High dimensional single cell analysis reveals unexpected immune cell types, and loss of motility and chemokine receptor expression of alveolar macrophages in chronic obstructive respiratory disease

Innate immune cells have been implicated to play a major role in the pathogenesis of chronic obstructive pulmonary disease (COPD) and asthma. Albeit there have been reports about changes in distribution and cellular functions in these diseases, we still do not fully understand them. By combining multi-color flow cytometry (MCFC), single-cell RNA sequencing (scRNA-seq) and functional tests, we established a detailed characterization of innate immune cells in the bronchoalveolar lavage (BAL) of 36 patients (pts) (13 controls, 17 COPD, 6 asthma pts). Based on MCFC, we found significant increase of neutrophils in BAL of COPD (2.4-fold) and asthma (3.8-fold) pts, and group 1 innate lymphoid cells (ILC1s) in COPD pts (7.5-fold) compared to controls. In addition, scRNA-seq revealed an unreported mast cell population in BAL of COPD pts. Further gene expression analysis showed a significant decrease of CCR5 expression in alveolar macrophages (AMs) of COPD pts. As a consequence, AMs of COPD pts showed less migration towards CCL3, a CCR5 ligand known to be a chemoattractant of AMs. Moreover, the transcription factor PPARγ, an upstream candidate for CCR5 was diminished in AMs of COPD pts. We here reveal an unexpected mast cell population, high levels of neutrophils and ILC1s in BAL of COPD pts, while AMs are changed functionally showing less motility to CCL3, less CCR5 and PPARγ expression. Thus, we have established a working model to determine whether this dysfunction is a consequence or a pre-requisite for COPD and whether it is also linked to the susceptibility of the pts to recurrent infections.