Download PDF Summer Bridge on Advanced Biomanufacturing for Medicines June 16, 2025 Volume 55 Issue 2 This issue of The Bridge features cutting-edge perspectives on the rapid progress and innovation in advanced biomanufacturing for medicines. Shaping Future Supply Chains with Bioindustrial Manufacturing Friday, June 13, 2025 Author: Melanie Tomczak and Penny Norquist Leveraging cutting-edge bioindustrial manufacturing technologies will enhance domestic supply chain resilience. From natural disasters and cyberattacks to growing sociopolitical tensions around the world, global supply chains are more unstable than any time in recent history. This instability has forced many countries to evaluate their manufacturing capacity, as domestic production of vital necessities becomes an increasing priority to bolster resilience against inevitable supply chain disruptions. The COVID-19 pandemic exposed major weaknesses in the US supply chain. While most Americans likely remember toilet paper shortages or the struggle to find their favorite snacks, the pandemic also revealed a major supply chain challenge for the healthcare and pharmaceutical industries. Cut off from the rest of the world and forced to end reliance on foreign materials, scientists raced to produce COVID-19 vaccines and test kits domestically and deliver them to the public. Addressing these hurdles proved vital to a worldwide return to normalcy, as well as to our future preparedness for a reality with increasing uncertainty. To address this, the National Institute of Standards and Technology (NIST) announced the Rapid Assistance for Coronavirus Economic Response (RACER) grant program. Introducing NIST RACER: BioMADE’s Call to Action The NIST RACER grant program awarded nearly $54M to Manufacturing USA institutes to support research, development, and testbeds for preventing, preparing for, and responding to coronavirus (NIST 2022). Manufacturing USA is a public-private network of 18 innovation institutes that convenes industry, academia, and government with a common goal of securing the future of US manufacturing through innovation, education, and collaboration. RACER funded 13 awards led by eight Manufacturing USA institutes for projects that developed point-of-care sensors for virus detection, enhanced personal protective equipment, innovated production of therapeutic countermeasures, accelerated manufacturing processes and automation for therapeutics, developed systems to strengthen medical supply chains, and created specialized training programs for technicians and operators in advanced biomanufacturing. The impact of these projects extends beyond coronavirus and pandemic preparedness. The outcomes bolster the US infrastructure and capacity for onshoring therapeutic production, drive medical device innovation for detecting a broad range of pathogens, advance automation in domestic manufacturing, reinforce our supply chain resilience, enhance the safety for our healthcare professionals, and equip our workforce with skills for high-quality biomanufacturing jobs. BioMADE (biomade.org) is one of these Manufacturing USA institutes, specifically dedicated to supporting US bioindustrial manufacturing, or the use of fermentation technology and American-grown crops, like corn, soybeans, and sugar beets, to produce items we use every day, such as plant-based nylon, dandelion rubber tires, and biobased cement. BioMADE was established in 2020, and its public-private partnership works closely with the US Department of Defense to secure a domestic supply chain for critical materials, chemicals, and more. BioMADE’s over 300-member network consists of leading companies, small businesses, start-ups, top research universities, community colleges, and non-profits across 38 states. BioMADE had two member-led projects funded through the RACER program: 1) Distributed Manufacturing of Antigen for Serological Testing and Countermeasures and 2) Domestic Supply Chains for Vaccine Manufacturing. Calling upon idea submissions from its members, BioMADE reviewed more than 50 responses and built collaborative projects that combined the strengths of related pitches to increase the scope and impact of the final proposals. Encouraging teamwork across its member network is a key part of BioMADE’s mission. Now, as these multiyear projects near completion, with support from BioMADE, we are confident that leveraging cutting-edge bioindustrial manufacturing technologies will enhance domestic supply chain resilience. Biomanufacturing Antigens: A Multi-University Collaboration Viral antigens (viral proteins or portions of them) are important for use as research reagents, diagnostics for serological testing, and subunit vaccines. As viruses mutate, there is an urgent need to design and produce new viral antigens in an efficient, rapid, scalable, and cost-effective way. Distributed manufacturing that utilizes a variety of platforms, in various US geographical locations, can reduce supply chain limitations and constraints, improve response resiliency, enhance US biomanufacturing, and expand the biomanufacturing workforce. This BioMADE-led collaboration brought together research teams from six universities—University of California, Davis; University of Texas, Austin; University of Georgia, Athens; Johns Hopkins University; Boston University; and Rensselaer Polytechnic Institute (RPI)—to design, develop, quantitatively assess, and compare seven different production platforms for SARS-CoV-2 antigens, utilizing bacterial, yeast, fungal, plant, and mammalian cell hosts. The goal was to identify development challenges and timelines, supply chain requirements, and scaling strategies; to quantify volumetric productivity, costs, production timelines, and product quality attributes for the different approaches; and to identify strategies that would increase flexibility in choice of production platform. To do this, this team leveraged research strengths and capabilities at each of the partner institutions. For example, the team established common analytical methods for use across platforms and project locations to compare platform capabilities effectively. Production of anti-SARS-CoV-2 monoclonal antibodies (mAbs) for quantification of antigen products was successfully performed at Johns Hopkins, purification of the mAbs was performed by RPI, and plasmid constructs were designed and delivered by UT Austin. Next, Johns Hopkins provided the mAb purified by RPI to UC Davis for testing via ELISA and Western blot. Specifically, UC Davis developed the ELISA protocol for the S2H97 antibody and H87G7 antibody produced in C1 filamentous fungi, then shared results with the project teams. Because antigen-binding properties, an intrinsic measure of antigen function, can depend on host-specific glycosylation, the team developed methods for in vitro glycosylation modification of antigens (UC Davis) (Chen 2024; Zhang et al. 2023). This groundbreaking work not only enables flexibility in choice of production platform but also will be used to tune antigen binding properties, no matter which production host is used. They developed and utilized computational modelling tools for prediction of antigen binding to targets. We are confident that leveraging cutting-edge bioindustrial manufacturing technologies will enhance domestic supply chain resilience. Alternative platforms were developed for production of COVID-19 spike and receptor binding domain (RBD) variants, including walnut embryo (UC Davis) (Zaini et al. 2024), Nicotiana benthamiana plants (UC Davis), Bacillus subtilis bacterial spore display (UT Austin) (Quezada et al. 2024), Aspergillus fungal strains (Johns Hopkins), Thermothelomyces heterothallica (C1) fungi (UC Davis), Pichia yeast strains (University of Georgia), and Chinese Hamster Ovary (CHO) mammalian cell culture (UC Davis). They are now accessing platforms based on a set of metrics determined by the project team and conducting technoeconomic analyses to develop the most promising platforms. Boston University has shared the initial outline of collaborative software developed for beta testing that will allow all collaborators on the project to work together on protocols, data files, and comment on uploaded materials. The team has identified one platform based on the fungal host C1 that appears very promising due to the high volumetric productivity of both extracellular SARS-CoV-2 RBD and full-length spike variants, low media costs, and ease of culturing. UC Davis has expressed RBD (Wuhan, Delta, and Omicron variants) and spike (Wuhan variant) variants in C1 filamentous fungi platform in 5L bioreactors. Gram levels of RBD and spike variants have been purified, and the antigens were glycan-modified (showing increased sialic acid composition) in vitro at UC Davis. Additionally, partial characterizations have been completed (e.g., thermal shift assay, biolayer interferometry [BLI], circular dichroism [CD] analysis, MALDI-TOF, and site-specific glycan analysis before and after in vitro glycan modification) and show comparable activity with commercially available controls. C1-produced spike variant stability studies at 37oC showed no significant difference up to seven days. BLI also showed functional binding of glycan-modified C1-produced RBD and spike variants to the ACE2 receptor protein and H87G7 (C1-produced mAb) in comparison to the glycan-unmodified version of the spike variant. ELISA showed no difference in binding of post-lyophilized C1-produced spike variants compared to un-lyophilized, which is important from an antigen distribution perspective. A detailed technoeconomic analysis of C1 fermentation-based antigen production is underway. This project illustrated the power of bringing together research teams with complementary but distinct expertise to collaborate on an important project and work towards the common goal of building flexible, responsive, and distributed biomanufacturing capability. The team’s accomplishments will aid in onshoring of biomanufacturing capacity and rapid development of both therapeutics and diagnostics in response to future health threats. Biomanufacturing Adjuvants: Attacking an Issue from Multiple Angles BioMADE’s second project brought together three research teams to address multiple bottlenecks in the supply chain for lipid adjuvants, key ingredients in vaccines that increase efficacy by stimulating the immune system to make the body respond more effectively. Two of the five approved-for-human-use adjuvants, squalene and quillaja saponin QS-21, come from threatened sources that limit the quantity of vaccines produced. The purest form of squalene is sourced from deep-sea shark liver oil, and saponins are derived from the bark of the Chilean tree