Cell-free RNA analysis of plasma samples collected from six astronauts in JAXA Cell-Free Epigenome (CFE) Study

A detailed understanding of how the human body responds to spaceflight will be important to develop countermeasures for long-term space exploration. Liquid biopsies offer minimally invasive alternatives to traditional tissue biopsies, while also permitting the extraction of cell-free nucleic acids, which may resolve molecular heterogeneity and extend the multi-omics scope better than standard methods. Full-body molecular profiling using cell-free nucleic acids isolated from liquid biopsies is hence one viable avenue for advancing space healthcare. Here, we perform a liquid biopsy study with six astronauts who resided on the International Space Station (ISS) for more than 120 days, and show that plasma cell-free RNA (cfRNA) can capture longitudinal gene expression responses of internal tissues to the spaceflight environment. Analysis of cfRNA collected before, during, and after spaceflight confirmed previously reported mitochondria dysregulation in space. Screening with 361 cell surface marker antibodies identified an extracellular mitochondria (exMT)-enriched fraction associated with the scavenger receptor CD36. RNA-sequencing analysis of the CD36 fraction revealed various tissue origins, some of which have not been well characterized due to their conventional inaccessibility. We compared our data to plasma cfRNA mouse data from a JAXA mission, in which on-board artificial gravity had been used, and discovered that microgravity induced the observed systemic responses. Our study used minimally invasive approaches to demonstrate exMT release as a conserved process in space and establishes the impact of gravity on Earth as an essential signal for normal homeostasis.