single-cell transcriptomics in patients with anti-citrullinated peptide antibody-positive early rheumatoid arthritis

Despite known differences in immunologic features between anti-citrullinated peptide antibody (ACPA)-positive (ACPA+) and ACPA-negative (ACPA-) early rheumatoid arthritis (eRA) patients, our understanding is still incomplete. To address this, we performed single-cell RNA sequencing of CD45+ cells from peripheral blood samples of drug-naïve ACPA+ and ACPA- eRA patients and compared distribution and functional characteristics of cell subsets based on ACPA presence. We obtained peripheral blood samples from untreated (drug-naïve), early, and active stage of RA patients who met the 2010 ACR/EULAR Rheumatoid Arthritis classification criteria. Peripheral blood mononuclear cells were isolated using Ficoll-Paque gradient centrifugation. Cell quantity and viability were then determined by Trypan Blue staining. We next conducted scRNA-seq to characterize and compare transcriptome profiles of CD45+ cells from PBMCs obtained from healthy controls (n = 4), drug-naïve ACPA- eRA patients (n = 6), and drug-naïve ACPA+ eRA patients (n = 6). Raw data were processed using BD Rhapsody software. Human transcriptome GRCh38-1.2.0 was used as the reference.