Redesigning RNA Delivery and Production: Unlocking the Full Potential of Personalized Cancer Therapeutics

Colin McKinlay- Senior Director of Chemistry and Delivery Technologies, Nutcracker Therapeutics; Sam Deutsch- Chief Scientific Officer, Nutcracker Therapeutics

The therapeutic promise of RNA-based medicines has never been more visible. From pandemic-era vaccines to next-generation cancer treatments, RNA is fast becoming a leading modality for precision medicine. Among its most exciting applications are personalized cancer therapeutics (PCTs) - custom-designed mRNA therapies tailored to a specific patient’s tumor profile. But as the PCT field matures, new bottlenecks are emerging in the areas of delivery and manufacturing, which need to be resolved before we see widespread usage.

RNA Delivery: The First Bottleneck

Delivering RNA in a therapeutic context is a simple concept, but it is nuanced and complex in practice. mRNA molecules are readily recognized and degraded by native enzymes, and their large size and negative charge preclude their ability to cross cell membranes to the cytosol, where their therapeutic action takes place. Therefore, robust strategies – which we refer to as “delivery vehicles” – are necessary to stabilize and protect mRNA as it is ferried into target cells.

To date, the field of mRNA delivery has been dominated by the lipid nanoparticle (LNP). LNPs were first approved for the delivery of siRNA molecules in the approved drug Onpattro™, and more recently gained global attention through the success of the COVID-19 vaccines. But as with any modality, they have limitations. LNPs have thus far only been approved for local delivery of vaccines or to the liver, and expanding their biodistribution to other organs has been an ongoing challenge, particularly where precise tissue targeting is required.¹ Their immunogenicity poses risks for repeat dosing and has a limited in vivo half-life, and as formulation complexity grows - such as with tumor-specific payloads - LNP manufacturing and consistency falter.²

Next-generation delivery platforms must meet a specific set of criteria: biocompatibility; tunability; high cargo capacity; efficient cell entry; cryostability; and scalable, reproducible manufacturing. This is a tall order, and one that traditional LNPs struggle to adequately address. Fortunately, novel delivery technologies are emerging that can complement LNPs.

Challenges Facing Viral Delivery

Viral vectors, such as adeno-associated virus (AAV) and lentivirus, have long been the workhorses of genetic medicine, but they face critical hurdles that have slowed their adoption for RNA delivery. Manufacturing these vectors is complex, expensive, and difficult to scale - even small clinical batches can require massive bioreactor volumes, with yields and quality often varying from run to run. However, their immunogenicity is the biggest limitation: a high-dose systemic delivery can cause severe or even fatal immune responses that often limit treatment to a single dose, as re-dosing is thwarted by immune memory.

Payload size is also constrained - AAV’s nearly 4.7 kilobase capacity is insufficient for many RNA-based therapeutics - and achieving precise tissue targeting without off-target effects remains challenging despite capsid engineering advances. Together, these factors make viral delivery a powerful but limited tool, prompting intense interest in alternative, non-viral RNA delivery platforms.

Polymer Nanoparticles

Polymer nanoparticles use cationic polymers to form complexes with negatively charged RNA, offering a highly customizable approach to targeted delivery. These particles are often very stable and don’t require the lipid excipients present in lipid nanoparticles. However, their ability to strongly bind often precludes mRNA release, and so their widespread adoption is still forthcoming. Additionally, since they are typically made using a non-discreet polymerization strategy, control of their manufacturing consistency is often a concern.⁵ While computational tools have accelerated development, challenges in stability and release control must be overcome before their full potential can be realized.

Exosomes

Exosomes are naturally produced by cells, and so, are highly biocompatible and less likely to trigger immune responses. They deliver RNA efficiently by fusing with cell membranes and releasing cargo directly into the cytoplasm, making them ideal for in vivo applications.6 However, their clinical utility is limited by manufacturing hurdles, including the difficulty of isolating pure, consistent exosome populations and maintaining stability during large-scale production and transport. These challenges lead to low yields and inconsistent quality, slowing their path toward broader therapeutic use.

