Fig. 1: Cellular overview of CIP after immunotherapy.

a Workflow showing biopsy collection sites, processing of single-cell suspensions for scRNA-seq and scTCR/BCR sequencing, and validation using blood and BALF samples. Created in BioRender. Lin, X. (2025) https://BioRender.com/viqeiga. b Summary of the patient samples. The figure shows only a subset of the patients validated by IHC/IF, while information on the other validated patients is provided in Supplementary Table 2. c Uniform manifold approximation and projection (UMAP) visualization of all cells captured, colored by major cell type. The left panel displays the overall clustering, while the right panel illustrates the cellular composition of samples from different sources, including the tissue, BALF and blood. d A bar plot illustrating the main cellular composition of samples from different sources. e Violin plots display the expression of canonical marker genes across major clusters, with the y-axis representing normalized gene expression values. f Stacked bar plot showing the fractions of major cell types between CTL and CIP groups. g Volcano plot showing the log2 fold change of gene expression across all cells. P values were calculated using a two-tailed Gaussian approximation of the U statistic and adjusted with the Benjamini–Hochberg procedure. h Reactome signaling analysis based on the DEGs identified in (g). P values were derived from the hypergeometric test and corrected using the Benjamini–Hochberg procedure. CIP checkpoint inhibitor-related pneumonitis, BALF bronchoalveolar lavage fluid.