Jonathan Gootenberg: Exploring New CRISPR Enzymes

Jonathan Gootenberg '09 is a McGovern fellow and recent Systems Biology Ph.D. graduate from the Broad Institute of MIT and Harvard, where he was co-advised by Feng Zhang and Aviv Regev, exploring microbial biology and turning new discoveries into tools for diagnostics and therapeutics. Recently, he talked with Xinyi Zhou '10 about his early interest in STEM, his thesis work and his thoughts on the value of a Ph.D. and what aspiring Ph.D.’s should look for in a mentor.

Jonathan GootenbergLet's start from the beginning - how'd you get interested in STEM?

My parents are both in medicine -- they're both doctors, and my dad did research -- so I've always had that influence growing up . . . In high school, I [became more interested in] the biosciences, and I got involved with a lot of [activities] in school like the Biology Olympiad. So by the end of my time at Blair I honed in on all things biology. 
 
So you did USABO (USA Biology Olympiad)? [Silver Chips August 2, 2009: Blair alumnus wins gold in international science competition]

USA Biology Team 2008
When I was in 10th grade biology, Ms. Bosse offered the qualifying exam and I got to the semi-finals. I didn't make it that year, . . . so the next year I read the whole biology textbook cover to cover, I looked at a bunch of practice tests, and I [qualified for] the camp [in 2008], and the next year I made it again! But it was really great that Blair gave us the opportunity to do all these different [competitions] in computer science, chemistry, biology, physics . . . a lot of schools don't offer all these, so the opportunity to have that was really enabling. 
 
And did you do a SRP (Senior Research Project)?

I did an SRP at NCI [the National Cancer Institute] at NIH. [It was the] first time I got into cell culture, looking at small hairpin RNA. [The project] didn't get very far but I ran my first Western blot, and it was a fun time. The opportunity was really nice, going to undergrad having a small idea of how to actually do science. The difference between what's taught at schools and the actual experience of doing science is so diametrically opposed; you need to have both -- you can't learn to be a scientist just by taking classes. 
 
Give us the spiel -- what was your thesis work on?

My thesis work has been exploring microbial diversity and turning that into tools for things like gene editing and diagnostics. So I work on clustered regularly interspaced short palindromic repeats (CRISPR), which, a lot of people recognize as a genome editing system, but it's a microbial adaptive immune system. It’s a way that bacteria and archaea can learn from phages and mobile elements can build a memory and build a defense against invasions. We have an adaptive immune system of millions of cells, while they have one cell which is a genomic record of what they've been exposed to. Part of the system is that the memories are turned into programming for enzymes. So [microbes] program these enzymes, and [the enzymes are] really advanced scissors -- they'll cut [DNA or RNA] sequences, so that's how the defense works. 
 

Notable Publications

J.S. Gootenberg, et al.Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6 (Science, Apr. 27, 2018).

J.S. Gootenberg, et al.Nucleic acid detection with CRISPR-Cas13a/C2c2 (Science, Apr. 27, 2018).

D.B.T. Cox, J.S. Gootenberg, et al.RNA editing with CRISPR-Cas13 (Science, Nov. 24, 2017).

O.O. Abudayyeh, J.S. Gootenberg, et al.RNA targeting with CRISPR–Cas13 (Nature, Oct. 12, 2017).

O.O. Abudayyeh, J.S. Gootenberg, et al. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector (Science, Aug. 5, 2016)
But what that means is that they are very programmable and modular scissors. The field of gene editing had really wanted specific scissors for a long time, to cut the genome and modify it. You can also inactivate the scissors -- you can turn genes on and off, you can put cut parts of the genome and stick them together, and you can image the genome. When I joined Feng [Zhang]'s lab there was this explosion of studying [CRISPR] Cas9 but there was this question: Can we find new CRISPR systems that can be new tools? So that's what my work has been on. I found and characterized two general classes of enzymes, Cas12 and Cas13. 
 
