1
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Aterido A, López-Lasanta M, Blanco F, Juan-Mas A, García-Vivar ML, Erra A, Pérez-García C, Sánchez-Fernández SÁ, Sanmartí R, Fernández-Nebro A, Alperi-López M, Tornero J, Ortiz AM, Fernández-Cid CM, Palau N, Pan W, Byrne-Steele M, Starenki D, Weber D, Rodriguez-Nunez I, Han J, Myers RM, Marsal S, Julià A. Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes. Genome Biol 2024; 25:68. [PMID: 38468286 PMCID: PMC10926600 DOI: 10.1186/s13059-024-03210-0] [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: 03/04/2022] [Accepted: 03/04/2024] [Indexed: 03/13/2024] Open
Abstract
BACKGROUND In rheumatoid arthritis (RA), the activation of T and B cell clones specific for self-antigens leads to the chronic inflammation of the synovium. Here, we perform an in-depth quantitative analysis of the seven chains that comprise the adaptive immune receptor repertoire (AIRR) in RA. RESULTS In comparison to controls, we show that RA patients have multiple and strong differences in the B cell receptor repertoire including reduced diversity as well as altered isotype, chain, and segment frequencies. We demonstrate that therapeutic tumor necrosis factor inhibition partially restores this alteration but find a profound difference in the underlying biochemical reactivities between responders and non-responders. Combining the AIRR with HLA typing, we identify the specific T cell receptor repertoire associated with disease risk variants. Integrating these features, we further develop a molecular classifier that shows the utility of the AIRR as a diagnostic tool. CONCLUSIONS Simultaneous sequencing of the seven chains of the human AIRR reveals novel features associated with the disease and clinically relevant phenotypes, including response to therapy. These findings show the unique potential of AIRR to address precision medicine in immune-related diseases.
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Affiliation(s)
- Adrià Aterido
- Rheumatology Research Group, Vall Hebron Research Institute, 08035, Barcelona, Spain
| | - María López-Lasanta
- Rheumatology Research Group, Vall Hebron Research Institute, 08035, Barcelona, Spain
| | - Francisco Blanco
- Rheumatology Department, Hospital Juan Canalejo, A Coruña, Spain
| | | | | | - Alba Erra
- Rheumatology Research Group, Vall Hebron Research Institute, 08035, Barcelona, Spain
- Rheumatology Department, Hospital Sant Rafael, Barcelona, Spain
| | | | | | - Raimon Sanmartí
- Rheumatology Department, Hospital Clínic de Barcelona and IDIBAPS, Barcelona, Spain
| | | | | | - Jesús Tornero
- Rheumatology Department, Hospital Universitario Guadalajara, Guadalajara, Spain
| | - Ana María Ortiz
- Rheumatology Department, Hospital Universitario La Princesa, IIS La Princesa, Madrid, Spain
| | | | - Núria Palau
- Rheumatology Research Group, Vall Hebron Research Institute, 08035, Barcelona, Spain
| | | | | | | | | | | | - Jian Han
- iRepertoire Inc, Huntsville, AL, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Sara Marsal
- Rheumatology Research Group, Vall Hebron Research Institute, 08035, Barcelona, Spain
| | - Antonio Julià
- Rheumatology Research Group, Vall Hebron Research Institute, 08035, Barcelona, Spain.
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2
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Mendis T, Filipova B, Wang JJ, Pietropaolo M, Jackson MW. Affinity purification of serum-derived anti-IA-2 autoantibodies in type 1 diabetes using a novel MBP-IA-2 fusion protein. Biochem Biophys Rep 2022; 33:101413. [PMID: 36578528 PMCID: PMC9791830 DOI: 10.1016/j.bbrep.2022.101413] [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: 11/30/2022] [Revised: 12/05/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Autoantibodies targeting epitopes contained within the intracellular domain (IC) of the protein phosphatase-like islet antigen 2 (IA-2) are a common marker of autoimmune type 1 diabetes (T1D), however the isolation of genuine, serum derived anti-IA-2 autoantibodies has proven challenging due to a lack of suitable bioassays. In the current study, an ELISA format was developed for affinity purification of human anti-IA-2ic autoantibodies utilizing a fusion protein (FP) incorporating maltose binding protein and the full-length IA-2IC domain. Using a T1D patient cohort validated for anti-IA-2ic autoantibodies by commercial ELISA, we demonstrate the MBP-IA-2ic FP ELISA detects serum anti-IA-2IC autoantibodies from 3 of 9 IA-2 positive patients. Further to this, a multi-plate MBP-IA-2ic FP ELISA protocol specifically affinity purifies IgG enriched for anti-IA-2ic autoantibodies. Interestingly, serum derived autoantibodies immobilised on the MBP-IA-2ic FP ELISA demonstrate increased Kappa light chain usage when compared to the respective total IgG derived from donor patients, suggesting a clonally restricted repertoire of anti-IA-2ic autoantigen specific B plasma cells is responsible for autoantibodies detect by the MBP-IA-2ic FP ELISA. This study is the first to demonstrate the generation of specific, genuine human derived anti-IA-2ic autoantibodies, thereby facilitating further investigation into the origin and functional significance of IA-2 autoantibodies in T1D.
