1
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Morgenlander WR, Chia WN, Parra B, Monaco DR, Ragan I, Pardo CA, Bowen R, Zhong D, Norris DE, Ruczinski I, Durbin A, Wang LF, Larman HB, Robinson ML. Precision arbovirus serology with a pan-arbovirus peptidome. Nat Commun 2024; 15:5833. [PMID: 38992033 PMCID: PMC11239951 DOI: 10.1038/s41467-024-49461-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 06/06/2024] [Indexed: 07/13/2024] Open
Abstract
Arthropod-borne viruses represent a crucial public health threat. Current arboviral serology assays are either labor intensive or incapable of distinguishing closely related viruses, and many zoonotic arboviruses that may transition to humans lack any serologic assays. In this study, we present a programmable phage display platform, ArboScan, that evaluates antibody binding to overlapping peptides that represent the proteomes of 691 human and zoonotic arboviruses. We confirm that ArboScan provides detailed antibody binding information from animal sera, human sera, and an arthropod blood meal. ArboScan identifies distinguishing features of antibody responses based on exposure history in a Colombian cohort of Zika patients. Finally, ArboScan details epitope level information that rapidly identifies candidate epitopes with potential protective significance. ArboScan thus represents a resource for characterizing human and animal arbovirus antibody responses at cohort scale.
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Affiliation(s)
- William R Morgenlander
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Wan Ni Chia
- Program in Emerging Infectious Diseases Duke-NUS Medical School, Singapore, Singapore
| | - Beatriz Parra
- Department of Microbiology, Universidad del Valle, Cali, Colombia
| | - Daniel R Monaco
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Izabela Ragan
- Department of Biomedical Sciences, Colorado State University College of Veterinary and Biomedical Sciences, Fort Collins, CO, USA
| | - Carlos A Pardo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Richard Bowen
- Department of Biomedical Sciences, Colorado State University College of Veterinary and Biomedical Sciences, Fort Collins, CO, USA
| | - Diana Zhong
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Douglas E Norris
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Anna Durbin
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Lin-Fa Wang
- Program in Emerging Infectious Diseases Duke-NUS Medical School, Singapore, Singapore
| | - H Benjamin Larman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Matthew L Robinson
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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2
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Liebhoff AM, Venkataraman T, Morgenlander WR, Na M, Kula T, Waugh K, Morrison C, Rewers M, Longman R, Round J, Elledge S, Ruczinski I, Langmead B, Larman HB. Efficient encoding of large antigenic spaces by epitope prioritization with Dolphyn. Nat Commun 2024; 15:1577. [PMID: 38383452 PMCID: PMC10881494 DOI: 10.1038/s41467-024-45601-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024] Open
Abstract
We investigate a relatively underexplored component of the gut-immune axis by profiling the antibody response to gut phages using Phage Immunoprecipitation Sequencing (PhIP-Seq). To cover large antigenic spaces, we develop Dolphyn, a method that uses machine learning to select peptides from protein sets and compresses the proteome through epitope-stitching. Dolphyn compresses the size of a peptide library by 78% compared to traditional tiling, increasing the antibody-reactive peptides from 10% to 31%. We find that the immune system develops antibodies to human gut bacteria-infecting viruses, particularly E.coli-infecting Myoviridae. Cost-effective PhIP-Seq libraries designed with Dolphyn enable the assessment of a wider range of proteins in a single experiment, thus facilitating the study of the gut-immune axis.
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Affiliation(s)
- Anna-Maria Liebhoff
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Institute of Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Thiagarajan Venkataraman
- Institute of Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - William R Morgenlander
- Institute of Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Miso Na
- Institute of Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Tomasz Kula
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA
| | - Kathleen Waugh
- Barbara Davis Center for Diabetes, University of Colorado Denver, Aurora, CO, USA
| | - Charles Morrison
- Behavioral, Clinical and Epidemiologic Sciences, FHI 360, Durham, NC, USA
| | - Marian Rewers
- Barbara Davis Center for Diabetes, University of Colorado Denver, Aurora, CO, USA
| | - Randy Longman
- Jill Roberts Institute for Research in IBD, Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - June Round
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Stephen Elledge
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA
| | - Ben Langmead
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - H Benjamin Larman
- Institute of Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA.
