaluated by means of various pathway analysis tools. Our results indicate that the immune signature of breast cancer patients shows a clear distinction from healthy individuals characterized by differentially reactive antigens involved in known disease relevant signaling pathways, such as VEGF, AKT/PI3K/mTOR or c-KIT, which is in close agreement with the findings from RNA-based expression profiles. Conclusion: Differential antigenic properties between breast cancer patients and healthy individual classes can be defined by serum-IgG profiling on protein microarrays. These immunome profiles provide an additional layer of molecular pathological information, which has the potential to refine and complete the systems biological map of neoplastic disease.
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Affiliation(s)
- István Gyurján
- Austrian Institute of Technology AIT, Center for Health & Environment, Molecular Diagnostics Unit, Vienna, Austria
| | - Sandra Rosskopf
- Austrian Institute of Technology AIT, Center for Health & Environment, Molecular Diagnostics Unit, Vienna, Austria
| | - Johana A Luna Coronell
- Austrian Institute of Technology AIT, Center for Health & Environment, Molecular Diagnostics Unit, Vienna, Austria
| | - Daniela Muhr
- Department of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | - Christian Singer
- Department of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | - Andreas Weinhäusel
- Austrian Institute of Technology AIT, Center for Health & Environment, Molecular Diagnostics Unit, Vienna, Austria
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17
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El-Chemaly S, Cheung F, Kotliarov Y, O'Brien KJ, Gahl WA, Chen J, Perl SY, Biancotto A, Gochuico BR. The Immunome in Two Inherited Forms of Pulmonary Fibrosis. Front Immunol 2018; 9:76. [PMID: 29445374 PMCID: PMC5797737 DOI: 10.3389/fimmu.2018.00076] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/11/2018] [Indexed: 02/01/2023] Open
Abstract
The immunome (immune cell phenotype, gene expression, and serum cytokines profiling) in pulmonary fibrosis is incompletely defined. Studies focusing on inherited forms of pulmonary fibrosis provide insights into mechanisms of fibrotic lung disease in general. To define the cellular and molecular immunologic phenotype in peripheral blood, high-dimensional flow cytometry and large-scale gene expression of peripheral blood mononuclear cells and serum proteomic multiplex analyses were performed and compared in a cohort with familial pulmonary fibrosis (FPF), an autosomal dominant disorder with incomplete penetrance; Hermansky-Pudlak syndrome pulmonary fibrosis (HPSPF), a rare autosomal recessive disorder; and their unaffected relatives. Our results showed high peripheral blood concentrations of activated central memory helper cells in patients with FPF. Proportions of CD38+ memory CD27- B-cells, IgA+ memory CD27+ B-cells, IgM+ and IgD+ B-cells, and CD39+ T helper cells were increased whereas those of CD39- T helper cells were reduced in patients affected with either familial or HPSPF. Gene expression and serum proteomic analyses revealed enrichment of upregulated genes associated with mitosis and cell cycle control in circulating mononuclear cells as well as altered levels of several analytes, including leptin, cytokines, and growth factors. In conclusion, dysregulation of the extra-pulmonary immunome is a phenotypic feature of FPF or HPSPF. Further studies investigating the blood immunome are indicated to determine the role of immune system dysregulation in the pathogenesis of pulmonary fibrosis. Clinical Trial Registration www.ClinicalTrials.gov, identifiers NCT00968084, NCT01200823, NCT00001456, and NCT00084305.
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Affiliation(s)
- Souheil El-Chemaly
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, United States
| | - Foo Cheung
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), National Institutes of Health, Bethesda, MD, United States
| | - Yuri Kotliarov
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), National Institutes of Health, Bethesda, MD, United States
| | - Kevin J O'Brien
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - William A Gahl
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States.,Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Jinguo Chen
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), National Institutes of Health, Bethesda, MD, United States
| | - Shira Y Perl
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), National Institutes of Health, Bethesda, MD, United States
| | - Angélique Biancotto
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), National Institutes of Health, Bethesda, MD, United States
| | - Bernadette R Gochuico
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
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18
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Abstract
Immunomics is a relatively new field of research which integrates the disciplines of immunology, genomics, proteomics, transcriptomics and bioinformatics to characterize the host-pathogen interface. Herein, we discuss how rapid advances in molecular immunology, sophisticated tools and molecular databases are facilitating in-depth exploration of the immunome. In our opinion, an immunomics-based approach presides over traditional antigen and vaccine discovery methods that have proved ineffective for highly complex pathogens such as the causative agents of malaria, tuberculosis and schistosomiasis that have evolved genetic and immunological host-parasite adaptations over time. By using an integrative multidisciplinary approach, immunomics offers enormous potential to advance 21st century antigen discovery and rational vaccine design against complex pathogens such as the Plasmodium parasite.
