A map of intra- and intercellular immune responses across diverse in vitro stimuli and inflammatory disease

In vitro stimulation of healthy human immune cells is widely used to model the immune states observed in disease, both to investigate pathology and to test therapeutic approaches. However, experiments typically focus on individual cell types or stimuli and a comprehensive cellular comparison of common immunomodulators and their relevance to disease is lacking.

We used single-cell transcriptomics to generate a reference profile of human peripheral blood mononuclear cells treated with 11 different in vitro stimuli, totalling over 150,000 cells across 21 immune cell types. We demonstrate its utility by performing comparative analyses across the immunomodulatory conditions and against peripheral blood profiles from patients with inflammatory disease.

We describe transcriptomic responses both unique to and shared across stimuli. For instance, stimulation via the T cell receptor (anti-CD3, CytoStim™) and IFN-α induced broad activation signatures, including indirect effects across multiple cell types, whereas TNF-α and LPS elicited more restricted, cell-specific responses. Ligand-receptor interaction mapping also uncovered the dominant intercellular signalling pathways in each stimulation. Comparing to patient datasets, we identified several aspects of inflammatory disease recapitulated by stimuli. For example, IFN-α stimulation induced SLE-like signatures across cell types, whereas LPS did so specifically within monocytes. However, comparative cell-cell network analysis showed that in vitro stimuli were only able to recapitulate some, but not all, aspects of intercellular interactions upregulated in SLE, highlighting the limitations of these model systems.

This dataset provides a valuable resource for understanding the effects of common in vitro blood stimuli, offering insights into their similarities and differences at cellular resolution, and, as demonstrated here, helping to guide the appropriate use of in vitro systems to model disease.