Q&A with Dr. Neville Sanjana on his career (so far) in CRISPR – PART 2

In case you missed the first part of the Front Line Genomics interview with Dr. Neville Sanjana, click here to check it out.
Read below for the conclusion of the interview and to learn about Neville’s current research projects, including how he has worked with Twist Bioscience to perform genome-scale CRISPR screens.


Image credit: Neville Sanjana

Front Line Genomics: Through all of this, we haven’t even talked about your move to New York yet. You’re now at The New York Genome Center and an assistant Professor of Biology at NYU. What attracted you to New York?
Neville Sanjana: I came from a very department-oriented background, through my PhD, as most people I interacted with were within the department. Towards the end of my time as a PhD student, I was able to work with two very talented postdoctoral fellows — Erez Levanon and Billy Li — in George Church’s Lab at Harvard Medical School. It was through a joint project with them that I really got exposed to this brave new world of high-throughput sequencing and the larger genomics community. I realized that just across the street from my neuroscience department, there was the Broad Institute which was making amazing discoveries using these new sequencing technologies. Through my friends in the Church Lab and in the neuroscience community, I was introduced to Feng Zhang and given the incredible opportunity to join the Zhang lab at the Broad.
I thought it was fantastic. I loved this idea of something that takes advantage of all the institutions around it and brings scientists together. It was a hotbed of new ideas and technologies and much of it was due to the tremendous cross-pollination. There are people from MIT, Harvard, Harvard Medical School, Massachusetts General Hospital, and many other Boston research centers. It’s just a very mixed environment that I thought was very attuned to the future of science, and the nature of what science should be, which is to say collaborative. I really enjoyed my time at the Broad. It’s a place that made me successful, and a place where I learned a lot from colleagues around me.
Out of all the places I went on to interview at, the New York Genome Center just stood out as being a place that had the same vision and the same kind of ideas that I first encountered at the Broad. There are no departments, really, here at the Genome Center, we have core faculty and core labs, but none of those traditional boundaries. Everybody works with everybody and that is fantastic. So there are two things that really brought me here: it felt like the best of what I’d seen in Cambridge and at the Broad, and also the junior faculty here were clearly the dream team of human genetics. Each of them also have an appointment somewhere else in New York, which makes the Genome Center really a cross-roads of great genomics for the city.
My joint appointment is with NYU’s Department of Biology, which was, of all the departments that I interviewed in across the country, the most friendly and collaborative department that I experienced. NYU Biology also has tremendous diversity. Coming from a neuroscience department, it’s refreshing to interact with everyone from plant biologists to computational scientists solving protein structures.
FLG: Your team is developing technologies to understand how human genetic variants cause disease of the nervous system and cancer. Can you tell us a bit more about the work you guys are doing and the people in your lab?
NS: I just started in April, but the lab is essentially focused in two directions. The vision for the first direction is new genome engineering technology development to understand the noncoding genome. One of the tools we rely upon are high-throughput CRISPR screens, which take advantage of the easy programmability of the CRISPR system to look at many genetic variants in parallel. In terms of the disease domains, we focus quite a lot on cancer. We’ve worked on drug resistance in melanoma and in vivo models of metastasis with lung cancer. We’re synthesizing large libraries of single guide RNAs (sgRNA) that are used to guide the CRISPR enzymes like Cas9 to different locations in the genome.
We’re doing this to ask genome-wide questions. For example, what are all the possible loss of function mutations that will trigger metastasis from a primary tumor into the lung? Or what are all possible mutations that can trigger resistance to a BRAF inhibitor? BRAF mutations are one of the most common mutations you find in melanoma, so we want to find out, before you get to a clinical trial, if you can predict what it is about a mutation that creates drug resistance and how to pair patients with more effective drug combinations.
A good example is the cocktail of drugs used in HIV: One drug by itself promotes resistance, but if you mix these three drugs together, it keeps the disease very well controlled. The other half of my lab kind of continues in the neuroscience direction along some of the interests I developed during my PhD. This side of the lab also uses genome engineering, but uses it in a very different way. Rather than testing hundreds and thousands of mutations in parallel, here we take some nominated mutations based on patient sequencing. Right now, we have invested significant efforts into understand the mechanisms underlying mutations found in autism. We are looking at de novo mutations, which means mutations that have arisen in the germ line cells of the parents. We look at them by putting them into human stem cells.
