Category: Bioprocessing

The emergence of increasingly complex biologics such as multi‑specific antibodies, cytokines, fusion proteins, and other structurally demanding modalities has exposed the limits of conventional bioprocessing. Many of these molecules are difficult to express at commercially viable yields, and their quality attributes can be highly sensitive to the cellular environment. As a result, productivity, consistency, and cost remain major constraints across the industry.

Traditional cell line development (CLD) relies on constitutive promoters that drive static expression throughout development and production. Because production is always on, cells must divide and manufacture protein simultaneously, even when the product is burdensome or toxic. While this model worked relatively well for easy-to-express monoclonal antibodies, it does not work well for next-generation biologics, where the inherent trade-off between higher specific productivity and rapid cell growth, both competing for the same cellular resources, is increased. Light‑controlled gene expression using optogenetics is emerging as a credible alternative.

This article explores the ten most important questions facing optogenetic biomanufacturing as it moves from proof‑of‑concept demonstrations toward mainstream adoption in modern bioprocessing.

1. What is optogenetics, and why is it relevant to biologics manufacturing?

Optogenetics uses light‑responsive proteins to control specific cellular functions. In biomanufacturing, the key application is regulating gene expression with light instead of relying on constitutive promoters or chemical inducers. When light‑controlled gene expression systems are engineered into production cell lines, illumination at defined wavelengths can switch expression on, off, or to intermediate levels.

This is important because it introduces a fundamentally different control modality. Conventional systems provide static expression, whereas optogenetics enables dynamic, reversible, and tunable control. As biologics become more complex and more sensitive to expression conditions, having a way to precisely modulate transcription directly, rather than perturbing the entire cell by modulating process parameters such as temperature, will become increasingly valuable.

2. What core limitation in biologics manufacturing does light‑based control address?

The main limitation is the inherent competition between cell growth and protein production. In constitutive systems, cells must divide and manufacture protein at the same time, drawing on the same finite pool of metabolic resources. This creates a structural trade‑off: clones that produce strongly have a slow doubling time and/or do not grow to viable densities, while clones that grow well often produce only modest titers. This trade‑off becomes much more pronounced for challenging molecules such as multi‑specific antibodies, cytokines, and fusion proteins that are aggregation‑prone or place a significant burden on the host cell.

Optogenetics addresses this by separating the growth and production phases. Cells can grow in an uninduced, low-burden state and then transition into a productive state upon illumination. As light acts directly on transcriptional regulators in a dose-dependent manner, expression can be tuned precisely rather than modulated indirectly through temperature shifts or coarsely and irreversibly by chemical induction. Chemical inducers can also negatively affect cell performance through off-target effects and are difficult to remove during downstream processing, which has limited their adoption in mammalian biomanufacturing. The direct, tunable control by light also enables more deliberate modulation of pathways that influence critical quality attributes such as post-translational modifications (PTMs), which is increasingly important for complex biologics and biosimilars.

3. How does optogenetic light exposure work, and is it safe for cells and media?

Optogenetics uses light as an informational cue rather than an energy source. Because photoreceptors respond to brief, low-intensity pulses and stay “on” for a tunable period of time before reverting to the off state, optogenetic systems can maintain precise control without continuous or high-power illumination.

The wavelengths used in bioprocessing are in the visible range and non-ionizing, operating well under established phototoxicity thresholds. At these levels, light does not harm cells or DNA, nor does it disrupt cellular physiology. Although certain media components are known to be light-sensitive, the illumination used for optogenetic induction has not shown detrimental effects on cellular performance.

4. What is the impact of optogenetics on lab operations?

Optogenetic workflows use standard lab equipment with the addition of illumination devices compatible with existing infrastructure, such as plates, shake flasks, or bioreactors. The main operational difference occurs during pool generation and single-cell cloning, where cells must remain uninduced. This is achieved by working under “safe light” conditions, visible wavelengths that do not activate the specific optogenetic system but allow the operator to handle the cell culture. Only small areas of the lab need to be adapted for this purpose. For all other operations, including biomanufacturing, local interventions to shield cells from room light are typically sufficient.

5. How many cellular functions can be controlled with light in a single cell line?

Current systems can independently regulate cellular functions using two or three different wavelengths. For example, one color may control production while another modulates a critical quality‑related pathway. Functions that require coordinated timing can be linked to the same wavelength. As genetic circuit design advances, the number of independently controllable functions is expected to increase.

