Concise Report Detection of putative autoantibodies in systemic lupus erythematous using a novel native-conformation protein microarray platform Anselm Mak 1,2 , Nien Yee Kow 1 , Nur Hafiza Ismail 3 , Nur Diana Anuar 3 , Nurul H Rutt 3 , Jiacai Cho 1,2 , Nurul Shielawati Binti Mohamed Rosli 3 and Bhushan Dharmahidari 4,5 Abstract Objective: Conventional immunoassays detect autoantibodies related to systemic lupus erythematosus (SLE) via rec- ognition of epitopes on autoantigens expressed in their denatured rather than native conformational state, casting difficulty in evaluating the genuine pathogenicity of the autoantibodies. We aimed to use a novel high-throughput protein microarray platform to identify autoantibodies against native autoantigens in SLE sera. Methods: Sera from SLE patients and those of gender-, age-, and ethnicity-matched healthy controls (HC) were screened against more than 1,600 immune-related antigens of native conformation. The relative fluorescent unit readout from post-assay imaging were subjected to bioinformatics pre-processing and composite normalization. A penetrance fold change (pFC) analysis between SLE and HC samples shortlisted 50 autoantigens that were subjected to an unsupervised cluster analysis. Correlations between the pFC of putative autoantigens and clinical parameters including SLE disease activity index (SLEDAI-2K) and recent SLE flares were explored. Results: 381 autoantigens were identified when 15 SLE and 15 HC serum samples were compared. The top 20 autoantigens which elicited autoantibody responses in SLE sera filtered based on the highest pFC were further analyzed. Autoantigens which the putative autoantibodies reacted against are those involved in chromatin organization such as DEK, regulation of transcription activity including REOX4 and ELF4, and negative regulation of NF k B activity such as TRIB3. Additionally, the pFC of these autoantibodies significantly and positively correlated with SLEDAI-2K and recent SLE flares. Conclusion: A high-throughput protein microarray platform allows detection and quantification of putative lupus- related autoantibodies which are of potential pathophysiological and prognostic significance in SLE patients. Keywords Autoantibody, lupus, high-throughput, microarrays, proteins Date received: 10 June 2020; accepted: 28 August 2020 Introduction Systemic lupus erythematosus is a prototype autoim- mune disease characterized by multifactorial aetiolo- gies and a plethora of autoantibodies which induce immune-complex mediated inflammation multi-system- ically. 1,2 Detection of the presence of autoantibodies and their relationships with specific clinical manifesta- tions is one of the fundamental strategies to further 1 Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore 2 Division of Rheumatology, University Medicine Cluster, National University Health System, Singapore, Singapore 3 Sengenics Corporation Pte Ltd, Sengenics, Singapore, Singapore 4 Department of Physiology, National University of Singapore, Singapore, Singapore 5 Immunology Program, National University of Singapore, Singapore, Singapore Corresponding author: Anselm Mak, Division of Rheumatology, Department of Medicine, 1E Kent Ridge Road, Level 10, NUHS Tower Block, Singapore 119228, Singapore. Email: mdcam@nus.edu.sg Lupus 0(0) 1–7 ! The Author(s) 2020 Article reuse guidelines: sagepub.com/journals-permissions DOI: 10.1177/0961203320959696 journals.sagepub.com/home/lup