Figure 3

FlowSOM metaclusters, which represent immune cell types, characterize differences in immune profiles between PBC and control. (A–D) FlowSOM metaclusters that varied in relative abundance, i.e., proportion, across study groups. Boxplots indicate relative abundances of Metacluster-3, Metacluster-4, Metacluster-16, and Metacluster-18, which corresponds to gamma-delta T cell (CD3⁺TCRgd⁺), CD8⁺ T cell (CD3⁺CD8⁺CD161⁺PD1⁺), memory B cell (CD3⁻CD19⁺CD27⁺CD38⁻), and naïve B cell (CD19⁺CD27⁻IgD⁺CCR7⁺) immune cell types, respectively. The ‘Cirrhosis’ and ‘Non-cirrhosis’ groups are subsets of the ‘PBC’ group. Numbers in parentheses indicate sample size of the group. Cirrhosis status was unavailable for one PBC patient. Horizontal bars indicate the Mann–Whitney U test performed on the respective group pairs (significance level: *0.01 ≤ p < 0.05; **0.001 ≤ p < 0.01; and ***p < 0.001). (E) Marker expression patterns for each of the nine FlowSOM clusters (derived from Metaclusters-3, -4, -16, and -18) found to be differentially abundant (i.e., fold-change ≥ 2.0 and p < 0.05) between PBC and control. Clusters from the same metacluster grouped according to their marker intensities. Color corresponds to marker intensity, which was scaled and centered for each marker.