6. When might optogenetically manufactured biologics reach clinical and commercial stages?

Optogenetic cell line development is already being explored for multiple programs. Regulatory agencies have established pathways for evaluating emerging bioprocess technologies, and optogenetic systems are beginning to move through these mechanisms. If early development proceeds as expected, optogenetically controlled processes could support clinical filings in the next two years, with commercial adoption following thereafter.

7. Can optogenetics be integrated into existing facilities?

Yes. Optogenetic manufacturing does not require new bioreactor designs; illumination hardware can be added to standard single‑use or stainless‑steel systems. For single‑use bags, light is delivered externally through the bag without breaching the sterility barrier; for stainless‑steel tanks, cultures can be circulated through illuminated loops. No cleanroom redesign is required.

8. How does optogenetic manufacturing scale to larger bioreactors?

Scaling optogenetic systems depends on three factors: the sensitivity of the photoreceptors, the lifetime of their activated state in the dark, and the mixing and light-scattering characteristics of the bioreactor. Modern optogenetic systems for biomanufacturing are designed to respond to very low light intensities, and once activated, they gradually return to the off state in the dark at a characteristic rate, typically over tens of minutes.

Since stirred-tank bioreactors mix continuously and scatter light throughout the vessel, cells receive sufficient illumination over the photoreceptor’s characteristic activation lifetime even at large volumes. Simulation studies and early pilot-scale experiments up to the 200 L scale suggest that optogenetic activation can be achieved at commercially relevant scales, including stainless steel and single-use systems.

9. What has convinced established players to evaluate this technology?

Biologics development and manufacturing are intentionally conservative, with new technologies adopted only when they demonstrate clear, reproducible benefits and maintain patient safety. For any emerging bioprocess platform, the threshold for evaluation is data showing that it can deliver meaningful improvements without introducing new risks or operational complexity.

In comparative studies, optogenetic induction has produced more than two‑fold increases in titer for standard monoclonal antibodies as well as for more difficult‑to‑express therapeutic proteins. These gains have been achieved while maintaining or improving critical quality attributes, including those influenced by folding, assembly, and post‑translational modification.

As the next generation of therapeutics become increasingly complex, leading biopharma and CDMO players see the need for novel biomanufacturing platforms capable of meeting that complexity without compromising titers, and for that reason several key players are actively evaluating optogenetic technology for potential integration.

10. Where is optogenetic biomanufacturing headed in the next decade?

If current trends continue, optogenetic control may become a standard tool for managing expression, quality, and other cellular functions in biologics manufacturing. The ability to modulate gene expression dynamically opens possibilities for more efficient production of complex therapeutics, more predictable quality profiles, and more flexible facility design. As the technology matures, it is likely to be adopted across CDMOs, biotech, and biopharma companies seeking greater control over their manufacturing processes.

Maximilian Hoerner, PhD, is the head of optogenetics at Prolific Machines

The technology underpinning RNA vaccines¹ and therapeutics² has been around for decades. However, until recently, only a handful of products were on the market.

Everything changed in 2020 when mRNA vaccines proved³ to be effective against SARS-CoV-2, the virus that causes COVID-19. In the years since, many more RNA products entered the clinic as developers recognized both their therapeutic and commercial potential.

The pandemic also kick-started efforts to optimize RNA manufacturing that will likely shape the sector for decades to come, according to David Sokolowski, global workflow manager for nucleic acid therapeutics at Cytiva.

“The COVID vaccines heralded the rapid industrialization of RNA and LNP [lipid nanoparticle] technologies, and due to the nature of a pandemic, large amounts of vaccine safety data were generated. However, it remains a nascent industry with limited applications commercially available, and this space is where developers are rushing to build.

“Manufacturing good quality RNA and LNP became easier with the proliferation of high-quality reports from successful studies, trials, and campaigns occurring all over the world.

“Now, we’re supporting the development of therapeutics with even grander aspirations and increasingly exotic biology—whether they are encoding and producing mAb via RNA, or enabling next-generation in vivo cell therapy, LNP-mediated therapeutics have no shortage of potential advances ahead,” he continued.

Manufacturability

The key to developing any RNA-based product—be it a vaccine or a therapeutic—is to ensure it can be produced in bulk in a cost-effective and efficient manner, says Luis Avila, PhD, a scientist at services firm Novoprotein Scientific.

