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Tokarz R, Guo C, Sanchez-Vicente S, Horn E, Eschman A, Turk SP, Lipkin WI, Marques A. Identification of reactive Borrelia burgdorferi peptides associated with Lyme disease. mBio 2024:e0236024. [PMID: 39248571 DOI: 10.1128/mbio.02360-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Accepted: 08/21/2024] [Indexed: 09/10/2024] Open
Abstract
Borrelia burgdorferi, the agent of Lyme disease, is estimated to cause >400,000 annual infections in the United States. Serology is the primary laboratory method to support the diagnosis of Lyme disease, but current methods have intrinsic limitations that require alternative approaches or targets. We used a high-density peptide array that contains >90,000 short overlapping peptides to catalog immunoreactive linear epitopes from >60 primary antigens of B. burgdorferi. We then pursued a machine learning approach to identify immunoreactive peptide panels that provide optimal Lyme disease serodiagnosis and can differentiate antibody responses at various stages of disease. We examined 226 serum samples from the Lyme Biobank and the National Institutes of Health, which included sera from 110 individuals diagnosed with Lyme disease, 31 probable cases from symptomatic individuals, and 85 healthy controls. Cases were grouped based on disease stage and presentation and included individuals with early localized, early disseminated, and late Lyme disease. We identified a peptide panel originating from 14 different epitopes that differentiated cases versus controls, whereas another peptide panel built from 12 unique epitopes differentiated subjects with various disease manifestations. Our method demonstrated an improvement in B. burgdorferi antibody detection over the current two-tiered testing approach and confirmed the key diagnostic role of VlsE and FlaB antigens at all stages of Lyme disease. We also uncovered epitopes that triggered a temporal antibody response that was useful for differentiation of early and late disease. Our findings can be used to streamline serologic targets and improve antibody-based diagnosis of Lyme disease. IMPORTANCE Serology is the primary method of Lyme disease diagnosis, but this approach has limitations, particularly early in disease. Currently employed antibody detection assays can be improved by the identification of alternative immunodominant epitopes and the selection of optimal diagnostic targets. We employed high-density peptide arrays that enabled precise epitope mapping for a wide range of B. burgdorferi antigens. In combination with machine learning, this approach facilitated the selection of serologic targets early in disease and the identification of serological indicators associated with different manifestations of Lyme disease. This study provides insights into differential antibody responses during infection and outlines a new approach for improved serologic diagnosis of Lyme disease.
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Affiliation(s)
- Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Cheng Guo
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Santiago Sanchez-Vicente
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | | | - Aleah Eschman
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Siu Ping Turk
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Adriana Marques
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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Sanchez-Vicente S, Tokarz R. Tick-Borne Co-Infections: Challenges in Molecular and Serologic Diagnoses. Pathogens 2023; 12:1371. [PMID: 38003835 PMCID: PMC10674443 DOI: 10.3390/pathogens12111371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/14/2023] [Accepted: 11/18/2023] [Indexed: 11/26/2023] Open
Abstract
Co-infections are a poorly understood aspect of tick-borne diseases. In the United States alone, nineteen different tick-borne pathogens have been identified. The majority of these agents are transmitted by only two tick species, Ixodes scapularis and Amblyomma americanum. Surveillance studies have demonstrated the presence of multiple pathogens in individual ticks suggesting a risk of polymicrobial transmission to humans. However, relatively few studies have explored this relationship and its impact on human disease. One of the key factors for this deficiency are the intrinsic limitations associated with molecular and serologic assays employed for the diagnosis of tick-borne diseases. Limitations in the sensitivity, specificity and most importantly, the capacity for inclusion of multiple agents within a single assay represent the primary challenges for the accurate detection of polymicrobial tick-borne infections. This review will focus on outlining these limitations and discuss potential solutions for the enhanced diagnosis of tick-borne co-infections.
