Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers (2021)
Figure 8

Figure 8. CRTAC1 protein abundance in BALF and plasma proteomes reports AT2 cell health.

(a) The scatter plots show the positive correlation of CFHR1 in BALF (MS-intensity, x-axis) with meta lung function (y-axis).

(b) UMAP visualizes embedding of single cells colored by gene expression for CRTAC1, which is specifically expressed in alveolar type-2 (AT2), Club and lymphatic endothelial (Lymp_EC) cells.

(c) Relative expression level of CRTAC1 across human organs.

(d) The box plots illustrate differences in mRNA detection for CRTAC1 in alveolar epithelial cells from fibrosis patients compared to control samples across the three indicated patient cohorts (Chicago cohort: ILD n = 9, controls n = 8; Nashville cohort: ILD n = 20, controls n = 10; Munich cohort: ILD n = 3, controls n = 11). The boxes represent the interquartile range, the horizontal line in the box is the median, and the whiskers represent 1.5 times the interquartile range.

(e) Relative gene expression levels of CRTAC1 in GSE47460. Dots represent average expression in the tissue of individual patients. The line represents the mean, error bars show SD. CRTAC1 is significantly downregulated in ILD but not COPD patients (p-value <0.0001) (One-way ANOVA) (control donors n = 91, ILD n = 194, COPD n = 144).

(f) For each single cell cohort, the gene-gene correlations with CRTAC1 within the SFTPC+ AT-2 cells were calculated. The indicated genes were selected based on their common direction of correlation across cohorts.

(g) The bar graph shows the gene categories most strongly correlated with CRTAC1 based on "Uniprot keywords". The dotted line marks a correlation coefficient of zero.

(h) The bar graph shows the gene categories most strongly correlated with CRTAC1 belonging to the GO category of "transcription regulators". The dotted line marks a correlation coefficient of zero.

(i) The bar graph shows the top correlated transcriptional regulators, predicted by ingenuity Pathway Analysis (IPA) for the CRTAC1 gene-gene correlations. The dotted line marks a correlation coefficient of zero.

(j) Diffusion map of human AT2 cells colored by cell type identity and inferred pseudotime.

(k) The line plot illustrates smoothed expression levels of the indicated genes across the human AT2 pseudotime trajectory.

(l) Diffusion map of mouse AT2 cells colored by cell type identity and inferred pseudotime.

(m) The line plot illustrates smoothed expression levels of the indicated genes across the m(Niu et al, 2019)ouse AT2 pseudotime trajectory.

(n) Immunofluorescence analysis of SPRR1A, KRT8 as well as SFTPC in IPF (n=3) and control samples (n=2).

(o) A high throughput experimental workflow for plasma proteomics(Niu et al, 2019) allowed for profiling of two independent cohorts of ILD patients (Munich, n=30 and Hannover, n=81; healthy age matched controls, n=30). All proteins quantified in plasma are shown, ranked by their abundance measured by mass spectrometry (MS-intensity).

(p) The indicated proteins from the plasma analysis were selected based on their common direction of correlation with patient lung function in two independent patient cohorts with distinct clinical characteristics.

(q) The heatmap shows the predicted relative contribution of lung cell types to the association of protein biomarker signatures in plasma with lung function (forced vital capacity - FVC). Patients were split in two groups, one with a mild decline in lung function [FVC 60-100%] and one with severe loss of lung function [FVC 20-60%] and compared to healthy age matched controls.