SHERLOCK CRISPR Kit: The Next Generation of Diagnostics (with Podcast)

CRISPR is well known for its powerful potential in therapeutics but this tool does more than gene editing. CRISPR’s search function is being utilized in diagnostics—the latest example being the newly-invented CRISPR-Chip for target DNA detection.

Today, we chat with Omar Abudayyeh and Jonathan Gootenberg, co-founders of Sherlock Biosciences, one of the top CRISPR start-up companies already making news in the medical diagnostic industry. This dynamic duo is famous for discovering the Cas13 enzyme, developing the SHERLOCK CRISPR diagnostic kit, and balancing academia and their own company.

Learn more about their journey from grad student life to co-founding Sherlock Biosciences in this interview.

Listen to the podcast here, or jump down and start learning & reading the podcast transcript — the choice is yours!

A CRISPR diagnostic test harnesses the “search” function of CRISPR nucleases to detect DNA or RNA mutations associated with a disease. Several researchers are leveraging this unique property of CRISPR to develop diagnostic kits that can detect diseases using patient samples such as blood, urine, or saliva.

A CRISPR system typically consists of two components––an endonuclease and a guide RNA (gRNA). The gRNA locates the specified DNA sequence and the Cas nuclease then makes a double stranded cut at the target location. For diagnostic applications, the most popularly used nucleases are Cas12 and Cas13.

CRISPR diagnostic tests have many advantages over the traditional assays, including:

1. Single reaction - Traditional assays such as PCR require multiple steps, while CRISPR-based diagnostic assays can be run as a single reaction test.
2. Minimal equipment - CRISPR diagnostics require minimal to no equipment.
3. Speed - These tests can be run quickly.
4. Accuracy - CRISPR diagnostic tests are more accurate than traditional tests.
5. Easy to use - Because of the minimal equipment necessary, CRISPR diagnostics could be made available as handheld devices.

The discovery of Cas13 nuclease was the breakthrough that lead to the development of SHERLOCK.

Time in podcast: 2:34

Cas13 can be used to detect both DNA and RNA. During the amplification stage, a T7 promoter can be added to convert DNA into RNA, which is then detected by Cas13.

Time in podcast: 7:24

While an exact timeline is hard to predict, Abudayyeh and Gootenberg hope to have the CRISPR diagnostics kits available soon. They say that the technology is easy to design and test, which makes it easier for things to progress rapidly.

Time in podcast: 11:13

Omar Abudayyeh: I did my undergrad at MIT a while ago in mechanical engineering and biological engineering. I went in very interested in working with biomedical devices and biotechnology, and that led me to doing an M.D./Ph.D. program at Harvard. I did the first year as a medical school student, and then completed my Ph.D. about a year ago from MIT. I have now put my medical training on hold to start a lab with Jonathan at MIT to continue tackling questions surrounding gene therapy and gene editing technology development.

Jonathan Gootenberg: I also did my undergrad at MIT — that's actually how Omar and I met. I was studying biological engineering and math. Then I went to Harvard to get my Ph.D. in systems biology, and I graduated about eight months ago. Since then, we've been running this new lab where we are exploring new questions in biological diversity.

Minu: So, both of you met in undergrad, and that's when you realized you liked working on similar things. Was it planned to work together later or did that just happen?

Omar & Jonathan: We didn't plan to both join Feng Zhang’s lab, but we had worked together on a senior design project that was actually a fun, crazy idea about engineering bacteria-like probiotics for some inflammatory disease, and it was a fun opportunity to work together. We actually continued doing some research together after that on new microscopy modalities. I think it was pretty fortuitous that we both ended up in Feng's lab.

Minu: You are now also working at the McGovern Research Institute, where both of you have your own labs. Could you tell us a little bit about other projects that you are working on or are interested in?

Omar & Jonathan: I think both of us are pretty interested in furthering gene editing and gene delivery technology. Gene editing still has limitations in that it's not efficient in all cell types, especially brain cells. Current gene editing tools still can't insert DNA well either. I think a lot of our work is looking at technologies that go beyond CRISPR, that can manipulate even more efficiently in more tissues, so that more diseases can be targeted.

Beyond that, we're also interested in a second problem with gene therapy which is that even if you have the perfect genome editor, it would still be hard to deliver these tools to the right tissue and right cells, and have them go in efficiently. We're currently trying to explore certain new types of viruses and other types of modalities that can better get nucleic acid into cells for that purpose. Those are our main two technology development approaches.

Beyond that, we're also understanding how using these tools to probe aging biology, and understand why cells become dysfunctional, and why they become senescent. If we can understand that better, we can determine if we can use our tools to actually reverse senescence and regenerate tissues across multiple aging-associated diseases.

Minu: And for a fun question, because you have such an interesting name of your company and your kit, between the two of you, who is Sherlock, and who is Watson?

Jonathan: I think the better question is who is Moriarty? The important thing about having a good working relationship is that we both have to have flexibility with our roles. It depends on the day, of course, but in general, it's probably half-half.

Minu: So it depends on the day?

