A distinct cross-reactive autoimmune response in multisystem inflammatory syndrome in children (MIS-C)

Multisystem inflammatory syndrome in children (MIS-C) is a severe, post-infectious sequela of SARS-CoV-2 infection, yet the pathophysiological mechanism connecting the infection to the broad inflammatory syndrome remains unknown. Here we leveraged a large set of MIS-C patient samples (n=199) to identify a distinct set of host proteins that are differentially targeted by patient autoantibodies relative to matched controls. We identified an autoreactive epitope within SNX8, a protein expressed primarily in immune cells which regulates an antiviral pathway associated with MIS-C pathogenesis. In parallel, we also probed the SARS-CoV-2 proteome-wide MIS-C patient antibody response and found it to be differentially reactive to a distinct domain of the SARS-CoV-2 nucleocapsid (N) protein relative to controls. This viral N region and the mapped SNX8 epitope bear remarkable biochemical similarity. Furthermore, we find that many children with anti-SNX8 autoantibodies also have T-cells cross-reactive to both SNX8 and this distinct domain of the SARS-CoV-2 N protein. Together, these findings suggest that MIS-C patients develop a distinct immune response against the SARS-CoV-2 N protein that is associated with cross reactivity to the self-protein SNX8, demonstrating a link from the infection to the inflammatory syndrome. ### Competing Interest Statement J.D.R. reports being a founder and paid consultant for Delve Bio, Inc., and a paid consultant for the Public Health Company and Allen & Co. M.A.S. receives unrelated research funding from the NIH, the CDC, Cepheid and Merck and unrelated Honoria from UpToDate, Inc. M.R.W. receives unrelated research grant funding from Roche/Genentech and Novartis, and received speaking honoraria from Genentech, Takeda, WebMD, and Novartis. J.C. reports consulting fees from GLG group, payments from Elsevier for work as an Associate Editor, a patent pending for methods and compositions for treating and preventing T cell-driven diseases, payments related to participation on a Data Safety Monitoring Board or Advisory Board for Enzyvant and is a member of the Diagnostic Laboratory Immunology Committee of the Clinical Immunology Society. M.S.Z. receives unrelated funding from NHLBI and consults for Sobi. N.B.H reporst unrelated previous grant support from Sanofi and Qudiel, and current grant support from Merck. C.V.H. reports being a speaker fo Biofire, and a reviewer for UpToDate, Inc, and Dynamed.com. A.G.R. receives royalties as a section editor for Pediatric Critical Care Medicine UpToDate, Inc, and also received Honoraria for MIS-C-related Grand Round Presentations. A.G.R. is also on the medical advisor board of Families Fighting Flu and is Chair of the International Sepsis Forum which is supported by industry and has received reagents from Illumina, Inc. ### Funding Statement This work was supported by the Pediatric Scientist Development Program and the Eunice Kennedy Shriver National Institute of Child Health and Human Development (K12-HD000850 to A.B.) and the Chan Zuckerberg Biohub SF (J.L.D. and M.S.A.). Overcoming COVID-19 Study Network enrollment, patient data, and specimen collections supported by the CDC contracts 75D30120C07725, 75D30121C10297 and 75D30122C13330 from the Centers for Disease Control and Prevention to Boston Childrens Hospital to A.G.R. and the National Institute of Allergy and Infectious Diseases (R01AI154470) to A.G.R. Patient clinical data and specimens also collected at Boston Childrens Hospital for the Taking on COVID-19 Together (TOCT) study supported in part by the Boston Childrens Hospital Emerging Pathogens and Epidemic Response Cluster of Clinical Research Excellence and the Institutional Centers for Clinical and Translational Research to A.G.R. and K.L.M. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Central IRB of Boston Children's Hospital gave ethical approval for this work. IRB of the Centers for Disease Control (CDC) gave ethical approval for this work. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors. Complete data will be made available via a Dryad repository upon peer-reviewed publication: doi:10.7272/Q6SJ1HVH