Extended Data Fig. 12: Patterns of conserved and divergent gene expression across human and mouse lung cell types.
From: A molecular cell atlas of the human lung from single-cell RNA sequencing
a, Dot plots of PTPRC and MYL6 expression in mouse and human lung cell types (SS2 datasets) showing two examples of conserved (type 0) expression pattern. Blue shading, homologous cell types with conserved expression. b, Dot plots showing gain of expression (type 1 change) in several human cell types of RNASE1 (left) and all human cell types of TRIM38 (right). Red shading, cell types with divergent (gained) expression. c, Alveolar section of adult mouse lung probed by smFISH for general alveolar epithelial marker Nkx2-1, AT2 marker Sftpc, and transcription factor Myrf. Note Myrf is selectively expressed in mouse AT1 cells (Nkx2-1+ Sftpc− cells), as it is in humans (Extended Data Fig. 6c). Scale bar, 5 μm. Staining repeated on three mice. d, Dot plots of expression of CGRP and ADM hormone receptor genes showing expansion of expression (type 2 change) in human endothelial cells (10x data sets). e, Dot plots of expression of emphysema-associated gene SERPINA1 showing switched expression (type 3 change) from mouse pericytes (top) to human AT2 cells (bottom) (SS2 datasets). f, Dot plots comparing expression and conservation of HHIP with those of other Hedgehog pathway genes including ligands (SHH, DHH, IHH), receptors (PTCH1, PTCH2, SMO), and transducers (GLI1, GLI2, GLI3) (SS2 datasets). g, Dot plots of expression of serous cell markers LTF, LYZ, BPIFBP1 and HP showing switched expression (type 3 change) from mouse airway epithelial cells to human serous cells, which mice lack (asterisk). Dot plots of expression of lipid handling genes APOE, PLIN2 and FST show switched expression (type 3 change) from mouse alveolar stromal cells to human lipofibroblasts, which mice lack (asterisks). ‘Mm()’ or ‘Hs()’, genes in which duplications between mouse and human were collapsed to HomologyIDs (10x and SS2 datasets). h, Pie chart of fraction of expressed genes in lung showing each of the four types of evolutionary changes in cellular expression patterns from mouse to human. Histogram below shows number of lung cell types that the 602 genes with perfectly conserved cellular expression patterns (type 0) are expressed in; note that almost all are expressed in either a single cell type (67%) or nearly all cell types (33%). For more details on statistics and reproducibility, see Methods.
