Creating a “Smoke Detector” for Genetically Engineered Organisms

The increased ease in which gene editing techniques such as CRISPR can be performed, coupled with their increasing affordability, means that we are potentially on the verge of a gene editing revolution.

A pertinent question, therefore, is if a genetically or synthetically engineered organism was to escape or be released into the environment, how would we know? Would we be able to tell it apart from the array of microorganisms that naturally exist in the environment?

In partnership with researchers from Raytheon and other universities, Eric young, assistant professor of chemical engineering at Worcester Polytechnic Institute, is creating a method for using DNA signatures to identify genetically engineered organisms in the wild. We spoke with Young to learn more about why such tools are needed and the process of their development.

Molly Campbell (MC): What are the risks associated with a genetically or synthetically engineered organism being released into the environment?

Eric Young (EY): Right now, the risks are low. An engineered organism is typically “sick” in many ways. First, it is usually engineered from a microbe that has been “domesticated,” and cannot survive well in the wild – kind of like a housecat or a dairy cow. Second, the microbe must spend much of its energy to make the product it is engineered for, like a biofuel or a medicine, which makes it easily outcompeted by microbes that do not have this burden. Finally, many engineered organisms are engineered with a “kill switch” or are engineered to need an essential nutrient that is not present in the wild, so they actually die if released.

The primary risk is that release of an engineered organism into the environment provides competitors access to millions of dollars of intellectual property, because the engineering is written in the DNA code that can be easily sequenced.

MC: What are the aims of your research project?

EY: The research project aims to create a kind of “smoke detector” that gives a simple yes-no readout for if a sample contains engineered organisms. Just like a smoke detector, this tool doesn’t say anything about why the “smoke” is there.

MC: Please can you tell us about your tool and how it works, including the technology required to create it?

EY: The tool relies on next-generation sequencing and software to search the sequencing data for DNA signatures that would only be there if engineering occurred.

MC: What challenges do you face in the development of the tool and how will you overcome these?

EY: A lot of DNA sequence used to engineer organisms is natural – that is, the sequence is the same as what we would find in nature – but the “parts” are put together in different combinations. That means that we often aren’t looking just for a sequence, but if the sequence is out of place. And that’s a hard problem, because there are many natural ways for DNA to be rearranged.

MC: Documentaries such as Code of the Wild are shining light on the more "secretive" research taking place in the field of genetic engineering. How can we look to regulate genetic engineering and what conversations do we need to be having? 

EY: I can’t comment specifically on this because it is not my expertise – there are others who are very involved in the field and speak about these issues. The regulation issue has many sides, and many people in the synthetic biology community and the government work together on these issues. In our work we follow strict regulations for the proper disposal of biological material that have been established for a long time.

MC: Biohackers such as the company Odin are selling kits so that individuals can genetically modify organisms in their own homes. What is your opinion on biohacking and how is it related to your work?

EY: My opinion is mixed. Some of the greatest innovations of the past century have been achieved by people working out of their garages. At the same time, working with microbes in a laboratory environment with enforced, established, regulated safety procedures is currently the best way to limit release. We design, build, and test engineered microbes in our laboratory, following all established biosafety regulations.

MC: What do you anticipate the field of genetic engineering to look like in 10 years' time?

EY: It will look much different. We are able to design and build much larger pieces of DNA than we were able to five years ago. It’s not unreasonable that in 10 years we could be writing whole genomes, rather than just small parts. This opens up a whole new set of possibilities and design challenges that I can’t wait to be a part of solving.

I think we will also see even more products made with genetic engineering come to market in the next 10 years. We already make human insulin for diabetics, recombinant chymosin for cheese, and better laundry detergents (among other things) with genetic engineering. But there are many other products that are nearing the market including spider silk clothing, better baby formulas that more closely mimic human breast milk, renewable plastics, biofuels, and treatments for diseases. 

Eric Young was speaking with Molly Campbell, Science Writer for Technology Networks.