Fig 2: Lung monocytes and macrophages of severe COVID-19 patients express reduced levels of efferocytic receptors.(A–B) Representative histological findings in post-mortem lung tissue from control patients (Cntrl) and COVID-19 patients, obtained by ultrasound-guided minimally invasive autopsy. Tissue samples were immunolabeled with anti-S100A9 (phagocytes, green), (A) anti-CD36 (red), or (B) anti-MERTK (red) and stained with DAPI (nuclei, blue). Representative images show cropped details of lung tissues scanned by wide-?eld epifluorescence imaging. Scale bar: 10 µm. The mean fluorescence intensity (MFI) of CD36 and MERTK of at least 300 S1009+ cells are shown (n=6 control and four COVID-19 patient samples). Dots represent an S1009+ cell (A and B), the crossing line represents the mean, and error bars are ± S.E.M. Significance was calculated by Mann-Whitney test (A and B), *p<0.05, **p<0.001, ***p<0.0001, comparing the indicated groups. (C) Gene set enrichment analysis for efferocytosis-related gene sets in early infiltrating phagocytes (S1009+ CCL18-) and in anti-inflammatory monocytes-derived macrophages (CD14+ S11009- CCL18+) clusters from the bronchoalveolar lavage of mild (-M Figure) and severe (-S) COVID-19 patients versus healthy individuals. The corrplot depicts the normalized enrichment score (NES), and p value for the gene sets indicated on the y-axis. (D) Enriched efferocytosis-related gene ontology (GO) terms in genes repressed in virus-positive versus virus-negative alveolar macrophages. Figure 5—source data 1.Source data for Figure 5.