Panel A: A dot plot shows that the x-axis lists various immune cell types, and the y-axis lists marker genes. The size of the dots indicates the percent expression, and the color represents the average expression level. Panel B: A heatmap displays the GSEA leading-edge genes for the Hallmark IFN-gamma response gene set common to IL-23R-deficient and IL-12R1-deficient classic monocytes. The x-axis lists different patient groups, and the y-axis lists genes. The color scale indicates normalized Z-transformed pseudobulk read counts. Panel C: A scatter plot shows the fold-change in IFNG mRNA levels following IL-23 stimulation in leukocytes from patients and healthy controls. The x-axis lists different immune cell types, and the y-axis shows the delta IFNG mRNA levels. Different colors represent different patient groups. Panel D: Four two-dimensional plots show the fold-change difference in IFNG mRNA levels following IL-23 stimulation. The x-axis shows the fold-change difference for various patient groups relative to controls, and the y-axis shows the same parameter for IL-23R knockout patients. The color of the circles indicates the median fold-change difference in normalized IFNG mRNA levels in controls for the corresponding subsets. MAIT, NK, and Vd2 positive T cells are highlighted.
Impaired IL-23–mediated IFNG mRNA induction in patients homozygous for hypomorphic IL23R variants. (A) Dotplot of the expression of lineage- and state-specific marker genes across predicted immune cell types. (B) Heatmap analysis of the GSEA leading-edge genes for the Hallmark IFN-γ response gene set common to IL-23R–deficient and IL-12Rβ1–deficient classic monocytes. Normalized Z-transformed pseudobulk read counts are shown. Three IL12RB1−/−, three IL23R−/−, three TYK2P1104A/P1104A, one IL23RG149R/G149R, two IL23RG300V/G300V, three IL23RR381Q/R381Q patients and 12 healthy controls were included. (C) The fold-change in IFNG mRNA levels following IL-23 stimulation in leukocytes from three IL23RR381Q/R381Q, two IL23RG300V/G300V, one IL23RG149R/G149R and two TYK2P1104A/P1104A, one IL12RB1−/− and two IL23R−/− patients, and nine healthy controls was normalized against housekeeping genes across immune cells. Bulk RNAseq pseudobulk expression counts for IFNG were normalized by this factor to obtain IFNG.HKG values. The delta score is the difference in normalized expression between IL-23 stimulation and non-stimulation (NS) conditions (IL-23 − NS), reflecting the magnitude of gene induction upon stimulation. (D) Two-dimensional plots of IL-23–induced delta IFNG expression. The fold-change difference in IFNG mRNA levels following IL-23 stimulation in leukocytes from IL23RR381Q/R381Q, IL23RG300V/G300V, IL23RG149R/G149R, and TYK2P1104A/P1104A patients relative to controls is shown on the x-axis. The y-axis shows the same parameter for IL23R−/− patients as a comparison. The color of the circles indicates the median fold-change difference (IL-23 versus NS) in normalized IFNG mRNA levels in controls for the corresponding subsets. MAIT, NK, and Vδ2+ γδT cells are highlighted.