CRISPR in space

David Li, Aarthi Vijayakumar, Deniz Atabay, Guy Bushkin, Michelle Sung, and Rebecca Li by a Saturn V rocket during a trip to NASA's Johnson Space Center

From left to right, David Li, Aarthi Vijayakumar, Deniz Atabay, Guy Bushkin, Michelle Sung, and Rebecca Li by a Saturn V rocket during a trip to NASA's Johnson Space Center

May 4, 2019

Tags: Fink LabReddien Lab

On May 4, as a SpaceX Falcon 9 rocket roared to life at Cape Canaveral Air Force Station and thundered skywards, launching a Dragon spacecraft to the International Space Station (ISS), four teenagers from Minnesota closely monitored its journey. The spacecraft carried components of a science experiment devised by the teens as high school students, soon to be implemented by astronauts on the ISS. Also celebrating the launch was the students’ mentor, Massachusetts Institute of Technology (MIT) graduate student Kutay Deniz Atabay, a researcher in Whitehead Institute Member Peter Reddien’s lab, and fellow advisor Guy Bushkin, previously a postdoctoral fellow in the lab of Whitehead Institute Member Gerald Fink, and now a senior scientist in Former Whitehead Institute Fellow David Pincus’ lab at the University of Chicago. The students and mentors had been brought together by Genes in Space, an annual challenge co-founded by miniPCR and Boeing, which invites students in grades seven to twelve to propose investigations into pressing biological questions in space. The winning proposal is carried out on the ISS.

“Genes in Space is a special program because it’s not just theoretical; these students actually get to see their experiments performed in space,” Atabay says. “Contributing to this unique and incredibly inspirational experience, mentoring the kids and getting to be a part of it ourselves, is wonderful.”

Every year when the Genes in Space challenge begins, hundreds of students from across the country submit proposals for an experiment that uses PCR technology and needs to be done in the ISS’s microgravity space environment. A group of five researchers from MIT and Harvard University help the Genes in Space team to select five finalist proposals, and then each of the researchers is assigned as a mentor to one of the finalist teams to help them get their proposal ready for presentation. This year, both Atabay and Bushkin — avid aficionados of space and space research — were mentors, and Bushkin later joined Atabay in advising the winning team. This was Atabay’s fourth year as a mentor; in 2016 he mentored challenge winner Julian Rubinfien, whose experiment targeted and amplified telomeric sequences, as well as establishing a diagnostic assay novel to space.

Atabay’s team this year were David Li from Woodbury High School in Minnesota, now an undergraduate at MIT, and Michelle Sung, Aarthi Vijayakumar, and Rebecca Li from Mounds View High School in Minnesota. Their winning proposal, a version of which will be completed on the ISS in coming weeks and months, was to look at which DNA repair mechanism cells favor in microgravity to remedy double stranded breaks. The winning idea was selected after all five finalists gave presentations at the annual ISS Research and Development Conference in front of astronauts, scientists, teachers, and engineers from NASA and Boeing. Atabay and Bushkin agree that all of the finalists gave impressive presentations, but Atabay was blown away by the presentation skills of his team.

“The students are incredibly well-versed in the science,” Atabay says. “They didn’t just memorize the facts they needed, they understood in depth what they were talking about, and answered increasingly complex questions from the audience.”

The students proposed using the CRISPR/Cas9 gene editing tool in space, in order to create double stranded breaks such as might occur in astronauts’ DNA due to increased radiation exposure during long duration spaceflight missions. Errors introduced during DNA repair can lead to cancer and other disease risks, so understanding how cells cope with double stranded breaks during spaceflight is important. This will be the first use of CRISPR/Cas9 in space, and the first experiment in which every step from introducing DNA into cells to reading the outcome of DNA repair will occur in space.

After the team’s proposal was selected, they began to work with miniPCR and NASA scientists to redesign the experiment in order to fit the requirements and restrictions of the ISS. The students had originally proposed looking at DNA repair in human cells, but the team realized that this would not be feasible within the given timeframe. Atabay then tapped Bushkin, whose Whitehead Institute research involved designing CRISPR tools for yeast, to help redesign the experiment using yeast cells. The final protocol uses two strains of Saccharomyces cerevisiae, commonly known as baker’s yeast. A strain found in the wild favors the DNA repair mechanism homologous recombination (HR), while a mutant strain favors non-homologous end joining (NHEJ), which is more-error prone and likely to lead to genes becoming nonfunctional or deleterious. Yeast cells that use HR to fix breaks require an additional piece of DNA to stitch into the repair; in this case, the researchers have provided a piece of additional DNA, known as a repair template, that when inserted will cause the typically white yeast cells to turn pink. In this way, astronauts on the ISS will have an easy visual cue to see whether and when the yeast colonies have repaired their DNA using HR. The cells’ DNA will then be amplified and sequenced to analyze changes introduced during HR and NHEJ repair.

“Because of its simplicity, efficiency, and the ease of visually distinguishing the mutated colonies, this system is ideal for the challenging environment on-board the International Space Station,” Bushkin says.

Getting the experiment ready for its trip to space was a large undertaking with many participants. Genes in Space representatives from Boeing and miniPCR were excellent collaborators, and NASA scientists Sarah Wallace and Sarah Stahl were instrumental to the process of finalizing the experimental protocol and testing the design, Atabay and Bushkin say. Further staff helped to store, prepare, and transport the experiment components. With the arrival of the Dragon spacecraft at the ISS, the experiment will be turned over to the astronauts onboard, but that doesn’t mean the project is over for the teammates on the ground. Students and mentors will be able to watch the astronauts begin the experiment on a live video feed. After the astronauts have completed the experiments, the team will analyze the results and write them up for publication.

“I think I can speak for everyone involved when I say it’s a thrill and an honor to be involved in this part of human history, expanding our knowledge about biology in space,” Atabay says.

 

Written by Greta Friar

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