Rice Computer Scientist leads biosecurity training at BioMADE

Todd Treangen's training program raises awareness of bioerror or bioterror outcomes on synthetic DNA projects

Todd Treangen

Rice University Computer Scientist Todd Treangen is co-leading the development of biosecurity training program materials announced with the kickoff of the White House Summit on the National Biotechnology and Biomanufacturing Initiative. The training program for scientists working on synthetic DNA projects will raise awareness about the possibility of bioerror or bioterror outcomes and set up guidelines for preventing and mitigating these issues.

"Rice University Computer Scientist Todd Treangen is co-leading the development of biosecurity training program materials announced with the kickoff of the White House Summit on the National Biotechnology and Biomanufacturing Initiative. The training program for scientists working on synthetic DNA projects will raise awareness about the possibility of bioerror or bioterror outcomes and set up guidelines for preventing and mitigating these issues. This biosecurity training program is well aligned with the executive order issued on September 12th, 2022 specific to enabling a safe, sustainable, and secure bioeconomy.

The biosecurity training program is part of a $20.6 million project launched by the nonprofit organization Bioindustrial Manufacturing and Design Ecosystem (BioMADE) and leverages research begun in 2017 by Treangen and colleagues to determine methods for detecting known and emerging pathogens in clinical and environmental biological samples.

“Under IARPA’s FunGCAT program, our team produced two primary deliverables — S2Fast and SeqScreen — to rapidly characterize and identify potentially threatening DNA sequences,” said Treangen. “Rather than follow in the footsteps of previous approaches that focused matches to lists of known select agents and toxins, we developed an entirely new platform that is based upon functional information that is linked to pathogenic potential and virulence of a given sequence."  

Those health threatening bits of genomic sequence are called functions of sequences of concern (FunSoCs) by the team; FunGCAT set about developing a curated set of FunSoCs and a machine learning-based platform where they could compare new samples of short nucleotide sequences against their base of known pathogenic sequences.

To accomplish this task, the working group relied on the deep expertise of diverse partners in industry, academia, and a research center: genomics, microbiologists, and bioinformatics experts at Signature Science, data science researchers and computational biologists at the University of Maryland, Rice’s Treangen and Electrical and Computer Engineering assistant professor Santiago Segarra, and research scientists in the experimental software engineering group at Fraunhofer USA Center Mid-Atlantic CMA.

Their five-year program was funded by the Intelligence Advanced Research Projects Activity— the high risk, high reward research arm of the United States Intelligence Community— and resulted in open-source software that can be freely downloaded and utilized by scientists and researchers checking their samples for pathogenic sequences.

Treangen said his interest in biosecurity arose from his work on SeqScreen and S2Fast. “Frequent meetings with the FunGCAT partners and S2FAST team members exposed me to work being accomplished on the screening side of synthetic DNA manufacturing. I’ve been educated by true performers in that community; everyone is excited by their work but also concerned about the risks of the new developments. The adage, ‘With great power comes great responsibility,’ is highly applicable to the scientists driving the rapidly expanding biomanufacturing industry.

“How can we realize the greatest impact of manufacturing new biological solutions while safeguarding the process and the outcomes? History is full of examples of tools that were invented for the good of humankind being subverted by malicious intent. So, we must think carefully with biomanufacturing stakeholders about how to best protect the science and the world.”

BioMADE emphasizes biosecurity

The security aspect of biomanufacturing aligns with the goals of BioMADE, an organization created to build a domestic, end-to-end bioindustrial manufacturing ecosystem in the United States. The group, composed of about 100 academic and industry partners spanning 31 states, is an independent and nonprofit manufacturing innovation institute that was launched with over $87 million in funding from the U.S. Department of Defense in 2021.

To kick off the September 14 biotechnology and biomanufacturing summit at the White House, BioMADE announced nine new projects including the biosecurity training program. The training program will teach scientists how to best use SeqScreen and other tools to check their newly developed DNA sequences for pathogens and other biological threats.

“This biosecurity training course is the first of its kind and will provide a key resource to the entire BioMADE community” said Paul Cherukuri, Rice’s new chief innovation officer. Cherukuri, a medical technology entrepreneur, completed his Ph.D. in physical chemistry at Rice under Nobel laureate Richard Smalley. He returned to the university in 2014 to lead the Institute of Biosciences and Bioengineering. In that role, he recognized the potential for BioMADE and ensured Rice’s role as an early partner.