Peptoid Nanoparticles

Among the most promising alternatives to traditional LNPs are peptoids, engineered analogs of peptides with improved stability and tunability, but whose vehicles function and behave similarly. By placing functional groups on the amide nitrogen rather than the alpha carbon, peptoids allow for a great degree of control over chemical properties and thus nanoparticle architecture, which has dramatic impacts on in vivo performance and tissue selectivity. Recent work from Nutcracker Therapeutics benchmarked over 200 peptoid-based configurations, ultimately identifying not only candidates that outperformed traditional MC3 LNPs - a commonly used ionizable lipid formulation -but also formulations that targeted the spleen and lung with high fidelity.³

Equally important, they produced negligible proinflammatory responses and no visible liver toxicity, making them highly promising for repeat dosing in immunologically sensitive contexts such as cancer immunotherapy. Additionally, the peptoid particles demonstrated six-month cryostability at –80 °C with no increase in particle size or loss of encapsulation.³

The Manufacturing Challenge: PCTs at Scale

Even with an optimal delivery system, PCTs face great production and logistics hurdles. Each therapy must be designed based on a patient’s unique tumor mutations and then manufactured from scratch. This means the entire process, from biopsy to administration, must occur within weeks and cross large distances.

Traditional biomanufacturing models, designed for large-batch uniform production (low-mix, high-volume), are fundamentally misaligned with the needs of PCTs (high-mix, low-volume). Running a 100-liter bioreactor to make a few doses is economically and operationally inefficient. Worse, switching from one patient-specific sequence to another creates delays due to frequent changeovers from one patient’s drug to the next and introduces contamination risks. Legacy setups are ill-equipped to support the parallel development of dozens of unique products.

A New Manufacturing Paradigm

To bring PCTs into real-world clinical practice, we need a fundamentally different way of making medicine, one that is highly integrated throughout the entire process and remains consistent regardless of the variability in patients’ tumor sequences. Fortunately, insights from high-precision fields, such as semiconductor manufacturing, along with parallels to CAR T therapies, offer invaluable examples of how to approach this challenge.

A logical first step is to miniaturize and automate the manufacturing process - scale down production to the required output volume and remove variability caused by the human element. While some approach this through compact bioreactors or modular cleanroom pods, others, such as Nutcracker Therapeutics and its NMU Symphony™, turn to microfluidics and closed-loop systems. Using this approach, the entire RNA manufacturing workflow is compressed onto one instrument via three single-use biochips that execute core processes including DNA template synthesis, in vitro transcription and purification, and formulation. This enables dramatic gains in efficiency, enabling turnaround times as short as three weeks from sequence design to final drug product, while also optimizing raw material use and minimizing manual interventions.⁷

Another key component within this process is real-time, embedded quality control. Unlike traditional methods that rely on post-production testing, integrated sensors on the biochips monitor more than 20 parameters throughout the manufacturing cycle.⁷ This allows for continuous assurance that each batch meets clinical standards as it is being made, eliminating the need to reserve product for off-the-line testing and allowing more of the therapy to go directly to the patient.

The Design Dilemma: Making Each Therapy Count

Patient-specific sequence design remains one of the most intricate - and in a way, artistic - steps of PCT production. This process involves far more than simply identifying mutations present in the tumor. It requires selecting the ones that can produce neoantigens capable of triggering a robust and specific immune response, while avoiding those that may be poorly expressed or shared with healthy tissue.

Initial tumor profiling may uncover hundreds of mutations, but only a select few can be harnessed to generate mRNA-encoded neoantigens capable of eliciting a robust, tumor-specific T-cell response.⁸ This requires a thorough understanding of the mechanics of antigen presentation, immune escape mechanisms, and the patient’s immune repertoire. Even after targets are selected, the mRNA sequence must be engineered for expression, stability, and manufacturability. Codon usage, RNA secondary structure, untranslated regions (UTRs), and avoidance of off-target immunogenicity must all be considered.