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Affiliation(s)
- Thilini Mendis
- Department of Immunology, Allergy & Arthritis, Flinders Medical Centre and Flinders University, Bedford Park, 5042, South Australia, Australia
| | - Barbora Filipova
- Department of Immunology, Allergy & Arthritis, Flinders Medical Centre and Flinders University, Bedford Park, 5042, South Australia, Australia
| | - Jing Jing Wang
- Department of Immunology, Allergy & Arthritis, Flinders Medical Centre and Flinders University, Bedford Park, 5042, South Australia, Australia
| | - Massimo Pietropaolo
- Dept of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Michael W. Jackson
- Department of Immunology, Allergy & Arthritis, Flinders Medical Centre and Flinders University, Bedford Park, 5042, South Australia, Australia,Corresponding author. Department of Immunology, Allergy and Arthritis, Flinders University, GPO Box 2100, Adelaide, South Australia, 5001, Australia.
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3
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Jaffe DB, Shahi P, Adams BA, Chrisman AM, Finnegan PM, Raman N, Royall AE, Tsai F, Vollbrecht T, Reyes DS, Hepler NL, McDonnell WJ. Functional antibodies exhibit light chain coherence. Nature 2022; 611:352-357. [PMID: 36289331 PMCID: PMC9607724 DOI: 10.1038/s41586-022-05371-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 09/21/2022] [Indexed: 11/08/2022]
Abstract
The vertebrate adaptive immune system modifies the genome of individual B cells to encode antibodies that bind particular antigens1. In most mammals, antibodies are composed of heavy and light chains that are generated sequentially by recombination of V, D (for heavy chains), J and C gene segments. Each chain contains three complementarity-determining regions (CDR1-CDR3), which contribute to antigen specificity. Certain heavy and light chains are preferred for particular antigens2-22. Here we consider pairs of B cells that share the same heavy chain V gene and CDRH3 amino acid sequence and were isolated from different donors, also known as public clonotypes23,24. We show that for naive antibodies (those not yet adapted to antigens), the probability that they use the same light chain V gene is around 10%, whereas for memory (functional) antibodies, it is around 80%, even if only one cell per clonotype is used. This property of functional antibodies is a phenomenon that we call light chain coherence. We also observe this phenomenon when similar heavy chains recur within a donor. Thus, although naive antibodies seem to recur by chance, the recurrence of functional antibodies reveals surprising constraint and determinism in the processes of V(D)J recombination and immune selection. For most functional antibodies, the heavy chain determines the light chain.
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4
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Reed JH. Transforming mutations in the development of pathogenic B cell clones and autoantibodies. Immunol Rev 2022; 307:101-115. [PMID: 35001403 DOI: 10.1111/imr.13064] [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: 12/06/2021] [Revised: 12/31/2021] [Accepted: 01/01/2022] [Indexed: 12/16/2022]
Abstract
Autoimmune diseases are characterized by serum autoantibodies, some of which are pathogenic, causing severe manifestations and organ injury. However, autoantibodies of the same antigenic reactivity are also present in the serum of asymptomatic people years before they develop any clinical signs of autoimmunity. Autoantibodies can arise during multiple stages of B cell development, and various genetic and environmental factors drive their production. However, what drives the development of pathogenic autoantibodies is poorly understood. Advances in single-cell technology have enabled the deep analysis of rare B cell clones producing pathogenic autoantibodies responsible for vasculitis in patients with primary Sjögren's syndrome complicated by mixed cryoglobulinaemia. These findings demonstrated a cascade of genetic events involving stereotypic immunoglobulin V(D)J recombination and transforming somatic mutations in lymphoma genes and V(D)J regions that disrupted antibody quality control mechanisms and decreased autoantibody solubility. Most studies consider V(D)J mutations that enhance autoantibody affinity to drive pathology; however, V(D)J mutations that increase autoantibody propensity to form insoluble complexes could be a major contributor to autoantibody pathogenicity. Defining the molecular characteristics of pathogenic autoantibodies and failed tolerance checkpoints driving their formation will improve prognostication, enabling early treatment to prevent escalating organ damage and B cell malignancy.
