The Transcriptional and Phenotypic Characteristics that Define Alveolar Macrophage Subsets in Acute Hypoxemic Respiratory Failure
The transcriptional and phenotypic characteristics that define alveolar monocyte and macrophage subsets in acute hypoxemic respiratory failure (AHRF) are poorly understood.  We applied CITE-seq (single-cell RNA-sequencing + cell-surface protein quantification) to bronchoalveolar lavage fluid and peripheral blood cells longitudinally collected from subjects with AHRF to identify novel alveolar monocyte/macrophage subsets, and then validated their identity in an external cohort using flow cytometry.  We identified 2 monocyte and 6 macrophage subsets in alveolar samples using CITE-seq data.  Some of the subsets had similar transcriptional profiles as those reported in healthy subjects (metallothionein genes) or patients with COVID-19 (LGMN-expressing).  We also identified novel subsets with transcriptional signatures that straddled previously reported monocyte and macrophage subsets.  We used information from CITE-seq to determine cell-surface proteins that distinguish transcriptional subsets (CD14, CD163, CD123, CD71, CD48, CD86, and CD44).  In the external cohort, we found a higher proportion of CD163/LGMN alveolar macrophages was associated with mortality.  We report a parsimonious set of cell-surface proteins that can distinguish alveolar monocyte/macrophage subsets using scalable approaches that can be applied to clinical cohorts. Overall design: These data contain 10x Gene Expression and Feature Barcode (CITE-seq) data from Bronchial Alveolar Lavage samples from twelve samples taken from eight intubated patients at two timepoints. Each bam file corresponds to a single sample from a single patient at a timepoints (denoted v1 or v2 for time). Four patients were suffering from Acute Respiratory Distress Syndrom (ARDS) at time of first sample (SLK3, SLK7, SLK22, SLK23).