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Affiliation(s)
- Santiago Sanchez-Vicente
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA;
| | - Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA;
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
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3
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Cleveland DW, Anderson CC, Brissette CA. Borrelia miyamotoi: A Comprehensive Review. Pathogens 2023; 12:267. [PMID: 36839539 PMCID: PMC9967256 DOI: 10.3390/pathogens12020267] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
Borrelia miyamotoi is an emerging tick-borne pathogen in the Northern Hemisphere and is the causative agent of Borrelia miyamotoi disease (BMD). Borrelia miyamotoi is vectored by the same hard-bodied ticks as Lyme disease Borrelia, yet phylogenetically groups with relapsing fever Borrelia, and thus, has been uniquely labeled a hard tick-borne relapsing fever Borrelia. Burgeoning research has uncovered new aspects of B. miyamotoi in human patients, nature, and the lab. Of particular interest are novel findings on disease pathology, prevalence, diagnostic methods, ecological maintenance, transmission, and genetic characteristics. Herein, we review recent literature on B. miyamotoi, discuss how findings adapt to current Borrelia doctrines, and briefly consider what remains unknown about B. miyamotoi.
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Affiliation(s)
| | | | - Catherine A. Brissette
- Department of Biomedical Sciences, University of North Dakota, Grand Forks, ND 58202, USA
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4
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Hoornstra D, Stukolova OA, Karan LS, Sarksyan DS, Kolyasnikova NM, Markelov ML, Cherkashina AS, Dolgova AS, Sudina AE, Sokolova MI, Platonov AE, Hovius JW. Development and Validation of a Protein Array for Detection of Antibodies against the Tick-Borne Pathogen Borrelia miyamotoi. Microbiol Spectr 2022; 10:e0203622. [PMID: 36314925 PMCID: PMC9769530 DOI: 10.1128/spectrum.02036-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/26/2022] [Indexed: 11/06/2022] Open
Abstract
Current serological tests for the emerging tick-borne pathogen Borrelia miyamotoi lack diagnostic accuracy. To improve serodiagnosis, we investigated a protein array simultaneously screening for IgM and IgG reactivity against multiple recombinant B. miyamotoi antigens. The array included six B. miyamotoi antigens: glycerophosphodiester phosphodiesterase (GlpQ), multiple variable major proteins (Vmps), and flagellin. Sera included samples from cases of PCR-proven Borrelia miyamotoi disease (BMD), multiple potentially cross-reactive control groups (including patients with culture-proven Lyme borreliosis, confirmed Epstein-Barr virus, cytomegalovirus, or other spirochetal infections), and several healthy control groups from regions where Ixodes is endemic and regions where it is nonendemic. Based on receiver operating characteristic (ROC) analyses, the cutoff for reactivity per antigen was set at 5 μg/mL for IgM and IgG. The individual antigens demonstrated high sensitivity but relatively low specificity for both IgM and IgG. The best-performing single antigen (GlpQ) showed a sensitivity of 88.0% (95% confidence interval [CI], 78.9 to 93.5) and a specificity of 94.2% (95% CI, 92.7 to 95.6) for IgM/IgG. Applying the previous published diagnostic algorithm-defining seroreactivity as reactivity against GlpQ and any Vmp-revealed a significantly higher specificity of 98.5% (95% CI, 97.6 to 99.2) but a significantly lower sensitivity of 79.5% (95% CI, 69.3 to 87.0) for IgM/IgG compared to GlpQ alone. Therefore, we propose to define seroreactivity as reactivity against GlpQ and any Vmp or flagellin which resulted in a comparable sensitivity of 84.3% (95% CI, 74.7 to 90.8) and a significantly higher specificity of 97.9% (95% CI, 96.9 to 98.7) for IgM/IgG compared to GlpQ alone. In conclusion, we have developed and validated a novel serological tool to diagnose BMD that could be implemented in clinical practice and epidemiological studies. IMPORTANCE This paper describes the protein array as a novel serological test for the diagnosis of Borrelia miyamotoi disease (BMD), by reporting the methodology, the development of a diagnostic algorithm, and its extensive validation. With rising numbers of ticks and tick bites, tick-borne diseases, such as BMD, urgently deserve further societal and medical attention. B. miyamotoi is prevalent in Ixodes ticks across the northern hemisphere. Humans are exposed to, and infected by, B. miyamotoi and develop BMD in Asia, in North America, and to a lesser extent in Europe. However, the burden of infection and disease remains largely unknown, due to the noncharacteristic clinical presentation, together with the lack of awareness and availability of diagnostic tools. With this paper, we offer a novel diagnostic tool which will assist in assessing the burden of disease and could be implemented in clinical care.