To streamline this process, some companies are building tightly integrated design platforms that bring together sequencing data, bioinformatics, and sequence engineering into a seamless pipeline. Nutcracker Therapeutics, for example, has developed a proprietary system known as CodonCracker™ software. The platform balances the competing priorities of PCT design, such as manufacturability and therapeutic potency, through a rules-based framework informed by experimental and clinical data.

Navigating Regulatory Complexity

Traditional regulatory frameworks, especially for cell and gene therapies, are designed around batch-based consistency, lengthy validation timelines, and large-scale production. Going through the entire regulatory review process is difficult, especially when every drug is a one-off. For companies developing PCTs, this creates uncertainty about what qualifies as sufficient evidence for product quality and clinical readiness, especially in early development stages.

There is growing momentum, however, for platform-based regulatory models. Under such a model, once a delivery vehicle, a manufacturing system, and other shared components are validated, new therapies using that backbone can undergo accelerated review.⁹ This approach, borrowed from vaccine platforms, could dramatically lower barriers for PCT approval, so long as rigorous documentation and control are maintained.

The Future of RNA Therapeutics is Personalized

The convergence of delivery innovation, microfluidic manufacturing, and computational design has made something previously unimaginable now attainable: cancer therapies built for one, delivered at scale. But to make PCTs truly accessible, we must continue innovating beyond LNPs and beyond conventional infrastructure. Peptoids, protein cages, polymers, and exosomes each offer tools to solve the delivery challenge, but none will succeed without equal advances in manufacturing and regulatory readiness.

The science is here. The platforms are here. What is needed now is the regulatory, clinical, and technological ecosystem to support this new model of medicine - one in which each treatment is as unique as the person receiving it.

References:

1. Mehta M, Bui TA, Yang X, Aksoy Y, Goldys EM, Deng W. Lipid-Based Nanoparticles for Drug/ Gene Delivery: An Overview of the Production Techniques and Difficulties Encountered in Their Industrial Development. ACS Mater Au. 2023;3(6):600-619. Published 2023 Aug 21. doi:10.1021/acsmaterialsau.3c00032
2. Wang J, Ding Y, Chong K, et al. Recent Advances in Lipid Nanoparticles and Their Safety Concerns for mRNA Delivery. Vaccines (Basel). 2024;12(10):1148. Published 2024 Oct 8. doi:10.3390/vaccines12101148
3. Webster ER, Peck NE, Echeverri JD, et al. Discovery of a Peptoid-Based Nanoparticle Platform for Therapeutic mRNA Delivery via Diverse Library Clustering and Structural Parametrization. ACS Nano. 2024;18(33):22181-22193. doi:10.1021/acsnano.4c05513
4. Bhaskar S, Lim S. Engineering protein nanocages as carriers for biomedical applications. NPG Asia Mater. 2017;9(4):e371. doi:10.1038/am.2016.128
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6. Iqbal Z, Rehman K, Mahmood A, et al. Exosome for mRNA delivery: strategies and therapeutic applications. J Nanobiotechnology. 2024;22(1):395. Published 2024 Jul 4. doi:10.1186/s12951-024-02634-x
7. Nutcracker Therapeutics. Nutcracker Therapeutics Unveils NMU-Symphony™ System for On-demand, Individualized Manufacture of RNA-based Personalized Therapeutics, 2025. Accessed June 25, 2025. https://www.nutcrackerx.com/news-overview/press-releases/ press-detail/?press_id=2431
8. Huang X, Zhang G, Tang TY, Gao X, Liang TB. Personalized pancreatic cancer therapy: from the perspective of mRan NA vaccine. Mil Med Res. 2022;9(1):53. Published 2022 Oct 13. doi:10.1186/s40779-022-00416-w
9. U.S. Food and Drug Administration. Considerations for the Development of Chimeric Antigen Receptor (CAR) T Cell Products: Guidance for Industry. Published April 2024. Accessed June 24, 2025. https://www.fda.gov/media/178938/download

 

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