Quality, Compliance, and Scale in Modern Cell Therapy Manufacturing

Since the first FDA approval of a CAR T-cell therapy in 2017,¹ the cell and gene therapy field has seen substantial market expansion. Manufacturing alone is projected to grow at an annual rate of 30% through 2035.² The steady rise in cell therapies represents a shift in treatment for a multitude of diseases, including hematological malignancies.

Yet, the production of CAR T-cell therapies presents unique challenges in translating candidate therapeutics into robust, clinically validated products. Autologous cell therapies rely on sourcing cells from patients, which are then engineered to express a chimeric antigen receptor (CAR). Hurdles exist within the manufacturing landscape that are not seen with conventional therapeutics, including variability of starting materials, logistics with engineering, scalability, and regulatory considerations that both companies and regulatory agencies are working to address.

This article aims to explain the current landscape of cell therapy manufacturing, including its challenges and solutions.    

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Managing variability in cell therapy processing

Autologous therapies rely on engineering a patient's own immune cells. This is achieved through apheresis, which involves collecting patient blood, isolating and activating T cells, genetically engineering the receptor, amplifying the cells, performing quality control, and finally administering the cells to the patient. While conventional therapies rely on a fixed starting material, autologous cell therapy uses the patient's own cells. This introduces variability and multiple challenges in the manufacturing process.

“There's never just one challenge. There are multiple challenges,” said Dr. Bruce Levine, the Barbara and Edward Netter Professor in Cancer Gene Therapy in the Perelman School of Medicine at the University of Pennsylvania. “We have a manufacturing process that is not fully automated as the apheresis product collected from patients is inherently inconsistent.”

Indeed, the starting material will contain a mixture of immune cells, including red blood cells, platelets, monocytes, granulocytes, and lymphocytes. However, the crucial challenge arises from native consistency. T cells vary significantly depending on the patient's disease state and prior treatment history.³

Key considerations include standardizing the starting material to fit the bioprocess while also reducing costs, as each patient's cells have to be treated differently. Apheresis products are tested early in potency assays to assess purity, T-cell phenotypes, and subsets, as well as pre-activation biomarkers.⁴ Only the material that fits the acceptance criteria is fed into the process. This is a modern process development approach that helps reduce variability within the process. Next to this is the need to increase automation to lower costs for patients. Ultimately, characterization of the starting material is essential to de-risk the standardized engineering process. 

Challenges in process analytics

Levine highlighted that two of the most significant hurdles for analytics are potency and sterility. Defining potency for a living drug is notoriously difficult. “[For a new drug] how can you develop a potency assay until you understand the mechanism of action?” he stated. The problem is compounded by the fact that the product changes post-infusion. “With a living cell product that is dividing, how can you design a potency assay for what the product will be that kills the tumor? You can only correlate backwards.”

A complete mechanism of action is not a prerequisite for defining potency. Instead, a quantitative measurement of biologic activity linked to clinically relevant effects with a hypothesized method of action is accepted, with iterative refinements.⁵

With newer manufacturing processes coming online, which shorten current 9–12 day processes down to 2–3 days, measuring potency becomes more challenging as historical correlations become less reliable.⁶ With rapid CAR T-cell platforms, activation/killing assays and multiomics-based phenotyping are being investigated to capture product quality better to fit quality measurements to a 24-hour timeline.⁷   

The second major bottleneck is sterility testing. Traditional culture-based sterility tests take upwards of 14 days. Yet for patients with rapidly progressing disease, a two-week window post-production and pre-administration can be life or death.

New alternatives are being tested using sensitive flow cytometry assays,⁸ non-growth-based assays with machine learning,⁹ and sequencing-based assays.¹⁰ The concept is to define markers that can gauge product sterility in a fraction of the two-week window, enabling lot release and patient infusion as quickly as possible.  

CAR T-cell developability

Today, most clinically approved CAR T-cell therapeutics originated in academic research labs; however, there is currently less momentum for advancing early-stage discovery, with most investments shifting toward late-stage products.¹¹ “Funding is probably the biggest bottleneck because it limits access, and it limits development,” said Dr. Emily Hopewell, director of cell and gene therapy manufacturing and assistant professor in clinical medical and molecular genetics at Indiana University.

Many start-up biopharmaceutical companies producing CAR T-cell products do not make it far past conceptualization due to these funding limitations. But even for those with adequate capital, significant developmental hurdles remain. “Some of the common issues include challenges with scalability, considerations on available instrumentation, quality of supplies and reagents, and robust documentation,” Hopewell noted. 

Cell therapy scalability and GMP  

The ability to produce cell therapies at scale remains a considerable challenge. Scalability means to scale out the process to handle thousands of individual patient batches simultaneously. This presents a unique tension between early-stage process design and commercial viability. Hopewell argued that “funding dictates strategy,” often forcing teams to rely on manual, open-processing techniques in early trials because they are cheaper upfront, even though they are challenging to scale to be high-throughput later.¹²

A major operational bottleneck is the transition of instrumentation. Available academic instrumentation is a frequent stumbling block in moving towards commercial production. Research-grade equipment often lacks the automation and data integration necessary for commercial-scale applications.¹³ If a process is built around manual instrumentation, scaling out requires a linear increase in facility size and headcount, a model that quickly becomes unsustainable.

“I think one of the biggest things that is underappreciated is actually what it costs to run even a small facility to meet early GMP requirements,” Hopewell said. The infrastructure burden, including environmental monitoring, documentation, and cryogenic logistics, imposes a ceiling on the number of doses a centralized facility can reliably produce.¹⁴

To bypass these bottlenecks, the industry is increasingly exploring distributed or point-of-care manufacturing. By placing automated units directly in hospitals, manufacturers could theoretically scale by using these hubs within the network rather than relying on a central plant.^15,16 This would shift the scalability challenge from facility size to ensuring quality control, necessitating advanced in-line sensors and remote monitoring to ensure that a dose produced between two facilities is identical.¹⁷  

Regulatory considerations

For early-stage companies, Hopewell noted that a major challenge often stems from foundational elements. For example, the adequate documentation and the thoughtful design of preclinical studies, which could raise questions from regulatory bodies.  

However, once in the clinic, the challenge shifts to modernizing the process. Altering the manufacturing process creates a new product requiring new authorization. However, updating the analytics, such as swapping a 14-day sterility test for a rapid 3-day PCR, is often accepted via a supplemental application because the product itself remains unchanged. Finally, as manufacturing scales, robust potency assays are essential to prove comparability, ensuring cells produced at a new regional hub are identical to those from the original site. 

Future of cell therapies

Looking ahead to the next decade of cell therapy, the industry will continue moving towards a diverse ecosystem of technological solutions rather than a single approach. “I don't think it's just one thing because of the breadth of possible indications,” said Hopewell. She envisions a future where automation enhances the reliability of current autologous products, while new modalities expand patient access.

Simultaneously, there is a push to transition from ex vivo engineering to in vivo engineering. Here, genetic material is delivered directly to the patient's body using viral vectors or lipid nanoparticles, thereby bypassing the need for ex vivo cell culture entirely. With clinical trials already underway,¹⁸ Levine is optimistic about this paradigm shift, predicting that “somewhere between 5 and 10 years from now, we will have multiple approvals of in vivo cell therapies.”

However, Levine does not believe this will render current methods obsolete immediately. “Those will coexist for quite some time because we're still very early in the field,” he noted. Ex vivo manipulation still allows for complex engineering, such as multiple gene knockouts, that is currently more challenging to achieve with in vivo therapy.¹⁹