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Graphical representation of the methodology of this study. To control for biological differences across the span of the colon, we collected 810 tissue biopsies only from the right colon. Our patient cohort included patients with PSC, patients with IBD with a history of right-sided colitis and patients with no history of IBD or PSC (HCs). Patients were retrospectively determined to have right-sided dysplasia. From one biopsy, we isolated RNA for whole-tissue bulk RNA-seq. The remainder of the biopsies were mechanically and enzymatically disrupted to isolate lamina propria CD4 + T cells and plasma cells for analysis via flow cytometry, scRNA-seq, and TCR and B cell receptor (BCR) analysis.

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