Figure 3
Evaluation of CODEX Results using scRNA-seq and CyTOF. Initial clustering results for scRNA-seq of colonic biopsies (A). UMAP representation and visualization of canonical markers identifies primary topographical features of interest: MS4A1 is a B-cell marker, CD3E is a T-cell marker, CD38 is a plasma cell marker (B). CD4 and PDCD1 (CD279) are displayed in the T-cell cluster ((C), red inset). Orange arrows indicate the PDCD1 + CD4 + T-cell region in UC samples ((C), red inset, right), as well as the corresponding depleted region in healthy controls (3C, red inset, left). CR2 (CD21) and PCNA (Ki67 surrogate) are displayed in the proliferating B-cell cluster ((C), black inset). Blue arrows indicate the PDNA + area of the MS4A1 + B-cell island in UC samples (3C, black inset, right) as well as the corresponding depleted region in healthy controls ((C), black inset, left). CyTOF reveals CD56 + B-cells and exhausted CD4 T-cells in UC patient colonic biopsies, though adjacent uninflamed controls have elevated proliferating B-cells (D). CD56 + B-cells as a fraction of all plasmablasts are reduced in blood during disease flare, relative to remission and healthy control (E), though similar differences are not observed as a fraction of all CD19 + cells.