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Affiliation(s)
- Dieuwertje Hoornstra
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Academic Medical Center, Amsterdam, The Netherlands
| | | | | | | | - Nadezhda M. Kolyasnikova
- Central Research Institute of Epidemiology, Moscow, Russia
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Anna S. Dolgova
- St. Petersburg Pasteur Institute of Epidemiology and Microbiology, Saint Petersburg, Russia
| | - Anna E. Sudina
- Central Research Institute of Epidemiology, Moscow, Russia
| | | | | | - Joppe W. Hovius
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Academic Medical Center, Amsterdam, The Netherlands
- Amsterdam Infection & Immunity Institute, Amsterdam University Medical Centers, Academic Medical Center, Amsterdam, The Netherlands
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Clinical Evaluation of a Borrelia Modified Two-Tiered Testing (MTTT) Shows Increased Early Sensitivity for Borrelia burgdorferi But Not Other Endemic Borrelia Species in A High Incidence Region for Lyme Disease in Wisconsin. Diagn Microbiol Infect Dis 2022; 105:115837. [DOI: 10.1016/j.diagmicrobio.2022.115837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/27/2022] [Accepted: 10/12/2022] [Indexed: 11/24/2022]
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6
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Zhou J, Chen J, Peng Y, Xie Y, Xiao Y. A Promising Tool in Serological Diagnosis: Current Research Progress of Antigenic Epitopes in Infectious Diseases. Pathogens 2022; 11:1095. [PMID: 36297152 PMCID: PMC9609281 DOI: 10.3390/pathogens11101095] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 07/30/2023] Open
Abstract
Infectious diseases, caused by various pathogens in the clinic, threaten the safety of human life, are harmful to physical and mental health, and also increase economic burdens on society. Infections are a complex mechanism of interaction between pathogenic microorganisms and their host. Identification of the causative agent of the infection is vital for the diagnosis and treatment of diseases. Etiological laboratory diagnostic tests are therefore essential to identify pathogens. However, due to its rapidity and automation, the serological diagnostic test is among the methods of great significance for the diagnosis of infections with the basis of detecting antigens or antibodies in body fluids clinically. Epitopes, as a special chemical group that determines the specificity of antigens and the basic unit of inducing immune responses, play an important role in the study of immune responses. Identifying the epitopes of a pathogen may contribute to the development of a vaccine to prevent disease, the diagnosis of the corresponding disease, and the determination of different stages of the disease. Moreover, both the preparation of neutralizing antibodies based on useful epitopes and the assembly of several associated epitopes can be used in the treatment of disease. Epitopes can be divided into B cell epitopes and T cell epitopes; B cell epitopes stimulate the body to produce antibodies and are therefore commonly used as targets for the design of serological diagnostic experiments. Meanwhile, epitopes can fall into two possible categories: linear and conformational. This article reviews the role of B cell epitopes in the clinical diagnosis of infectious diseases.
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7
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Röttgerding F, Njeru J, Schlüfter E, Latz A, Mahdavi R, Steinhoff U, Cutler SJ, Besier S, Kempf VAJ, Fingerle V, Kraiczy P. Novel approaches for the serodiagnosis of louse-borne relapsing fever. Front Cell Infect Microbiol 2022; 12:983770. [PMID: 36204641 PMCID: PMC9530196 DOI: 10.3389/fcimb.2022.983770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/26/2022] [Indexed: 11/13/2022] Open
Abstract
Louse-borne relapsing fever (LBRF) caused by B. recurrentis is a poverty-related and neglected infectious disease with an endemic focus in the Horn of Africa. Re-emergence of the disease occurred in Europe during the refugee crisis in 2015 and sporadic outbreaks were frequently reported in Eastern Africa where poor settings lack affordable diagnostics. Currently, there are no validated in vitro assays available for the serodiagnosis of LBRF. The aim of this study was to develop novel and reliable immunoassays by investigating clinically suspected and culture-confirmed serum samples from LBRF patients and a broad panel of serum samples from patients with other spirochetal, bacterial, and parasitic diseases. We identified two immunoreactive antigens (complement-inhibiting protein CihC and the glycerophosphodiester phosphodiesterase GlpQ of B. recurrentis) as the most promising target candidates leading to the evaluation of two immunoassays (line immunoblot and ELISA) for IgM and IgG. To optimize the IgM immunoassay, we conducted a bioinformatic approach to localize the relevant immunogenic regions within CihC. By utilizing a N-terminal CihC fragment, the sensitivity and specificity of both immunoassays (CihC and GlpQ) were high (IgM: sensitivity 100%, specificity of 89.9%, IgG: sensitivity 100%, specificity 99.2%). In conclusion, our findings indicate the diagnostic potential of CihC and GlpQ as valuable markers for the serodiagnosis of LBRF even at early time points of infection. Here, we provide strong evidence for the utilization of these immunoassays as reliable tools in clinical practice.