Omar: I guess I have more of the medical background, so maybe I'm closer to Watson in that regard. I think the more important thing is what's the next acronym that we can think up because that was certainly the hardest part of SHERLOCK — figuring that out! There were a lot of different iterations it went through. I think it's really important to have fun with the day-to-day; that's what makes it a great experience.

Minu: Absolutely. I think you guys have done a great job, and you've certainly set the bar for abbreviations really high! Every CRISPR researcher now has to step up to that level if they want to come up with any abbreviations. We are looking forward to what your next one will be!

Minu: One of the main things in your project was the discovery of Cas13, which was fundamental to the development of SHERLOCK. Can you talk a little bit about how you came to find this enzyme and how that led you to where you are now?

Omar & Jonathan: SHERLOCK is our highly-sensitive and specific CRISPR diagnostics platform. It is really exciting that CRISPR can be used for sensing nucleic acids with implications for disease detection, but we definitely didn't go into graduate school interested in diagnostics. I was much more excited about molecular tool development, gene therapy, and treating diseases.

As a part of that, both of us were really interested in exploring the diversity of CRISPR enzymes, so everyone was really excited about Cas9 six years ago. We had this question about what other enzymes in the CRISPR world existed, and if there are any that might have unique features that could be useful for things we hadn’t even conceived of yet.

We did a lot of bioinformatics to find the CRISPR system we characterized biochemically in bacteria. One of the really interesting ones was this Cas13 enzyme. It was unique because it targeted RNA instead of DNA, and that was fairly unique because the enzymes known at the time that we used for those tools were all DNA-targeted. Being able to go after RNA allows you to do so much: you can modulate genes, and you can edit residues on genes temporally so it's like a temporary gene modification.

We later realized you could use this for diagnostics as well, because when this enzyme is bound to its target, it would not only cleave its target, but it would also cleave other molecules in the solution. That property is kind of like saying "hey, I just found my target and I'm just going to cleave everything and tell everyone that I found this target." It's sort of a more abstract way of thinking about it.

We realized that we could put in these fluorescent reporters. When they would cleave they would become fluorescent, and this Cas13 would basically release fluorescence when they found a nucleic acid target. We were also able to make this test sensitive to a single molecule, so it was very quick and cheap. We went down this path very fortuitously from just asking these questions about CRISPR biology, and not really knowing what we would find. And we took that path to many different areas — including CRISPR diagnostics.

Minu: I remember reading about SHERLOCK for the first time, and then I think about a year later, there was an upgraded version which was even more sensitive. What struck me most was that the readout is so simple. Is it correct that the method is so sensitive that it can actually use strips in your sample, and you can actually see a readout on the strip?

Omar & Jonathan: Yes, that's correct. One of the great things about this CRISPR diagnostic platform is that by changing the piece of RNA or DNA that is cleaved by this activity that Omar talked about, we can change it from a readout by fluorescence to something that could be read out by a paper strip. There are also a few who have done it so it actually changes the optical properties of a fluid or even potentially electronic readouts. So, this kind of lateral flow paper-based diagnostic is really powerful because the modularity of the platform allows you to swap the readouts depending on the application.

It was just really fun to think about different ways to develop things. That's the cool thing about being in the lab and having these enzymes. It's really thrilling first to discover them. I remember when we first characterized Cas12, back when it was called Cpf1. It's like people thought there was only Cas9 and now, this is an entirely new thing.

That’s the discovery aspect, but even beyond that, once we have the technologies, you can kind of let your imagination run wild, and ask “what can we detect?” Can we detect cancer? Can we detect different patient mutations, viral DNA, bacterial DNA? Or, can we detect using a different color metric or other readouts? And the thing you don't see, of course, is there are so many things that we tried that failed. But you just have to keep trying and letting your imagination play with it. It can make really interesting stuff like this lateral flow readout.

Minu: If you had to estimate, when do you think these diagnostic kits would be available in the market, and, would they be available for just anyone to buy, or will you be sending them to doctors only?

Omar & Jonathan: The future vision will be easy accessibility, because one of the really powerful aspects of the technology is that we can do testing wherever. Of course, there are many different iterations of the technology, and each of those has to go through different aspects of regulatory approval. I think that we will probably initially focus on not giving them directly to patients.

As for the timeline, that's always hard to predict, but we're moving quickly. We’re hoping to have products quite soon; because the technology is so easy to design and test, it’s easier to get something out rapidly.

Another thing, of course, is that the technology is not only being adopted by the company, but there's many different applications across human health, agriculture, and even the environment. We have collaborators who are interested in using it to track different ecological populations, for example, fish migrating on the West Coast or looking at different types of beetles.

It's really exciting to see how a foundational technology like this RNA detection can really be adopted by so many people to make a difference in so many areas.

Broad Institute video explaining the SHERLOCK diagnostic kit

In this video, you can learn about the Cas13 nuclease and how it is being used for DNA/RNA detection in SHERLOCK, a CRISPR based diagnostic platform.

Article introducing SHERLOCK (2017)

In this article, you can learn more about SHERLOCK, the CRISPR-based diagnostic tool that is highly sensitive and specific.

Refined version of SHERLOCK announced (2018)

In this article, learn about how the SHERLOCK team developed a simple paper test to demonstrate whether or not a target molecule is present in the sample.