Cell-free DNA (cfDNA) and Exosome Profiling from a Year-Long Human Spaceflight Reveals Circulating Biomarkers

Abstract

Summary Liquid biopsies based on cell-free DNA (cfDNA) or exosomes provide a noninvasive approach to monitor human health and disease but have not been utilized for astronauts. Here, we profile cfDNA characteristics, including fragment size, cellular deconvolution, and nucleosome positioning, in an astronaut during a year-long mission on the International Space Station, compared to his identical twin on Earth and healthy donors. We observed a significant increase in the proportion of cell-free mitochondrial DNA (cf-mtDNA) inflight, and analysis of post-flight exosomes in plasma revealed a 30-fold increase in circulating exosomes and patient-specific protein cargo (including brain-derived peptides) after the year-long mission. This longitudinal analysis of astronaut cfDNA during spaceflight and the exosome profiles highlights their utility for astronaut health monitoring, as well as cf-mtDNA levels as a potential biomarker for physiological stress or immune system responses related to microgravity, radiation exposure, and the other unique environmental conditions of spaceflight.

Plasma derived cell-free mitochondrial DNA originates mainly from circulating cell-free mitochondria

“…Consequently, our findings led to a profound revision of previous assumptions regarding the significance of the cir-mtDNA amounts detected in our and other previous works (10,34,51,55,59,69–71). First, it can no longer be considered valid to examine cir-mtDNA with WGS or to discuss cir-mtDNA fragmentation under 1000 bp when discussing the overall cir-mtDNA population, since it accounts for a very tiny part of the cir-mtDNA amount.…”

“…Note, other circulating nucleic acid species include viral, bacterial and fungal DNA or RNA. These whole types of circulating nucleic acids are now accurately characterized by high throughput sequencing (6,25,34,38,50,51). Despite previous efforts at designing methods, particularly Q-PCR based, for detecting mtDNA from blood cells (13,14,15,20), the standardization of cir-mtDNA quantification has proved to be a challenge, in particular concerning the issue of calibration.…”

“…The accurate differentiation of cirDNA of nuclear and mitochondrial origin is feasible (10,31,33), and may offer diagnostic information in specific physiological or pathological situations (32,34,35). Note, we hypothesized that the respective quantitation of cir-mtDNA and cir-nDNA may have potential cancer screening capacity (10,36,37).…”

Circulating miRNA Spaceflight Signature Reveals Targets for Countermeasure Development

“…Despite the demonstrated contribution of CD14 + monocytes to increases in the circulating miRNAs, it is also possible that the miRNAs could be coming from another organ where they are more abundantly expressed. Thus, further studies will be necessary to determine the exact origin of the increased miRNAs and tissue response, such as with cell-free DNA profiling (Bezdan et al, 2020), which will be beneficial for mapping and developing effective countermeasures. Finally, the successful prevention of vascular damage through antagomir therapy in our proof-of-concept human tissue model demonstrates the need for further experiments to fully characterize antagomir therapies in vivo to understand their clinical safety and efficacy and to examine which components of the spaceflight miRNA signature make effective targets for antagomir therapies.…”

Genomic Changes Driven by Radiation-Induced DNA Damage and Microgravity in Human Cells

“…Notably, mitochondria, by generating mitochondrial ROS during cellular respiration, contribute to an increase in oxidative stress. Different studies have demonstrated that OsaD has a significant impact on human physiology as the changes in oxidative levels of irradiated cells may remain for days after exposure leading to long-term effects [ 38 ] in addition to serving as a plasma biomarker [ 39 ].…”