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Affiliation(s)
- Florian Röttgerding
- Institute of Medical Microbiology and Infection Control, University Hospital of Frankfurt, Goethe-University Frankfurt, Frankfurt, Germany
| | - John Njeru
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | | | - Andreas Latz
- NovaTec Immundiagnostica GmbH, Dietzenbach, Germany
| | - Rouzbeh Mahdavi
- Institute for Medical Microbiology and Hygiene, Philipps-University Marburg, Marburg, Germany
| | - Ulrich Steinhoff
- Institute for Medical Microbiology and Hygiene, Philipps-University Marburg, Marburg, Germany
| | - Sally J. Cutler
- School of Health, Sports & Bioscience, University of East London, London, United Kingdom
| | - Silke Besier
- Institute of Medical Microbiology and Infection Control, University Hospital of Frankfurt, Goethe-University Frankfurt, Frankfurt, Germany
| | - Volkhard A. J. Kempf
- Institute of Medical Microbiology and Infection Control, University Hospital of Frankfurt, Goethe-University Frankfurt, Frankfurt, Germany
| | - Volker Fingerle
- National Reference Center for Borrelia, Bavarian Health and Food Safety Authority, Oberschleissheim, Germany
| | - Peter Kraiczy
- Institute of Medical Microbiology and Infection Control, University Hospital of Frankfurt, Goethe-University Frankfurt, Frankfurt, Germany
- *Correspondence: Peter Kraiczy,
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8
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Tagliafierro T, Joshi S, Sameroff S, Marques A, Dumler JS, Mishra N, Sanchez-Vicente S, Wormser GP, Marcos LA, Lipkin WI, Tokarz R. Detection of antibodies to Anaplasma phagocytophilum and Babesia microti using linear peptides. Ticks Tick Borne Dis 2022; 13:101999. [DOI: 10.1016/j.ttbdis.2022.101999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 06/03/2022] [Accepted: 06/25/2022] [Indexed: 11/30/2022]
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Mishra M, Zahra A, Chauhan LV, Thakkar R, Ng J, Joshi S, Spitzer ED, Marcos LA, Lipkin WI, Mishra N. A Short Series of Case Reports of COVID-19 in Immunocompromised Patients. Viruses 2022; 14:v14050934. [PMID: 35632677 PMCID: PMC9145915 DOI: 10.3390/v14050934] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/13/2022] [Accepted: 04/26/2022] [Indexed: 01/08/2023] Open
Abstract
Immunocompromised individuals are at risk of prolonged SARS-CoV-2 infection due to weaker immunity, co-morbidities, and lowered vaccine effectiveness, which may evolve highly mutated variants of SARS-CoV-2. Nonetheless, limited data are available on the immune responses elicited by SARS-CoV-2 infection, reinfections, and vaccinations with emerging variants in immunocompromised patients. We analyzed clinical samples that were opportunistically collected from eight immunocompromised individuals for mutations in SARS-CoV-2 genomes, neutralizing antibody (NAb) titers against different SARS-CoV-2 variants, and the identification of immunoreactive epitopes using a high-throughput coronavirus peptide array. The viral genome analysis revealed two SARS-CoV-2 variants (20A from a deceased patient and an Alpha variant from a recovered patient) with an eight amino-acid (aa) deletion within the N-terminal domain (NTD) of the surface glycoprotein. A higher NAb titer was present against the prototypic USA/WA1/2020 strain in vaccinated immunocompromised patients. NAb titer was absent against the Omicron variant and the cultured virus of the 20A variant with eight aa deletions in non-vaccinated patients. Our data suggest that fatal SARS-CoV-2 infections may occur in immunocompromised individuals even with high titers of NAb post-vaccination. Moreover, persistent SARS-CoV-2 infection may lead to the emergence of newer variants with additional mutations favoring the survival and fitness of the pathogen that include deletions in NAb binding sites in the SARS-CoV-2 surface glycoprotein.
