PhIP-Seq uncovers novel autoantibodies and unique endotypes in interstitial lung disease

Interstitial lung diseases (ILDs) are a heterogeneous group of disorders that can develop in patients with connective tissue diseases (CTD). Establishing autoimmunity in ILD impacts prognosis and treatment. ILD patients are screened for autoimmunity by assaying for anti-nuclear autoantibodies, rheumatoid factors and other non-specific tests. However, this approach has not been rigorously validated and may miss autoimmunity that manifests as autoantibodies to tissue antigens not previously defined in ILD. Here, we use Phage Immunoprecipitation-Sequencing (PhIP-Seq) to conduct a large, multi-center unbiased autoantibody discovery screen of ILD patients and controls. PhIP-Seq identified 17 novel autoreactive targets, and machine learning classifiers derived from these targets discriminated ILD serum from controls. Among these 17 candidates, we validated Cadherin Related Family Member 5 (CDHR5) as an autoantigen and found CDHR5 autoantibodies in patients with rheumatologic disorders and importantly, subjects not previously diagnosed with autoimmunity. Lung tissue of CDHR5 autoreactive patients showed transcriptional profiles consistent with activation of NFκB signaling and upregulation of chitotriosidase (CHIT1), a molecular pathway linked to fibrosis. Our study shows PhIP-Seq uncovers novel autoantibodies in ILD patients not revealed by standard clinical tests. Furthermore, CDHR5 autoantibodies may define a novel molecular endotype of ILD characterized by inflammation and fibrosis. ### Competing Interest Statement P.W. received grants from Roche, Sanofi, Pliant, Boehringer Ingelheim and personal fees from; Sanofi, Boehringer Ingelheim, and Blade Therapeutics. M.E.S. received grants and editorial assistance from Boehringer Ingelheim and personal fees from Fibrogen. M.S.A. owns stock in Medtronic and Merck and has consulted for Sana and Imcyse. J.D. is a paid scientific consultant for The Public Health Company, Inc., Allen & Co., and Delve Bio. There is no direct overlap between the current study and these consulting duties. The other authors declare no conflicts of interest.