As the field of advanced therapies expands, the push for sustainability grows increasingly critical. Manufacturers face substantial hurdles due to the high costs and scalability challenges of traditional methods, which could limit the widespread adoption of new therapies. Embracing more sustainable production techniques not only mitigates these issues but also diminishes the environmental footprint of therapy manufacturing. A standout approach is the shift from historical methods to produce plasmid DNA (pDNA) via fermentation to the use of enzymatic processes that are superior in their resource efficiency. Touchlight's innovative dbDNATM (doggyboneTM DNA) technology exemplifies this shift, offering a smaller production footprint, freedom from bacterial impurities, and enhanced sustainability, setting a new standard in the manufacturing of diverse advanced therapies.
Growing Emphasis on Sustainability in Pharma Manufacturing
Whilst the pharmaceutical industry is committed to improving and saving lives, the full impact of pharmaceutical manufacturing practices on the health of our planet and people has only received considerable attention in the last decade. The production of both small and large molecule drugs is highly energy-intensive, typically involving substantial water use, hazardous chemicals and generating considerable waste. Additional environmental concerns arise from packaging, distribution practices, the disposal of medical waste, and unused medications.
In 2023, it was estimated that the healthcare sector was responsible for 4% of global carbon dioxide (CO2) emissions, with projections suggesting a more than threefold increase by 2050 if no mitigative action is taken.1 Remarkably, the pharmaceutical industry's emissions surpass those of the automotive sector, and the currently-employed manufacturing processes pose significantly greater risks to the environment than those employed in the petrochemical industry.2
The increasing awareness of climate change worldwide has catalysed the pharmaceutical industry to acknowledge and act upon its environmental responsibilities.3 Drug manufacturers are adopting more energy-efficient equipment, utilizing renewable energy sources, applying green chemistry principles to minimize resource use and waste and finding ways to recycle and reuse solvents and water. Sustainable packaging solutions are also being introduced. Expectations for similar sustainable practices are extending throughout the supply chain, from raw material suppliers to contract service providers, as the sustainability focus is shifting towards Scope 3 emissions.
Given the complexity of advanced therapies and the many challenges manufacturers face when navigating an emerging field and establishing new processes and technologies, sustainability has not yet been a focus for most companies active in this area. This contrasts with traditional biologics, where sustainability efforts have gained more traction due to established production processes that have been optimized over time. Traditional biologic manufacturing often benefits from decades of process refinement, allowing for the implementation of energy-efficient equipment, waste-reduction strategies, and green chemistry principles. In contrast, advanced therapies, such as gene and cell therapies, face heightened scalability challenges and higher resource demands due to the nascent and highly specialized nature of their manufacturing. However, as issues of cost and scalability become more pressing, sustainability is gaining importance in advanced therapy production, as these factors could jeopardize the widespread application of many new therapeutic modalities.
Adopting more sustainable production methods can mitigate these issues while also reducing the environmental impact of manufacturing advanced therapies. Some drug developers, for example, are discovering that the implementation of intensified processes can diminish environmental footprints, reduce resource consumption and waste and enhance yields and scalability.4 Technological advancements such as digital technologies are significantly contributing to the reduction of waste and optimization of resource use throughout the pharmaceutical supply chain. As the sector evolves, more sustainable solutions will become necessary. Therefore, addressing these concerns from the start is not only prudent in the long term but could also yield immediate benefits.
Reassessing Production Methods for Sustainable Advanced Therapies
Advanced therapeutics are revolutionizing the manner in which diseases are treated. For example, gene therapies, gene-modified cell therapies and nucleic acid–based medicines offer potential cures, not just treatments for disease symptoms. However, the manufacturing processes for these innovative drugs are highly inefficient, affecting both their scalability and overall sustainability.
A significant challenge is the production of pDNA, which serves as an essential building block for a wide range of genetic medicine applications, including mRNA and most cell and gene therapies. Currently, most pDNA is produced through bacterial fermentation — a process that is not only resource-intensive and lengthy but also complex.
The Challenges of Fermentation for Plasmid DNA Production
The historical bacterial fermentation process for synthesizing pDNA faces significant challenges, including slow production and the risk of carrying bacterial cell components, such as genomic DNA and endotoxins. The use of Escherichia coli–based bacterial fermentation, which harbors antibiotic-resistance genes and endotoxins, can pose safety risks if administered to patients. Moreover, the presence of antibiotic resistance markers contributes to the unsustainable spread of multidrug-resistant bacteria. Consequently, these impurities must be rigorously and complexly purified.
The inefficiencies of the fermentation process are further compounded by its costliness. Low yields necessitate large-volume processes, consuming substantial amounts of water and generating significant waste from spent bacterial cells. This waste not only includes biomass but also various impurities like RNA, host-cell genomic DNA, host-cell proteins, and endotoxins, which must be removed through complex and waste-intensive purification steps. Moreover, clarified lysates typically contain less than 3% pDNA, complicating the purification process and increasing waste.5 Additionally, traditional pDNA production requires high energy and substantial water for clean-in-place (CIP) operations of fermentation vessels. Although some pDNA manufacturers have transitioned towards single-use systems to reduce these resource demands, the majority of pDNA continues to be produced in bioreactors requiring regular CIP and intensive resource usage.
