Fig. 1

Combined single-cell transcriptional and proteomics immunophenotyping provides a high-resolution map of human primary CD4⁺ T cells in the blood. a Summary of the experimental workflow. FACS plot depicting the sorting strategy for the isolation of the three assessed CD4⁺ T cell populations. b Two-dimensional plot depicting the expression of IL-7R and IL-2RA at the protein level using oligo-conjugated antibodies (AbSeq). Cells are coloured according to their respective sorting gate, as assessed using oligo-conjugated sample-tagging antibodies. c Uniform Manifold Approximation Projection (UMAP) plot depicting the clustering of all captured CD4⁺ single cells using the combined proteomics and transcriptomics data. Expression levels of the CD45RA (black to green) and CD45RO (black to red) isoforms obtained using the AbSeq technology are depicted in the plot. d UMAP plot depicting the clustering of resting primary CD4⁺ T cells (n = 9708) isolated from the blood of a systemic lupus erythematosus (SLE) patient. Dashed lines delineate the naive Teff (black), memory Teff (red), and Treg (blue) clusters, annotated manually based on their respective protein and mRNA expression profiles. e Heatmap displaying the top 10 differentially expressed genes in each resting CD4⁺ Teff cluster. f UMAP plots depicting the expression of the CD4⁺ T cell lineage-defining transcription factors TBET (Th1) and RORγt (Th17) in resting CD4⁺ T cells. Arrows recapitulate the identified axis of Th1 and Th17 differentiation and are supported both on the gradient of expression of the respective lineage-restricted transcription factors (TBET and RORγt, respectively) and on the developmental trajectories identified by the pseudotime analysis depicted in Fig. 3. g Expression of the effector-type cytokine transcripts IFNG, NKG7, PRF1, CCL5, GZMH and GZMK in resting CD4⁺ T cells