An autoantigen profile of human A549 lung cells reveals viral and host etiologic molecular attributes of autoimmunity in COVID-19

Abstract

We aim to establish a comprehensive COVID-19 autoantigen atlas in order to understand autoimmune diseases caused by SARS-CoV-2 infection. Based on the unique affinity between dermatan sulfate and autoantigens, we identified 348 proteins from human lung A549 cells, of which 198 are known targets of autoantibodies. Comparison with current COVID data identified 291 proteins that are altered at protein or transcript level in SARS-CoV-2 infection, with 191 being known autoantigens. These known and putative autoantigens are significantly associated with viral replication and trafficking processes, including gene expression, ribonucleoprotein biogenesis, mRNA metabolism, translation, vesicle and vesicle-mediated transport, and apoptosis. They are also associated with cytoskeleton, platelet degranulation, IL-12 signaling, and smooth muscle contraction. Host proteins that interact with and that are perturbed by viral proteins are a major source of autoantigens. Orf3 induces the largest number of protein alterations, Orf9 affects the mitochondrial ribosome, and they and E, M, N, and Nsp proteins affect protein localization to membrane, immune responses, and apoptosis. Phosphorylation and ubiquitination alterations by viral infection define major molecular changes in autoantigen origination. This study provides a large list of autoantigens as well as new targets for future investigation, e.g., UBA1, UCHL1, USP7, CDK11A, PRKDC, PLD3, PSAT1, RAB1A, SLC2A1, platelet activating factor acetylhydrolase, and mitochondrial ribosomal proteins. This study illustrates how viral infection can modify host cellular proteins extensively, yield diverse autoantigens, and trigger a myriad of autoimmune sequelae. Our work provides a rich resource for studies into "long COVID" and related autoimmune sequelae.

Keywords: Atlas; Autoantigens; Autoimmunity; COVID-19; Lung; Resource.

Fig. 1.

The autoantigenome from A549 cells identified by DS-affinity. Marked proteins are associated with translation (69 proteins, red), mRNA metabolic processing (69 proteins, pink), ribosome biogenesis (43 proteins, blue), vesicles (87 proteins, green) and vesicle-mediated transport (72 proteins, dark green), chromosomes (40 proteins, aqua), and cytoskeleton (65 proteins, gold).

Fig. 2.

COVID-altered proteins shared with the A549 autoantigenome. Marked proteins are associated with translation (53 proteins, red), mRNA metabolic process (63 proteins, pink), vesicle (79 proteins, green) and vesicle-mediated transport (64 proteins, dark green), cytoskeleton (58 proteins, gold), chromosomes (35 proteins, aqua), and ribosome biogenesis (29 proteins, blue).

Fig. 3.

Top 40 enriched GO biological processes among COVID-altered proteins shared with the A549 autoantigenome. Bigger dots indicate more significant p-values.

Fig. 4.

Top 20 enriched pathways and processes among COVID-altered autoAgs. Top: 298 COVID-altered autoAgs. Middle: 231 up-regulated autoAgs in COVID. Bottom: 252 down-regulated autoAgs in COVID.

Fig. 5.

DS-affinity proteins that interact with SARS-CoV-2 viral proteins or are perturbed in A549 cells expressing individual viral proteins. Orf3: regulation of gene expression (pink), cytoplasmic vesicle (green), monosaccharide biosynthetic process (blue), response to stress (brown), and hydrolase activity (gold). Orf9b: mitochondrial translation (red), mitochondrion localization (pink), autophagosome maturation (gold). E: establishment of protein localization to membrane (red), translation initiation (pink), mRNA splicing (green), regulation of macroautophagy (brown), post-translational protein modification (gold), RNA polymerase II transcription (blue). M: establishment of protein localization to membrane (red), intracellular protein transport (gold), organelle organization (green), nicotinamide nucleotide metabolic process (aqua), regulation of apoptotic process (blue), and symbiont process (pink). N: maintenance of location in cell (pink), protein localization to ER (red), protein folding (aqua), mitochondrial nucleoid (amber), RNA polymerase II transcription (blue), and RNA-binding (green). Nsp1: protein localization (green), gene expression (red), protein processing in ER (blue), and phagosome (gold). Nsp13: cytoskeleton (gold), regulation of muscle contraction (green), and melanosome (brown).

Fig. 6.

Known and putative autoAgs derived from ubiquitination alteration in SARS-CoV-2 infected A549 cells. Marked proteins are associated with catabolic process (37 proteins, blue), ubiquitin protein ligase binding (12 proteins, aqua), gene expression (46 proteins, pink), regulation of apoptotic process (22 proteins, brown), cytoplasmic vesicles (28 proteins, green), and cytoskeleton (26 proteins, gold).

Fig. 7.

Known and putative autoAgs derived from phosphorylation alteration in SARS-CoV-2 infected cells. Marked proteins are associated with gene expression (52 proteins, red), vesicle-mediated transport (25 proteins, green), ATP binding (18 proteins, gold), and kinase binding (12 proteins, aqua).