“RNA design fundamentally determines both manufacturability and biological performance, but optimizing for one often comes at the expense of the other.” The best approach is to design for manufacturability from the start,” he says, adding “the right template architecture can contribute with optimized promoter design, transcription initiation sequences, encoded polyA tails, transcript boundaries, and sequence composition to improve IVT [in vitro transcription] performance while minimizing problematic secondary structures.”

“Combined with other factors, such as engineered RNA polymerases, optimized reaction chemistries and advanced capping technologies, these design strategies will improve RNA yield, integrity, and translational performance all while reducing the generation of dsRNA,” he tells GEN.

The type of RNA being made should be the key consideration in any assessment of manufacturability, according to Avila, who cites the differences between messenger RNA and self-amplifying RNA to illustrate the point.

“For mRNA, coding-sequence composition, transcript length, GC content, and secondary structure strongly influence IVT efficiency. Whereas optimized UTRs [untranslated regions], cap structures, and poly(A) tails primarily govern RNA stability and translational efficiency.

“For saRNA, the incorporation of the large alphavirus replicase cassette substantially increases transcript length and structural complexity, thus making IVT more challenging while enabling intracellular RNA amplification that dramatically lowers the therapeutic dose required,” he says.

Producing circular RNA—a covalently closed-loop structure that is stable and resistant to exonuclease degradation—can be even harder, according to Avila.

“circRNA presents an even greater manufacturing challenge because linear IVT is followed by an additional circularization step whose efficiency remains a major bottleneck. Following circularization, translation relies on efficient cap-independent initiation through optimized IRES [internal ribosome entry site] elements and RNA architecture.”

Characterization

So, designing an RNA therapeutic or vaccine with manufacturing in mind is critical. However, the ability to realize that optimized blueprint on the factory floor is entirely dependent on being able to characterize the product in real-time, as it is being made.

And, unfortunately for the industry, RNA characterization is a complex challenge, says Matthew Ranaghan, PhD, applications scientist at analysis technology firm Refeyn.

“Thorough Characterization of RNA is critical to ensuring the safety, stability, and efficacy of next-generation RNA therapeutics, yet it remains a significant analytical bottleneck.”

“Current methods are limited to various types of chromatography, which struggle with poor resolution for large RNAs, or mass spectrometry, which requires digesting samples into smaller oligos with RNases. While both have advantages, they demand extensive and time-consuming method development.”

Traditional RNA analysis usually consists of separate assays looking at specific characteristics. For example, size exclusion chromatography is used to assess aggregation while enzyme-linked immunosorbent assays are used to check for trace amounts of double-stranded RNA.

One promising alternative is mass photometry (MP), a technique that can analyze RNA molecules within minutes based on only nanograms of material within minutes in a single experiment. There are multiple potential advantages according to Ranaghan.

“A single readout replaces the need for multiple instruments, drastically reducing hands-on time, reagent costs, and the need for extensive method development across different platforms. A single readout also enables at-line process monitoring, allowing for immediate go/no-go decisions during bioprocessing and purification.”

“We envision the faster speed and higher resolution of MP to enable its use as a multi-attribute tool for at-line assessment of the various critical quality attributes (CQAs) of RNA therapeutics,” he says.

“We have already demonstrated how MP can rapidly assess integrity, fragments, multimer, and purity in a single measurement. We are also actively building out more applications,” Ranaghan adds.

Commercial concerns

Manufacturers of RNA products also need to develop commercialization plans as early as possible—in parallel with process development—to ensure they reach the patients who need them and garner the revenues needed to fund future research.

And, for some firms, developing such plans can be a steep learning curve, says Rajiv Gangurde, PhD, vice president of chemistry, manufacturing, and controls (CMC) for cell and gene therapies at contract research organization Parexel International.

“Like many newer modalities, RNA-based therapies typically emerge out of academia or start-up biotech, and transitioning from academia to industry can be challenging due to differences in objectives, differences in expertise, fundraising, etc.”

“In addition, newer modalities require heavier than usual investment in CMC activities to establish proof-of-concept as well as manufacturability. There is heavy reliance on external partners, creating capability and capacity constraints.

“Most importantly,” Gangurde continued, “a phase-appropriate CMC strategy aimed at global approvals can significantly derisk development and help minimize costs and timelines.”

