Dr. Stephen C. Ekker and Jarryd Campbell of the Mayo Clinic’s Ekker Lab purchased an OpenTrons robot during our 2014 Kickstarter campaign. In March of this year, they started a new company, Lifengine, and we've since partnered with them to sell Lifengine’s first product: FusX, “the world’s first all-inclusive, in-house, automated gene editor production system."
I spoke with Ekker and Campbell over the phone to better understand their work, what FusX is, and how they put their OT-One robot to use. (Conversations have been edited.)
Edith Zimmerman, OpenTrons: What are you working on at the Ekker Lab?
Campbell: We use gene editing to make specific manipulations to a model system called zebrafish. They have mutations in their genome that are similar to disease-causing mutations in the human genome, so we study the model system of the animal to try to understand what’s going on in people.
And a cool thing about zebrafish is that after an egg has been fertilized and while it’s beginning to divide, it stays at the one-cell stage for [the relatively long time of] about 45 minutes, at which point you can microinject into the cell — literally, with a glass needle — to give it gene editing tools to alter its DNA.
We published a paper a few years ago that was the first of its kind to show that you can directly edit an animal by programming with an artificial DNA fragment to achieve a specific desired result. It’s called “knocking in” something. So you can “knock in” a piece of DNA, and the organism will grow up to have those traits. And then when it reproduces, its offspring will also have those traits. The idea was to demonstrate that you can really do disease modeling down to the single-nucleotide level, with precision, using this technology. The genome engineering field has exploded in the intervening four years.
How did your research lead you to OpenTrons?
Ekker: We’ve been interested in using robotics in biology for a long time. I’ve had some applications in my lab for potential use for automation, and I even helped bring in a rather expensive liquid-handling robot to the Mayo Clinic, but I don’t use it, because the software is such a challenge to deploy for new applications.
Campbell: We couldn’t program that robot ourselves, because the company essentially locked us out of the software. They also wouldn’t provide support unless we purchased new components for it each time we wanted to do a new experiment, and we don’t really like that business model. So Steve was a bit fed up, and one day he was on Kickstarter — he’s an early adopter of a lot of cool technologies and totally a junkie when it comes to tech — and I think he just came across the OpenTrons and bought it, immediately.
Ekker: My son had connected me with Kickstarter over the years — we’d helped fund the Pebble watch, for instance, and some other projects. But it’s always seemed ridiculous to me that automation has taken so long to arrive in the life sciences. And because I had a very specific application, I figured that if all the robot did was solve this one thing, it would justify its existence. It seemed low-risk.
What was that specific application?
Campbell: We had an easy-to-assemble protocol for making transcription activator-like effector nucleases (TALENs) that we were doing by hand, but it had a lot of individual components, so we’d had to increase its complexity. TALENs are like CRISPR-Cas9 in that they can target anywhere in the genome and edit, but TALENs are able to target more sequences and, on average, show very high efficacy. And we figured out that if we put our protocol on the robot, we could make the protocol as complex as we wanted, because the robot can handle complexity without making errors — without the human aspects of having to do pipetting by hand.
And somewhere in there you launched your new company, Lifengine.
Campbell: Right. So, once we had our OpenTrons and TALEN system working for us, we thought, “Okay, we have this robot, and we’ve built this cool system…”
Ekker: “...Why aren’t we making it commercially available?” Because channels like AddGene don’t allow their DNA plasmids to be made available to commercial enterprises. And we already had a few companies asking us for access to this tool at the time, which also made it easy to launch Lifengine. Factoring in the OpenTrons connection — the first accessible liquid-handling robot for life science labs — it seemed like a good bet to start a commercial operation to help other scientists, engineers, and entrepreneurs to use these great genome editing reagents — like the FusX system.
Campbell: Basically, the OpenTrons simplified everything for us. So much so that we spun off the system we’d developed and are now selling it as FusX, a gene editing tool-building application that works on the OpenTrons robot.
FusX is described in detail in the peer-reviewed journal Human Gene Therapy (abstract below), but can you summarize it here?
Campbell: FusX is essentially an all-in-one system for gene editing. It contains all the material you need to target any DNA sequence; you only need one kit, and you can make 25 custom TALENs without having to order more synthetic DNA.
Ekker: The TALE systems, especially the TALENs, are some of the most precise and active gene editing tools in the field, but the ability to manufacture them has been a challenge. This is because of how TALENs actually target DNA; many large, repetitive DNA sequences need to be assembled in order, which is difficult to do quickly. The FusX system solved this problem and allows you to rapidly make these tools so that you can get to doing your DNA-editing for your interesting biological questions.
Campbell: We also worked with OpenTrons to build a simple web interface for FusX that allows you to copy and paste the DNA sequence you want to target into the OpenTrons software, which then spits out the protocol file for the robot to assemble. (Although everything we’re making can still be done by hand.)
What types of experiments could people run with the FusX kits?
Campbell: At Recombinetics, they’re using this kind of science to do what’s called accelerated breeding, which is the process of putting traits into an animal’s DNA that are naturally occurring but difficult to breed for in traditional ways. Using TALENs, for example, they were able to gene edit a dairy cow so that it was born without its horns. And why that’s interesting is because dairy cows typically have horns, but the way you get rid of them — so that they don’t gouge one another — is to saw them off, basically. It’s a very common process, but it’s incredibly inhumane.
Another company, Calyxt, is using the same technology for agriculture. They’re interested in making — not gluten-free, but gluten-less foods, like finding a sweet spot for gluten where it maintains its properties in bread-making but also allows for people with celiac disease to tolerate it.
Ekker: I’m interested to see if having the robot available and accessible makes scientists more willing to do certain kinds of complex protocols. I’m looking for: “Well, you’d never do a Golden Gate System,” for instance, “because that’d mean making 300 plasmids, and pipetting that much is a pain.” But if you set that Golden Gate reaction up with an OpenTrons, it isn’t a pain, because the robot does the pain point. That’s the kind of cultural change I’m looking for.
You have to multiply it slowly — you have to multiply it by the scientific community — but there will be more of these that come out. More protocols and ideas made possible that would normally be too complex.
What’s next for Lifengine?
Ekker: It’s the camel’s nose in the tent, right? We have a very specific use case, and the robot is good for that. But that individual use case begs the question: “Okay, what else can you do with it?” We have a follow-up genome-engineering idea that will use the robot in a strictly analogous way — same kind of a deal, roughly 300 plasmids — and we’re building those plasmids right now.
But I’m particularly excited to see the second generation of tools — to see life science labs solve medical mysteries by using approaches that manual pipetting would have rendered impossible.
Campbell: We see FusX as the first in a suite of many gene editing applications that the OpenTrons robot can do. This kind of science is still mostly in the hands of academics and companies who can use it to make product, but now is just the beginning. Where it can go is really up to the creativity of the people who are using it.