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Affiliation(s)
- Joanne H Reed
- Westmead Institute for Medical Research, Centre for Immunology and Allergy Research, Westmead, NSW, Australia.,Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
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5
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Adamson PJ, Wang JJ, Anosova NG, Colella AD, Chataway TK, Kleanthous H, Gordon TP, Gordon DL. Proteomic profiling of precipitated Clostridioides difficile toxin A and B antibodies. Vaccine 2019; 38:2077-2087. [PMID: 31718902 DOI: 10.1016/j.vaccine.2019.10.096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/24/2019] [Accepted: 10/29/2019] [Indexed: 01/01/2023]
Abstract
Clostridioides difficile infection is the leading cause of nosocomial diarrhoea globally. Immune responses to toxins produced by C. difficile are important in disease progression and outcome. Here, we analysed the anti-toxin A and anti-toxin B serum antibody proteomes following natural infection or vaccination with a C. difficile toxoid A/toxoid B vaccine using a modified miniaturised proteomic approach based on de novo mass spectrometric sequencing. Analysis of immunoglobulin variable region (IgV) subfamily expression in immunoprecipitated toxin A and toxin B antibodies from four and seven participants of a vaccine trial, respectively, revealed a polyclonal proteome with restricted IGHV, IGKV and IGLV subfamily usage. No dominant IGHV subfamily was observed in the toxin A response, however the dominant anti-toxin B heavy (H)-chain was encoded by IGHV3-23. Light (L)-chain usage was convergent for both anti-toxin A and anti-toxin B proteomes with IGKV3-11, 3-15, 3-20 and 4-1 shared among all subjects in both cohorts. Peptide mapping of common IgV families showed extensive public and private amino acid substitutions. The cohort responses to toxin A and toxin B showed limited similarity in shared IGHV subfamilies. L-chain subfamily usage was more similar in the anti-toxin A and anti-toxin B responses, however the mutational signatures for each subfamily were toxin-dependent. Samples taken both post vaccination (n = 5) or at baseline, indicating previous exposure (n = 2), showed similar anti-toxin B IgV subfamily usage and mutational profiles. In summary, this study provides the first sequence-based proteomic analysis of the antibody response to the major disease-mediating toxins of C. difficile, toxin A and toxin B, and demonstrates that despite the potential for extreme diversity, the immunoglobulin repertoire can raise convergent responses to specific pathogens whether through natural infection or following vaccination.
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Affiliation(s)
- Penelope J Adamson
- Department of Microbiology and Infectious Diseases, Flinders University and SA Pathology, Flinders Medical Centre, Bedford Park, SA 5042, Australia.
| | - Jing J Wang
- Department of Immunology, Flinders University and SA Pathology, Flinders Medical Centre, Bedford Park, SA 5042, Australia.
| | | | - Alex D Colella
- Flinders Proteomic Facility, Flinders University, Flinders Medical Centre, Bedford Park, SA 5042, Australia.
| | - Timothy K Chataway
- Flinders Proteomic Facility, Flinders University, Flinders Medical Centre, Bedford Park, SA 5042, Australia.
| | | | - Tom P Gordon
- Department of Immunology, Flinders University and SA Pathology, Flinders Medical Centre, Bedford Park, SA 5042, Australia.
| | - David L Gordon
- Department of Microbiology and Infectious Diseases, Flinders University and SA Pathology, Flinders Medical Centre, Bedford Park, SA 5042, Australia.
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6
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Chang YT, Chang MC, Tsai YJ, Ferng C, Shih HC, Kuo YP, Chen CH, Tsai IL. Method development of immunoglobulin G purification from micro-volumes of human serum for untargeted and targeted proteomics-based antibody repertoire studies. J Food Drug Anal 2019; 27:475-482. [PMID: 30987718 PMCID: PMC9296204 DOI: 10.1016/j.jfda.2018.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 10/05/2018] [Accepted: 10/08/2018] [Indexed: 11/20/2022] Open
Abstract
Immunoglobulins (Igs) are major serum proteins which play important roles in immunity. Both untargeted and targeted proteomic workflows can be applied to investigate antigen-binding sites and the glycosylation profiles of Igs. For a more-comprehensive picture of IgG from human serum, we developed an IgG purification process and coupled the standardized method to untargeted and targeted proteomic workflows for IgG investigations. Parameters such as the type of purification beads, volume of the bead slurry, incubation conditions, and binding capacities were evaluated in this study. Only 2 μL of human serum was required for each sample. The performance of coupling the purification process to untargeted proteomics in the IgG analysis was evaluated by comparing normalized abundances of IgG subclass-specific peptides with quantification results from an ELISA. Pearson’s correlation values were all >0.82. Targeted proteomic workflow was applied to serum samples from patients with autoimmune pancreatitis and from healthy controls, and the results corresponded to clinical findings that IgG4-related peptides/glycopeptides showed higher abundances in the diseased group. The developed IgG purification process is simple and requires small sample volume, and it can be coupled to targeted and untargeted proteomic workflows for clinical investigations in the future.
