Multi-tiered proteome analysis displays the hyper-permeability of the rheumatoid synovial compartment for plasma proteins

Rheumatoid arthritis (RA) is characterized by synovial hyperplasia, cartilage/bone destruction and stiffness. RA affects the joints, the synovial membrane and consequently also the proteome of synovial fluid. Most of the RA studies are focusing on the role of T cells, but antibodies as well as other proteins may also play a role in joint destruction. As the proteomic signature of liquid biopsies can provide insights into the underlying (inflammatory) processes, we analysed using the protein composition of plasma and synovial fluid at three distinct levels of depth using mass spectrometry, namely the total proteome, the clonal IgG1 repertoire and the RA-related clonal IgG1 ACPA autoantibody repertoire. We compared paired synovial/plasma liquid biopsies from 9 individual patients diagnosed with RA and assessed the similarity in protein composition between plasma and synovial fluid within each patient at these three molecular levels. Intriguingly, at the total proteome level, the synovial fluid proteome aligned qualitatively and quantitatively with the plasma proteome from the same patient, independent of the size and/or other biochemical features of the observed ~300 proteins. Although dominated by plasma proteins, the synovial fluid contained additional lower abundant proteins primarily related to cartilage and several, mainly neutrophil-derived, cellular proteins. Strikingly, also the synovial IgG1 repertoire and ACPA autoantibody repertoire, monitored quantitatively and with clonal resolution, containing several hundred of distinctive clones, resembled very well the plasma IgG1 repertoires within the same patient. Our comprehensive multilayer proteomics data reveals not only that the synovial fluid in RA patients is a direct, unbiased, filtrate from the plasma, but also that, within the same patient, all the dominant abundant IgG1 (auto)antibody clones are equivalently present between the two. We argue that the huge infiltration of plasma into the synovium, as reported here, may reduce the normal lubricating function of synovial fluid and partially clarify the key phenotype of RA stiffness