Single Cell Analysis Identifies Conserved Features of Immune Dysfunction in Simulated Microgravity and Spaceflight [scRNA-Seq]

Microgravity is associated with immunological dysfunction, though the underlying mechanisms are poorly understood. Here, using single cell analysis of human peripheral blood mononuclear cells (PBMC)s exposed to short term (25 hours) simulated microgravity, we characterize altered genes and pathways across immune cells under basal and stimulated states with a Toll like Receptor-7/8 agonist. At basal state, simulated microgravity altered the transcriptional landscape across immune cells, with monocyte subsets showing most pathway changes. Remarkably, short term simulated microgravity was sufficient to increase endogenous retroviral and mycobacterial transcripts. Under stimulation in simulated microgravity, nearly all immune cells demonstrated differences in functional pathways. Results from single cell analysis were validated against additional PBMC samples, including by RNA sequencing and super-resolution microscopy, and against data from the Inspiration-4 (i4) mission, JAXA6 mission, Twins study, and spleens from mice housed on the international space station. Combined results show significant impacts of microgravity on pathways essential for optimal immunity, including the cytoskeleton, interferon signaling, pyroptosis, temperature-shock, nuclear receptors, IL-6 signaling, HIF1α, and sirtuin signaling. Using machine learning, we identified numerous compounds linking microgravity to immune cell transcription, and demonstrate that the flavonol, quercetin, can reverse most abnormal pathways. These results offer insight into maladaptation of the immune system in microgravity, and provide opportunities to develop countermeasures that maintain normal immunity in space. Comparative gene expression profiling analysis of RNA-seq data for PBMCs under basal and stimulated states with a Toll like Receptor-7/8 agonist in simulated microgravity and normal gravity.