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19
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Teltsh O, Porgador A, Rubin E. Extracting tumor tissue immune status from expression profiles: correlating renal cancer prognosis with tumor-associated immunome. Oncotarget 2015; 6:33191-205. [PMID: 26384298 DOI: 10.18632/oncotarget.5052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 08/28/2015] [Indexed: 01/25/2023] Open
Abstract
Investigating the expression of genes in cancer-associated immune cells (immunome) is imperative for prognosis prediction. However, evaluating the expression of immune-associated genes within cancer biopsy is subject to significant inconsistencies related to the sampling methodology. Here, we present immFocus, a method for extracting immune signals from total RNA sequencing of tumor biopsies, intended for immunity depiction and prognosis evaluation. It is based on reducing the variation which biopsy preparation adds to the apparent expression levels of immune genes. We employed immFocus to normalize gene expression with an immune index using data obtained from renal clear cell carcinoma biopsies. Genes that became less variable due to normalization were found to be preferentially immune-related. Moreover, immune-related genes tended to become more prognostic due to the normalization. These results demonstrate, for the first time, that whole transcriptome sequencing can be used for interrogation of a cancer immunome and for advancing immune-based prognosis.
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20
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Pellon A, Ramirez-Garcia A, Buldain I, Antoran A, Rementeria A, Hernando FL. Immunoproteomics-Based Analysis of the Immunocompetent Serological Response to Lomentospora prolificans. J Proteome Res 2016; 15:595-607. [PMID: 26732945 DOI: 10.1021/acs.jproteome.5b00978] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The filamentous fungus Lomentospora prolificans is an emerging pathogen causing severe infections mainly among the immunocompromised population. These diseases course with high mortality rates due to great virulence of the fungus, its inherent resistance to available antifungals, and absence of specific diagnostic tools. Despite being widespread in humanized environments, L. prolificans rarely causes infections in immunocompetent individuals likely due to their developed protective immune response. In this study, conidial and hyphal immunomes against healthy human serum IgG were analyzed, identifying immunodominant antigens and establishing their prevalence among the immunocompetent population. Thirteen protein spots from each morph were detected as reactive against at least 70% of serum samples, and identified by liquid chromatography tandem mass spectrometry (LC-MS/MS). Hence, the most seroprevalent antigens were WD40 repeat 2 protein, malate dehydrogenase, and DHN1, in conidia, and heat shock protein (Hsp) 70, Hsp90, ATP synthase β subunit, and glyceraldehyde-3-phosphate dehydrogenase, in hyphae. More interestingly, the presence of some of these seroprevalent antigens was determined on the cell surface, as Hsp70, enolase, or Hsp90. Thus, we have identified a diverse set of antigenic proteins, both in the entire proteome and cell surface subproteome, which may be used as targets to develop innovative therapeutic or diagnostic tools.