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3
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Chong AY, Brenner N, Jimenez-Kaufmann A, Cortes A, Hill M, Littlejohns TJ, Gilchrist JJ, Fairfax BP, Knight JC, Hodel F, Fellay J, McVean G, Moreno-Estrada A, Waterboer T, Hill AVS, Mentzer AJ. A common NFKB1 variant detected through antibody analysis in UK Biobank predicts risk of infection and allergy. Am J Hum Genet 2024; 111:295-308. [PMID: 38232728 PMCID: PMC10870136 DOI: 10.1016/j.ajhg.2023.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 12/07/2023] [Accepted: 12/10/2023] [Indexed: 01/19/2024] Open
Abstract
Infectious agents contribute significantly to the global burden of diseases through both acute infection and their chronic sequelae. We leveraged the UK Biobank to identify genetic loci that influence humoral immune response to multiple infections. From 45 genome-wide association studies in 9,611 participants from UK Biobank, we identified NFKB1 as a locus associated with quantitative antibody responses to multiple pathogens, including those from the herpes, retro-, and polyoma-virus families. An insertion-deletion variant thought to affect NFKB1 expression (rs28362491), was mapped as the likely causal variant and could play a key role in regulation of the immune response. Using 121 infection- and inflammation-related traits in 487,297 UK Biobank participants, we show that the deletion allele was associated with an increased risk of infection from diverse pathogens but had a protective effect against allergic disease. We propose that altered expression of NFKB1, as a result of the deletion, modulates hematopoietic pathways and likely impacts cell survival, antibody production, and inflammation. Taken together, we show that disruptions to the tightly regulated immune processes may tip the balance between exacerbated immune responses and allergy, or increased risk of infection and impaired resolution of inflammation.
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Affiliation(s)
- Amanda Y Chong
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Nicole Brenner
- Division of Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andres Jimenez-Kaufmann
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Mexico
| | - Adrian Cortes
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Michael Hill
- MRC-Population Health Research Unit, University of Oxford, Oxford, UK
| | | | - James J Gilchrist
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK; Department of Paediatrics, University of Oxford, Oxford, UK
| | | | - Julian C Knight
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Flavia Hodel
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jacques Fellay
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Andres Moreno-Estrada
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Mexico
| | - Tim Waterboer
- Division of Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Adrian V S Hill
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK; The Jenner Institute, University of Oxford, Oxford, UK
| | - Alexander J Mentzer
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
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4
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Filimonova I, Innocenti G, Vogl T. Phage Immunoprecipitation Sequencing (PhIP-Seq) for Analyzing Antibody Epitope Repertoires Against Food Antigens. Methods Mol Biol 2024; 2717:101-122. [PMID: 37737980 DOI: 10.1007/978-1-0716-3453-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
While thousands of food and environmental allergens have been reported, conventional methods for allergy testing typically rely on measuring immunoglobulin E (IgE) binding against panels of dozens to hundreds of antigens. Beyond IgE, also the specificity of other Ig (sub-)classes such as IgG4, has gained interest because of a potential protective role toward allergy.Phage immunoprecipitation sequencing (PhIP-Seq) allows to study hundreds of thousands of rationally selected peptide antigens and to resolve binding specificities of different Ig classes. This technology combines synthetic DNA libraries encoding antigens, with the display on the surface of T7 bacteriophages and next-generation sequencing (NGS) for quantitative readouts. Thereby binding of entire Ig repertoires can be measured to detect the exact epitopes of food allergens and to study potential cross-reactivity.In this chapter, we provide a summary of both the key experimental steps and various strategies for analyzing PhIP-Seq datasets, as well as comparing the advantages and disadvantages of this methodology for measuring antibody responses against food antigens.
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Affiliation(s)
- Ioanna Filimonova
- Medical University of Vienna, Center for Cancer Research, Vienna, Austria
| | - Gabriel Innocenti
- Medical University of Vienna, Center for Cancer Research, Vienna, Austria
| | - Thomas Vogl
- Medical University of Vienna, Center for Cancer Research, Vienna, Austria.
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5
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Do WL, Wang L, Forgues M, Liu J, Rabibhadana S, Pupacdi B, Zhao Y, Gholian H, Bhudhisawasdi V, Pairojkul C, Sukeepaisarnjaroen W, Pugkhem A, Luvira V, Lertprasertsuke N, Chotirosniramit A, Auewarakul CU, Ungtrakul T, Sricharunrat T, Sangrajrang S, Phornphutkul K, Budhu A, Harris CC, Mahidol C, Ruchirawat M, Wang XW. Pan-viral serology uncovers distinct virome patterns as risk predictors of hepatocellular carcinoma and intrahepatic cholangiocarcinoma. Cell Rep Med 2023; 4:101328. [PMID: 38118412 PMCID: PMC10772458 DOI: 10.1016/j.xcrm.2023.101328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/31/2023] [Accepted: 11/17/2023] [Indexed: 12/22/2023]
Abstract
This study evaluates the pan-serological profiles of hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA) compared to several diseased and non-diseased control populations to identify risk factors and biomarkers of liver cancer. We used phage immunoprecipitation sequencing, an anti-viral antibody screening method using a synthetic-phage-displayed human virome epitope library, to screen patient serum samples for exposure to over 1,280 strains of pathogenic and non-pathogenic viruses. Using machine learning methods to develop an HCC or iCCA viral score, we discovered that both viral scores were positively associated with several liver function markers in two separate at-risk populations independent of viral hepatitis status. The HCC score predicted all-cause mortality over 8 years in patients with chronic liver disease at risk of HCC, while the viral hepatitis status was not predictive of survival. These results suggest that non-hepatitis viral infections may contribute to HCC and iCCA development and could be biomarkers in at-risk populations.
