First Genome-Editing Experiment Conducted in Space
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For the first time, scientists have used a CRISPR-Cas9 mutagenesis strategy on eukaryotes in an unlikely laboratory – the International Space Station (ISS). The research is published in the journal PLoS ONE.1
DNA on Earth
Here on Earth, we know that there are many factors – intrinsic and extrinsic – that can contribute to the damage of our "molecular blueprint", or DNA code. These factors include intracellular metabolism and exposure to external factors such as UV light, pollution and some therapeutics such as chemotherapy.2 To prevent unwanted genetic mutations that could lead to adverse changes in the status of our health, our cells are tasked with repairing this damage through a number of different molecular pathways. Efficient DNA repair has been linked to "extreme longevity" in centurions, while unrepaired DNA damage appears to be associated with increased aging.
But what happens to our DNA when we are not on Earth? The majority of us will not leave the planet in our lifetime, nonetheless, space exploration is extremely important when it comes to navigating and understanding human life. "Human space exploration helps to address fundamental questions about our place in the Universe and the history of our solar system. Through addressing the challenges related to human space exploration we expand technology, create new industries and help to foster a peaceful connection with other nations," National Aeronautics and Space Administration (NASA) states. It is therefore important that we have a comprehensive understanding of how space travel impacts astronauts at the molecular and cellular level. Research continues to explore this, particularly in reference to DNA damage and how the mechanisms used to repair such damage might differ on Earth and in space.
Repairing DNA breaks
DNA can "break" in different ways, but double-strand breaks, whereby the phosphate "backbone" of the DNA helix is hydrolyzed, are especially problematic. If left unrepaired, double-strand breaks can lead to cell death, or their improper repair can result in the formation of cancerous cells. Eukaryotic organisms on earth can repair such breaks via two approaches: homologous recombination and non-homologous end joining.
DNA damage in space
In a 2017 review, Moreno-Villanueva and colleagues concluded that space environmental factors can cause damage to DNA, which may contribute to adverse health in astronauts.3 However, they also acknowledged that this field of research was burdened with conflicting results obtained from different studies. Consequently, it has remained unclear which DNA repair mechanisms are adopted in space, largely because a large portion of previous research had utilized DNA samples in which the breaks had been induced on Earth before being sent to space for repair analysis. More carefully designed experiments with "higher levels of DNA damage that is intentionally induced in space" were called for, but this remained challenging from both a logistical and safety standpoint.
Sarah Stahl-Rommel is a microbiologist at NASA’s Johnson Space Center (JSC). She is also part of the Genes in Space initiative, a collaboration between Boeing and miniPCR bio that offers young students the opportunity to design a DNA experiment that could address challenges in space exploration. In the latest PloS ONE publication, Stahl-Rommel and colleagues present a novel technology that was born from the Gene in Space contest: a CRISPR-based assay for DNA break induction and the assessment of double-strand break repair pathway choices. The workflow can be conducted entirely in space.
What is CRISPR?
CRISPR is an acronym for Clustered Regularly Interspaced Short Palindromic Repeats. These are short sequences of DNA that repeat themselves in bacteria. In between the repeats, viral DNA sequences can be found. When that virus infects the bacteria, the bacteria transcribe the viral DNA sequences to RNA which then guides a specific protein, known as a nuclease (or Cas), to the viral DNA, and cuts it. Over proceeding years, scientists harnessed this naturally-occurring immune response to create an in vitro and eventually in vivo genome-editing technology. The RNA is engineered to guide the Cas nuclease to a specific location in the genome, where it will cut.
An out of this world experiment
"On Earth, we use radiation and other tools to induce double-strand DNA breaks in a more controlled way, but it isn’t safe to use radiation on the space station because the protective equipment needed to safely irradiate cells would be difficult to bring to space," explains Emily Gleason, biologist and curriculum specialist at miniPCR bio. "The 2018 winners of the Genes in Space experiment proposed using CRISPR-Cas9 genome editing to introduce double strand breaks into DNA in a known location and in a way that is safe for the astronauts performing the experiment." Impressively, the winners of the contest, were four high school students from Minnesota: David Li, Michelle Sung, Rebecca Li and Aarthi Vijayakumar.
In the present study, the team used Saccharomyces cerevisiae, a type of yeast, to test the technique. This is because yeast is safe to grow and handle, has a nucleus like human cells and DNA repair in yeast has been extensively studied.
"First, we needed to insert the instructions for making the components of the CRISPR-Cas9 genome editing system into yeast cells. These components, when assembled inside the cell, would cut the yeast DNA at a particular site. If left alone, this cut would result in the death of the yeast cells, however we also provided the instructions for repairing the DNA lesion," Gleason says. Inserting foreign DNA into cells had not been performed in space prior to this study, so this initial step was an ambitious goal. Once the CRISPR-Cas9 system was inserted into the cells, it would damage the DNA at the specified location, which would be visibly detectable as a color change in the yeast from red to white. "Additionally, we assessed the DNA sequence at the lesion site to see if it had been edited using the instructions we provided. These techniques confirmed that the cells had used the instructions we provided to repair the damage caused by the CRISPRCas9 system," Gleason explains.
In other words, the researchers had performed the first successful CRISPR-Cas9 genome editing experiment in space. "The ability to perform this all-encompassing, end-to-end investigation is a huge step forward for space biology," says Sarah Castro-Wallace researcher at the NASA JSC and co-author of the study.
A complex molecular biology workflow in space
The research was a technical demonstration that showed it was possible to perform a complex molecular biology workflow entirely in space. "While this was quite complex, the data we collected isn't sufficient to answer the question posed by the high school students who inspired this study – how is DNA repair pathway choice impacted by microgravity?" Gleason notes. However, the project does provide a framework for experiments that are of a larger-scale and that could generate enough data to answer this question.
"By giving these students a voice, we have seen the adoption of new projects expanding the scope of the established research agenda," Gleason adds. The final result? An experiment that has pushed the field of space biology forward.
1. Stahl-Rommel S, Li D, Sung M, Li R, Vijayakumar A, Atabay KD, et al. A CRISPR-based assay for the study of eukaryotic DNA repair onboard the International Space Station. PLoS ONE. 2021;16(6): e0253403. doi: 10.1371/journal.pone.0253403.
2. Williamson EA, Wray JW, Bansal P, Hromas R. Overview for the histone codes for DNA repair. In: Doetsch PW, ed. Progress in Molecular Biology and Translational Science. Vol 110. Academic Press; 2012:207-227. doi:10.1016/B978-0-12-387665-2.00008-0.
3. Moreno-Villanueva M, Wong M, Lu T, Zhang Y, Wu H. Interplay of space radiation and microgravity in DNA damage and DNA damage response. npj Microgravity. 2017;3(1):14. doi: 10.1038/s41526-017-0019-7.