Yet preparing a CMC strategy that will win approval in multiple markets is no small undertaking, particularly, as Gangurde points out, because regulatory guidelines for RNA-based therapies are still evolving.

Another challenge is the lack of consistency. For instance, the U.S. Food and Drug Administration (FDA) and EU EMA use different definitions and guidelines for CMC.

Gangurde told us, “Harmonization of guidelines and expectations across the two agencies will be hugely beneficial to developers of RNA therapies. For example, while both agencies recognize potency/efficacy assessment as a critical quality attribute (CQA), there are some differences in method validation requirements, timing, and regulatory expectations across clinical phases.”

“While the FDA accepts real-world experience and surrogate endpoints, particularly for rare or life-threatening diseases, EMA requires more comprehensive clinical data and demonstration of long-term efficacy for approval. The EMA also mandates an appropriate degree of method validation at each stage of development, whereas the FDA does not expect validation of the potency assays during Phase I,” he added.

The product component designations used by regulatory agencies can also differ. For example, the lipid nanoparticle for the COVID-19 vaccine, Spikevax, consists of four lipids: SM-102, PEG2000-DMG, DSPC, and cholesterol.

The FDA designates each of these components as a “drug substance,” whereas the EMA designates them as “novel excipients”—each designation has differing data submission requirements.

Continuous process

In the future, RNA manufacturing methods are likely to keep improving, according to Novoprotein’s Avila, who says continuous production processes are likely to have a major impact.

“One of the most exciting developments is the emergence of continuous or flow-based IVT manufacturing. This has the potential to improve productivity, reduce costs, and enable more consistent large-scale RNA production through continuous enzyme utilization and process integration.”

“As equally transformative are advances in engineered low-dsRNA T7 RNA polymerases, improved co-transcriptional capping chemistries, and integrated continuous purification. All of which will enable improvements in RNA quality, simplify downstream processing, and accelerate GMP manufacturing,” he added.

This view is shared by Ranaghan from Refeyn, who cites the shift toward continuous flow manufacturing as one of the most exciting advances in the field.

“Moving away from traditional batch processing to a continuous flow model is highly logical because it minimizes the time that the fragile mRNA product spends exposed to active reaction components that drive fragmentation and aggregation. This shift not only improves overall yield and intactness, especially for massive transcripts like saRNA, but it also creates a mandate for faster, real-time analytics.”

For Parexel’s Gangurde, efforts to make production more efficient and sustainable will drive innovation, with the WHO’s recently launched mRNA Technology Transfer Programme Phase 2.0⁴ being a case in point.

“This is a major global initiative aimed at scaling up commercially viable mRNA-based vaccine and therapeutic production in low- and middle-income countries—where the need for these therapies is most critical.”

Launched in 2021 in collaboration with the Medicines Patent Pool (MPP), the initiative has enabled 15 partners across Latin America, Africa, Eastern Europe, and Asia to receive foundational mRNA technology.

Phase 2.0 focuses on building local manufacturing capacity so countries can make mRNA vaccines and therapeutics for future outbreaks and diseases like influenza, TB, HIV, malaria, dengue, and leishmaniasis, as well as oncology drugs and mAbs.

Gangurde says, “By decentralizing production, the program reduces reliance on a few high-income countries for mRNA supply, supporting global access for mRNA-based therapies.”

References

1. Beyrer C. The Long History of mRNA Vaccines. Johns Hopkins Bloomberg School of Public Health; 2021. Accessed August 12, 2026.
2. Chatterjee S, Bhattacharya M, Lee SS, Chakraborty C. An insight of different classes of RNA-based therapeutic, nanodelivery and clinical status: Current landscape. Current Research in Biotechnology 2023;6:100150-100150. doi:10.1016/j.crbiot.2023.100150
3. Parvin N, Mandal TK, Joo SW. The Impact of COVID-19 on RNA Therapeutics: A Surge in Lipid Nanoparticles and Alternative Delivery Systems, Systems. Pharmaceutics 2024; 16(11): 1366. Doi: 10.3390/pharmaceutics16111366
4. World Health Organization: WHO. mRNA Technology Transfer Programme’s Phase 2.0 discussed with partners on the sidelines of G20 Summit. Who. June 13, 2025. Accessed August 12, 2026.