1
|
Rebak AS, Hendriks IA, Elsborg JD, Buch-Larsen SC, Nielsen CH, Terslev L, Kirsch R, Damgaard D, Doncheva NT, Lennartsson C, Rykær M, Jensen LJ, Christophorou MA, Nielsen ML. A quantitative and site-specific atlas of the citrullinome reveals widespread existence of citrullination and insights into PADI4 substrates. Nat Struct Mol Biol 2024; 31:977-995. [PMID: 38321148 PMCID: PMC11189309 DOI: 10.1038/s41594-024-01214-9] [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: 12/22/2022] [Accepted: 01/04/2024] [Indexed: 02/08/2024]
Abstract
Despite the importance of citrullination in physiology and disease, global identification of citrullinated proteins, and the precise targeted sites, has remained challenging. Here we employed quantitative-mass-spectrometry-based proteomics to generate a comprehensive atlas of citrullination sites within the HL60 leukemia cell line following differentiation into neutrophil-like cells. We identified 14,056 citrullination sites within 4,008 proteins and quantified their regulation upon inhibition of the citrullinating enzyme PADI4. With this resource, we provide quantitative and site-specific information on thousands of PADI4 substrates, including signature histone marks and transcriptional regulators. Additionally, using peptide microarrays, we demonstrate the potential clinical relevance of certain identified sites, through distinct reactivities of antibodies contained in synovial fluid from anti-CCP-positive and anti-CCP-negative people with rheumatoid arthritis. Collectively, we describe the human citrullinome at a systems-wide level, provide a resource for understanding citrullination at the mechanistic level and link the identified targeted sites to rheumatoid arthritis.
Collapse
Affiliation(s)
- Alexandra S Rebak
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ivo A Hendriks
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jonas D Elsborg
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sara C Buch-Larsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claus H Nielsen
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Lene Terslev
- Copenhagen Center for Arthritis Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Rebecca Kirsch
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dres Damgaard
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Nadezhda T Doncheva
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Caroline Lennartsson
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martin Rykær
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars J Jensen
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
2
|
Lastwika KJ, Lampe PD. Breaking tolerance: autoantibodies can target protein posttranslational modifications. Curr Opin Biotechnol 2024; 85:103056. [PMID: 38141322 PMCID: PMC10922400 DOI: 10.1016/j.copbio.2023.103056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 11/28/2023] [Accepted: 12/03/2023] [Indexed: 12/25/2023]
Abstract
Autoantibodies (AAb) are an immunological resource ripe for exploitation in cancer detection and treatment. Key to this translation is a better understanding of the self-epitope that AAb target in tumor tissue, but do not bind to in normal tissue. Posttranslational modifications (PTMs) on self-proteins are known to break tolerance in many autoimmune diseases and have also recently been described in cancer. This scope of possible autoantigens is quite broad and new high-dimensional and -throughput technologies to probe this repertoire will be necessary to fully exploit their potential. Here, we discuss the strengths and weaknesses of existing high-throughput platforms to detect AAb, review the current methods for characterizing immunogenic PTMs, describe the main challenges to identifying disease-relevant antigens and suggest the properties of future technologies that may be able to address these challenges. We conclude that exploiting the evolutionary power of the immune system to distinguish between self and nonself has great potential to be translated into antibody-based clinical applications.