Additionally, the scalability of pDNA manufacturing is severely constrained by yield and purity challenges inherent to the fermentation process. These challenges are exacerbated when producing larger plasmids or those with complex genetic payloads, which can impose metabolic stresses on host cells and reduce overall yield. For instance, plasmid titers in fermentation are significantly lower than those observed for recombinant proteins and monoclonal antibodies, and the quality of plasmid DNA can be compromised by factors such as shear stress and prolonged processing times during lysis, leading to degradation.
Real-time monitoring of critical process parameters (CPPs) like agitation, pH, and temperature is essential to maximize yields and ensure quality.6 Despite such measures, achieving the necessary high percentage of supercoiled DNA isoforms — greater than 90% as per modern regulatory expectations — remains a formidable challenge.7 Consequently, minimizing the cost of goods sold (COGS) while maintaining the required quality standards at scale presents a substantial challenge, with pDNA often accounting for the largest proportion (15–50%) of raw material costs per GMP batch of adeno-associated viral (AAV) vector used in gene therapy applications.
Synthetic dbDNA Presents a Sustainable Alternative
There are several potential alternative methods for producing DNA that are suitable for use as a critical raw material in advanced therapy manufacturing. One particularly promising method, in terms of sustainability, involves the use of enzymes in vitro. Enzymatic amplification of DNA streamlines the production process, reducing the manufacturing footprint, which in turn lowers energy and resource consumption, contributing to a more environmentally sustainable production method. Since bacterial cells are not involved, bacterial sequences and antibiotics are entirely absent, eliminating the need for lengthy purification processes. Therefore, enzymatic methods are not only more efficient but also produce high-quality DNA with a significantly improved safety profile.
dbDNA is a double-stranded, linear, covalently closed DNA construct produced through rolling circle amplification from a circular template. The process uses an amplification enzyme and a processing enzyme to swiftly produce high-quality products. During dbDNA amplification, a circular DNA template and φ29 DNA polymerase generate long double-stranded concatemers of DNA. Protelomerase is then used to cleave at specific recognition sites and covalently close the linear DNA, producing multiple copies of dbDNA, while restriction enzymes and exonucleases break down the backbone sequences. The DNA undergoes purification through a series of chromatography steps, tangential flow filtration, and further enzymatic processing before being subjected to filtration and filling.
The entire process occupies a small manufacturing footprint relative to pDNA manufacturing via fermentation. Processes that currently operate on scales smaller than 5 liters can achieve yields comparable to those requiring fermentation volumes of over 50 liters, sometimes up to 300 liters. Going forward, yields of dbDNA are expected to increase. Production of dbDNA also scales linearly, avoiding the impurities and contamination risks associated with fermentation, thus reducing the high waste generation typical of that method.
Touchlight’s dbDNA manufacturing process stands out from competing technologies owing to its highly optimized approach to scalability and the production of complex sequences. The dbDNA process avoids thermal cycling, and patented reagent compositions enable Touchlight to produce high-yield sequences with complex features, such as homopolymers, secondary structures and repetitive sequences. Furthermore, Touchlight’s process technology circumvents ligation-based methods in downstream purification, which often require large reaction volumes and can generate non-target DNA species.
Another significant advantage of dbDNA production over traditional pDNA fermentation is the dramatic reduction in solvent use and waste generation. Conventional pDNA manufacturing relies on hazardous solvents such as ethanol, isopropanol, chloroform, and phenol — some of which are regulated under both the EU's REACH (Registration, Evaluation, Authorisation, and Restriction of Chemicals) and the UK's post-Brexit UK REACH, due to their environmental and health risks. These solvents not only contribute to environmental pollution but also pose significant disposal challenges and safety concerns. In contrast, the enzymatic dbDNA process eliminates the need for these solvents by removing bacterial cells from the equation, streamlining purification and reducing the overall environmental footprint. By avoiding these waste-intensive steps, dbDNA offers a cleaner, safer, and more sustainable approach to DNA manufacturing.
Comparison of Water Usage in dbDNA vs. pDNA Production
One of the key sustainability advantages of Touchlight’s dbDNA technology is its significantly lower water usage compared with traditional pDNA fermentation processes. In the Global Risks Report 2024, the World Economic Forum cites resource shortages, including water scarcity, as the fourth most severe risk projected to worsen significantly over the next decade, with potential widespread impacts on industries, economies, and ecosystems worldwide. This highlights the growing importance of sustainable water consumption.