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Affiliation(s)
- Aize Pellon
- Fungal and Bacterial Biomics Research Group. Department of Immunology, Microbiology and Parasitology. Faculty of Science and Technology. University of the Basque Country (UPV/EHU) , Leioa 48940, Spain
| | - Andoni Ramirez-Garcia
- Fungal and Bacterial Biomics Research Group. Department of Immunology, Microbiology and Parasitology. Faculty of Science and Technology. University of the Basque Country (UPV/EHU) , Leioa 48940, Spain
| | - Idoia Buldain
- Fungal and Bacterial Biomics Research Group. Department of Immunology, Microbiology and Parasitology. Faculty of Science and Technology. University of the Basque Country (UPV/EHU) , Leioa 48940, Spain
| | - Aitziber Antoran
- Fungal and Bacterial Biomics Research Group. Department of Immunology, Microbiology and Parasitology. Faculty of Science and Technology. University of the Basque Country (UPV/EHU) , Leioa 48940, Spain
| | - Aitor Rementeria
- Fungal and Bacterial Biomics Research Group. Department of Immunology, Microbiology and Parasitology. Faculty of Science and Technology. University of the Basque Country (UPV/EHU) , Leioa 48940, Spain
| | - Fernando L Hernando
- Fungal and Bacterial Biomics Research Group. Department of Immunology, Microbiology and Parasitology. Faculty of Science and Technology. University of the Basque Country (UPV/EHU) , Leioa 48940, Spain
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21
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Pitarch A, Nombela C, Gil C. Serum antibody signature directed against Candida albicans Hsp90 and enolase detects invasive candidiasis in non-neutropenic patients. J Proteome Res 2014; 13:5165-84. [PMID: 25377742 DOI: 10.1021/pr500681x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Invasive candidiasis (IC) adds significantly to the morbidity and mortality of non-neutropenic patients if not diagnosed and treated early. To uncover serologic biomarkers that alone or in combination could reliably detect IC in this population, IgG antibody-reactivity profiles to the Candida albicans intracellular proteome were examined by serological proteome analysis (SERPA) and data mining procedures in a training set of 24 non-neutropenic patients. Despite the high interindividual molecular heterogeneity, unsupervised clustering analyses revealed that serum 22-IgG antibody-reactivity patterns differentiated IC from non-IC patients. Univariate analyses further highlighted that 15 out of the 22 SERPA-identified IgG antibodies could be useful candidate IC biomarkers. The diagnostic performance of one of these candidates (anti-Hsp90 IgG antibodies) was validated using an ELISA prototype in a test set of 59 non-neutropenic patients. We then formulated an IC discriminator based on the combined immunoproteomic fingerprints of this and another SERPA-detected and previously validated IC biomarker (anti-Eno1 IgG antibodies) in the training set. Its consistency was substantiated using their ELISA prototypes in the test set. Receiver-operating-characteristic curve analyses showed that this two-biomarker signature accurately identified IC in non-neutropenic patients and provided better IC diagnostic accuracy than the individual biomarkers alone. We conclude that this serum IgG antibody signature directed against C. albicans Hsp90 and Eno1, if confirmed prospectively, may be useful for IC diagnosis in non-neutropenic patients.
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Affiliation(s)
- Aida Pitarch
- Department of Microbiology II, Faculty of Pharmacy, Complutense University of Madrid and Ramón y Cajal Institute of Health Research (IRYCIS) , Plaza Ramón y Cajal s/n, 28040 Madrid, Spain
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Duramad P, Holland NT. Biomarkers of immunotoxicity for environmental and public health research. Int J Environ Res Public Health 2011; 8:1388-401. [PMID: 21655126 PMCID: PMC3108116 DOI: 10.3390/ijerph8051388] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 03/26/2011] [Accepted: 04/25/2011] [Indexed: 02/07/2023]
Abstract
The immune response plays an important role in the pathophysiology of numerous diseases including asthma, autoimmunity and cancer. Application of biomarkers of immunotoxicity in epidemiology studies and human clinical trials can improve our understanding of the mechanisms that underlie the associations between environmental exposures and development of these immune-mediated diseases. Immunological biomarkers currently used in environmental health studies include detection of key components of innate and adaptive immunity (e.g., complement, immunoglobulin and cell subsets) as well as functional responses and activation of key immune cells. The use of high-throughput assays, including flow cytometry, Luminex, and Multi-spot cytokine detection methods can further provide quantitative analysis of immune effects. Due to the complexity and redundancy of the immune response, an integrated assessment of several components of the immune responses is needed. The rapidly expanding field of immunoinformatics will also aid in the synthesis of the vast amount of data being generated. This review discusses and provides examples of how the identification and development of immunological biomarkers for use in studies of environmental exposures and immune-mediated disorders can be achieved.
