Tissue availability remains an important limitation of single-cell genomic technologies for investigating cellular heterogeneity in human health and disease. Bronchoalveolar lavage (BAL) represents a minimally invasive approach to assess an individual's lung cellular environment for diagnosis and research. However, the lack of high-quality healthy lung reference data is a major obstacle to using single-cell approaches to study a plethora of lung diseases. Here, we performed single-cell RNA-sequencing (scRNA-seq) on over 40,000 cells isolated from BAL of four healthy volunteers. Of the six cell types or lineages that we identified, macrophages were consistently the most numerous across individuals. Our analysis confirmed the expression of marker genes defining cell types despite background signal due to the ambient RNA found in many single-cell studies. We assessed variability of gene expression across macrophages and defined a distinct subpopulation of cells expressing a set of genes associated with the Macrophage Inflammatory Protein (MIP-1). RNA in situ hybridization and re-analysis of published lung single-cell data validated the presence of this macrophage subpopulation. Thus, our study characterizes lung macrophage heterogeneity in healthy individuals and provides a valuable resource for future studies to understand the lung environment in health and disease.
Keywords: Bronchoalveolar lavage (BAL); genomics; heterogeneity; lung immunology; macrophage.