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Affiliation(s)
- Yu-Ting Chang
- Department of Internal Medicine, National Taiwan University Hospital,
Taiwan
- Department of Internal Medicine, College of Medicine, National Taiwan University,
Taiwan
| | - Ming-Chu Chang
- Department of Internal Medicine, National Taiwan University Hospital,
Taiwan
- Department of Internal Medicine, College of Medicine, National Taiwan University,
Taiwan
| | - Yun-Jung Tsai
- School of Pharmacy, Taipei Medical University,
Taiwan
| | | | | | - Ya-Po Kuo
- Genomics Research Center, Academia Sinica,
Taiwan
| | | | - I-Lin Tsai
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University,
Taiwan
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University,
Taiwan
- Corresponding author. Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, 250 Wuxing Street, Taipei, 11031, Taiwan., E-mail address: (I.-L. Tsai)
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7
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Abdulwahab RA, Alaiya A, Shinwari Z, Allaith AAA, Giha HA. LC‑MS/MS proteomic analysis revealed novel associations of 37 proteins with T2DM and notable upregulation of immunoglobulins. Int J Mol Med 2019; 43:2118-2132. [PMID: 30864687 PMCID: PMC6443330 DOI: 10.3892/ijmm.2019.4127] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/04/2019] [Indexed: 12/29/2022] Open
Abstract
Type 2 diabetes mellitus (T2DM) is a disease associated with a number of metabolic disturbances, including protein metabolism. In the present study, blood samples were obtained from Bahraini subjects, including 6 patients with T2DM and 6 age‑ and sex‑matched, non‑diabetic, healthy controls. Depleted and non‑depleted sera were prepared from the collected blood, and the global protein expression changes were evaluated by liquid chromatography tandem mass spectrometry. Only significantly and markedly differentially‑expressed proteins (P<0.05, analysis of variance; maximum fold change ≥1.5) were considered as candidate proteins for informatics analysis. Accordingly, a total of 62 proteins were identified to be differentially expressed in T2DM, compared with control subjects, and they were grouped functionally into 16 classes of proteins. The largest class was that of the immune‑associated proteins. Additionally, ~25 of these proteins (40%) had previously been associated with DM; however, the association of the other 37 proteins with T2DM was a novel observation. The majority of the identified proteins were upregulated in T2DM. The identified proteins could be involved in the pathogenesis of the disease or serve as disease biomarkers. Further validation of the identified proteins in a large study cohort is required, in order to fully access their potential clinical usefulness.
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Affiliation(s)
- Rabab Asghar Abdulwahab
- Integrated Science Division, College of Health Sciences, University of Bahrain, Manama 32038, Kingdom of Bahrain
| | - Ayodele Alaiya
- Proteomics Unit, Stem Cell and Tissue Re‑Engineering Program, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Zakia Shinwari
- Proteomics Unit, Stem Cell and Tissue Re‑Engineering Program, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Abdul Ameer A Allaith
- Department of Biology College of Science, University of Bahrain, Zallaq 32038, Kingdom of Bahrain
| | - Hayder A Giha
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama 26671, Kingdom of Bahrain
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8
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Wang Z, Liu X, Muther J, James JA, Smith K, Wu S. Top-down Mass Spectrometry Analysis of Human Serum Autoantibody Antigen-Binding Fragments. Sci Rep 2019; 9:2345. [PMID: 30787393 PMCID: PMC6382847 DOI: 10.1038/s41598-018-38380-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/18/2018] [Indexed: 12/26/2022] Open
Abstract
Detecting autoimmune diseases at an early stage is crucial for effective treatment and disease management to slow disease progression and prevent irreversible organ damage. In many autoimmune diseases, disease-specific autoantibodies are produced by B cells in response to soluble autoantigens due to defects in B cell tolerance mechanisms. Autoantibodies accrue early in disease development, and several are so disease-specific they serve as classification criteria. In this study, we established a high-throughput, sensitive, intact serum autoantibody analysis platform based on the optimization of a one dimensional ultra-high-pressure liquid chromatography top-down mass spectrometry platform (1D UPLC-TDMS). This approach has been successfully applied to a 12 standard monoclonal antibody antigen-binding fragment (Fab) mixture, demonstrating the feasibility to separate and sequence intact antibodies with high sequence coverage and high sensitivity. We then applied the optimized platform to characterize total serum antibody Fabs in a systemic lupus erythematosus (SLE) patient sample and compared it to healthy control samples. From this analysis, we show that the SLE sample has many dominant antibody Fab-related mass features unlike the healthy controls. To our knowledge, this is the first top-down demonstration of serum autoantibody pool analysis. Our proposed approach holds great promise for discovering novel serum autoantibody biomarkers that are of interest for diagnosis, prognosis, and tolerance induction, as well as improving our understanding of pathogenic autoimmune processes.
