Cell and Gene Therapy Manufacturing: Challenges, Technologies, and Scale-Up

By Pooja Toshniwal PahariaReviewed by Lauren Hardaker

Introduction
Why Is Cell & Gene Therapy Manufacturing Difficult?
The Scale-Up Gap in Bioprocessing
Technologies Helping Close the Gap
Regulatory and Quality Considerations
Future Outlook
References
Further reading

Cell and gene therapy manufacturing relies on complex cell processing, viral vector production, quality control, and GMP-compliant workflows to consistently produce safe and effective therapies at commercial scale. Advances in automation, bioprocessing, digital manufacturing, and integrated production models are improving manufacturing efficiency, regulatory compliance, and the widespread clinical adoption of these advanced therapies.

Image credit: Anton Vierietin/Shutterstock.com

Introduction

Cell and gene therapies (CGT) are increasingly integrated into modern medical practice for genetic, oncologic, and degenerative diseases. Scientists inject cells, genes, or gene-modified cells, along with recombinant nucleic acids, into a patient to prevent or treat a disease. Approved therapies include chimeric antigen receptor (CAR-T) treatments and gene-editing approaches. These approaches provide curative options for conditions with limited therapeutic alternatives.^1,2

However, manufacturing scalability has become a major industry challenge. Although several products have reached commercialization, advancing new therapies into late-stage trials and routine clinical practice remains challenging. The transition from laboratory-scale process development to robust, good manufacturing practice (GMP)-compliant commercial manufacturing remains one of the principal barriers to broader clinical adoption. Manufacturing processes must consistently deliver product quality, safety, potency, and regulatory compliance while accommodating increasing demand and reducing production costs. Manufacturers need to improve their production processes and incorporate next-generation techniques to scale up and accelerate the transition from clinical development to commercial manufacturing.^3,4,5

Why Is Cell & Gene Therapy Manufacturing Difficult?

Cell-based therapies use cells such as mesenchymal stem cells (MSCs), while gene-based therapies use vectors such as adeno-associated viral vectors (AAV) or lentiviral vectors (LVs) for disease management. For cell-based therapies, key challenges include maintaining the source material under appropriate conditions, eliminating contamination, and simplifying multistep procedures. For gene-based therapies, scientists are working to develop stable producer cell lines that do not require plasmid deoxyribonucleic acid (DNA) for vector production and that maximize AAV and LV titers while minimizing manufacturing costs. Efforts are ongoing to improve separation of empty from full AAV capsids and remove residual impurities and xenogeneic serum during LV vector-based treatments. To date, manufacturing sufficient quantities of recombinant AAV products to meet rapidly expanding clinical demand remains a bottleneck in the industry.^1,4

Manufacturing platforms that depend on transient transfection for vector generation are often limited by scale and cell density. Large amounts of transfection reagents and genetic material (DNA) are required to scale up transient expression systems, leading to increased production costs and potential batch-to-batch variability. Achieving sufficient yield and purity of raw materials, such as plasmid DNA, while also maintaining potency can be challenging since some viral vectors are fragile. Autologous cell therapy approaches using blood or stem cells are difficult to transfect. Isolating cells from the patient (for autologous therapies) and from matched donors (for allogeneic therapies) can be challenging, as these cells may be highly variable and behave differently.^1,3

Cell therapy manufacturing also requires stringent control of donor variability, tissue procurement, cell isolation, expansion, harvesting, formulation, cryopreservation, storage, and shipment. Variability introduced during prolonged cell expansion can alter potency, proliferation capacity, and therapeutic efficacy, making process standardization and quality control particularly important.¹

Efforts should be undertaken to develop technologies that can improve the quality of the starting material or the process, so that the final product ultimately conforms to release criteria. Raw materials such as cytokines and growth factors are often unavailable, very expensive, or not obtainable under the appropriate conditions. In addition, continuous manual media feeding/changing for growth factor replenishment and waste removal is laborious. Cell isolation methods also need to be more cost-effective and reliable to scale up manufacturing. Whether producing a smaller batch from patient cells for an autologous therapy or a large batch from healthy donor cells, major challenges include maintaining sterility and avoiding adventitious agents, which are difficult to ensure in the open systems widely used today.³

Beyond technical hurdles, manufacturers frequently encounter workforce shortages, limited GMP expertise, funding constraints for early-stage developers, and increasingly stringent regulatory documentation requirements. These operational challenges contribute significantly to delays in clinical translation and commercialization.⁵

