Fig. 4: Composition and expression differences between COVID-19 and healthy lungs and between infected and uninfected regions within COVID-19 lungs.

a, Example of analysed regions. Top: RNAscope (left) and immunofluorescent staining (right) of donor D20 with collection regions of interest (ROIs) and matched areas in white rectangles. Bottom: one ROI (yellow rectangle) from each scan (left and middle) and the segmented collection areas of illumination (AOIs) (right). b, Cell composition differences between PanCK⁺ and PanCK⁻ alveolar AOIs and between AOIs from COVID-19 (n = 9, 190 AOIs) and healthy (D22–24, 38 AOIs) lungs. Expression scores (colour bar) of cell type signatures (rows) in PanCK⁺ (left) and PanCK⁻ (right) alveolar AOIs (columns) in whole transcriptome (WTA) data from different donors (top colour bar). c, Differential gene expression in COVID-19 versus healthy lung. Left: significance (−log₁₀(P), y axis) and magnitude (log₂(fold change), x axis) of differential expression of each gene (dots) in WTA data between PanCK⁺ alveoli AOIs from COVID-19 (n = 78) and healthy (n = 18) lung. Right: significance (−log₁₀(q)) of enrichment (permutation test) of different pathways (rows). d, e, Changes in gene expression in SARS-CoV-2 high versus low AOIs within COVID-19 lungs in WTA data. d, SARS-CoV-2 high and low alveolar AOIs. PanCK⁺ alveolar AOIs (dots) rank ordered by their SARS-CoV-2 signature score (y axis) in WTA data, and partitioned to high (red), medium (grey) and low (blue) SARS-CoV-2 AOIs. e, Significance (−log₁₀(P), y axis) and magnitude (log₂(fold change), x axis) of differential expression of each gene (dots) in WTA data between SARS-CoV-2 high and low AOIs for PanCK⁺ alveoli (AOIs: 17 high, 3 medium, 58 low). Horizontal dashed line, FDR = 0.05; vertical dashed lines, |log₂(fold change)| = 2. FC, fold change. The top 10 differentially expressed genes by fold change are marked.