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Affiliation(s)
- Whitney L Do
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Limin Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Marshonna Forgues
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Jinping Liu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | | | - Yongmei Zhao
- Office of Science and Technology Resources, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Heelah Gholian
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | | | | | | | - Vor Luvira
- Khon Kaen University, Khon Kaen, Thailand
| | | | | | | | | | | | | | | | - Anuradha Budhu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA; Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Curtis C Harris
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | - Mathuros Ruchirawat
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA; Center of Excellence on Environmental Health and Toxicology, Office of Higher Education Commission, Ministry of Education, Bangkok, Thailand.
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA; Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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6
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Liechti T, Van Gassen S, Beddall M, Ballard R, Iftikhar Y, Du R, Venkataraman T, Novak D, Mangino M, Perfetto S, Larman HB, Spector T, Saeys Y, Roederer M. A robust pipeline for high-content, high-throughput immunophenotyping reveals age- and genetics-dependent changes in blood leukocytes. CELL REPORTS METHODS 2023; 3:100619. [PMID: 37883924 PMCID: PMC10626267 DOI: 10.1016/j.crmeth.2023.100619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 05/29/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023]
Abstract
High-dimensional flow cytometry is the gold standard to study the human immune system in large cohorts. However, large sample sizes increase inter-experimental variation because of technical and experimental inaccuracies introduced by batch variability. Our high-throughput sample processing pipeline in combination with 28-color flow cytometry focuses on increased throughput (192 samples/experiment) and high reproducibility. We implemented quality control checkpoints to reduce technical and experimental variation. Finally, we integrated FlowSOM clustering to facilitate automated data analysis and demonstrate the reproducibility of our pipeline in a study with 3,357 samples. We reveal age-associated immune dynamics in 2,300 individuals, signified by decreasing T and B cell subsets with age. In addition, by combining genetic analyses, our approach revealed unique immune signatures associated with a single nucleotide polymorphism (SNP) that abrogates CD45 isoform splicing. In summary, we provide a versatile and reliable high-throughput, flow cytometry-based pipeline for immune discovery and exploration in large cohorts.
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Affiliation(s)
- Thomas Liechti
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA.
| | - Sofie Van Gassen
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Margaret Beddall
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Reid Ballard
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Yaser Iftikhar
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Renguang Du
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Thiagarajan Venkataraman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - David Novak
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Massimo Mangino
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK; National Heart and Lung Institute, Cardiovascular Science Division, Imperial College London, London, UK
| | - Stephen Perfetto
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - H Benjamin Larman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Tim Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Yvan Saeys
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Mario Roederer
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA.
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7
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Duggal P. Who Lives, Who Dies, Who Tells Your Story? J Infect Dis 2023; 228:811-813. [PMID: 37282664 DOI: 10.1093/infdis/jiad201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 06/06/2023] [Indexed: 06/08/2023] Open
Affiliation(s)
- Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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8
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Liebhoff AM, Venkataraman T, Morgenlander WR, Na M, Kula T, Waugh K, Morrison C, Rewers M, Longman R, Round J, Elledge S, Ruczinski I, Langmead B, Larman HB. Efficient encoding of large antigenic spaces by epitope prioritization with Dolphyn. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.30.551179. [PMID: 37577562 PMCID: PMC10418057 DOI: 10.1101/2023.07.30.551179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
We investigated a relatively underexplored component of the gut-immune axis by profiling the antibody response to gut phages using Phage Immunoprecipitation Sequencing (PhIP-Seq). To enhance this approach, we developed Dolphyn, a novel method that uses machine learning to select peptides from protein sets and compresses the proteome through epitope-stitching. Dolphyn improves the fraction of gut phage library peptides bound by antibodies from 10% to 31% in healthy individuals, while also reducing the number of synthesized peptides by 78%. In our study on gut phages, we discovered that the immune system develops antibodies to bacteria-infecting viruses in the human gut, particularly E.coli-infecting Myoviridae. Cost-effective PhIP-Seq libraries designed with Dolphyn enable the assessment of a wider range of proteins in a single experiment, thus facilitating the study of the gut-immune axis.