We worked for many years on making very efficient ways to rapidly differentiate those stem cells into specific kinds of neurons. Neurons are something that we obviously can’t get directly from human patients. Thus, gene editing in stem cells and differentiating the stem cells into cortical neurons gives us a powerful platform for understanding what is going wrong in neuron with autism-associated mutations. It means we can try to understand the mechanisms that lead to autism. We hope that in the future we might be able to develop this into a platform that could be used for something like a drug screen, or a high throughput CRISPR screen, to help develop therapeutics.
Right now, we’re at the stage where we might be able to diagnose some of these kids based on genome sequencing, as the cost of sequencing becomes cheaper and establishes itself in the clinic. But what we want to do is the next step: To understand the mechanism, so we can actually think about treatments. At a future stage, I hope to develop gene therapies that can help people where no drugs exist. And of course, there are many more things that don’t have to do with human health or disease. There is tremendous potential to apply these tools in plant and crop biotechnology, looking at DNA as a storage medium, and other things that will be enabled by making writing DNA a routine procedure. Right now, we can plan out experiments easily that just four years ago we could not do. We could not really easily modify genomes of human cells. That’s the bottom line; that’s something that enabled so much that science can do today.
FLG: How have you found the jump from being part of someone else’s lab to having your own lab and calling all the shots?
NS: You know, I feel very lucky. Anybody who’s doing a PhD or a post doc knows, it’s an incredibly competitive job. I’m very grateful for the opportunities that I’ve been given. I’m very positive that this is an opportunity where we can do a lot and hopefully have a big impact on diseases that affect so many people. The really great thing about the New York Genome Center is that everybody here is new and that itself provides a lot of raw energy. Even the veterans have only been here 2 or 3 years. There’s something really powerful about being in a new place and building an organization together.
FLG: Twist Bioscience very kindly introduced us to you, so it’d be great to hear about what your relationship is with them. What do you look for in partnerships with suppliers?
NS: The key thing for us with pooled CRISPR screens is having a way to quickly use the sgRNA libraries that we design. Most labs don’t have the capability to do very high throughput oligonucleotide synthesis in house and oligo libraries have historically been hard to purchase anywhere. Twist Bioscience seemed genuinely very interested in developing libraries for pooled CRISPR screens. They saw it as something that a lot of people might find useful. They’ve been ideal partners, in that they’ve wanted to understand our needs, and have helped us test things out. I think Twist Bioscience has done a nice job in recognizing this market for pooled screening reagents, and thinking about how to make something that is both accessible and useful for anyone wanting to do a CRISPR pooled screen. Many other companies in this space have just been either confused or extremely protective in a way that doesn’t encourage innovation.
The people that I’ve worked with at Twist, Maria Ramirez and Scott McCuine, have been great partners with a real interest in enabling others to do great science. In our own work, we’re always thinking about how we can get these ideas and technologies out to as many people as possible. Since our first genome-wide CRISPR screen maybe a little over two years ago, I see one or two new papers being published using the technology every week. Overall, it’s been wonderful to see the technology take off and even better to see industry collaborators interested in fostering that.
FLG: You’re still early on in your career. Are there specific things you’re hoping to achieve?
NS: I feel incredibly lucky to be here at a time where genome engineering is really becoming a reality. Every time we have new tools, you can just see much, much further and that naturally leads to better experiments and new results. So, I’m very grateful to have been a part of this genome engineering community and I feel like I want to continue developing these tools in order to understand the basic mechanisms of human
FLG: What advice would you give to people just starting out now, struggling through their PhD’s?
NS: I feel that being fearless is the hardest thing to do and also the most important. In new fields like genome engineering, you don’t need a whole lot of experience but you do need a willingness to try many kinds of experiments, fail, and quickly move on. It’s surprising how quickly expertise can develop. I knew almost nothing about molecular biology when I started my post doc. With the fantastic training environment where I was surrounded by people like Feng — people who are risk takers and innovators, eager to just try new experiments and put together new tools — I saw that you can actually cover a lot of ground pretty quickly. Even as a PhD student or technician in the lab, you have the ability to try out new things. If you thrown a lot of darts before you pick one direction, you will have many opportunities to hit the bullseye.
We at Twist Bioscience look forward to seeing what comes next from Dr. Neville Sanjana’s lab as he continues to help move the genome editing field forward.
Interview reproduced with permission from Front Line Genomics.