Trajectory mapping of primary Sjögren's syndrome via transcriptome learning demonstrates limitations of peripheral blood sequencing.

Primary Sjögren's syndrome (pSS) is a complex autoimmune disease characterized by aberrant immune cell action against secretory glands throughout the body. A number of studies have previously identified unique characteristics in the circulating expression profile of white blood cells of pSS patients. However, the molecular progression pattern of pSS is unclear. Through a systematic analysis of pSS transcriptome information, we found that pSS transcriptomes display broad heterogeneity, but cannot be distinguished from the broad range of possible profiles of healthy controls. Instead, only sample learning using a subset of pre-identified signature genes could achieve partial separation through a trajectory governed by interferon activity. Interestingly, this trajectory is correlated with a decrease in dendritic cell counts. Our study thus highlights a major limitation to the utility of broad blood transcriptome analysis in the context of pSS, while also identifying several factors that influence the divergence between patient samples.