Fig. 3: Reverse phenotyping reveals systematic biases induced by antigenic stimulation and allows precise definition of ex vivo transcriptional profiles of SARS-CoV-2 antigen-reactive T cells.

a Dot plots of log-normalized expression of selected marker genes by clonotype group (reactive and non-reactive) and by condition (stimulated: “stim”, unstimulated: “unstim”) for CD4 T cells (stimulated reactive n = 68, unstimulated reactive n = 178, unstimulated nonreactive n = 539, stimulated nonreactive n = 249). b Fraction of gene-positive cells with >0 UMIs on the presented gene by clonotype and condition (+: stimulated, −: unstimulated). c UMAPs indicating cells from the unstimulated condition in colors with cells from the stimulated condition shown in gray (n = 11,460 cells in total); CD4 or CD8 T cell state (top left panel), clonotype size as defined through cell number (bottom left panel); reactive CD8 clonotypes as defined in (a) (top middle panel) or reactive CD4 clonotypes as defined in (b) (bottom middle panel), with all other cells not belonging to that clonotype also shown in gray; CD8 (top right panel) and CD4 (bottom right panel) Leiden clusters, including manual annotation of cluster groups for the sake of clarity. d Volcano plots of differential expression test of cells from non-reactive versus reactive clonotypes in unstimulated CD8 (top) and CD4 (bottom) T cells. For the sake of clarity, TYROBP (l2fc −0.48; qval 7 × 10⁻¹³¹), KIR2DL3 (l2fc −0.15; qval 3 × 10⁻⁶⁰), and KLRC3 (l2fc −0.13; qval 3 × 10⁻⁵⁵) are not displayed (CD8). Data are shown for patient GT_3.