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Affiliation(s)
- Mitali Mishra
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (M.M.); (L.V.C.); (R.T.); (J.N.); (S.J.)
| | - Aleena Zahra
- Division of Infectious Diseases, Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; (A.Z.); (E.D.S.); (L.A.M.)
| | - Lokendra V. Chauhan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (M.M.); (L.V.C.); (R.T.); (J.N.); (S.J.)
| | - Riddhi Thakkar
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (M.M.); (L.V.C.); (R.T.); (J.N.); (S.J.)
| | - James Ng
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (M.M.); (L.V.C.); (R.T.); (J.N.); (S.J.)
| | - Shreyas Joshi
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (M.M.); (L.V.C.); (R.T.); (J.N.); (S.J.)
| | - Eric D. Spitzer
- Division of Infectious Diseases, Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; (A.Z.); (E.D.S.); (L.A.M.)
| | - Luis A. Marcos
- Division of Infectious Diseases, Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; (A.Z.); (E.D.S.); (L.A.M.)
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (M.M.); (L.V.C.); (R.T.); (J.N.); (S.J.)
- Correspondence: (W.I.L.); (N.M.)
| | - Nischay Mishra
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (M.M.); (L.V.C.); (R.T.); (J.N.); (S.J.)
- Correspondence: (W.I.L.); (N.M.)
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10
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Zheng Z, Mergaert AM, Ong IM, Shelef MA, Newton MA. MixTwice: large-scale hypothesis testing for peptide arrays by variance mixing. Bioinformatics 2021; 37:2637-2643. [PMID: 33693483 PMCID: PMC8428605 DOI: 10.1093/bioinformatics/btab162] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/13/2021] [Accepted: 03/05/2021] [Indexed: 01/03/2023] Open
Abstract
SUMMARY Peptide microarrays have emerged as a powerful technology in immunoproteomics as they provide a tool to measure the abundance of different antibodies in patient serum samples. The high dimensionality and small sample size of many experiments challenge conventional statistical approaches, including those aiming to control the false discovery rate (FDR). Motivated by limitations in reproducibility and power of current methods, we advance an empirical Bayesian tool that computes local FDR statistics and local false sign rate statistics when provided with data on estimated effects and estimated standard errors from all the measured peptides. As the name suggests, the MixTwice tool involves the estimation of two mixing distributions, one on underlying effects and one on underlying variance parameters. Constrained optimization techniques provide for model fitting of mixing distributions under weak shape constraints (unimodality of the effect distribution). Numerical experiments show that MixTwice can accurately estimate generative parameters and powerfully identify non-null peptides. In a peptide array study of rheumatoid arthritis, MixTwice recovers meaningful peptide markers in one case where the signal is weak, and has strong reproducibility properties in one case where the signal is strong. AVAILABILITYAND IMPLEMENTATION MixTwice is available as an R software package https://cran.r-project.org/web/packages/MixTwice/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zihao Zheng
- Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Aisha M. Mergaert
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53705-2281, USA
| | - Irene M. Ong
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53726, USA
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI 53792, USA
- University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Miriam A. Shelef
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA
| | - Michael A. Newton
- Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53726, USA
- University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, Madison, WI 53792, USA
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11
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Abstract
Serodiagnosis of SARS-CoV-2 infection is impeded by immunological cross-reactivity among the human coronaviruses (HCoVs): SARS-CoV-2, SARS-CoV-1, MERS-CoV, OC43, 229E, HKU1, and NL63. Here we report the identification of humoral immune responses to SARS-CoV-2 peptides that may enable discrimination between exposure to SARS-CoV-2 and other HCoVs. We used a high-density peptide microarray and plasma samples collected at two time points from 50 subjects with SARS-CoV-2 infection confirmed by qPCR, samples collected in 2004–2005 from 11 subjects with IgG antibodies to SARS-CoV-1, 11 subjects with IgG antibodies to other seasonal human coronaviruses (HCoV), and 10 healthy human subjects. Through statistical modeling with linear regression and multidimensional scaling we identified specific peptides that were reassembled to identify 29 linear SARS-CoV-2 epitopes that were immunoreactive with plasma from individuals who had asymptomatic, mild or severe SARS-CoV-2 infections. Larger studies will be required to determine whether these peptides may be useful in serodiagnostics. Mishra, Huang et al. identify 29 linear SARS-CoV-2 epitopes that are immunoreactive with the plasma from individuals who had asymptomatic, mild, or severe SARS-CoV-2 infections. This study suggests the possibility of using these peptides to discriminate the exposure to SARS-CoV-2 and other human coronaviruses.
