Integrated Proteomics and Single-Cell Mass Cytometry Analysis Dissects the Immune Landscape of Ankylosing Spondylitis

Mass cytometry is a powerful single-cell technology widely
adopted
to depict immune cell heterogeneity in different contexts. However,
this method is only capable of examining several dozens of proteins
simultaneously and requires a prior knowledge of the markers to be
analyzed. Here we propose that the integration of mass cytometry with
shot-gun proteomics may serve as a valuable tool to achieve an in-depth
understanding of the immune system. By implementing such a strategy,
we investigated the immune landscape of ankylosing spondylitis (AS),
a chronic inflammatory arthritis with unclear etiology. The proteome
alteration in peripheral blood mononuclear cells (PBMCs) was investigated
by quantitative proteomics, and then mass cytometry analysis was conducted
to decipher the immunome by considering the signaling molecules identified
with differential expression by proteomics. As a result, we identified
a wide spectrum of proteins dysregulated in AS, e.g., upregulation
of glycolytic enzymes, downregulation of lipid transporters, and dysregulation
of chemokine signaling molecules involved in proinflammatory cytokine
production and leucocyte migration. Moreover, the single-cell analysis
showed the upregulation of chemokine signaling regulators in subclusters
of both innate and adaptive immune cells in AS. In addition, correlation
analysis unveiled the interplay among Phenograph-identified subclusters
of monocytes, CD4+ T cells, and CD8+ T cells. Taken together, our
findings demonstrated that the integration of mass spectrometry-based
proteomics and single-cell mass cytometry may serve as a useful tool
to reveal clinically relevant information regarding useful targets
and cellular phenotypes that could be further exploited to develop
novel therapeutic strategies.