Cas12's target DNA, but cut DNA slightly differently than Cas9, which makes them more versatile and specific. Cas13's target RNA. The idea is that you can bind to RNA inside a live cell, you can see where it is, you can cut it and destroy it, and you can change where it goes. We also found that Cas13 had this activity which is: when it binds to the RNA it wants, it starts cutting other RNA it's not targeting. We call this the collateral effect. We turn that into a detection system, so you target it to [the RNA transcript of interest] and you dope in something that will detect it [such as a fluorescent or colorimetric readout]. We can detect as little as a single molar in a microliter (which is an attomolar). We've applied this to different bacteria: Zika, Dengue, and cell free DNA (so if you have a tumor and it's shedding DNA that has mutations, we can detect those mutations). It's really portable and inexpensive. We've also applied Cas13 to RNA editing, so we're working on ways to change bases in RNA, which doesn't have the permanence of [editing] DNA. So any problems are only temporary. It's been pretty exciting. 
  
When did you decide you wanted to do a PhD? 

I feel like I always wanted to do a PhD because I was really excited about research. The idea of learning something about the world -- it becomes cliché at this point -- but it's exciting to know something that you've uncovered. And it's also exciting to take in the knowledge of the whole community, and to build collaborations. There's relatively less competition in science so [being able to work] with people to understand the natural world, that's really thrilling. A PhD in biology is kind of necessary to do anything [further in biology], whether academia or industry. And that dichotomy is not as strict as people think. 

Let's talk more about that, since faculty positions are getting more and more competitive -- why do you think should students still consider a PhD?

A PhD is not academia -- It's experience, an opportunity to learn. I think you should take everything in life as an opportunity to learn, but, a PhD is school. Some people see it as "I'm going to do this and publish papers and go into academia," and others say, "I don't care how much I publish, I'll just get a job," but both of those [attitudes] are focusing on the wrong thing. [A PhD is] much more like a process of apprenticeship, which doesn't exist in many fields in such an organized fashion. It gets you the opportunity to have a fantastic mentor, and having that is really really vital. It gives you a sense of how you can operate in the world, how you can connect to people, and to see how someone thinks. That's the biggest thing about the research -- it's not as much about what you do, it's what you learn . . . Over the 4-5 years, I learned so much on how to operate, how to be a scientist, to manage people, and to interact with people.

The biggest thing about a PhD is who you're working with, and that really comes down to the advisor. I was lucky because Feng was [very involved], really dedicated to [his students'] careers. That's what academia [should be] about -- this tree of mentorship, and training the next generation of science.

What are some specific things that people should look for in a mentor?

Empirical signs -- if you have a mentor who has trained a lot of good mentees, that publishes a lot per person in the lab, and has a lot of grad students who are happy and have good relationships with their mentor, those are good signs. Of course you also want someone who has time for you. Someone who is much more established may have many more obligations. My advisor now is different from when I joined -- he has more obligations, he isn't in lab as much, and he has a family. You want to find a mentorship style that works for you, and someone who will attract good people in the lab -- that's a sign of a good PI (principal investigator). And someone who you feel like you can connect with. I took a class with Feng and I really liked it . . . That's not something you can always get. I think that you have to kind of feel it out -- you really want someone who can give you time -- you want someone with whom you can build a personal relationship that you can build on throughout your entire life.

What are you working on now post-PhD?

I'm currently wrapping up some projects in Feng's lab, and then I'm starting a lab at MIT together with Omar Abudayyeh -- we're going to be McGovern fellows [at the McGovern Institute for Brain Research].
 
What's for you 10 years out?

I think doing biological discovery and also applying those tools is really awesome; it gives you the opportunity to give things to the community that are really useful . . . So I think I want to explore that, thinking about things beyond CRISPR -- how we can find additional tools useful for gene therapy. I've always been interested in aging, so I'm writing a couple of new grants on understanding aging. I'd like to still be academic but have interactions with different companies. But more so I think it's just important to see yourself making an impact and enjoying what you do. I think these boxes of academia and getting saddled to that is not important. You can make a new model. You can say I'm going to create a new institute and do that. And these things are not as hard as people think -- Just explore. 
 
Anything other advice you'd give?

It's really important to focus on who you work with and who you interact with. Those relationships support you throughout your life. One of the biggest predictors of happiness is having a good support group. I'm not saying that you should explicitly network, but find people you like. Build rewarding relationships -- those are really the most important things.