Quillaja Saponaria, which only becomes a viable source after maturing for 25 years. In addition to their use as vaccine adjuvants, saponin and squalene ingredients provide emulsification, foaming and antioxidant properties to various food and skincare products. One of BioMADE’s greatest strengths is its ability to bring together research teams to address a common issue from many different angles. In this case, Amyris, a leading synthetic biotechnology and renewable chemical company, and two laboratories at UC Berkeley have developed viable methods for adjuvant production in the short and long term, taking advantage of both microbial and plant-based solutions. Amyris: Manufacturing Biofermentation-Based Squalene Amyris has been a maverick in reducing supply chain volatility since its inception. By engineering yeast strains and determining how to ferment those strains at a large scale, Amyris has pioneered the ability to convert basic plant sugars into high-value molecules used across end-markets. To date, the company has commercialized 15 different molecules used in more than 3,000 top global brands. Amyris technology is highly relevant to the production of raw materials used in the pharmaceutical supply chain. The goal of this RACER project was to scale up technology to produce hundreds of kilograms of sustainable, fermentation-derived squalene, which could be used to replace shark-derived squalene currently used in vaccine adjuvants. Establishing this technology at commercial scale will simplify supply chains, improve the quality and consistency of materials, eliminate reliance on threatened and endangered animals, and enhance readiness to ramp up excipient production should there be an acute future need. With the support of BioMADE, Amyris successfully completed a demonstration campaign with a domestic partner in 2023, producing and purifying more than 400 killograms of squalene. This campaign was critical in establishing the commercial viability of this novel technology, which is now commercialized in an agreement between Amyris and CRODA, a global leader in vaccine ingredient technology. UC Berkeley: Biomanufacturing Saponins from Sustainable Plants Through a pioneering two-year project at UC Berkeley, they have developed a sustainable source of quillaja saponins. By cultivating Quillaja Saponaria in California and extracting saponins from the leaves of 2–3-year-old shrubs, this innovation reduces reliance on wild-harvested bark from Chile’s dwindling population of 30-year-old trees. The trees are successfully grown in greenhouses, hydroponic systems, and open fields. Through selective genetic and environmental controls, saponin yields and profiles are optimized, and leaves are harvested at peak accumulation. The foliage regenerates, enabling a fully renewable, seasonal harvest. With respect to dry biomass, yields are 4–5 times higher than those from bark. As part of this project, they produced 3 kilograms, and they are now working on options for scale-up and pilot extraction and purification of the saponins at higher yields. By establishing a domestic, renewable supply, this project mitigates pressure on wild populations, addressing sustainability concerns and regulatory constraints. Its success strengthens pharmaceutical supply chains, ensuring a stable, long-term source of this essential vaccine ingredient. UC Berkeley: Biomanufacturing Saponins from Yeast The other lab at UC Berkeley comprising the RACER team has been focusing on leveraging synthetic biology approaches to produce lifesaving saponins sustainably in Saccharomyces cerevisiae (baker’s yeast). Yeast is an ideal platform for saponin production due to its ability to grow using only simple sugars both rapidly and in a scalable manner. Additionally, yeast possesses a eukaryotic subcellular environment similar to plants and benefits from robust toolkits for genetic modification. By incorporating 38 heterologous enzymes from six different organisms, the team was able to produce QS-21 successfully in engineered yeast that is chemically indistinguishable from QS-21 isolated from Q. saponaria. Beyond simply introducing the biosynthetic genes responsible for QS-21 production into the yeast genome, this endeavor required refactoring the primary metabolic pathways for producing non-native nucleotide sugars in yeast, which are required to produce the complex glycosylation pattern largely responsible for QS-21’s immunomodulatory activity. These projects only scratch the surface of what we can achieve with bioindustrial manufacturing. Building off this accomplishment and incorporating lessons learned, they have since focused on improving TRY (titers, rates, and yields) of QS-21 heterologously produced in yeast with the goal of providing a bioproduction platform that rivals traditional isolation from Q. saponaria plants. This pathway optimization entails a granular analysis of each transformation in the complex QS-21 biosynthetic pathway that holistically evaluates biosynthetic flux, pathway bottlenecks, and feedback inhibition, as well as finely tunes expression of heterologous enzymes to achieve maximal production. These efforts have led to increased production of key intermediates by up to 500% and are poised to enhance QS-21 production in yeast significantly. The Future of Biomanufacturing: Looking Beyond Healthcare and Pharma These