Five (more) questions for David Root

Four years ago, David Root talked with us about the fundamentals of RNA interference (RNAi) technology. But, since then, the group that Root oversees – Broad’s erstwhile RNAi Platform – has taken on a new identity: it’s now known as the Genetic Perturbation Platform (GPP).

While at first glance the name change might appear to signal a shift in the group’s focus, the team’s mission hasn’t really changed: it continues to develop tools to investigate the function of the 20,000 genes that make up the human genome and, in parallel, help Broad researchers adapt and apply these tools to diverse biological questions. What has changed, however, are the approaches used to conduct such research; the team’s new moniker reflects the growing arsenal of tools the platform is now using to investigate gene function.

Recognizing that the name change may have raised a few questions (not the least of which may be, “What exactly is ‘genetic perturbation’ anyway?”), we caught up with Root (now director of GPP) for this installment of “Five Questions.”

Q1: Can you sum up what the Genetics Perturbation Platform does?

DR: In short, our platform is interested in using experimental approaches to discover gene function.

All of our cells’ workings are the result of genes and the molecules they produce – RNAs and proteins – and genes play many different roles to make cellular systems work. For example, one type of gene might turn other genes on and off; another might support the structure of a cell; or a gene might be responsible for signaling with other cells. Not only do genes have important functions on their own, but it is also important to know how they interact with each other. Plus, their roles can vary a lot depending on cell context, say in different types of tissue. The Genetic Perturbation Platform is interested in improving the tools that one uses to discover the function of genes, in every cell type, in normal and disease biology.

Q2: How do you go about discovering the various functions of genes?

DR: The main strategy we use is to alter the activity of a gene in some manner so that we can see how it changes a cell’s behavior, and in that way infer the gene’s function in that context. That’s the essence of “perturbation”: we tweak the gene is some way and we see what happens.

These experiments generally all have three parts: we need to alter the function of the gene in some manner; we need to choose what kind of cells and context to do that in; and then we need some way of assessing the consequences, to see how altering the gene changed the behavior of cells or tissue. By observing those functional consequences, you can often infer what the gene’s role is in that context.

Our platform is interested in enabling those types of experiments. We give special attention to the first part – the genetic perturbation – by developing various mechanisms by which one can perturb genes, but we also work hard on combining all three critical components of these experiments in whatever way is most effective.

Q3: Can you describe some of the tools that your team uses to conduct these experiments?

DR: Our first main work (which of course related to the platform’s original name) was using RNAi to suppress gene expression at the transcript level for loss-of-function screens. We designed and tested RNAi reagents, made genome-wide libraries, and then defined best practices for using them. We’ve done similar work – we’ve developed libraries and assessed their performance – for methods that overexpress genes, where we essentially just introduce an artificial, extra, turned-on copy of the gene. A new major focus – an approach that everybody is excited about – is using the CRISPR-Cas9 system to target a specific region of the genome to knockout or modify gene expression.

Q4: What can studying gene function tell us? In other words, what is the upshot of your research in terms of human health?

DR: One analogy that people often use is a fuse box; if you want to know which lights are controlled by which circuit, you can systematically test the switches in the fuse box to see which one turns out the lights. It’s an oversimplification, but what we do is similar: by systematically perturbing genes and seeing how it affects the function of biological systems, we can figure out what these individual genes do in models of normal biology or disease. This can yield valuable insights into the genetic mechanisms underlying human disease and inform and accelerate research on treatment strategies.

Q5: “Genetic Perturbation Platform” can be quite a mouthful. How did you come up with the name?

DR: True. We’ve become known as “GPP” for short. We liked “Functional Genomics Platform” which certainly would have rolled off the tongue better, but there were concerns that it had been used in the past to mean different things. “Perturbation” reflects a key, common aspect of our experimental approaches: namely, actively intervening to perturb genes’ activities in order to learn their causal roles.

To learn more about the Genetic Perturbation Platform, check out the platform's website.

If you want to learn more about the ways functional genomics is helping to uncover disease-relevant biology, check out these papers, which were co-authored by GPP scientists:

Egan, ES et al. “Malaria. A forward genetic screen identifies erythrocyte CD55 as essential for Plasmodium falciparum invasion.” Science, 348:711-4. 8 May 2015. DOI: 10.1126/science.aaa3526.

Ramirez-Ortiz, ZG et al. “The receptor TREML4 amplifies TLR7-mediated signaling during antiviral responses and autoimmunity.” Nature Immunology. 16, 495–504. Online April 6, 2015. DOI: 10.1038/ni.3143. [See also, "Fanning the flames of lupus" on the BroadMinded blog.]

Wilson, FH et al. "A Functional Landscape of Resistance to ALK Inhibition in Lung Cancer.” Cancer Cell. 9 March 2015. DOI: 10.1016/j.ccell.2015.02.005. [See also, "Cancer drug resistance-from laundry list to paradigms" on the BroadMinded blog.]

Shema, R et al. “Synthetic lethal screening in the mammalian central nervous system identifies Gpx6 as a modulator of Huntington's disease.” Proceedings of the National Academy of Sciences. 2015. DOI: 10.1073/pnas.1417231112.

Knoechel, B et al. “An epigenetic mechanism of resistance to targeted therapy in T cell acute lymphoblastic leukemia.” Nature Genetics. March 2, 2014. DOI: 10.1038/ng.2913 [See also, "Insights into drug resistance for a rare leukemia" on the BroadMinded blog.]

Zhou, P et al. "In vivo discovery of immunotherapy targets in the tumour microenvironment.” Nature. Online 29 January 2014. DOI: 10.1038/nature12988.