Analysis of Autoantibody Profiles in Osteoarthritis Using Comprehensive Protein Array Concepts Frauke Henjes, †,▽ Lucı ́ a Lourido, ‡,▽ Cristina Ruiz-Romero, ‡,§ Juan Ferna ́ ndez-Tajes, ‡,# Jochen M. Schwenk, † María Gonzalez-Gonzalez, ⊥ Francisco J. Blanco, ‡,∥ Peter Nilsson,* ,† and Manuel Fuentes* ,⊥ † Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm SE 171- 21, Sweden ‡ Rheumatology Division, ProteoRed/ISCIII Proteomics Group, INIBIC − Hospital Universitario de A Coruñ a, A Coruñ a 15006, Spain § CIBER-BBN Instituto de Salud Carlos III, INIBIC-CHUAC, A Coruñ a 15006, Spain ∥ RIER-RED de Inflamació n y Enfermedades Reuma ́ ticas, INIBIC-CHUAC, A Coruñ a 15006, Spain ⊥ Cancer Research Center (CIC), Department of Medicine, Proteomics Unit ProteoRed/ISCIII, IBSAL. University of Salamanca, Salamanca 37007, Spain # Wellcome Trust Centre For Human Genetics, McCarthy’s Group, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom * S Supporting Information ABSTRACT: Osteoarthritis (OA) is the most common rheumatic disease and one of the most disabling pathologies worldwide. To date, the diagnostic methods of OA are very limited, and there are no available medications capable of halting its characteristic cartilage degeneration. Therefore, there is a significant interest in new biomarkers useful for the early diagnosis, prognosis, and therapeutic monitoring. In the recent years, protein microarrays have emerged as a powerful proteomic tool to search for new biomarkers. In this study, we have used two concepts for generating protein arrays, antigen microarrays, and NAPPA (nucleic acid programmable protein arrays), to characterize differential autoantibody profiles in a set of 62 samples from OA, rheumatoid arthritis (RA), and healthy controls. An untargeted screen was performed on 3840 protein fragments spotted on planar antigen arrays, and 373 antigens were selected for validation on bead-based arrays. In the NAPPA approach, a targeted screening was performed on 80 preselected proteins. The autoantibody targeting CHST14 was validated by ELISA in the same set of patients. Altogether, nine and seven disease related autoantibody target candidates were identified, and this work demonstrates a combination of these two array concepts for biomarker discovery and their usefulness for characterizing disease-specific autoantibody profiles. KEYWORDS: Protein microarrays, autoantibody profiles, osteoarthritis, NAPPA ■ INTRODUCTION OA as Multifactor Disease Osteoarthritis (OA) is the most common arthritic disease, and it is thereby among the most frequent symptomatic diseases for middle aged and elderly people. Worldwide estimates are that 10% of men and 18% of women over 60 years of age have symptomatic osteoarthritis. About 80% of those with OA have significant limitations of movement, and 25% cannot perform their major activities of daily living. 1 Therefore, OA is already Special Issue: Proteomics of Human Diseases: Pathogenesis, Diagnosis, Prognosis, and Treatment Received: July 28, 2014 Published: September 16, 2014 Article pubs.acs.org/jpr © 2014 American Chemical Society 5218 dx.doi.org/10.1021/pr500775a | J. Proteome Res. 2014, 13, 5218−5229