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Affiliation(s)
- Zhe Wang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Xiaowen Liu
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Jennifer Muther
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Judith A James
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
- Departments of Medicine and Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Kenneth Smith
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA.
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA.
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9
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Wang JJ, Colella AD, Beroukas D, Chataway TK, Gordon TP. Precipitating anti-dsDNA peptide repertoires in lupus. Clin Exp Immunol 2018; 194:273-282. [PMID: 30086185 DOI: 10.1111/cei.13197] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2018] [Indexed: 12/15/2022] Open
Abstract
Anti-double-stranded (ds)DNA autoantibodies are prototypical serological markers of systemic lupus erythematosus (SLE), but little is known about their immunoglobulin variable (IgV) region composition at the level of the secreted (serum) proteome. Here, we use a novel proteomic workflow based on de novo mass spectrometric sequencing of anti-dsDNA precipitins to analyse IgV subfamily expression and mutational signatures of high-affinity, precipitating anti-dsDNA responses. Serum anti-dsDNA proteomes were oligoclonal with shared (public) expression of immunoglobulin (Ig)G heavy chain variable region (IGHV) and kappa chain variable region (IGKV) subfamilies. IgV peptide maps from eight subjects showed extensive public and random (private) amino acid replacement mutations with prominent arginine substitutions across heavy (H)- and light (L)-chains. Shared sets of L-chain complementarity determining region 3 (CDR3) peptides specified by arginine substitutions were sequenced from the dominantly expressed IGKV3-20 subfamily, with changes in expression levels of a clonal L-chain CDR3 peptide by quantitative multiple reaction monitoring (MRM) paralleling the rise and fall of anti-dsDNA levels by Farr radioimmunoassays (RIA). The heavily mutated IgV peptide signatures of precipitating anti-dsDNA autoantibody proteomes reflect the strong selective forces that shape humoral anti-dsDNA responses in germinal centres. Direct sequencing of agarose gel precipitins using microlitre volumes of stored sera streamlines the antibody sequencing workflow and is generalizable to other precipitating serum antibodies.
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Affiliation(s)
- J J Wang
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park, SA, Australia
| | - A D Colella
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park, SA, Australia
| | - D Beroukas
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park, SA, Australia
| | - T K Chataway
- Flinders Proteomics Facility, Flinders University, Bedford Park, SA, Australia
| | - T P Gordon
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park, SA, Australia
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10
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Wang JJ, Reed JH, Colella AD, Russell AJ, Murray-Brown W, Chataway TK, Jackson KJL, Goodnow CC, Gordon TP. Molecular Profiling and Clonal Tracking of Secreted Rheumatoid Factors in Primary Sjögren's Syndrome. Arthritis Rheumatol 2018; 70:1617-1625. [PMID: 29697211 DOI: 10.1002/art.40539] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 04/19/2018] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Rheumatoid factors (RFs) are associated with systemic disease in primary Sjögren's syndrome (SS) and may be pathogenic as mixed cryoglobulins. Current detection methods cannot resolve RFs at a molecular level. This study was undertaken to perform the first proteomic and transcriptomic analysis of secreted and membrane-bound IgM-RF in primary SS and identify unique heavy-chain peptide signatures for RF clonotype tracking. METHODS Purified heavy chains of serum RFs from 15 patients with primary SS were subjected to de novo mass spectrometric sequencing. The circulating B cell Ig repertoire was determined by massively parallel sequencing of IGH RNA from matched peripheral blood mononuclear cells (n = 7). RF-specific heavy-chain third complementarity-determining region (CDR3) peptides were identified by searching RF heavy-chain peptide sequences against the corresponding IGH RNA sequence libraries. Heavy-chain CDR3 peptides were used as biomarkers to track serum RF clonotypes using quantitative multiple reaction monitoring. RESULTS Serum RFs were clonally restricted and composed of shared sets of IgM heavy-chain variable region (Ig VH ) 1-69, 3-15, 3-7, and 3-74 subfamilies. Cryoprecipitable RFs from patients with mixed cryoglobulinemia (MC) were distinguishable from nonprecipitating RFs by a higher frequency of amino acid substitutions and identification of stereotypic heavy-chain CDR3 transcripts. Potentially pathogenic RF clonotypes were detected in serum by multiple reaction monitoring years before patients presented with MC. Levels of Ig VH 4-34 IgM-RF decreased following immunosuppression and remission of MC. CONCLUSION Cryoprecipitable RF clonotypes linked to vasculitis in primary SS have different molecular profiles than nonprecipitating RFs, suggesting different underlying mechanisms of production. The combined omics workflow presented herein provides molecular biomarkers for tracking and removal of pathogenic RF clones.
