Extended Data Fig. 4: Associations between immune cell populations and clinical traits in COPD.
a, Immunofluorescence staining for CD3 (red), CD19 (green), and CHIT1 (yellow) in lung tissue from study participants without COPD and GOLD IV COPD; nuclei are stained with DAPI (blue). Scale bars, 500 μm. b, Box plots of IM1 as a proportion of all macrophages stratified by GOLD stage (n = 140). c, Correlation between AMCSF (proportion of all macrophages) and exacerbation scores (n = 140). d, MDM as a proportion of all cells stratified by semiquantitative lobe emphysema (n = 127). e, Box plots of Macdiv as a proportion of all cells stratified by semiquantitative lobe emphysema (n = 127). f, Mast cells as a proportion of all cells stratified by lobe-specific semiquantitative emphysema (n = 127). g, B/plasma cells as a proportion of all cells stratified by smoking status (N: never, F: former, C: current), GOLD stage (n = 122), and semiquantitative lobe emphysema (n = 127). h, Migratory dendritic cells (mDCs) as a proportion of all cells, stratified by GOLD stage (n = 122) and semiquantitative lobe emphysema (n = 127). i, UMAP of lymphocyte cell populations, including CD4⁺ T cells, CD8⁺ T cells, regulatory T cells (Treg), mucosal-associated invariant T cells (MAIT), B cells, plasma cells, and natural killer (NK) cells. j, Feature plots of representative marker genes for immune cell populations shown in i. b,e,f,g,h, Proportions multiplied by 100 and plotted on a log10 scale. b–h, Differential composition by sccomp (Bayesian sum-constrained β binomial with posterior probabilities converted to Benjamini–Hochberg adjusted probabilities), adjusted for age, sex, BMI, and smoking status; emphysema traits additionally adjusted for lobe. (*FDR < 0.10, **FDR < 0.05, ***FDR < 0.01). b,d–h, Box plots depict the median (centerline), interquartile range (box), and 1.5× IQR whiskers.
