Fig. 2: Spatial RNA sequencing analysis reveals upregulated inflammatory cytokines/chemokines in the lungs of Atg 7 cKO mice during NTM infection.

a–g Spatial transcriptomics data obtained lung tissues from Mav-infected (1 × 10⁷ CFU) Atg7 cWT and Atg7 cKO mice at 21 dpi. a Representative H&E staining images of spatial transcriptomics data generated using the 10× Genomics Visium platform. b UMAP plot of Louvain clustering with 6971 spots from 2 spatial transcriptomics samples. Hierarchical clustering tree divided into major nodes, each represented by a distinct color. c UMAP plot of 8 major nodal clusters and comparison of cluster composition in each sample. UMAP clusters are mapped into spatial context. d Heatmap of the expression of cell type specific gene signatures of epithelial cells, endothelial cells, fibroblasts, myeloid cells, and lymphoid cells among 8 major nodal clusters. e Heatmap comparing expression profiles between the 8 major nodal clusters and the 13 cell types resulting from deconvolution with scRNA sequencing data (GSE151974). f Pathway enrichment analysis (GO Biological Process) comparing total spatial transcriptomic spots between Atg7 cWT (n = 3152 spots) and Atg7 cKO (n = 3798 spots), showing the top enriched pathways per group. Enriched GO terms were identified using one-sided hypergeometric tests, and p-values were adjusted for multiple comparisons using the Benjamini-Hochberg method. g UMAP plots of the module scores for the inflammatory pathway (HALLMARK: INFLAMMATORY_ RESPONSE), mapped to both the total and cluster five regions within the spatial context, comparing Atg7 cWT and Atg7 cKO. Violin plot shows a significant difference in cluster 5, assessed using a two-sided unpaired Welch’s t-test (P < 2.2 × 10⁻¹⁶; Atg7 cWT: n = 490 spots; Atg7 cKO: n = 1,275 spots). a is representative of at least three independent experiments performed. Alv Alveolar, Int interstitial, NK natural killer. Source data are provided as a Source Data file.