58 Supplemental Figure 1: Additional Clinical Parameters. a. The patient’s thrush. b. The patient’s platelet counts over time. c. Schematic of JAK-STAT signaling showing interferon-y binding its receptor, activating JAK1 and JAK2 to phosphorylate STAT1. STAT1 dimerizes, translocates to the nucleus, and activates target genes. d. Laboratory values as part of an infectious and rheumatologic workup of pancytopenia.
Supplemental Figure 2: Immunophenotyping. Flow cytometric immunophenotyping gating strategy is shown, and gated cell types are labeled (left). Antibodies and fluorophores used can be found in supplemental methods. Cell type frequencies for each cell type are plotted by condition (Healthy control, pre-itacitinib, or post- itacitinib) (right).
a. Flow cytometric intracellular cytokine staining gating strategy (left) and memory CD4+ T cell IL-17A-secreting cell frequencies (right). CD4+ T cell interferon-y-secreting cell frequencies are found in Figure 2 of the main manuscript, as are CD8+ T cell interferon-y-secreting cell frequencies. All P values calculated using unpaired t-test.
Supplemental Figure 3: Single-Cell RNA-Sequencing. a. Single-cell RNA-sequencing was performed on PBMCs from four different healthy controls and the patient at six different time points pre- and post-itacitinib treatment. For each sample, median unique molecular identifiers (UMIs) per cell, median genes detected per cell, and number of cells for each sample are shown.
b. Cluster-defining genes for each cell type (top); cluster defining genes across T cell containing subclusters (bottom left); and cluster defining genes across myeloid subclusters (bottom right) are shown. c. T cell-containing subclusters are shown by condition (Healthy control, pre-itacitinib, or post- itacitinib) (top left) and by sample (one of four healthy controls or one of six time points from the patient) (bottom left). The same is plotted for myeloid subclusters (top right) and (bottom right).
Supplemental Figure 4: Single-cell Assay for Transposase-Accessible Chromatin with Sequencing a. Shown are the number of cells sequenced per time point sample (left) and a representative plot from one sample where each point is a cell plotted by log 10 number of fragments on the x- axis and by the fraction of reads in called peak regions (FRIP) on the y-axis. b. Clustering of cell types using scATAC-seq, plotted in UMAP space, and labeled by cell type (top) and by time-point (bottom). N = 3 pre-itacitinib time points and n = 2 post-itacitinib time points.