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Affiliation(s)
- Paurene Duramad
- Genentech, Inc., 1 DNA Way MS #59, South San Francisco, CA 94080, USA; E-Mail:
| | - Nina T. Holland
- School of Public Health, University of California, Berkeley, 733 University Hall, Berkeley, CA 94720-7360, USA
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Maciel M, Kellathur SN, Chikhlikar P, Dhalia R, Sidney J, Sette A, August TJ, Marques ET. Comprehensive analysis of T cell epitope discovery strategies using 17DD yellow fever virus structural proteins and BALB/c (H2d) mice model. Virology 2008; 378:105-17. [PMID: 18579176 PMCID: PMC2615555 DOI: 10.1016/j.virol.2008.04.043] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Revised: 04/07/2008] [Accepted: 04/30/2008] [Indexed: 01/19/2023]
Abstract
Immunomics research uses in silico epitope prediction, as well as in vivo and in vitro approaches. We inoculated BALB/c (H2d) mice with 17DD yellow fever vaccine to investigate the correlations between approaches used for epitope discovery: ELISPOT assays, binding assays, and prediction software. Our results showed a good agreement between ELISPOT and binding assays, which seemed to correlate with the protein immunogenicity. PREDBALB/c prediction software partially agreed with the ELISPOT and binding assay results, but presented low specificity. The use of prediction software to exclude peptides containing no epitopes, followed by high throughput screening of the remaining peptides by ELISPOT, and the use of MHC-biding assays to characterize the MHC restrictions demonstrated to be an efficient strategy. The results allowed the characterization of 2 MHC class I and 17 class II epitopes in the envelope protein of the YF virus in BALB/c (H2d) mice.
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Affiliation(s)
- Milton Maciel
- Johns Hopkins University, School of Medicine, Pharmacology Department, Baltimore, USA
| | - Srinivasan N. Kellathur
- Johns Hopkins University, School of Medicine, Pharmacology Department, Baltimore, USA,Johns Hopkins Singapore, Singapore
| | - Pryia Chikhlikar
- Johns Hopkins University, School of Medicine, Pharmacology Department, Baltimore, USA
| | - Rafael Dhalia
- Oswaldo Cruz Foundation (FIOCRUZ), Instituto Aggeu Magalhaes, Recife, Brazil
| | | | | | - Thomas J. August
- Johns Hopkins University, School of Medicine, Pharmacology Department, Baltimore, USA
| | - Ernesto T.A. Marques
- Johns Hopkins University, School of Medicine, Pharmacology Department, Baltimore, USA,Johns Hopkins, School of Medicine, Department of Infectious Diseases, Baltimore, USA,Oswaldo Cruz Foundation (FIOCRUZ), Instituto Aggeu Magalhaes, Recife, Brazil,Corresponding author. Johns Hopkins University, School of Medicine, Pharmacology Department, Baltimore, USA
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De Groot AS, Moise L, Mcmurry JA, Martin W. Epitope-Based Immunome-Derived Vaccines: A Strategy for Improved Design and Safety. Clinical Applications of Immunomics 2009. [DOI: 10.1007/978-0-387-79208-8_3] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Vaccine science has extended beyond genomics to proteomics and has come to also encompass ‘immunomics,’ the study of the universe of pathogen-derived or neoplasm-derived peptides that interface with B and T cells of the host immune system. It has been theorized that effective vaccines can be developed using the minimum essential subset of T cell and B cell epitopes that comprise the ‘immunome.’ Researchers are therefore using bioinformatics sequence analysis tools, epitope-mapping tools, microarrays, and high-throughput immunology assays to discover the minimal essential components of the immunome. When these minimal components, or epitopes, are packaged with adjuvants in an appropriate delivery vehicle, the complete package comprises an epitope-based immunome-derived vaccine. Such vaccines may have a significant advantage over conventional vaccines, as the careful selection of the components may diminish undesired side effects such as have been observed with whole pathogen and protein subunit vaccines. This chapter will review the pre-clinical and anticipated clinical development of computer-driven vaccine design and the validation of epitope-based immunome-derived vaccines in animal models; it will also include an overview of heterologous immunity and other emerging issues that will need to be addressed by vaccines of all types in the future.
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