An Autoantigen-ome from HS-Sultan B-Lymphoblasts Offers a Molecular Map for Investigating Autoimmune Sequelae of COVID-19

Abstract

To understand how COVID-19 may induce autoimmune diseases, we have been compiling an atlas of COVID-autoantigens (autoAgs). Using dermatan sulfate (DS) affinity enrichment of autoantigenic proteins extracted from HS-Sultan lymphoblasts, we identified 362 DS-affinity proteins, of which at least 201 (56%) are confirmed autoAgs. Comparison with available multi-omic COVID data shows that 315 (87%) of the 362 proteins are affected in SARS-CoV-2 infection via altered expression, interaction with viral components, or modification by phosphorylation or ubiquitination, at least 186 (59%) of which are known autoAgs. These proteins are associated with gene expression, mRNA processing, mRNA splicing, translation, protein folding, vesicles, and chromosome organization. Numerous nuclear autoAgs were identified, including both classical ANAs and ENAs of systemic autoimmune diseases and unique autoAgs involved in the DNA replication fork, mitotic cell cycle, or telomerase maintenance. We also identified many uncommon autoAgs involved in nucleic acid and peptide biosynthesis and nucleocytoplasmic transport, such as aminoacyl-tRNA synthetases. In addition, this study found autoAgs that potentially interact with multiple SARS-CoV-2 Nsp and Orf components, including CCT/TriC chaperonin, insulin degrading enzyme, platelet-activating factor acetylhydrolase, and the ezrin-moesin-radixin family. Furthermore, B-cell-specific IgM-associated ER complex (including MBZ1, BiP, heat shock proteins, and protein disulfide-isomerases) is enriched by DS-affinity and up-regulated in B-cells of COVID-19 patients, and a similar IgH-associated ER complex was also identified in autoreactive pre-B1 cells in our previous study, which suggests a role of autoreactive B1 cells in COVID-19 that merits further investigation. In summary, this study demonstrates that virally infected cells are characterized by alterations of proteins with propensity to become autoAgs, thereby providing a possible explanation for infection-induced autoimmunity. The COVID autoantigen-ome provides a valuable molecular resource and map for investigation of COVID-related autoimmune sequelae and considerations for vaccine design.

Dermatan Sulfate Is a Potential Regulator of IgH via Interactions With Pre-BCR, GTF2I, and BiP ER Complex in Pre-B Lymphoblasts

“…Based on these findings and our previous studies ( 1 – 9 ), we propose an (DS•autoAg)-autoBCR dual-signal model for initiating autoreactive B1 cell activation ( Figure 6 ): (i) DS and autoAgs from dying cells form non-covalent autoAg•DS complexes; (ii) upon encountering autoreactive B cells, an autoAg engages an autoBCR and binds to part of the variable domain (e.g., CDR1 and CDR2); (iii) because of its complexation with the autoAg, DS is brought into close contact with the autoBCR and binds to the IgH portion of the autoBCR (e.g., CDR3); (iv) (DS•autoAg)-autoBCR complexes internalize, and DS/IgH complexes accumulate in the ER where they may recruit IgH-associated protein processing complexes to facilitate folding and assembly of newly synthesized Ig; (v) somewhere along the way, DS binds GTF2I and transports it to nucleus, and in the nucleus, GTF2I upregulates transcription of the IgH locus and other gene targets. In summary, the intricate interactions of DS with Ig-associated complex in the ER and GTF2I may provide a positive feedback loop to upregulate IgH at gene and protein levels.…”

“…We then tested clinical autoantibody standard sera and sera from patients with autoimmune diseases such as lupus and Sjögren syndrome and demonstrated that DS affinity enabled the identification of many more autoAgs than current clinical tests are able to (2). Based on our DS•autoAg affinity hypothesis, we have thus far identified over 200 potential protein autoAgs from cells lines and murine liver and kidney tissues (2,(4)(5)(6) and autoAgs related to autoimmunity in COVID-19 (7)(8)(9).…”

A Master Autoantigen-ome Links Alternative Splicing, Female Predilection, and COVID-19 to Autoimmune Diseases

“…Potential autoAgs were identified by DS-affinity from protein extracts from six human cell lines as previously described, including HFL1 fetal lung fibroblasts [1], A549 lung epithelial cells [2], HS-Sultan B-lymphoblasts [4], Wil2-NS B-lymphoblasts [7], Jurkat T-lymphoblasts [5], and HEp-2 fibroblasts [11].…”

“…To gain a better understanding of autoimmune sequelae due to COVID-19, we present a master autoantigen atlas of over 750 potential autoAgs identified from six human cell types [1, 2, 4, 5, 7, 11]. These autoAgs show significant correlation with pathways and processes that are crucial in viral infection and mRNA vaccine action, reveal common autoAgs associated with apoptosis and cell stress which may serve as markers for systemic autoimmune diseases, and provide a detailed molecular map for understanding and for investigating diverse autoimmune sequalae of COVID-19 and potential rare side-effects to viral vector- and mRNA-based vaccines.…”

An Autoantigen Profile from Jurkat T-Lymphoblasts Provides a Molecular Guide for Investigating Autoimmune Sequelae of COVID-19

“…DS and autoAgs can form affinity complexes and cooperatively stimulate autoreactive B1 cells and autoantibody production [5, 7, 8]. Based on autoAg-DS affinity, we have identified several hundred autoAgs from various cells and tissues [1–3, 9–11].…”