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Affiliation(s)
- Anna-Maria Liebhoff
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | | | - William R Morgenlander
- Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Miso Na
- Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Tomasz Kula
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA
| | - Kathleen Waugh
- Barbara Davis Center for Diabetes, University of Colorado Denver, Aurora, Colorado, USA
| | - Charles Morrison
- Behavioral, Clinical and Epidemiologic Sciences, FHI 360, Durham, NC, USA
| | - Marian Rewers
- Barbara Davis Center for Diabetes, University of Colorado Denver, Aurora, Colorado, USA
| | - Randy Longman
- Jill Roberts Institute for Research in IBD, Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - June Round
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Stephen Elledge
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA
| | - Ben Langmead
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - H Benjamin Larman
- Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
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9
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Andreu-Sánchez S, Bourgonje AR, Vogl T, Kurilshikov A, Leviatan S, Ruiz-Moreno AJ, Hu S, Sinha T, Vich Vila A, Klompus S, Kalka IN, de Leeuw K, Arends S, Jonkers I, Withoff S, Brouwer E, Weinberger A, Wijmenga C, Segal E, Weersma RK, Fu J, Zhernakova A. Phage display sequencing reveals that genetic, environmental, and intrinsic factors influence variation of human antibody epitope repertoire. Immunity 2023; 56:1376-1392.e8. [PMID: 37164013 DOI: 10.1016/j.immuni.2023.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/13/2022] [Accepted: 04/06/2023] [Indexed: 05/12/2023]
Abstract
Phage-displayed immunoprecipitation sequencing (PhIP-seq) has enabled high-throughput profiling of human antibody repertoires. However, a comprehensive overview of environmental and genetic determinants shaping human adaptive immunity is lacking. In this study, we investigated the effects of genetic, environmental, and intrinsic factors on the variation in human antibody repertoires. We characterized serological antibody repertoires against 344,000 peptides using PhIP-seq libraries from a wide range of microbial and environmental antigens in 1,443 participants from a population cohort. We detected individual-specificity, temporal consistency, and co-housing similarities in antibody repertoires. Genetic analyses showed the involvement of the HLA, IGHV, and FUT2 gene regions in antibody-bound peptide reactivity. Furthermore, we uncovered associations between phenotypic factors (including age, cell counts, sex, smoking behavior, and allergies, among others) and particular antibody-bound peptides. Our results indicate that human antibody epitope repertoires are shaped by both genetics and environmental exposures and highlight specific signatures of distinct phenotypes and genotypes.
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Affiliation(s)
- Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arno R Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Thomas Vogl
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria; Center for Cancer Research, Medical University of Vienna, Wien, Austria.
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sigal Leviatan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Angel J Ruiz-Moreno
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Shixian Hu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Trishla Sinha
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Shelley Klompus
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Iris N Kalka
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Karina de Leeuw
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Suzanne Arends
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Iris Jonkers
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sebo Withoff
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Elisabeth Brouwer
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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10
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Immunoglobulin germline gene polymorphisms influence the function of SARS-CoV-2 neutralizing antibodies. Immunity 2023; 56:193-206.e7. [PMID: 36574772 PMCID: PMC9742198 DOI: 10.1016/j.immuni.2022.12.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/23/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
The human immunoglobulin heavy-chain (IGH) locus is exceptionally polymorphic, with high levels of allelic and structural variation. Thus, germline IGH genotypes are personal, which may influence responses to infection and vaccination. For an improved understanding of inter-individual differences in antibody responses, we isolated SARS-CoV-2 spike-specific monoclonal antibodies from convalescent health care workers, focusing on the IGHV1-69 gene, which has the highest level of allelic variation of all IGHV genes. The IGHV1-69∗20-using CAB-I47 antibody and two similar antibodies isolated from an independent donor were critically dependent on allele usage. Neutralization was retained when reverting the V region to the germline IGHV1-69∗20 allele but lost when reverting to other IGHV1-69 alleles. Structural data confirmed that two germline-encoded polymorphisms, R50 and F55, in the IGHV1-69 gene were required for high-affinity receptor-binding domain interaction. These results demonstrate that polymorphisms in IGH genes can influence the function of SARS-CoV-2 neutralizing antibodies.
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11
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Allergenic food protein consumption is associated with systemic IgG antibody responses in non-allergic individuals. Immunity 2022; 55:2454-2469.e6. [PMID: 36473469 DOI: 10.1016/j.immuni.2022.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 06/01/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022]
Abstract
Although food-directed immunoglobulin E (IgE) has been studied in the context of allergies, the prevalence and magnitude of IgG responses against dietary antigens are incompletely characterized in the general population. Here, we measured IgG binding against food and environmental antigens obtained from allergen databases and the immune epitope database (IEDB), represented in a phage displayed library of 58,233 peptides. By profiling blood samples of a large cohort representing the average adult Israeli population (n = 1,003), we showed that many food antigens elicited systemic IgG in up to 50% of individuals. Dietary intake of specific food protein correlated with antibody binding, suggesting that diet can shape the IgG epitope repertoire. Our work documents abundant systemic IgG responses against food antigens and provides a reference map of the exact immunogenic epitopes on a population scale, laying the foundation to unravel the role of food- and environmental antigen-directed antibody binding in disease contexts.
