Characterization of CD4 ⁺ T cells in the colon lamina propria by CITE-seq. (A) Schematic overview of the entire experimental workflow covering all procedures in Figs. 1–8. (B) UMAP plot visualizing colonic lamina propria CD4⁺ T cells from CD (n = 3, Patient 1–3 in Table S1) and control (n = 3, Ctrl-Patient 1–3 in Table S1) samples. Annotations are shown in C. (C and D) Expression levels of selected RNA (C) and protein (D) markers across identified clusters. The dot size indicates the percentage of cells expressing the gene within each cluster, while color intensity reflects average expression level. (E) Cluster proportion across disease conditions. Each bar represents 100% of cells from a given disease, with segments denoting the relative abundance of each cluster. (F) Distribution of CD-derived (red) and control-derived (blue) cells. (G) Left: Graph representation of neighborhoods (Nhoods) identified by Milo. Nodes represent Nhoods, colored by their log₂ FC between CD and control samples. Nondifferential abundance Nhoods (FDR ≥ 0.1) are white, and sizes correspond to cell number within a Nhood. Edges depict shared cells between adjacent Nhoods. Right: Beeswarm plot displaying adjusted log₂ FC distribution in abundance between CD and control samples within Nhoods, stratified by 15 cell types. Colors match the UMAP. (H and I) Feature plots showing the expression of key marker genes (H) and proteins (I) that characterize the T_RM_2 cluster. Color intensity represents expression levels, with darker shades indicating higher expression. FC, fold change.