High dimensional single cell analysis reveals unexpected immune cell types, and loss of motility of alveolar macrophages regulated by PPARγ in chronic obstructive pulmonary 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 due to heterogeneity of these diseases. To resolve it, we applied multi-color flow cytometry (MCFC) and single-cell RNA sequencing (scRNA-seq) combined with cellular functional tests and established a detailed characterization of innate immune cells in the bronchoalveolar lavage (BAL) of 55 patients (pts) (20 controls, 26 COPD, 9 asthma pts). Based on MCFC, we found significant increase of neutrophils in BAL of COPD (2.4-fold) and asthma (8.8-fold) pts, and group 1 innate lymphoid cells (ILC1s) in COPD pts (17.4-fold) compared to controls. In addition, scRNA-seq revealed an unexpected mast cell population in BAL of COPD pts. Further gene expression analysis showed increased gene expression associated with cell adhesion and decreased CCR5 gene 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 was diminished in AMs of COPD pts. We also found that the activation of PPARγ with its ligand restored impaired migration ability of AMs from COPD pts, whereas suppression of PPARγ with siRNA transfection decreased the migration ability of AMs, indicating that PPARγ regulates the migration ability of AMs.

We here reveal an unexpected mast cell population, high levels of neutrophils and ILC1s in BAL of COPD pts, while AMs are changed transcriptionally and functionally showing less migration which is regulated by PPARγ. 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.