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12
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Gemmati D, Longo G, Gallo I, Silva JA, Secchiero P, Zauli G, Hanau S, Passaro A, Pellegatti P, Pizzicotti S, Serino ML, Singh AV, Tisato V. Host genetics impact on SARS-CoV-2 vaccine-induced immunoglobulin levels and dynamics: The role of TP53, ABO, APOE, ACE2, HLA-A, and CRP genes. Front Genet 2022; 13:1028081. [PMID: 36531241 PMCID: PMC9748098 DOI: 10.3389/fgene.2022.1028081] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/18/2022] [Indexed: 08/26/2023] Open
Abstract
Background: Development and worldwide availability of safe and effective vaccines against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) to fight severe symptoms of coronavirus disease 2019 (COVID-19) and block the pandemic have been a great achievement and stimulated researchers on understanding the efficacy and duration of different vaccine types. Methods: We investigated the levels of anti-SARS-CoV-2 antibodies (IgG) and neutralizing antibodies (NAbs) in 195 healthy adult subjects belonging to the staff of the University-Hospital of Ferrara (Italy) starting from 15 days up to 190 days (about 6 months) after the second dose of the BNT162b2 (Pfizer-BioNTech) mRNA-based vaccine (n = 128) or ChAdOx1 (AstraZeneca) adenovirus-based vaccine (n = 67) using a combined approach of serological and genomics investigations. Results: A strong correlation between IgG and NAb levels was detected during the 190 days of follow-up (r 2 = 0.807; p < 0.0001) and was confirmed during the first 90 days (T1) after vaccination (r 2 = 0.789; p = 0.0001) and 91-190 days (T2) after vaccination (r 2 = 0.764; p = 0.0001) for both vaccine types (r 2 = 0.842; p = 0.0001 and r 2 = 0.780; p = 0.0001 for mRNA- and adenovirus-based vaccine, respectively). In addition to age (p < 0.01), sex (p = 0.03), and type of vaccine (p < 0.0001), which partially accounted for the remarkable individual differences observed in the antibody levels and dynamics, interesting genetic determinants appeared as significant modifiers of both IgG and NAb responses among the selected genes investigated (TP53, rs1042522; APOE, rs7412/rs429358; ABO, rs657152; ACE2, rs2285666; HLA-A rs2571381/rs2499; CRP, rs2808635/rs876538; LZTFL1, rs35044562; OAS3, rs10735079; SLC6A20, rs11385942; CFH, rs1061170; and ACE1, ins/del, rs4646994). In detail, regression analysis and mean antibody level comparison yielded appreciable differences after genotype stratification (P1 and P2, respectively, for IgG and NAb distribution) in the whole cohort and/or in the mRNA-based vaccine in the following genes: TP53, rs1042522 (P1 = 0.03; P2 = 0.04); ABO, rs657152 (P1 = 0.01; P2 = 0.03); APOE, rs7412/rs429358 (P1 = 0.0018; P2 = 0.0002); ACE2, rs2285666 (P1 = 0.014; P2 = 0.009); HLA-A, rs2571381/rs2499 (P1 = 0.02; P2 = 0.03); and CRP, rs2808635/rs876538 (P1 = 0.01 and P2 = 0.09). Conclusion: High- or low-responsive subjects can be identified among healthy adult vaccinated subjects after targeted genetic screening. This suggests that favorable genetic backgrounds may support the progression of an effective vaccine-induced immune response, though no definite conclusions can be drawn on the real effectiveness ascribed to a specific vaccine or to the different extent of a genotype-driven humoral response. The interplay between data from the polygenic predictive markers and serological screening stratified by demogeographic information can help to recognize the individual humoral response, accounting for ethnic and geographical differences, in both COVID-19 and anti-SARS-CoV-2 vaccinations.
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Affiliation(s)
- Donato Gemmati
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Centre Haemostasis & Thrombosis, University of Ferrara, Ferrara, Italy
- University Centre for Gender Medicine Studies, University of Ferrara, Ferrara, Italy
| | - Giovanna Longo
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Centre Haemostasis & Thrombosis, University of Ferrara, Ferrara, Italy
| | - Ines Gallo
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Centre Haemostasis & Thrombosis, University of Ferrara, Ferrara, Italy
| | - Juliana Araujo Silva
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Centre Haemostasis & Thrombosis, University of Ferrara, Ferrara, Italy
| | - Paola Secchiero
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Giorgio Zauli
- Research Department, King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
| | - Stefania Hanau
- Department of Neuroscience & Rehabilitation, University of Ferrara, Ferrara, Italy
| | - Angelina Passaro
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | | | | | | | - Ajay Vikram Singh
- Department of Chemical & Product Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Veronica Tisato
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- University Centre for Gender Medicine Studies, University of Ferrara, Ferrara, Italy
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13
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Qi H, Xue JB, Lai DY, Li A, Tao SC. Current advances in antibody-based serum biomarker studies: From protein microarray to phage display. Proteomics Clin Appl 2022; 16:e2100098. [PMID: 36071670 DOI: 10.1002/prca.202100098] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 08/16/2022] [Accepted: 09/05/2022] [Indexed: 12/30/2022]
Abstract
PURPOSE This review aims to summarize the technological advances in the field of antibody-based biomarker studies by proteome microarray and phage display. In addition, the possible development directions of this field are also discussed. EXPERIMENTAL DESIGN We have focused on the antibody profiling by proteome microarray and phage display, including the technological advances, the tools/resources constructed, and the characteristics of both platforms. RESULTS With the help of tools/resources and technological advances in proteome microarray and phage display, the efficiency of profiling antibody-based biomarkers in serum samples has been greatly improved. CONCLUSIONS In the past few years, proteome microarray and phage display, especially the latter one, have already demonstrated their capacity and efficiency for biomarker identification. In the near future, we believe that more antibody-based biomarkers could be identified, and some of them could eventually be developed into real clinical applications.