Collapse
Affiliation(s)
- Kristin J Lastwika
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Paul D Lampe
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Lingasamy P, Modhukur V, Mändar R, Salumets A. Exploring Immunome and Microbiome Interplay in Reproductive Health: Current Knowledge, Challenges, and Novel Diagnostic Tools. Semin Reprod Med 2023; 41:172-189. [PMID: 38262441 PMCID: PMC10846929 DOI: 10.1055/s-0043-1778017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
The dynamic interplay between the immunome and microbiome in reproductive health is a complex and rapidly advancing research field, holding tremendously vast possibilities for the development of reproductive medicine. This immunome-microbiome relationship influences the innate and adaptive immune responses, thereby affecting the onset and progression of reproductive disorders. However, the mechanisms governing these interactions remain elusive and require innovative approaches to gather more understanding. This comprehensive review examines the current knowledge on reproductive microbiomes across various parts of female reproductive tract, with special consideration of bidirectional interactions between microbiomes and the immune system. Additionally, it explores innate and adaptive immunity, focusing on immunoglobulin (Ig) A and IgM antibodies, their regulation, self-antigen tolerance mechanisms, and their roles in immune homeostasis. This review also highlights ongoing technological innovations in microbiota research, emphasizing the need for standardized detection and analysis methods. For instance, we evaluate the clinical utility of innovative technologies such as Phage ImmunoPrecipitation Sequencing (PhIP-Seq) and Microbial Flow Cytometry coupled to Next-Generation Sequencing (mFLOW-Seq). Despite ongoing advancements, we emphasize the need for further exploration in this field, as a deeper understanding of immunome-microbiome interactions holds promise for innovative diagnostic and therapeutic strategies for reproductive health, like infertility treatment and management of pregnancy.
Collapse
Affiliation(s)
| | - Vijayachitra Modhukur
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Reet Mändar
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
Curran AM, Girgis AA, Jang Y, Crawford JD, Thomas MA, Kawalerski R, Coller J, Bingham CO, Na CH, Darrah E. Citrullination modulates antigen processing and presentation by revealing cryptic epitopes in rheumatoid arthritis. Nat Commun 2023; 14:1061. [PMID: 36828807 PMCID: PMC9958131 DOI: 10.1038/s41467-023-36620-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 02/06/2023] [Indexed: 02/26/2023] Open
Abstract
Cryptic peptides, hidden from the immune system under physiologic conditions, are revealed by changes to MHC class II processing and hypothesized to drive the loss of immune tolerance to self-antigens in autoimmunity. Rheumatoid arthritis (RA) is an autoimmune disease characterized by immune responses to citrullinated self-antigens, in which arginine residues are converted to citrullines. Here, we investigate the hypothesis that citrullination exposes cryptic peptides by modifying protein structure and proteolytic cleavage. We show that citrullination alters processing and presentation of autoantigens, resulting in the generation of a unique citrullination-dependent repertoire composed primarily of native sequences. This repertoire stimulates T cells from RA patients with anti-citrullinated protein antibodies more robustly than controls. The generation of this unique repertoire is achieved through altered protease cleavage and protein destabilization, rather than direct presentation of citrulline-containing epitopes, suggesting a novel paradigm for the role of protein citrullination in the breach of immune tolerance in RA.
Collapse
Affiliation(s)
- Ashley M Curran
- Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alexander A Girgis
- Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Yura Jang
- Neurology, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Laboratory of Immunology, Office of Biotechnology Products, Center for Drugs Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Jonathan D Crawford
- Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mekha A Thomas
- Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ryan Kawalerski
- Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jeff Coller
- Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Clifton O Bingham
- Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chan Hyun Na
- Neurology, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Erika Darrah
- Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
7
|
