Supplementary Figures Legends
Figure S1. Representative intracellular cytokine staining and CD107a degranulation from patient R1. PBMCs were stimulated as described in Methods with either cognate peptide or DMSO control and gated on viable CD8+, CD3+ cells to analyze the expression of each cytokine/marker. (A) Representative expression of IFN-g, IL-2, CD107a gated on viable CD8+, CD3+ T cells. (B, C) IFN-g+ gates were then analyzed using PESTLE and SPICE softwares to determine the poly-functionality of the cells.
Figure S2. CD127 expression delineates a unique poly-functional T cell subset in patient R1 with spontaneously resolved HCV infection. CD3+ T cells from PBMCs of patient R1 at week 57 PDV were sorted into CD127neg and CD127hi cells and tested for their proliferative capacity and cytokine production. (A) CFSE proliferation, sorted CD127neg and CD127hi cells, numbers in the upper left quadrant represent the percentage of proliferating (CFSElo) tet+ cells, numbers in the bottom left quadrant represent the percentage of cells in each quadrant. (B) Summary of ICS and degranulation on CD127neg and CD127hi cells. (C) Poly-functional analysis for CD127neg and CD127hi cells stimulated with NS3-1073 peptide, gated on viable CD3+, CD8+, IFN-g+ cells. Red represents 3 functions (IFN-g+, IL-2+ and CD107a+), blue represents 2 functions (IFN-g+ and CD107a+), green represents 2 functions (IFN-g+ and IL-2+) and yellow represents one function (IFN-g), numbers on the pie chart represent the percentage of each population. The frequency of IFN-g producing cells in CD127neg cells was too low to perform poly-functionality analysis.
Figure S3. IFN therapy does not alter the phenotype of non-HCV-specific CD8+ T cells. Control tetramer staining and phenotyping before, during and after IFN therapy is shown for: (A) Patient T1 with A2-CMVpp65 tetramer, (B) Patient T3 with B7/CMV-pp65 tetramer, (C) Patient T4 with A2/CMV-pp65 tetramer and (D) Patient T4 with A2/Flu-M tetramer. Black represents expression tetramer positive cells and red represents expression on total CD3+CD8+ T cells, in the same patient. Percentages of tetramer positive cells in each quadrant are shown.