projects only scratch the surface of what we can achieve with bioindustrial manufacturing. Our partnership with the Department of Defense truly symbolizes that bioindustrial manufacturing is a national security imperative. Specifically, these technologies have the potential to compress the US supply chain for vital military resources and commercial applications, like chemicals, solvents, reagents, electronic films, fabrics, polymers, and more. By making use of local crops as feedstocks to power domestic fermentation facilities, bioindustrial manufacturing ends reliance on foreign imports and ensures that we can produce critical items on US soil. Lastly, bioindustrial manufacturing holds the potential to transform the US economy, boosting resilience and creating jobs that will withstand the test of time. The US bioeconomy is currently worth $950 billion (NASEM 2020). And even more importantly, experts estimate that biology can be leveraged to produce up to 60% of materials (Chui et al. 2020) in the global consumer supply chain, representing ample opportunity for continued economic growth. This economic boost will be felt throughout the American public. Farmers will gain access to new sources of revenue, as bioindustrial manufacturing creates new markets for their crops and even waste streams. Bioindustrial manufacturing will also lead to job creation for a globally competitive STEM workforce. In 2023, the US industrial bioeconomy supported nearly 644,000 (TEConomy Partners, LLC 2024). As our industry continues to grow, experts now project more than 1.1 million additional jobs added to the US economy by 2030, exclusively driven by the rapidly expanding bioeconomy. Bioindustrial manufacturing defies categorization into a single industry or sector. Whether we are transforming vaccines or designing the military uniforms of tomorrow, BioMADE and its members will continue to push the boundaries of what we can produce in the United States by unleashing the power of biology. Team Participants Antigens Project Team: Michael Betenbaugh (JHU), Andrew Pekosz (JHU), Pricila Hauk (JHU), Ilya Finkelstein (UTA), Andrew Ellington (UTA), Jason McLellen (UTA), Steven Cramer (RPI), Jeff Rapp (UGA), Doug Densmore (BU), Priya Shah (UCD), Roland Faller (UCD), Xi Chen (UCD), Abhaya Dandekar (UCD), Carlito Lebrilla (UCD), Justin Siegel (UCD). Adjuvants Project Team: Jay Keasling (UCB), Graham Hudson (UCB), Maria Clara Tavares Astolfi (UCB) XiXi Zhao (UCB). Acknowledgement This work was performed under the following financial assistance award 70NANB22H016 & 70NANB22H017 from US Department of Commerce, National Institute of Standards and Technology. References Amyris and University of California, Berkeley. 2022. Domestic Supply Chains for Vaccine Manufacturing. BioMADE. Chen X. 2024. Enabling chemoenzymatic strategies and enzymes for synthesizing Sialyl Glycans and Sialyl Glycoconjugates. Acc. Chem. Res. 57(2):234–46. Chui M, Evers M, Manyika J, Zheng A, Nisbet T. 2020. The Bio Revolution: Innovations transforming economies, societies, and our lives. McKinsey Global Institute. NASEM [National Academies of Sciences, Engineering, and Medicine]. 2020. Safeguarding the bioeconomy. The National Academies Press. NIST [National Institute of Standards and Technology]. 2022. Commerce department awards $54 million in American Rescue Act grants to increase access to advanced manufacturing opportunities, Feb 28. Quezada A, Annapareddy A, Javanmardi K, Cooper J, Finkelstein IJ. 2024. Mammalian antigen display for pandemic countermeasures. Methods in Molecular Biology 2762:191–216. Rogers JN, Stokes B, Dunn J, Cai H, Wu M, Haq Z, Baumes H. An assessment of the potential products and economic and environmental impacts resulting from a billion ton bioeconomy. Biofuels, Bioprod. Bioref. 11:110–128. TEConomy Partners LLC. 2024. The Economic Impact of the U.S. Industrial Bioeconomy. University of California Davis, Boston University, University of Texas-Austin, Johns Hopkins University, University of Georgia, Rensselaer Polytechnic Institute. 2022. Distributed Manufacturing of Antigen for Serological Testing and Countermeasures. BioMADE. Online at https://www.biomade.org/antigen-manufacturing. Zaini PA, Haddad KR, Feinberg NG, Ophir Y, Nandi S, McDonald KA, Dandekar AM. 2024. Leveraging walnut somatic embryos as a biomanufacturing platform for recombinant proteins and metabolites. BioTech 13(4):50. Zhang L, Li Y, Li R, Yang X, Zheng Z, Fu J, Yu H, Chen X. 2023. Glycoprotein in vitro N-Glycan processing using enzymes expressed in E. coli. Molecules 28(6):2753. Related Publications Crowe SA, Liu Y, Zhao X, Scheller HV, Keasling JD. 2024. Advances in engineering nucleotide sugar metabolism for natural product glycosylation in Saccharomyces cerevisiae. ACS Synth. Biol. 13(6):1589–99. Crowe SA, Zhao X, Gan F, Chen X, Hudson GA, Astolfi MCT, Scheller HV, Liu Y, Keasling JD. 2024. Engineered Saccharomyces cerevisiae as a biosynthetic platform for nucleotide sugars. ACS Synth. Biol. 13(4):1215–24. Liu Y, Gan F, Chen X, Crowe SA, Hudson GA, Belcher MS, Schmidt M, Zhao X, Astolfi MCT, Pang B, and 21 others. 2024. Complete biosynthesis of QS-21 in engineered yeast. Nature 629:937–94. About the Author:Melanie Tomczak is head of programs and chief technology officer at BioMADE. Penny Norquist is program director—technology and innovation at BioMADE.