Fig. 6: Receptor-ligand analysis between aberrant basaloid intermediates and CD206hi macrophages.
From: Temporo-spatial cellular atlas of the regenerating alveolar niche in idiopathic pulmonary fibrosis
a Data extracted from of single cell RNA sequencing of lung digest cells from IPF (n = 12) and healthy control (n = 12) lungs deposited by Habermann et al.9 reproduced here to demonstrate starting point for further clustering of macrophages. This UMAP retains Habermann’s annotations. Text in red identifies Habermann’s aberrant basaloid intermediate cells (KRT5-KRT17+ cells) and transitional AT II cells, and in blue the two clusters of DCs. Monocytes (Mono) and Macrophage (Mac) cell clusters in broken blue circle are re-clustered (using 0.7 resolution in Seurat) to discriminate levels of CD206 (MRC1) gene expression and where there is a clear CD206hi subcluster (subcluster 9) shown in (b) and (c). Cluster 9 (in broken box) (c) showing the highest CD206 expression is annotated as CD206hi macrophages. d–e Receptor-ligand analysis using CellChat, with ABI as sender and CD206hi macrophages, cDC and pDC as receivers (d) and vice versa (e). Red circles - highest probability of communication (>0.5); large bubbles indicate probability of communication > 0.3, and small bubble < 0.3; no bubble—no communication detected. Colour of the bubble represents levels of communication probability. Y axis – ligand-receptor; x axis ABI - immune cell pairs. tAT2—Transitional ATII; 'prob'—communication probability (f) Marker gene list for Cluster 9 (CD206hi macrophages) compared to the established macrophage subclusters (FABP4+ macrophage and SPP1+ macrophage)8,24,25 found in IPF. Note that cluster 9 (CD206hi macrophages) shows a distinct difference in fibronectin (FN) expression compared to FABP4+ macrophage and SPP1+ macrophage subsets. g Confocal picture of immunofluorescent staining of FN in CD206+ macrophages in one of our IPF lungs (one of 16 ROIs shown, n = 3 patients). h Schema proposing location of ABIs and CD206hi macrophages, and functional consequences of receptor-ligand engagement. 'MIF' - macrophage migration inhibitory factor, 'mac' - macrophages.
