Extended Data Fig. 7: Mitochondrial OXPHOS pathway changes across all cell types and analysis of T-cells following IAV infection with or without DCCs or CD4 depletion.

The top heatmap in (a) displays statistically significant changes in custom mitochondrial OXPHOS pathways, ranked by normalized enrichment score (NES) and identified through fGSEA analysis. Only pathways with a false discovery rate (FDR) < 0.25 are shown. The bottom heatmap shows individual log₂(Fold-Change) values for custom innate immune genes across the experimental groups: Her2+IAV vs. HER2 + PBS, Her2+IAV vs. WT + IAV, and Her2+IAV+anti-CD4 vs. Her2+IAV. All genes are included, with statistical significance marked by * for adjusted p-value < 0.05 and # for raw p-value < 0.05. Note that for groups with depletion of CD4⁺ cells using anti-CD4 antibody, the residual cells in CD4⁺ effector, CD4⁺ memory and regulatory T-cell clusters expressed minimal CD4, and thus are not analyzed. Flow cytometric detection of Cxcr4 and western blotting for Dusp5 protein (b) (n = 4/group). Heatmap of top 20 differentially expressed genes from scRNAseq comparing CD4⁺ memory T-cells (c), CD8⁺ effector T-cells (d), CD8⁺ memory T-cells (e) in MMTV-Her2+IAV versus WT + IAV mice at 15dpi. Proportion of T-cell subtypes identified in scRNAseq (f). Mean fluorescence intensity of MitoTracker stain in CD4⁺ and CD8⁺ cells (g) (n = 4/group) from lungs of 15 dpi IAV infected WT or MMTV-Her2 mice. Significance is determined by two tailed Student’s t test. CD4 and CD8 cell populations used to gate for MitoTracker staining (h) (n = 4/group). All box-and-whisker plots are presented as maximum value (top line), median value (middle line), minimum value (bottom line) with all data points shown (dots).

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