Figure 6. Phenotypic characterization and multidimensional analysis of patient liver biopsies.

Intrahepatic lymphocytes (IHLs) were isolated from fresh liver biopsy tissue obtained from chronically hepatitis C virus–infected patients either carrying the IFNλ4 ΔG or TT allele. IHLs were subjected to multicolor FACS analysis. (A) t tests identified no significant differences (P > 0.05) in the percent of cells with a positive phenotype for any cell surface marker between patients with ΔG (n = 9) or TT (n = 4) IFNλ4 alleles. (B, C) tSNE dimensional reduction and clustering enabled identification of clusters enriched for either IFNλ4 allele (C) using a Poisson test (false discovery rate < 0.001; colored dots) while maintaining within-cluster representation of patients with each IFNλ4 allele (B). Cells not selected for further analysis are gray. (B, C, D) Hierarchical clustering of the median marker expression of selected clusters from (B) and (C), revealing three groups (1, 2, 3) of CD8⁺ clusters with opposing expression of exhaustion and senescence markers CD57, CD127, KLRG1, PD1, and 2B4.