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Affiliation(s)
- Jing J Wang
- Flinders University and SA Pathology, Bedford Park, South Australia, Australia
| | - Joanne H Reed
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Alex D Colella
- Flinders University and SA Pathology, Bedford Park, South Australia, Australia
| | - Amanda J Russell
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | | | - Tim K Chataway
- Flinders University, Bedford Park, South Australia, Australia
| | | | | | - Tom P Gordon
- Flinders University and SA Pathology, Bedford Park, South Australia, Australia
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11
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Adamson PJ, Al Kindi MA, Wang JJ, Colella AD, Chataway TK, Petrovsky N, Gordon TP, Gordon DL. Proteomic analysis of influenza haemagglutinin-specific antibodies following vaccination reveals convergent immunoglobulin variable region signatures. Vaccine 2017; 35:5576-5580. [PMID: 28888340 DOI: 10.1016/j.vaccine.2017.08.053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 08/02/2017] [Accepted: 08/27/2017] [Indexed: 10/18/2022]
Abstract
Analysis of the anti-haemagglutinin serum antibody proteome from six H1N1pdm09 influenza A vaccinated subjects demonstrated restricted IgG1 heavy chain species encoded by IGHV5-51 and IGHV3-7 gene families in 2 subjects and either IGHV5-51 or IGHV3-7 in 4 individuals. All subjects exhibited a dominant IGKV3-20 light chain, however 5 subjects also exhibited IGKV3-11 and IGKV4-1 families. Sequences were closely aligned with the matched germline sequence, with few shared mutations. This study illustrates the feasibility of using a proteomic approach to determine the expressed V region signatures of serum antibodies induced by vaccination.
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Affiliation(s)
- Penelope J Adamson
- Department of Microbiology and Infectious Diseases, Flinders University and SA Pathology, Flinders Medical Centre, Bedford Park, SA 5042, Australia.
| | - Mahmood A Al Kindi
- Department of Immunology, Flinders University and SA Pathology, Flinders Medical Centre, Bedford Park, SA 5042, Australia.
| | - Jing J Wang
- Department of Immunology, Flinders University and SA Pathology, Flinders Medical Centre, Bedford Park, SA 5042, Australia.
| | - Alex D Colella
- Flinders Proteomic Facility, Flinders University, Flinders Medical Centre, Bedford Park, SA 5042, Australia.
| | - Timothy K Chataway
- Flinders Proteomic Facility, Flinders University, Flinders Medical Centre, Bedford Park, SA 5042, Australia.
| | - Nikolai Petrovsky
- Department of Endocrinology, Flinders University and Vaxine Pty Ltd., Flinders Medical Centre, Bedford Park, SA 5042, Australia.
| | - Tom P Gordon
- Department of Immunology, Flinders University and SA Pathology, Flinders Medical Centre, Bedford Park, SA 5042, Australia.
| | - David L Gordon
- Department of Microbiology and Infectious Diseases, Flinders University and SA Pathology, Flinders Medical Centre, Bedford Park, SA 5042, Australia.
