Fig. 6: scRNA sequencing analysis reveals that neutrophils contribute to excessive inflammation and cell death in Atg7 cKO lungs during NTM infection.
a–e Atg7 cWT and Atg7 cKO mice infected with Mav (1 × 107 CFU) for 21 days. scRNA sequencing data were obtained under the same experimental conditions as the spatial transcriptomics data from lung tissues. a UMAP plot of all scRNA sequencing data, comprising a total of 25,040 cells from two samples: Atg7 cWT and Atg7 cKO. The plot shows cells from 22 distinct cell types (left), with an enlarged view of 5 innate immune cell types (right). b Dot Plot of marker gene expression for innate immune cell populations. c, d Violin plots of the module scores for the inflammatory pathway and three cell death pathways (same as Figs. 2g and 5a) in innate immune cell populations, comparing Atg7 cWT (n = 3457 cells) and Atg7 cKO (n = 3389 cells). The distribution of module scores across all cell types is shown on the UMAP plot. Statistical significance was assessed using a two-sided unpaired Welch’s t-test for each plot (P = 7.7 × 10−5, P = 5.8 × 10−8, P = 0.025, P = 3.5 × 10−12, listed in the order of plots). e Violin plots across innate immune cells in Atg7 cKO (Int Macrophages, n = 1512 cells; Alv Macrophages, n = 268 cells; Neutrophils, n = 419 cells; Monocytes, n = 753 cells; DCs, n = 437 cells), showing the module scores for the pathways from Fig. 6c, d. For multi-group comparisons, normality was assessed using the Shapiro-Wilk test, and homogeneity of variance was evaluated using Levene’s test. One-way ANOVA followed by Tukey’s HSD test was used for post-hoc pairwise comparisons. Exact p-values for each plot are provided in the Source data file. AT alveolar type cell, Ciliated ciliated cell, Cap capillary endothelial cell, Vein venous endothelial cell, Lymph lymphatic endothelial cell, Int interstitial, Alv alveolar, DC dendritic cell. Source data are provided as a Source Data file.