Many pDNA constructs used in genetic medicine are complex, containing high GC content, AAV inverted terminal repeats (ITRs), homopolymers (polyA), and other toxic or unstable sequences. As such, pDNA fermentation yields can vary by 1–2 orders of magnitude. An analysis of client-reported pDNA yields is shown in contrast to that of dbDNA (Figure 1). On average, dbDNA typically has up to a 40-fold lower upstream processing volume for equivalent DNA yield, resulting in substantially lower biomass, water, and waste volumes. A further analysis comparing the full workflows of dbDNA versus pDNA water usage indicates that GMP production of dbDNA would typically use ~65% less than pDNA fermentation processes, and even up to 81% when comparing with common low-productivity processes.
These analyses do not account for additional water used in cleaning steps, which can further increase overall water consumption. Because traditional pDNA fermentation involves large-scale bacterial culture, extensive cleaning and flushing protocols are required to prevent cross-contamination, particularly during the removal of bacterial biomass and endotoxins. This adds significantly to the total water consumption. In contrast, the enzymatic dbDNA process, which does not involve bacterial cells, requires far less intensive cleaning. As a result, the water consumption gap between pDNA and dbDNA is likely even wider when cleaning and flushing are considered, further highlighting the environmental benefits of the dbDNA approach.
Figure 1. Upstream water consumption for dbDNA vs. pDNA. pDNA productivity sources collected by Touchlight and Nice Insight and grouped into high productivity processes and low productivity processes. Total water consumption for entire process flow of pDNA manufacturing and dbDNA manufacturing was modeled and compared, showing a 65% reduction in total water consumption as an average for dbDNA production.
Additionally, the dbDNA process is significantly faster, taking five days to complete a GMP batch, compared with the three weeks required for a batch of pDNA using traditional fermentation methods. This reduction in process time not only speeds up production but also reduces overall energy consumption, as shorter processes require less sustained energy input. The substantial difference in both water use and production time highlights dbDNA’s role in fostering a more sustainable, energy-efficient, and cost-effective approach to producing genetic medicines.
Extended Downstream Sustainability Benefits of dbDNA
Because dbDNA can incorporate genes of interest up to 30 kilobases in size and with significantly higher complexity than those produced using conventional bacterial fermentation, it is ideally suited to a wide range of therapeutic applications. dbDNA has the potential to be pivotal in the development of DNA vaccines, non-viral gene therapies, viral vectors for gene and cell therapies, mRNA therapeutics and genome-editing technologies, marking it as a crucial enabler of the next generation of genetic medicines.
Furthermore, using dbDNA to produce advanced therapies enhances the sustainability of these manufacturing operations. It allows for the achievement of equivalent or improved titres for several AAV serotypes and lentiviral vectors using less DNA. AAV packaging efficiency is doubled on average, yielding more doses per batch. When used to create lipid nanoparticles (LNPs) for non-viral gene therapy applications, dbDNA facilitates the production of smaller, more uniform LNPs without compromising encapsulation efficiency. Additionally, DNA-based vaccines utilizing dbDNA achieve comparable immunogenicity at lower doses than those relying on conventional pDNA.
Employing high-purity, low-endotoxin, closed dbDNA for genome editing enhances editing efficiency and eliminates the need for generating viral vectors for the delivery of genetic material. dbDNA's short production timelines, scalability, and high-fidelity amplification of complex genetic constructs are also key advantages for mRNA manufacturing using z-dbDNA, a specialized product derived from dbDNA. Beyond these specific applications, dbDNA's versatility across genetic medicines not only enhances therapeutic outcomes but also contributes to establishing a new sustainable paradigm for the entire sector, reducing resource use and environmental impact while improving efficiency.
The Imperative of Sustainability in Pharma Manufacturing
Enhancing the sustainability of all aspects of pharmaceutical manufacturing is imperative. Significant progress has been made in reducing the environmental impacts of processes used to produce small molecule and conventional biologic drugs. Considering the emerging nature of advanced therapies, it is understandable that sustainability has not yet been prioritized. However, this issue needs to be addressed sooner rather than later, particularly given the predicted explosion of these therapies in the coming years and the ongoing need to reduce the associated COGS for their production to make advanced therapies commercially viable in the long term.
Substituting the costly and inefficient fermentation-based production of pDNA with the clearly more sustainable enzymatic method of producing dbDNA offers a straightforward solution to significantly enhance the sustainability of advanced therapy manufacturing operations. Already, more than 170 biotech and top 10 pharma companies involved in developing mRNA, gene editing, viral vectors, DNA vaccines, and non-viral gene therapy products have adopted this approach. Touchlight is actively supplying DNA and regulatory dossiers for clinical trials, with a major study scheduled for later in 2024. As a leader in the synthetic DNA market, Touchlight is committed to assisting biopharma clients in harnessing the full potential of the genetic revolution through the use of more sustainable DNA solutions. The future of sustainable advanced therapies depends not only on continued innovation but also on the widespread adoption of sustainable methods like dbDNA, which can revolutionize the environmental impact of genetic medicine manufacturing.
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