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12
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Moreira ALE, Oliveira MAP, Silva LOS, Inácio MM, Bailão AM, Parente-Rocha JA, Cruz-Leite VRM, Paccez JD, de Almeida Soares CM, Weber SS, Borges CL. Immunoproteomic Approach of Extracellular Antigens From Paracoccidioides Species Reveals Exclusive B-Cell Epitopes. Front Microbiol 2020; 10:2968. [PMID: 32117076 PMCID: PMC7015227 DOI: 10.3389/fmicb.2019.02968] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/09/2019] [Indexed: 11/16/2022] Open
Abstract
Fungi of the Paracoccidioides genus are the etiological agents of paracoccidioidomycosis (PCM), a systemic mycosis restricted to the countries of Latin America. Currently, the Paracoccidioides complex is represented by Paracoccidioides lutzii, Paracoccidioides americana, Paracoccidioides brasiliensis, Paracoccidioides restrepiensis, and Paracoccidioides venezuelensis. Even with advances in techniques used for diagnosing fungal diseases, high rates of false-positive results for PCM are still presented. Additionally, there is no efficient antigen that can be used to follow up the efficiency of patient treatment. The immunoproteomic is considered a powerful tool for the identification of antigens. In addition, antigens are molecules recognized by the immune system, which make them excellent targets for diagnostic testing of diseases caused by microorganisms. In this vein, we investigated which antigens are secreted by species representing Paracoccidioides complex to increase the spectrum of molecules that could be used for future diagnostic tests, patient follow-up, or PCM therapy. To identify the profile of antigens secreted by Paracoccidioides spp., immunoproteomic approaches were used combining immunoprecipitation, followed by antigen identification by nanoUPLC-MSE-based proteomics. Consequently, it was possible to verify differences in the exoantigen profiles present among the studied species. Through a mass spectrometry approach, it was possible to identify 79 exoantigens in Paracoccidioides species. Using bioinformatics tools, two unique exoantigens in P. lutzii species were identified, as well as 44 epitopes exclusive to the Paracoccidioides complex and 12 unique antigenic sequences that can differentiate between Paracoccidioides species. Therefore, these results demonstrate that Paracoccidioides species have a range of B-cell epitopes exclusive to the complex as well as specific to each Paracoccidioides species. In addition, these analyses allowed us the identification of excellent biomarker candidates for epidemiology screening, diagnosis, patient follow-up, as well as new candidates for PCM therapy.
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Affiliation(s)
- André Luís Elias Moreira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Milton Adriano Pelli Oliveira
- Laboratório de Citocinas, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Brazil
| | - Lana O'Hara Souza Silva
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Moisés Morais Inácio
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Alexandre Melo Bailão
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Juliana Alves Parente-Rocha
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | | | - Juliano Domiraci Paccez
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | | | - Simone Schneider Weber
- Laboratório de Biociência, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil.,Instituto de Ciências Exatas e Tecnologia, Universidade Federal do Amazonas, Itacoatiara, Brazil
| | - Clayton Luiz Borges
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
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