Fig. 2: CellNEST identifies T cell homing signals in human lymph node T cell zones.

a, Human lymph node tissue assayed with Visium and annotated with cell2location³⁴ (n = 4,035 spots). b, Histogram of ligand–receptor pairs (x axis) with the top 20% highest attention scores in T cell zones assigned by CellNEST in descending order of abundance (y axis). CCL19–CCR7 (red text with triangle) is a canonical T cell homing signal. c, Density plot of CCL19–CCR7 attention scores (red) compared to all other ligand–receptor pairs (gray) in T cell zones. d, Density plot of CCL19–CCR7 ligand–receptor coexpression scores (red) compared to all other ligand–receptor pairs (gray) in T cell zones. e, Selection of the top 5,000, 2,500 and 500 CCL19–CCR7 edges with the strongest attention scores (left to right) across the entire tissue. Stronger CCL19–CCR7 communication is found in T cell zones. f, Mean expression of the top 20% expressed genes encoding proteins downstream of CCR7 signaling mapped onto the human lymph node, which aligns with CellNEST-detected regions in T cell zones in e. g, Box and whisker plots comparing mean gene expression from f within (n = 417 spots) or outside (n = 3,618 spots) of T cell zones. Center line, median; box, interquartile range; whiskers, 1.5 × interquartile range; points, outliers. There is elevated expression of CCR7 downstream signaling genes in T cell zones (two-sided Mann–Whitney U-test, P = 6.42 × 10⁻¹⁶⁴). h, Application of COMMOT to the human lymph node, with red arrows indicating CCL19–CCR7 strength. Regions do not align well with T cell zones. i, Application of NICHES to the human lymph node. Using a cluster-based analysis (left), NICHES identified three signals but missed the CCL19–CCR7 signal (right).