International Space Station update: direct RNA sequencing in space

Photo (composite) courtesy of NASA Johnson Space Center

This week, for the first time, direct RNA sequencing (mapping the order of bases on a native strand of RNA) has been successfully carried out in space.

Aboard the International Space Station, NASA astronaut Ricky Arnold used the Oxford Nanopore MinION to sequence strands of RNA.  Nanopore sequencing is the only existing method by which native RNA strands can be sequenced, without using copies.

This builds on previous work that allowed astronauts Kate Rubins and Peggy Whitson to perform the first DNA sequencing in a microgravity environment, and to use DNA sequencing to analyse microbial DNA on board the ISS.

The ability to sequence both DNA and RNA in a microgravity environment opens up a range of potential biological analyses that could be performed in space.  NASA scientists are interested in identifying onboard microorganisms, monitoring changes in human health or microbiomes in response to spaceflight, performing biomedical research in microgravity, or even possibly aid in the detection of DNA- or RNA-based life elsewhere in the universe.

Why RNA?

Gaining information about RNA is particularly useful as it provides insight into how the DNA ‘code’ of an organism is interpreted at a given moment in time. Direct RNA sequencing also allows scientists to understand the epitranscriptomics of that sample, providing more insight into the biological processes within an organism.

Through RNA sequencing it is possible to obtain a snapshot of how a given cell or tissue is functioning at a given time point.  For example, a tumour cell will have different genes up- or down-regulated when compared to a normal cell of the same tissue type. RNA information also gives insights into other diseases of humans or plants – indeed viruses often have RNA based genomes.  RNA sequence data can be used to elucidate the identity of mixed microbiological populations in diverse ecosystems.

Why direct RNA analysis?

Directly sequencing RNA is only possible with nanopore technology; traditional DNA sequencing relies on converting RNA to another type of molecule - cDNA before sequencing can take place.  This process can result in loss of information.

NASA Researchers explain the impact of direct RNA analysis onboard the ISS in this blog:

“Because the MinION detects changes in current, it can directly sequence RNA as well as DNA,” said co-investigator Aaron Burton. “With most other platforms, you first have to convert RNA to DNA, and this additional processing could bias your data, causing you to miss what’s really going on. Direct RNA sequencing results in near real-time gene expression data.”

“With small modifications to our process, you can pretty much do any type of sequencing on the station,” said Sarah Wallace. “Until now, we had to bring samples back to the ground to see these changes. We know gene expression changes, but freezing a sample and bringing it back to the ground could result in alterations not caused by the spaceflight environment. If we could look at it while on the station, it might look very different. There is so much to be gained from that real-time snapshot of gene expression.”

This RNA space mission follows the success of teams back on earth using direct RNA sequencing across a number of applications, some of which are summarised in this white paper.

One team from UCSC, who also collaborated with NASA for these direct RNA experiments, has produced an entire human transcriptome using direct RNA sequencing.  They commented: "RNA sequencing is one of the most direct and unambiguous ways to measure the state of living cells. Native RNA sequencing of the type performed by Astronaut Arnold on the ISS is particularly exciting because it preserves information about nucleotide modifications that occur after transcription. We think that RNA sequencing will be invaluable for monitoring the health of astronauts on long missions -- to Mars for example."

lc18-speaker.jpg You can also hear about the latest in RNA sequencing with nanopore technology from speakers at the London Calling 2018 conference and in recent publications.