AAgAtlas 1.0: a human autoantigen database

Abstract

Autoantibodies refer to antibodies that target self-antigens, which can play pivotal roles in maintaining homeostasis, distinguishing normal from tumor tissue and trigger autoimmune diseases. In the last three decades, tremendous efforts have been devoted to elucidate the generation, evolution and functions of autoantibodies, as well as their target autoantigens. However, reports of these countless previously identified autoantigens are randomly dispersed in the literature. Here, we constructed an AAgAtlas database 1.0 using text-mining and manual curation. We extracted 45 830 autoantigen-related abstracts and 94 313 sentences from PubMed using the keywords of either ‘autoantigen’ or ‘autoantibody’ or their lexical variants, which were further refined to 25 520 abstracts, 43 253 sentences and 3984 candidates by our bio-entity recognizer based on the Protein Ontology. Finally, we identified 1126 genes as human autoantigens and 1071 related human diseases, with which we constructed a human autoantigen database (AAgAtlas database 1.0). The database provides a user-friendly interface to conveniently browse, retrieve and download human autoantigens as well as their associated diseases. The database is freely accessible at http://biokb.ncpsb.org/aagatlas/. We believe this database will be a valuable resource to track and understand human autoantigens as well as to investigate their functions in basic and translational research.

“Degradation of the extracellular matrix is part of the pathology of ulcerative colitis”

“…These autoantibodies against NET components have been suggested as possible explanations for the breakdown of tolerance to NET autoantigens, such as hypercitrullination. Of the NETs granule proteins identified in our study, LTF, MPO, and PRTN3 have been associated with autoantibody formation in relation to IBD and ECM-related processes (72). The release of active PAD2 and PAD4 isoforms into synovial fluid by neutrophil cell death is a plausible explanation for the generation of extracellular autoantigens in RA (73).…”

Degradation of the extracellular matrix is part of the pathology of ulcerative colitis

“…Of the NETs granule proteins identified in this study, LTF, MPO, and PRTN3 have been associated with autoantibody formation in relation to IBD and ECM-related processes. 74 The release of active PAD2 and PAD4 isoforms into synovial fluid by neutrophil cell death is a plausible explanation for the generation of extracellular autoantigens in RA. 75 The inhibition of PADs by either small molecule drugs or biologics has been This journal is © The Royal Society of Chemistry 2019 implicated in treatment strategies for autoimmune diseases such as RA but no evidence for such potential has been provided so far.…”

Antibody fingerprints in lyme disease deciphered with high density peptide arrays

“…Therefore, the query can either help in ruling out cross-targeted organisms for diagnostic purposes or serve for the identification of crosstargeted antigens. For the identification of human proteins that are involved in already known autoimmune disorders, all database entries of the query were cross-checked with the AAgAtlas, an online database of the National Center for Protein Sciences (Beijing) [28]. All potentially crossreacting human proteins are listed in Supporting Information Tables S2 -S6.…”

“…Table 3 lists the fingerprints, which were used for the database query. For the identification of human proteins that are involved in already known autoimmune disorders, all database entries of the query were cross-checked with the AAgAtlas, an online database of the National Center for Protein Sciences (Beijing) [28]. The database contains 1126 autoantigens that were collated from the literature.…”