How omics teaches us about the biology of space travel and charts a course for understanding health on earth

Space reshapes the human body in ways that don’t normally occur on Earth. The lack of gravity, the increase in radiation, and the isolation from other humans make space a uniquely hostile and extreme environment. After spending time in space, astronauts find that they have a decrease in muscle mass, a loss of bone density, and even an increase in height (Scott Kelly, who spent one year in space, temporarily “grew” about two inches while in space).

But what’s really going on beneath the surface on a molecular level?

On a recent episode of the Translating Proteomics podcast, we sat down with Afshin Beheshti, Professor of Surgery, Director of the Center for Space Biomedicine, and Associate Director of the McGowan Institute for Regenerative Medicine at the University of Pittsburgh, to discuss the impacts of microgravity and space radiation on the body, how scientists are studying these changes using omics technologies, and ways to mitigate their effects. Here, we cover some of the key takeaways from this fascinating conversation.

Check out our “What is multiomics?” blog post for some brief background on multiomics.

How multiomics provides a holistic view of spaceflight biology

To understand how space changes the human body, one thing researchers can do is take samples before, during, and after spaceflight or simulated space conditions. Samples such as blood, urine, and saliva are all rich sources of information about how the body is functioning. From these samples, transcriptomic, proteomic, and metabolomic analyses provide detailed looks at the state of the body during space travel and how it can change over time after returning from space.

In 2020, Beheshti’s team used a multiomic approach to analyze existing transcriptomic, proteomic, metabolomic, and epigenomic data from space missions, including data from human cell models, tissues, and mice. The team found alterations in many pathways, but one thing stood out: mitochondrial dysfunction. Their comprehensive study found impacts on mitochondrial function evidenced by the genomic, proteomic, and metabolomic effects observed on both the cellular and tissue level. Based on their data and data from previous studies, Beheshti thinks that many other processes such as immunity and metabolism that change during spaceflight are a result of mitochondrial dysfunction.

One advantage of multiomic approaches like this one is that they provide more comprehensive views of biological function at the molecular level. Beheshti explains that on their own, each omic technique can only “show you one piece of the puzzle.” In proteomics, for example, “you’re looking at all the protein levels changes,” he says. “But you might not see some proteins being expressed and you don’t know why.” The pairing of proteomics with another technique like transcriptomics could help pinpoint the exact cause of this.

Beheshti does exactly this in his research on the role of micro RNAs (miRNAs) in space biology. miRNAs are small RNA molecules that can bind complementary sequences in mRNA and silence their translation. He’s found miRNA signatures associated with spaceflight in simulated conditions and subsequently found that inhibiting these miRNAs could reduce inflammation, DNA damage, and mitochondria dysfunction.

Studies such as this one show the importance of using multiple approaches together to more fully grasp biological changes on multiple levels. “If [I] had just focused on the proteomic part, I would miss exactly what the microRNAs are doing that silence the proteins that are not expressed anymore,” he said. On the other hand, analyzing just the transcriptome would neglect to account for how these changes manifest at the protein level.

Bridging space biology and human health research

In the above example, we see that what scientists learn about biology in space can affect how we approach biology on Earth and vice versa. What scientists learn about mitigating damage to the body in space could also be applied to conditions on Earth. For instance, Beheshti’s findings on mitochondrial dysfunction suggest that already approved therapies for mitochondrial disease could be repurposed to alleviate these effects during spaceflight. Beheshti is currently working on how a nutraceutical called kaempferol reduces the effects of mitochondrial damage from space radiation by boosting mitochondrial biogenesis. He mentions that mitochondrial damage also occurs during long COVID and that kaempferol could help restore mitochondrial function in people with long COVID.

In addition, Beheshti’s work on frailty and aging biomarkers during spaceflight have direct parallels to aging on Earth: muscle loss, increased inflammation, and other age-related characteristics occur in space on a much accelerated schedule compared to on Earth. Countermeasures to mitigate frailty and aging due to space travel could have direct impacts on the health of aging or frail populations on Earth, where interventions could otherwise require decades-long studies to evaluate their effects.

Increasing the accessibility of multiomics in space biology

Getting samples before and after spaceflight isn’t very different from getting samples for any other earthbound study. But, as you can imagine, getting real-time information while in space can be difficult: you either need a way to run the samples in space or a way to preserve the samples so they can return to earth intact without degradation. Real-time measurements might be important for researchers to see direct effects that occur on short time scales, and in the future, interventions based on real-time measurements could also help improve astronaut health while in space.

Excitingly, we are arriving at a time where studying omics directly in space is becoming more accessible in many ways. Smaller sequencing platforms have allowed astronauts to sequence DNA in space – Kathleen Rubins was the first person to do this in 2016. And in 2024, scientists reported the first longitudinal long-read RNA sequencing done in space. However, for measuring other molecules like proteins in real-time during spaceflight, Beheshti says we’re not quite there yet. “Maybe in five years, someone will have a miniaturized proteomic machine they could [use] in space,” he says.

Despite this, omics has come a long way. The cost of RNA sequencing has come down and next-generation proteomics platforms like the Nautilus Voyager™ Platform are developing at a rapid pace. Up-and-coming omics tools may potentially enable researchers to study more than one -ome together in a single study especially if there’s publicly available data. Behenshti’s research often relies on such publicly available data and he frequently uses the NASA Open Science Data Repository as a starting point for many of his research papers. GeneLab, an open-access resource within this repository, contains omics data related to spaceflight. “You don’t need to go to space,” he explains. “If you have curiosity, you could go to this platform and start asking your favorite questions.” Another resource, the Space Omics Medical Atlas (SOMA), houses a collection of data from genomics, epigenomics, transcriptomics, proteomics, metabolomics, and microbiomes across a range of space missions. Using publicly available databases means that multiomic research becomes more cost-effective and enables more researchers to study space biology.

With the Nautilus Voyager Platform, we aim to make single-molecule proteomics accessible to all and hope the platform will be used to empower space biology in the not-so-distant future. If you’ve got a project you think can be advanced by scalable, single-molecule proteomic analysis, join our Iterative Mapping Early Access Program.