From our previous work we have shown a key miRNA signature that is associated with spaceflight can be used as a biomarker and countermeasure to mitigate the damage caused by space radiation. Here, we have further expanded on this work to determine key biological factors that are being rescued by the countermeasure treatment. We performed RNA-sequencing and transcriptomic analysis on our established 3D microvessel cell cultures exposed to simulated deep space radiation (0.5 Gy of Galactic Cosmic Radiation) with and without the antagonists to three microRNAs (i.e. antagomirs). Significant reduction of inflammation and DNA DSBs activity is observed, along with key mitochondria functions being rescued after antagomir treatment. Lastly, we compared the key genes and pathways involved with the antagomirs with astronaut data from Inspiration4 and JAXA missions to demonstrate that the key genes and pathways associated with these experiments occur in humans and this countermeasure strategy can potentially be utilized in astronauts to mitigate the space radiation response.