The Principal Project will characterize B cell responses in patients with autoimmune disease by using a DNA-barcoding technology recently developed in the Robinson lab, termed 'antibody repertoire capture'(ARC). The approach couples DNA barcoding with next-generation sequencing to enable large-scale characterization of the paired heavy-chain (HC) and light-chain (LC) immunoglobulin genes expressed by single plasmablasts or antigen-specific B cells. Although methods exist for profiling antibodies, none are able to comprehensively characterize the, antibodies involved in an active immune response and to then bioinformatically identify those most likely to be functional i.e., those that either drive the disease or serve as identifiers of the key antigens that trigger pathogenic autoimmune responses. The scale of the sequencing datasets generated by ARC enables bioinformatic generation of """"""""phylogenetic trees"""""""" of the antibody repertoire. These phylogenetic trees guide identification of clonal families of affinity-matured antibodies and thereby rational selection of key antibodies, which can then be expressed for direct analysis of their binding and functional properties. We propose to use ARC to sequence and comprehensively dissect the autoantibody responses in rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), and, leveraging resources from the other ACE Projects and Cores, to test the overarching hypothesis that monoclonal autoantibodies contribute to the pathogenesis of RA and SLE by forming proinflammatory immune complexes (ICs) that dual-stimulate immune cells (by simultaneously engaging a pattern recognition receptor and either the B-cell or the Fc receptor). For instance, we hypothesize that RA-associated anti-citrullinated proteins antibodies (ACPAs) form ICs that dual-stimulate macrophages to produce TNF, and B cells to produce ACPAs;and that SLE-associated anti-nuclear antibodies (ANAs) bind nuclear antigens and thereby form ICs that dual-stimulate dendritic cells to produce IFN, and B cells to produce ANAs.
In Aim 1, we will use ARC to sequence the antibody repertoires in patients with RA or SLE and identify antibody profiles that are associated with specific clinical subtypes or response to therapy.
In Aim 2, we will clone and express rationally selected, affinity-matured antibodies from individuals with RA or SLE, and elucidate their autoantigen targets.
In Aim 3, will characterize key RA and SLE recombinant antibodies identified in Aim 2 and uncover mechanisnis by which they contribute to autoimmune inflammation. Success would provide insights into the role of autoantibodies and the mechanisms by which they contribute to the pathogenesis of RA and SLE, and could lead to development of novel diagnostic tests and therapeutic approaches.

Public Health Relevance

RA and SLE together affect over 0.5% of the U.S. population. The proposed studies will investigate the role of autoantibodies and immune complexes in mediating the pathogenesis of RA and SLE. Success of the proposed studies would provide insights into pathogenesis of RA and SLE, and could lead to development of new diagnostic and therapeutic approaches for these and other autoimmune diseases

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Program--Cooperative Agreements (U19)
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Special Emphasis Panel (ZAI1)
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Stanford University
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Bongen, Erika; Vallania, Francesco; Utz, Paul J et al. (2018) KLRD1-expressing natural killer cells predict influenza susceptibility. Genome Med 10:45
Elliott, Serra E; Kongpachith, Sarah; Lingampalli, Nithya et al. (2018) Affinity Maturation Drives Epitope Spreading and Generation of Proinflammatory Anti-Citrullinated Protein Antibodies in Rheumatoid Arthritis. Arthritis Rheumatol 70:1946-1958
Cheung, Peggie; Vallania, Francesco; Warsinske, Hayley C et al. (2018) Single-Cell Chromatin Modification Profiling Reveals Increased Epigenetic Variations with Aging. Cell 173:1385-1397.e14
Rosenberg, Jacob M; Maccari, Maria E; Barzaghi, Federica et al. (2018) Neutralizing Anti-Cytokine Autoantibodies Against Interferon-? in Immunodysregulation Polyendocrinopathy Enteropathy X-Linked. Front Immunol 9:544
Lu, Daniel R; McDavid, Andrew N; Kongpachith, Sarah et al. (2018) T Cell-Dependent Affinity Maturation and Innate Immune Pathways Differentially Drive Autoreactive B Cell Responses in Rheumatoid Arthritis. Arthritis Rheumatol 70:1732-1744
Rizzi, Giovanni; Lee, Jung-Rok; Dahl, Christina et al. (2017) Simultaneous Profiling of DNA Mutation and Methylation by Melting Analysis Using Magnetoresistive Biosensor Array. ACS Nano 11:8864-8870
Haddon, D James; Wand, Hannah E; Jarrell, Justin A et al. (2017) Proteomic Analysis of Sera from Individuals with Diffuse Cutaneous Systemic Sclerosis Reveals a Multianalyte Signature Associated with Clinical Improvement during Imatinib Mesylate Treatment. J Rheumatol 44:631-638
Degn, Søren E; van der Poel, Cees E; Firl, Daniel J et al. (2017) Clonal Evolution of Autoreactive Germinal Centers. Cell 170:913-926.e19
de Bourcy, Charles F A; Dekker, Cornelia L; Davis, Mark M et al. (2017) Dynamics of the human antibody repertoire after B cell depletion in systemic sclerosis. Sci Immunol 2:
Perkins, Tiffany; Rosenberg, Jacob M; Le Coz, Carole et al. (2017) Smith-Magenis Syndrome Patients Often Display Antibody Deficiency but Not Other Immune Pathologies. J Allergy Clin Immunol Pract 5:1344-1350.e3

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