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Affiliation(s)
- Huan Qi
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Jun-Biao Xue
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Dan-Yun Lai
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Ang Li
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
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14
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Vogl T, Kalka IN, Klompus S, Leviatan S, Weinberger A, Segal E. Systemic antibody responses against human microbiota flagellins are overrepresented in chronic fatigue syndrome patients. SCIENCE ADVANCES 2022; 8:eabq2422. [PMID: 36149952 DOI: 10.1126/sciadv.abq2422] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating disease with an unclear etiology and pathogenesis. Both an involvement of the immune system and gut microbiota dysbiosis have been implicated in its pathophysiology. However, potential interactions between adaptive immune responses and the microbiota in ME/CFS have been incompletely characterized. Here, we profiled antibody responses of patients with severe ME/CFS and healthy controls against microbiota and viral antigens represented as a phage-displayed 244,000 variant library. Patients with severe ME/CFS exhibited distinct serum antibody epitope repertoires against flagellins of Lachnospiraceae bacteria. Training machine learning algorithms on this antibody-binding data demonstrated that immune responses against gut microbiota represent a unique layer of information beyond standard blood tests, providing improved molecular diagnostics for ME/CFS. Together, our results point toward an involvement of the microbiota-immune axis in ME/CFS and lay the foundation for comparative studies with inflammatory bowel diseases and illnesses characterized by long-term fatigue symptoms, including post-COVID-19 syndrome.
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Affiliation(s)
- Thomas Vogl
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
| | - Iris N Kalka
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Shelley Klompus
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sigal Leviatan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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15
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Chen A, Kammers K, Larman HB, Scharpf RB, Ruczinski I. Detecting antibody reactivities in Phage ImmunoPrecipitation Sequencing data. BMC Genomics 2022; 23:654. [PMID: 36109689 PMCID: PMC9476399 DOI: 10.1186/s12864-022-08869-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 08/31/2022] [Indexed: 11/10/2022] Open
Abstract
Phage ImmunoPrecipitation Sequencing (PhIP-Seq) is a recently developed technology to assess antibody reactivity, quantifying antibody binding towards hundreds of thousands of candidate epitopes. The output from PhIP-Seq experiments are read count matrices, similar to RNA-Seq data; however some important differences do exist. In this manuscript we investigated whether the publicly available method edgeR (Robinson et al., Bioinformatics 26(1):139-140, 2010) for normalization and analysis of RNA-Seq data is also suitable for PhIP-Seq data. We find that edgeR is remarkably effective, but improvements can be made and introduce a Bayesian framework specifically tailored for data from PhIP-Seq experiments (Bayesian Enrichment Estimation in R, BEER).
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Affiliation(s)
- Athena Chen
- grid.21107.350000 0001 2171 9311Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - Kai Kammers
- grid.21107.350000 0001 2171 9311Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - H Benjamin Larman
- grid.21107.350000 0001 2171 9311Department of Pathology and the Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Robert B. Scharpf
- grid.21107.350000 0001 2171 9311Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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16
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Credle JJ, Gunn J, Sangkhapreecha P, Monaco DR, Zheng XA, Tsai HJ, Wilbon A, Morgenlander WR, Rastegar A, Dong Y, Jayaraman S, Tosi L, Parekkadan B, Baer AN, Roederer M, Bloch EM, Tobian AAR, Zyskind I, Silverberg JI, Rosenberg AZ, Cox AL, Lloyd T, Mammen AL, Benjamin Larman H. Unbiased discovery of autoantibodies associated with severe COVID-19 via genome-scale self-assembled DNA-barcoded protein libraries. Nat Biomed Eng 2022; 6:992-1003. [PMID: 35986181 PMCID: PMC10034860 DOI: 10.1038/s41551-022-00925-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/14/2022] [Indexed: 12/13/2022]
Abstract
Pathogenic autoreactive antibodies that may be associated with life-threatening coronavirus disease 2019 (COVID-19) remain to be identified. Here, we show that self-assembled genome-scale libraries of full-length proteins covalently coupled to unique DNA barcodes for analysis by sequencing can be used for the unbiased identification of autoreactive antibodies in plasma samples. By screening 11,076 DNA-barcoded proteins expressed from a sequence-verified human ORFeome library, the method, which we named MIPSA (for Molecular Indexing of Proteins by Self-Assembly), allowed us to detect circulating neutralizing type-I and type-III interferon (IFN) autoantibodies in five plasma samples from 55 patients with life-threatening COVID-19. In addition to identifying neutralizing type-I IFN-α and IFN-ω autoantibodies and other previously known autoreactive antibodies in patient plasma, MIPSA enabled the detection of as yet unidentified neutralizing type-III anti-IFN-λ3 autoantibodies that were not seen in healthy plasma samples or in convalescent plasma from ten non-hospitalized individuals with COVID-19. The low cost and simple workflow of MIPSA will facilitate unbiased high-throughput analyses of protein-antibody, protein-protein and protein-small-molecule interactions.