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Wang JJ, Al Kindi MA, Colella AD, Dykes L, Jackson MW, Chataway TK, Reed JH, Gordon TP. IgV peptide mapping of native Ro60 autoantibody proteomes in primary Sjögren's syndrome reveals molecular markers of Ro/La diversification. Clin Immunol 2016; 173:57-63. [PMID: 27609500 DOI: 10.1016/j.clim.2016.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 08/18/2016] [Accepted: 09/01/2016] [Indexed: 01/25/2023]
Abstract
We have used high-resolution mass spectrometry to sequence precipitating anti-Ro60 proteomes from sera of patients with primary Sjögren's syndrome and compare immunoglobulin variable-region (IgV) peptide signatures in Ro/La autoantibody subsets. Anti-Ro60 were purified by elution from native Ro60-coated ELISA plates and subjected to combined de novo amino acid sequencing and database matching. Monospecific anti-Ro60 Igs comprised dominant public and minor private sets of IgG1 kappa and lambda restricted heavy and light chains. Specific IgV amino acid substitutions stratified anti-Ro60 from anti-Ro60/La responses, providing a molecular fingerprint of Ro60/La determinant spreading and suggesting that different forms of Ro60 antigen drive these responses. Sequencing of linked anti-Ro52 proteomes from individual patients and comparison with their anti-Ro60 partners revealed sharing of a dominant IGHV3-23/IGKV3-20 paired clonotype but with divergent IgV mutational signatures. In summary, anti-Ro60 IgV peptide mapping provides insights into Ro/La autoantibody diversification and reveals serum-based molecular markers of humoral Ro60 autoimmunity.
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Affiliation(s)
- Jing J Wang
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park 5042, South Australia, Australia
| | - Mahmood A Al Kindi
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park 5042, South Australia, Australia; Department of Microbiology and Immunology, Sultan Qaboos University Hospital, Muscat 123, Oman
| | - Alex D Colella
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park 5042, South Australia, Australia; Flinders Proteomics Facility, Flinders University, Bedford Park 5042, South Australia, Australia
| | - Lukah Dykes
- Flinders Proteomics Facility, Flinders University, Bedford Park 5042, South Australia, Australia
| | - Michael W Jackson
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park 5042, South Australia, Australia
| | - Tim K Chataway
- Flinders Proteomics Facility, Flinders University, Bedford Park 5042, South Australia, Australia
| | - Joanne H Reed
- Garvan Institute of Medical Research, Immunology Division, Immunogenomics Laboratory, 384 Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Tom P Gordon
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park 5042, South Australia, Australia.
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13
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Tao B, Bernardo K, Eldi P, Chegeni N, Wiese M, Colella A, Kral A, Hayball J, Smith W, Forsyth K, Chataway T. Extended boiling of peanut progressively reduces IgE allergenicity while retaining T cell reactivity. Clin Exp Allergy 2016; 46:1004-14. [DOI: 10.1111/cea.12740] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/09/2016] [Accepted: 03/31/2016] [Indexed: 11/30/2022]
Affiliation(s)
- B. Tao
- Department of Paediatrics and Child Health; Flinders University of South Australia; Adelaide SA Australia
- Flinders Proteomics Facility; Department of Human Physiology; Flinders University of South Australia; Adelaide SA Australia
| | - K. Bernardo
- Flinders Proteomics Facility; Department of Human Physiology; Flinders University of South Australia; Adelaide SA Australia
| | - P. Eldi
- School of Pharmacy and Medical Sciences; University of South Australia; Adelaide SA Australia
| | - N. Chegeni
- Flinders Proteomics Facility; Department of Human Physiology; Flinders University of South Australia; Adelaide SA Australia
| | - M. Wiese
- School of Pharmacy and Medical Sciences; University of South Australia; Adelaide SA Australia
| | - A. Colella
- Department of Immunology; Flinders University of South Australia; Adelaide SA Australia
| | - A. Kral
- Department and School of Medicine; University of Adelaide; Adelaide SA Australia
| | - J. Hayball
- School of Pharmacy and Medical Sciences; University of South Australia; Adelaide SA Australia
| | - W. Smith
- Department and School of Medicine; University of Adelaide; Adelaide SA Australia
| | - K. Forsyth
- Department of Paediatrics and Child Health; Flinders University of South Australia; Adelaide SA Australia
| | - T. Chataway
- Flinders Proteomics Facility; Department of Human Physiology; Flinders University of South Australia; Adelaide SA Australia
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Al Kindi MA, Colella AD, Beroukas D, Chataway TK, Gordon TP. Lupus anti-ribosomal P autoantibody proteomes express convergent biclonal signatures. Clin Exp Immunol 2016; 184:29-35. [PMID: 26646815 PMCID: PMC4778099 DOI: 10.1111/cei.12750] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2015] [Indexed: 11/30/2022] Open
Abstract
