Fig. 3: Characterization of T/NK cells in PT and BM samples reveal enrichment of immune-suppressive Cycling T cells in BMs.

A A UMAP plot of all T and NK cells, colored by identified cell clusters. B A heat map illustrating normalized expression of canonical T and NK cell marker genes across clusters; TRM denotes tissue-resident memory cells. C A dotplot showing average score of curated gene signatures among T cell clusters. D Box plots comparing the proportions of T and NK cell subclusters between primary (n = 8) and brain metastatic (n = 11) NSCLC samples. P-values from two-sided Wilcoxon Rank Sum tests are shown. E, F Enriched GO terms in CD4_IL7R (E) and cycling (F) cells. P-values were calculated using one-sided hypergeometric tests with Benjamini–Hochberg FDR correction. G, H Kaplan–Meier survival curves for patients with NSCLC in the Ravi (n = 122 patients) and Kim (n = 27 patients) cohorts, as stratified by high and low levels of CD4_IL7R (G) and cycling (H) cells signature score; optimal cutoff values were determined using “survminer.” Hazard ratios (HRs) with 95% confidence intervals (CIs) and P-values from two-sided log-rank tests are shown. Survival curves represent Kaplan–Meier estimates; +, censored observations. In box plots (D), center line represents the median, box bounds indicate the 25th and 75th percentiles (IQR), whiskers extend to 1.5× IQR from box bounds, and outliers are shown as individual points.