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Affiliation(s)
- Joel J Credle
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jonathan Gunn
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Puwanat Sangkhapreecha
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel R Monaco
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xuwen Alice Zheng
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hung-Ji Tsai
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Azaan Wilbon
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - William R Morgenlander
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andre Rastegar
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yi Dong
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sahana Jayaraman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lorenzo Tosi
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Biju Parekkadan
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Alan N Baer
- Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mario Roederer
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Evan M Bloch
- Division of Transfusion Medicine, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aaron A R Tobian
- Division of Transfusion Medicine, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Israel Zyskind
- Department of Pediatrics, NYU Langone Medical Center, New York City, NY, USA
- Department of Pediatrics, Maimonides Medical Center, Brooklyn, NY, USA
| | - Jonathan I Silverberg
- Department of Dermatology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Avi Z Rosenberg
- Division of Kidney-Urologic Pathology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrea L Cox
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tom Lloyd
- Department of Neurology and Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew L Mammen
- Department of Neurology and Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Muscle Disease Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - H Benjamin Larman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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17
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Angkeow JW, Monaco DR, Chen A, Venkataraman T, Jayaraman S, Valencia C, Sie BM, Liechti T, Farhadi PN, Funez-dePagnier G, Sherman-Baust CA, Wong MQ, Ruczinski I, Caturegli P, Sears CL, Simner PJ, Round JL, Duggal P, Laserson U, Steiner TS, Sen R, Lloyd TE, Roederer M, Mammen AL, Longman RS, Rider LG, Larman HB. Phage display of environmental protein toxins and virulence factors reveals the prevalence, persistence, and genetics of antibody responses. Immunity 2022; 55:1051-1066.e4. [PMID: 35649416 PMCID: PMC9203978 DOI: 10.1016/j.immuni.2022.05.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 02/17/2022] [Accepted: 05/03/2022] [Indexed: 11/19/2022]
Abstract
Microbial exposures are crucial environmental factors that impact healthspan by sculpting the immune system and microbiota. Antibody profiling via Phage ImmunoPrecipitation Sequencing (PhIP-Seq) provides a high-throughput, cost-effective approach for detecting exposure and response to microbial protein products. We designed and constructed a library of 95,601 56-amino acid peptide tiles spanning 14,430 proteins with "toxin" or "virulence factor" keyword annotations. We used PhIP-Seq to profile the antibodies of ∼1,000 individuals against this "ToxScan" library. In addition to enumerating immunodominant antibody epitopes, we studied the age-dependent stability of the ToxScan profile and used a genome-wide association study to find that the MHC-II locus modulates bacterial epitope selection. We detected previously described anti-flagellin antibody responses in a Crohn's disease cohort and identified an association between anti-flagellin antibodies and juvenile dermatomyositis. PhIP-Seq with the ToxScan library is thus an effective tool for studying the environmental determinants of health and disease at cohort scale.
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Affiliation(s)
- Julia W Angkeow
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel R Monaco
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Athena Chen
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Thiagarajan Venkataraman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sahana Jayaraman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Cristian Valencia
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Brandon M Sie
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thomas Liechti
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Payam N Farhadi
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, NIH, Bethesda, MD, USA
| | - Gabriela Funez-dePagnier
- Jill Roberts Institute for Research in IBD, Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Cheryl A Sherman-Baust
- Laboratory of Molecular Biology and Immunology, NIH/National Institute on Aging, Baltimore, MD, USA
| | - May Q Wong
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Patrizio Caturegli
- Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Cynthia L Sears
- Departments of Medicine and Oncology, Johns Hopkins University School of Medicine, and Department of Molecular Microbiology & Immunology, Bloomberg School of Public Health, Baltimore, MD, USA
| | - Patricia J Simner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - June L Round
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Uri Laserson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, NIH/National Institute on Aging, Baltimore, MD, USA
| | - Thomas E Lloyd
- Department of Neurology, Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Mario Roederer
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Andrew L Mammen
- Muscle Disease Unit, Laboratory of Muscle Stem Cells and Gene Regulations, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, USA
| | - Randy S Longman
- Jill Roberts Institute for Research in IBD, Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lisa G Rider
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, NIH, Bethesda, MD, USA
| | - H Benjamin Larman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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18
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Guerra G, Kachuri L, Wendt G, Hansen HM, Mack SJ, Molinaro AM, Rice T, Bracci P, Wiencke JK, Kasahara N, Eckel-Passow JE, Jenkins RB, Wrensch M, Francis SS. The immunogenetics of viral antigen response is associated with subtype-specific glioma risk and survival. Am J Hum Genet 2022; 109:1105-1116. [PMID: 35550063 PMCID: PMC9247888 DOI: 10.1016/j.ajhg.2022.04.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/18/2022] [Indexed: 12/14/2022] Open
Abstract