Lupus-specific anti-ribosomal P (anti-Rib-P) autoantibodies have been implicated in the pathogenesis of neurological complications in systemic lupus erythematosus (SLE). The aim of the present study was to determine variable (V)-region signatures of secreted autoantibody proteomes specific for the Rib-P heterocomplex and investigate the molecular basis of the reported cross-reactivity with Sm autoantigen. Anti-Rib-P immunoglobulins (IgGs) were purified from six anti-Rib-P-positive sera by elution from enzyme-linked immunosorbent assay (ELISA) plates coated with either native Rib-P proteins or an 11-amino acid peptide (11-C peptide) representing the conserved COOH-terminal P epitope. Rib-P- and 11-C peptide-specific IgGs were analysed for heavy (H) and light (L) chain clonality and V-region expression using an electrophoretic and de-novo and database-driven mass spectrometric sequencing workflow. Purified anti-Rib-P and anti-SmD IgGs were tested for cross-reactivity on ELISA and their proteome data sets analysed for shared clonotypes. Anti-Rib-P autoantibody proteomes were IgG1 kappa-restricted and comprised two public clonotypes defined by unique H/L chain pairings. The major clonotypic population was specific for the common COOH-terminal epitope, while the second shared the same pairing signature as a recently reported anti-SmD clonotype, accounting for two-way immunoassay cross-reactivity between these lupus autoantibodies. Sequence convergence of anti-Rib-P proteomes suggests common molecular pathways of autoantibody production and identifies stereotyped clonal populations that are thought to play a pathogenic role in neuropsychiatric lupus. Shared clonotypic structures for anti-Rib-P and anti-Sm responses suggest a common B cell clonal origin for subsets of these lupus-specific autoantibodies.
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Affiliation(s)
- M A Al Kindi
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology
| | - A D Colella
- Flinders Proteomic Facility, Flinders University, SA, Australia
| | - D Beroukas
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology
| | - T K Chataway
- Flinders Proteomic Facility, Flinders University, SA, Australia
| | - T P Gordon
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology
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15
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Al Kindi MA, Colella AD, Chataway TK, Jackson MW, Wang JJ, Gordon TP. Secreted autoantibody repertoires in Sjögren's syndrome and systemic lupus erythematosus: A proteomic approach. Autoimmun Rev 2016; 15:405-10. [PMID: 26804757 DOI: 10.1016/j.autrev.2016.01.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 01/13/2016] [Indexed: 12/18/2022]
Abstract
The structures of epitopes bound by autoantibodies against RNA-protein complexes have been well-defined over several decades, but little is known of the clonality, immunoglobulin (Ig) variable (V) gene usage and mutational status of the autoantibodies themselves at the level of the secreted (serum) proteome. A novel proteomic workflow is presented based on affinity purification of specific Igs from serum, high-resolution two-dimensional gel electrophoresis, and de novo and database-driven sequencing of V-region proteins by mass spectrometry. Analysis of anti-Ro52/Ro60/La proteomes in primary Sjögren's syndrome (SS) and anti-Sm and anti-ribosomal P proteomes in systemic lupus erythematosus (SLE) has revealed that these antibody responses are dominated by restricted sets of public (shared) clonotypes, consistent with common pathways of production across unrelated individuals. The discovery of shared sets of specific V-region peptides can be exploited for diagnostic biomarkers in targeted mass spectrometry platforms and for tracking and removal of pathogenic clones.
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Affiliation(s)
- Mahmood A Al Kindi
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park, 5042, South Australia, Australia
| | - Alex D Colella
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park, 5042, South Australia, Australia; Flinders Proteomic Facility, Flinders University, Australia
| | - Tim K Chataway
- Flinders Proteomic Facility, Flinders University, Australia
| | - Michael W Jackson
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park, 5042, South Australia, Australia
| | - Jing J Wang
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park, 5042, South Australia, Australia.
| | - Tom P Gordon
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park, 5042, South Australia, Australia.
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Barnidge DR, Lundström SL, Zhang B, Dasari S, Murray DL, Zubarev RA. Subset of Kappa and Lambda Germline Sequences Result in Light Chains with a Higher Molecular Mass Phenotype. J Proteome Res 2015; 14:5283-90. [DOI: 10.1021/acs.jproteome.5b00711] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Susanna L. Lundström
- Department of Medical Biochemistry & Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Bo Zhang
- Department of Medical Biochemistry & Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Roman A. Zubarev
- Department of Medical Biochemistry & Biophysics, Karolinska Institutet, Stockholm, Sweden
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