Vazquez SE, Mann SA, Bodansky A, Kung AF, Quandt Z, Ferré EMN, Landegren N, Eriksson D, Bastard P, Zhang SY, Liu J, Mitchell A, Proekt I, Yu D, Mandel-Brehm C, Wang CY, Miao B, Sowa G, Zorn K, Chan AY, Tagi VM, Shimizu C, Tremoulet A, Lynch K, Wilson MR, Kämpe O, Dobbs K, Delmonte OM, Bacchetta R, Notarangelo LD, Burns JC, Casanova JL, Lionakis MS, Torgerson TR, Anderson MS, DeRisi JL. Autoantibody discovery across monogenic, acquired, and COVID-19-associated autoimmunity with scalable PhIP-seq. eLife 2022; 11:e78550. [PMID: 36300623 PMCID: PMC9711525 DOI: 10.7554/elife.78550] [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: 03/23/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022] Open
Abstract
Phage immunoprecipitation sequencing (PhIP-seq) allows for unbiased, proteome-wide autoantibody discovery across a variety of disease settings, with identification of disease-specific autoantigens providing new insight into previously poorly understood forms of immune dysregulation. Despite several successful implementations of PhIP-seq for autoantigen discovery, including our previous work (Vazquez et al., 2020), current protocols are inherently difficult to scale to accommodate large cohorts of cases and importantly, healthy controls. Here, we develop and validate a high throughput extension of PhIP-seq in various etiologies of autoimmune and inflammatory diseases, including APS1, IPEX, RAG1/2 deficiency, Kawasaki disease (KD), multisystem inflammatory syndrome in children (MIS-C), and finally, mild and severe forms of COVID-19. We demonstrate that these scaled datasets enable machine-learning approaches that result in robust prediction of disease status, as well as the ability to detect both known and novel autoantigens, such as prodynorphin (PDYN) in APS1 patients, and intestinally expressed proteins BEST4 and BTNL8 in IPEX patients. Remarkably, BEST4 antibodies were also found in two patients with RAG1/2 deficiency, one of whom had very early onset IBD. Scaled PhIP-seq examination of both MIS-C and KD demonstrated rare, overlapping antigens, including CGNL1, as well as several strongly enriched putative pneumonia-associated antigens in severe COVID-19, including the endosomal protein EEA1. Together, scaled PhIP-seq provides a valuable tool for broadly assessing both rare and common autoantigen overlap between autoimmune diseases of varying origins and etiologies.
Collapse
Affiliation(s)
- Sara E Vazquez
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
- School of Medicine, University of California, San FranciscoSan FranciscoUnited States
| | - Sabrina A Mann
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Aaron Bodansky
- Department of Pediatric Critical Care Medicine, University of California, San FranciscoSan FranciscoUnited States
| | - Andrew F Kung
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Zoe Quandt
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
- Department of Medicine, University of California, San FranciscoSan FranciscoUnited States
| | - Elise MN Ferré
- Fungal Pathogenesis Unit, Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Nils Landegren
- Department of Medicine, Karolinska University Hospital, Karolinska InstituteStockholmSweden
- Science for life Laboratory, Department of Medical Sciences, Uppsala UniversityUppsalaSweden
| | - Daniel Eriksson
- Department of Medical Biochemistry and Microbiology, Uppsala UniversityUppsalaSweden
- Centre for Molecular Medicine, Department of Medicine, Karolinska InstitutetStockholmSweden
| | - Paul Bastard
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller UniversityNew YorkUnited States
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick ChildrenParisFrance
- Imagine Institute, University of ParisParisFrance
- Department of Pediatrics, Necker Hospital for Sick ChildrenParisFrance
| | - Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller UniversityNew YorkUnited States
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick ChildrenParisFrance
- Imagine Institute, University of ParisParisFrance
| | - Jamin Liu
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Berkeley-University of California, San Francisco Graduate Program in Bioengineering, University of California, San FranciscoSan FranciscoUnited States
| | - Anthea Mitchell
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Irina Proekt
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
| | - David Yu
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
| | - Caleigh Mandel-Brehm
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Chung-Yu Wang
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Brenda Miao
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Gavin Sowa
- School of Medicine, University of California, San FranciscoSan FranciscoUnited States
| | - Kelsey Zorn
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Alice Y Chan
- Department of Pediatrics, Division of Pediatric Allergy, Immunology, Bone and Marrow Transplantation, Division of Pediatric Rheumatology, University of California, San FranciscoSan FranciscoUnited States
| | - Veronica M Tagi
- Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
| | - Chisato Shimizu
- Kawasaki Disease Research Center, Rady Children’s Hospital and Department of Pediatrics, University of California, San DiegoLa JollaUnited States
| | - Adriana Tremoulet
- Kawasaki Disease Research Center, Rady Children’s Hospital and Department of Pediatrics, University of California, San DiegoLa JollaUnited States
| | - Kara Lynch
- Department of Laboratory Medicine, University of California, San FranciscoSan FranciscoUnited States
- Zuckerberg San Francisco GeneralSan FranciscoUnited States
| | - Michael R Wilson
- Weill Institute for Neurosciences, University of California, San FranciscoSan FranciscoUnited States
| | - Olle Kämpe
- Department of Medicine, Karolinska University Hospital, Karolinska InstituteStockholmSweden
- Department of Clinical Science and KG Jebsen Center for Autoimmune Disorders, University of BergenBergenNorway
- Center of Molecular Medicine, and Department of Endocrinology, Metabolism and Diabetes, Karolinska University HospitalStockholmSweden
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Rosa Bacchetta
- Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Jane C Burns
- Kawasaki Disease Research Center, Rady Children’s Hospital and Department of Pediatrics, University of California, San DiegoLa JollaUnited States
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller UniversityNew YorkUnited States
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick ChildrenParisFrance
- Imagine Institute, University of ParisParisFrance
- Department of Pediatrics, Necker Hospital for Sick ChildrenParisFrance
- Howard Hughes Medical InstituteNew YorkUnited States
| | - Michail S Lionakis
- Fungal Pathogenesis Unit, Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Troy R Torgerson
- Seattle Children's Research InstituteSeattleUnited States
- Department of Pediatrics, University of WashingtonSeattleUnited States
| | - Mark S Anderson
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| |
Collapse
|
8
|
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.
Collapse
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.
| |
Collapse
|
9
|
Tiu CK, Zhu F, Wang LF, de Alwis R. Phage ImmunoPrecipitation Sequencing (PhIP-Seq): The Promise of High Throughput Serology. Pathogens 2022; 11:pathogens11050568. [PMID: 35631089 PMCID: PMC9143919 DOI: 10.3390/pathogens11050568] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 11/24/2022] Open
Abstract
Simple Summary Determining the exposure or infection history of a person to a multitude of viruses is not an easy task. Typically, antibody tests detect antibodies against proteins (antigens) to only one or a few viruses. Here, we review an emerging technology called Phage ImmunoPrecipitation Sequencing (PhIP-Seq), that allows us to study the infection history of individuals to large numbers of viruses simultaneously. This technology uses bacteriophages to express and display viral antigens of choice, which are then bound by antigen-specific antibodies in patient samples. Antibody-bound bacteriophages are pulled down and identified through molecular techniques. This technology has been used in various infectious disease scenarios, including assessing exposure to different viruses, studying vaccine responses, and identifying viral cause of diseases. Despite inherent limitations in presenting only peptides, this technology holds great promise for future application in identifying novel pathogens, one health and pandemic preparedness. Abstract Phage ImmunoPrecipitation Sequencing (PhIP-Seq) is a high throughput serological technology that is revolutionizing the manner in which we track antibody profiles. In this review, we mainly focus on its application to viral infectious diseases. Through the pull-down of patient antibodies using peptide-tile-expressing T7 bacteriophages and detection using next-generation sequencing (NGS), PhIP-Seq allows the determination of antibody repertoires against peptide targets from hundreds of proteins and pathogens. It differs from conventional serological techniques in that PhIP-Seq does not require protein expression and purification. It also allows for the testing of many samples against the whole virome. PhIP-Seq has been successfully applied in many infectious disease investigations concerning seroprevalence, risk factors, time trends, etiology of disease, vaccinology, and emerging pathogens. Despite the inherent limitations of this technology, we foresee the future expansion of PhIP-Seq in both investigative studies and tracking of current, emerging, and novel viruses. Following the review of PhIP-Seq technology, its limitations, and applications, we recommend that PhIP-Seq be integrated into national surveillance programs and be used in conjunction with molecular techniques to support both One Health and pandemic preparedness efforts.