Glioma is a highly fatal cancer with prognostically significant molecular subtypes and few known risk factors. Multiple studies have implicated infections in glioma susceptibility, but evidence remains inconsistent. Genetic variants in the human leukocyte antigen (HLA) region modulate host response to infection and have been linked to glioma risk. In this study, we leveraged genetic predictors of antibody response to 12 viral antigens to investigate the relationship with glioma risk and survival. Genetic reactivity scores (GRSs) for each antigen were derived from genome-wide-significant (p < 5 × 10-8) variants associated with immunoglobulin G antibody response in the UK Biobank cohort. We conducted parallel analyses of glioma risk and survival for each GRS and HLA alleles imputed at two-field resolution by using data from 3,418 glioma-affected individuals subtyped by somatic mutations and 8,156 controls. Genetic reactivity scores to Epstein-Barr virus (EBV) ZEBRA and EBNA antigens and Merkel cell polyomavirus (MCV) VP1 antigen were associated with glioma risk and survival (Bonferroni-corrected p < 0.01). GRSZEBRA and GRSMCV were associated in opposite directions with risk of IDH wild-type gliomas (ORZEBRA = 0.91, p = 0.0099/ORMCV = 1.11, p = 0.0054). GRSEBNA was associated with both increased risk for IDH mutated gliomas (OR = 1.09, p = 0.040) and improved survival (HR = 0.86, p = 0.010). HLA-DQA1∗03:01 was significantly associated with decreased risk of glioma overall (OR = 0.85, p = 3.96 × 10-4) after multiple testing adjustment. This systematic investigation of the role of genetic determinants of viral antigen reactivity in glioma risk and survival provides insight into complex immunogenomic mechanisms of glioma pathogenesis. These results may inform applications of antiviral-based therapies in glioma treatment.
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Affiliation(s)
- Geno Guerra
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA.
| | - Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - George Wendt
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Helen M Hansen
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Steven J Mack
- Department of Pediatrics, University of California, San Francisco, Oakland, CA, USA
| | - Annette M Molinaro
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Terri Rice
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Paige Bracci
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - John K Wiencke
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA; Institute of Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Nori Kasahara
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, USA
| | | | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Margaret Wrensch
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA; Institute of Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Stephen S Francis
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, USA.
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19
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Abstract
Accumulating evidence implicates Epstein-Barr virus (EBV) as an etiological factor in multiple sclerosis (MS). If EBV is a "driver" that causes antiviral immunity with associated autoimmune components rather than a "trigger" that unleashes self-perpetuating autoimmunity, then elimination of EBV would be a rational therapy for MS.
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Affiliation(s)
- Ludvig M Sollid
- KG Jebsen Centre for Coeliac Disease Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway and Department of Immunology, Oslo University Hospital - Rikshospitalet, Oslo, Norway.
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20
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Kearns PKA. Prevention of MS Requires Intervention on the Causes of the Disease: Reconciling Genes, Epigenetics, and Epstein Barr Virus. Front Neurol 2022; 13:817677. [PMID: 35273557 PMCID: PMC8902355 DOI: 10.3389/fneur.2022.817677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/13/2022] [Indexed: 11/28/2022] Open
Abstract
Prevention of multiple sclerosis requires intervention on modifiable causes of the condition making it necessary to establish what those causes are. MS is often stated to be a polygenic disease, with causal contributions from environmental factors and gene-environment interactions, implying an additive and independent relationship of these factors. Mechanistically there are no independent contributions of genes or environmental factors to traits. This model is unrealistic but still useful and underlies the concept of heritability, a foundational parameter in population genetics. However, it perpetuates a debate on an irreconcilable dichotomy about whether MS is primarily genetic or environmental. In particular, epidemiological evidence now exists for a causal, possibly even necessary, role for Epstein Barr Virus in MS. The additive model makes it unintuitive to reconcile MS as a genetic disease but also independently a viral illness. In this perspective it is argued that starting from a realistic interaction only model, based on broadly accepted biological premises, and working forward to explain why the classical additive model gives useful results, there is actually no paradox. An integrated approach using population genetic studies, immunology and molecular virology offers a particularly promising route to establish the elusive role of EBV in MS pathology, as EBV is a large and complex virus and its latency, dysregulated in most EBV-related pathologies, is hard to study in vivo. This approach may offer a route to prevention of MS altogether.
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Affiliation(s)
- Patrick K A Kearns
- Chromatin Lab, MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom.,Anne Rowling Regenerative Neurology Clinic, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom.,Department of Clinical Neurosciences (Neurology), Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, United Kingdom
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21
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Castro Dopico X, Karlsson Hedestam GB. A family matter: Anti-viral antibody responses. Immunity 2022; 55:8-10. [PMID: 35021059 DOI: 10.1016/j.immuni.2021.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The immune response is an amalgam of heritable and non-heritable effects, although the contribution of each is generally unknown. In this issue of Immunity, Venkataraman et al. report heritable traits that govern anti-viral antibody epitope specificity and breadth controlled by the MHC class II region, indicating that your genes influence which pathogen-derived epitopes your B cells target during viral infections.
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Affiliation(s)
- Xaquin Castro Dopico
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden
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