Extended Data Fig. 8: Postnatal transitional cells from NDUFS2 cKO mice display distinct features compared to those identified in other postnatal or adult lung injury and repair models.
From: Mitochondrial integrated stress response controls lung epithelial cell fate
a–d, Re-analysis of postnatal lung epithelium from Negretti et al. (mouse lung development atlas, n = 11,807 cells)14 integrated with our single-cell RNA-seq data of epithelium (9,322 cells). ISR enrichment scores across the postnatal epithelial cell types within the single-cell mouse lung development atlas (a). Higher score indicates higher enrichment of the ISR signature genes. p < 2.2 × 10−16 by Kruskal-Wallis test. Transitional cells have more enriched ISR gene signatures than other epithelial cells (** adjusted p < 0.01 by post-hoc pairwise Mann-Whitney test with Holm method, p values are in the Source Data). Violin plots (b) showing ISR enrichment score in transitional cells from two single-cell RNA-seq data. p < 2.2 × 10−16 by Mann-Whitney test. UMAP embedding of integrated postnatal lung epithelial cells (c) colored by the cell types as annotated in original analyses. RNA-velocity vectors (d) were calculated and overlaid on the UMAP embedding. While normal postnatal transitional cells are predicted to differentiate to AT1 cells by RNA velocity analysis, transitional cells in NDUFS2 cKO mice are not. Please note that RNA velocity estimates should be interpreted with caution as they can be biased by a low-dimensional representation75. e–h, Re-analysis of lung epithelium from Hurskainen et al. (postnatal hyperoxia model, n = 9,975 cells)43 integrated with our single-cell RNA-seq data of epithelium (9,322 cells). ISR enrichment scores in AT2 cells from hyperoxia-exposed lungs and normoxia-exposed lungs are shown in violin plots (e). p = 1.3 × 10−12 by Mann-Whitney test. Violin plots showing ISR enrichment scores in transitional cells from NDUFS2 cKO mice and AT2 cells from hyperoxia-exposed mice (f). p < 2.2 × 10−16 by Mann-Whitney test. UMAP embedding of integrated lung epithelial cells (g) colored by the same cell type as annotated in original analyses. RNA-velocity vectors were calculated and overlaid on the UMAP plots depicting cell identity by experimental conditions (h). i–j, Re-analysis of lung epithelium from Strunz et al. (adult bleomycin injury model, n = 32,559 cells)23 integrated with our single-cell RNA-seq data of epithelium (9,322 cells). ISR enrichment scores across the epithelial cell types within Strunz et al. dataset (i). p < 2.2 × 10−16 by Kruskal-Wallis test. ISR gene signatures of Krt8+ ADI cells are more enriched compared to other cell types (*** adjusted p < 2.0 × 10−16 by post-hoc pairwise Mann-Whitney test with Holm method, p values are in the Source Data). Violin plots (j) showing ISR enrichment score in transitional cells from two single-cell RNA-seq data. p < 2.2 × 10−16 by Mann-Whitney test. k–l, Re-analysis of lung epithelium from Choi et al. (adult bleomycin injury model, n = 12,179 cells)24 integrated with our single-cell RNA-seq data of epithelium (9,322 cells). ISR enrichment scores across the epithelial cell types within Choi et al. dataset (k). p < 2.2 × 10−16 by Kruskal-Wallis test. ISR gene signatures of DATPs are more enriched than primed AT2, cycling AT2, and AT1 (*** adjusted p < 2.0 × 10−16 by post-hoc pairwise Mann-Whitney test with Holm method, p values are in the Source Data). Violin plots (l) showing ISR enrichment score in transitional cells from two single-cell RNA-seq data. p < 2.2 × 10−16 by Mann-Whitney test. m–n, Re-analysis of lung epithelium from Kobayashi et al. (mouse lung organoids, n = 5,705 cells)28 integrated with our single-cell RNA-seq data of epithelium (9,322 cells). ISR enrichment scores across the epithelial cell types within Kobayashi et al. dataset (m). p < 2.2 × 10−16 by Kruskal-Wallis test. ISR gene signatures of PATS are more enriched than those of other epithelial cells (* adjusted p < 0.05, *** adjusted p < 1.0 × 10−14 by post-hoc pairwise Mann-Whitney test with Holm method, p values are in the Source Data). Violin plots (n) showing ISR enrichment scores in transitional cells from two single-cell RNA-seq data. p < 2.2 × 10−16 by Kruskal-Wallis test. *** adjusted p < 2.0 × 10−16 by post-hoc pairwise Mann-Whitney test with Holm method.