Cherukuri said, “I anticipate this is the first of many fruitful partnerships between Rice and BioMADE as the global biomanufacturing and biotechnology industry continues to experience unprecedented growth, leaning into key areas of expertise of our faculty and research programs”

“BioMADE is bringing together many institutions, government, and industry partners, and it is privilege to participate at the early stage of this venture. But the truly unique aspect of this collaborative work is BioMADE’s prioritizing of security up front. It is obvious that BioMADE considers biosecurity a pillar of what we are going to build and they are intentionally bringing the community into this perspective ASAP,” said Treangen.

“We are doing more than our ‘due diligence.’ Security is more than just checkbox on a list. We have an actual obligation to educate community members about the threats to and in their work. With so many partners, we are receiving great input, feedback, use cases, anecdotes, and concrete reasons why and what is important to securing the labs and the work.”

He mentioned California as an example of a state that has taken the lead with recently passed legislation requiring the University of California to develop systemwide guidance to incorporate very clear screening protocols for the biological sequences they produce. Used properly, these screening protocols can help provide early detection of bioerrors.

Consortium working group explores security

When Treangen proposed a biosecurity training initiative to his partners at Signature Science and Aclid, he said he benefitted from thoughtful conversations and engagement with the Engineering Biology Resource Consortium (EBRC). One of seven Rice University faculty members in the consortium, Treangen is an active participant in the EBRC’s security working group.

“The EBRC security working group meets monthly and discusses various preventative and precautionary measures to safeguard biomanufacturing,” said Treangen. “The group has great leadership and spans many different institutions, drawing on a wide range of experiences as we share our thoughts about the challenges and opportunities ahead. Experts within this community have been thinking about this for a long time, spreading the word, and finding ways to dedicate more resources to the security side of manufacturing synthetic DNA. I’m fortunate to be part of this community”.

Biosecurity is a fundamental and critical aspect of biomanufacturing. Malicious attacks, simple errors, and lack of concern for long-range side effects can all result in unintended consequences. From cybersecurity hacks to environmental and residential clean up following leaks, explosions, and decades of dumping, we have many examples to draw on when it comes to the importance of building security and safeguards into new systems from the start.”

Planning defense and launching offense

Incorporating biosecurity into the biomanufacturing game plan is like launching a strong offensive line on the football field. Defense is critical, particularly when a project encounters an attack or a setback, but a champion offense locks a protective shield around the team’s key point makers. The biosecurity training program will stress the importance of creating and maintaining protections around the research and manufacture of synthetic biological products.

But accidents do happen and Treangen plans to counter these types of issues by preparing scientists to think like crisis managers. He said, “On a high level, we recognize that bioerrors will crop up from time to time. In a synthetic DNA manufacturing bioerror, something outside of the scope of the expected genomic sequence is inadvertently created. What security protocols do the researchers and the lab itself have in place to prevent bioerrors, and to limit the damage if a bioerror does occur?

“From the perspective of bioterror, we already know there is potential for misuse of today’s technologies and tomorrow’s innovations. So, we are thinking about how to shrink the space in which intentional harm can be initiated. It is not sufficient to look back after an incident and say, ‘We never expected anyone to do that with our solution.’ We have to expect misuse will be attempted and plan ways to diminish opportunities for and outcomes of these types of attacks.”

Treangen believes that awareness and use of screening tools, along with incorporating best practices and educating the biomanufacturing community at large about biosecurity, can go a long way to building biosecurity into the industrial process from the start.

Biosecurity training program opens in October

Screening protocols like SeqScreen are not helpful if scientists do not understand how to use them to their advantage. Fortunately, every member of the BioMADE community is eligible participate in the biosecurity training program to learn how to use SeqScreen and other tools.

To prepare for the training sessions, Treangen and his partners at Signature Science and Aclid are developing a course curriculum and creating training sets of DNA sequences and case studies. They plan to post their course materials on GitHub, and deliver the material through live sessions in Zoom. Recordings of those sessions will be made available to offline participants via freely accessible online platforms.

“It is exciting to see BioMADE building this kind of training into the biomanufacturing life cycle,” said Treangen. “With their funding, endorsement, and access to their community, our biosecurity training program can launch as early as next month.

“Once we develop and deploy these training materials, leaning on input from the BioMade community, scientists can begin learning how to use our tools and build safety guidelines into their own processes. All the stars are aligned. Now is the time to jump in and lean into the security arena for biomanufacturing.”


Carlyn Chatfield, contributing writer