Multi-modal single-cell sequencing reveals network transition in circulating monocytes that aligns with faster recovery in patients with trauma and favours a response to M-CSF

Background Previous transcriptomic studies demonstrated an acute genomic storm in circulating immune cells after trauma that gradually returns to baseline. The magnitude and duration of these changes is associated with post-injury complications. We hypothesised that other immune cell features emerging in the subacute timeframe should be associated with recovery. Methods We applied DOGMA-seq on peripheral blood mononuclear cells isolated at day 3 after injury from the patients undergoing slow or fast recovery from critical illness (n = 8/group), along with age-and-sex matched healthy controls. We explored the functional responses of newly identified gene co-expression networks using in vitro cell culture (GM-CSF or M-CSF induced macrophage differentiation) followed by scRNA-seq. Findings We identified a subset of CD172a hi/MHCII hi, CD14+ monocytes that were distinct from baseline, and overrepresented in patients that recovered faster and associated with changes in several key gene co-expression networks. A gene co-expression pattern associated with chemotaxis and cell adhesion was overrepresented in patients with fast recovery and, specifically associated with increased accessibility of AP1 family motifs, continuously deviating from baseline, and favouring a response to M-CSF rather than GM-CSF during macrophage differentiation. Interpretation Our findings add a new information layer to the current paradigm by demonstrating that recovery is not simply a return to the baseline state and instead involves the emergence of new monocyte subset with new transcriptomic programs that may influence the macrophage response. Funding National Institutes of Health R35 grant R35GM127027 (T.B.).