Collapse
Affiliation(s)
- Charles Kevin Tiu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (C.K.T.); (F.Z.); (L.-F.W.)
- SingHealth Duke-NUS Global Health Institute, Singapore 169857, Singapore
| | - Feng Zhu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (C.K.T.); (F.Z.); (L.-F.W.)
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (C.K.T.); (F.Z.); (L.-F.W.)
- SingHealth Duke-NUS Global Health Institute, Singapore 169857, Singapore
| | - Ruklanthi de Alwis
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (C.K.T.); (F.Z.); (L.-F.W.)
- Viral Research and Experimental Medicine Centre (ViREMiCS), SingHealth Duke-NUS Academic Medical Centre, Singapore 169856, Singapore
- Correspondence:
| |
Collapse
|
10
|
Vazquez SE, Mann SA, Bodansky A, Kung AF, Quandt Z, Ferré EMN, Landegren N, Eriksson D, Bastard P, Zhang S, Liu J, Mitchell A, Mandel-brehm C, Miao B, Sowa G, Zorn K, Chan AY, Shimizu C, Tremoulet A, Lynch K, Wilson MR, Kampe O, Dobbs K, Delmonte OM, Notarangelo LD, Burns JC, Casanova J, Lionakis MS, Torgerson TR, Anderson MS, Derisi JL. Autoantibody discovery across monogenic, acquired, and COVID19-associated autoimmunity with scalable PhIP-Seq.. [PMID: 35350199 PMCID: PMC8963698 DOI: 10.1101/2022.03.23.485509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phage Immunoprecipitation-Sequencing (PhIP-Seq) allows for unbiased, proteome-wide autoantibody discovery across a variety of disease settings, with identification of disease-specific autoantigens providing new insight into previously poorly understood forms of immune dysregulation. Despite several successful implementations of PhIP-Seq for autoantigen discovery, including our previous work (Vazquez et al. 2020), current protocols are inherently difficult to scale to accommodate large cohorts of cases and importantly, healthy controls. Here, we develop and validate a high throughput extension of PhIP-seq in various etiologies of autoimmune and inflammatory diseases, including APS1, IPEX, RAG1/2 deficiency, Kawasaki Disease (KD), Multisystem Inflammatory Syndrome in Children (MIS-C), and finally, mild and severe forms of COVID19. We demonstrate that these scaled datasets enable machine-learning approaches that result in robust prediction of disease status, as well as the ability to detect both known and novel autoantigens, such as PDYN in APS1 patients, and intestinally expressed proteins BEST4 and BTNL8 in IPEX patients. Remarkably, BEST4 antibodies were also found in 2 patients with RAG1/2 deficiency, one of whom had very early onset IBD. Scaled PhIP-Seq examination of both MIS-C and KD demonstrated rare, overlapping antigens, including CGNL1, as well as several strongly enriched putative pneumonia-associated antigens in severe COVID19, including the endosomal protein EEA1. Together, scaled PhIP-Seq provides a valuable tool for broadly assessing both rare and common autoantigen overlap between autoimmune diseases of varying origins and etiologies.
Collapse
|
11
|
Grönwall C, Malmström V. New technologies laying a foundation for next generation clinical serology. EBioMedicine 2021; 72:103585. [PMID: 34563922 PMCID: PMC8479613 DOI: 10.1016/j.ebiom.2021.103585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 09/03/2021] [Indexed: 11/25/2022] Open
Affiliation(s)
- Caroline Grönwall
- Division of Rheumatology, Department of Medicine, Karolinska University Hospital Solna, Karolinska Institutet, Stcokholm, Sweden
| | - Vivianne Malmström
- Division of Rheumatology, Department of Medicine, Karolinska University Hospital Solna, Karolinska Institutet, Stcokholm, Sweden.
| |
Collapse
|