The Scale-Up Gap in Bioprocessing

Processes optimized at laboratory scale often fail at commercial scale. Supply-chain logistics require further development. While blood products have shelf lives that allow for modest delays in the distribution process, the transit window for CGTs and precursor material is more stringent. Long-term inventory management remains largely dependent on cryopreservation. However, few clinics possess liquid nitrogen storage or −80°C freezers.²

Suspension transient transfection (sTT) enables rapid implementation; however, these processes are challenging to scale up and require expensive raw materials, such as plasmids and polyethylenimine (PEI). In baculovirus expression vector (BEV) systems, recombinant AAV is usually produced by coinfection of insect cells with two recombinant baculoviruses that supply crucial genes. These methods enable larger volumes than mammalian cell culture platforms. However, scientists face difficulties related to the genetic instability of recombinant baculovirus and the burden of baculovirus generation. In addition, there are safety concerns regarding helper-virus impurities. Purification continues to be a major hurdle for both AAVs and LVs.^1,4

Producer cell line (PCL) systems represent another scalable manufacturing platform capable of commercial-scale production. Although PCLs can improve robustness, reduce manufacturing costs, and achieve production at bioreactor scales exceeding 2,000 L, development of stable producer cell lines requires considerable time, specialized expertise, and GMP-qualified cell banks. Emerging inducible producer cell line technologies may further increase volumetric productivity by separating cell growth from vector production.⁴

Cell expansion can also be challenging, as large volumes of cells must be produced with consistent quality and free of foreign particles. These cells may also be sensitive to the chemical transfection reagents typically used to introduce the material that programs the cells. The quality of the starting leukapheresis material must be scrutinized to increase the efficacy and potency of CAR-T cell therapy. Establishing optimal control of nutrient, oxygen, and carbon dioxide levels at scale is also an issue, since reagents are very expensive and serum-free culture media may not be sustainable over the long term.^1,3,4

Researchers need to conduct sterility and potency testing as CAR-T cells are generally infused shortly after production. Cell preservation and cryostorage are additional logistical concerns. Scientists and healthcare providers are exploring new ways to contain cryopreserved materials and increase the availability of master cell banks (MCBs) to preserve long-term cell viability.^1,3,4

Scale-up challenges also extend to GMP facility utilization. Some commercial manufacturing facilities remain underused due to high operating costs, shortages of experienced personnel, and limited regulatory support, whereas academic and large pharmaceutical GMP facilities often operate near full capacity. Better coordination of manufacturing resources and greater adoption of digital quality management systems could improve facility efficiency and accelerate investigational new drug (IND) submissions.⁵

Technologies Helping Close the Gap

Automated and closed-system manufacturing technologies are playing an increasingly important role in overcoming the scalability challenges associated with CGT production. Traditional droplet-based flow sorting techniques are manual, open, labor-intensive, time-consuming, and highly technique-sensitive, making them unsuitable for the commercial manufacture of thousands of doses per year. Consequently, manufacturers are increasingly adopting automated manufacturing platforms that incorporate artificial intelligence (AI), digital twins, and advanced image-processing technologies to improve reproducibility and reduce operator-dependent variability.²

Several commercially available and emerging manufacturing platforms, including modular closed bioreactor systems, hollow-fiber expansion systems, automated cell processing workstations, and configurable microfactory platforms, are designed to standardize manufacturing processes while supporting decentralized production under good manufacturing practice (GMP) conditions. Self-contained microfactory systems use proprietary environmental controls, in situ sensors, and reconfigurable isolators to support multiple manufacturing layouts while minimizing contamination risks and reducing human intervention.₂

Digital manufacturing technologies are also transforming CGT production. Electronic quality management systems (QMS), real-time process monitoring, advanced analytics, automation, and data-driven process control improve batch consistency, reduce documentation burdens, enhance traceability, and facilitate regulatory compliance throughout the manufacturing lifecycle.⁵

Continuous manufacturing and closed, automated bioreactor technologies are increasingly being adopted to improve production efficiency and facilitate large-scale cell expansion while minimizing contamination and batch loss. However, further advances are required, particularly for automated harvesting of adherent cell therapies, where manual processing remains a significant source of variability. Standardized automated harvesting technologies could improve the consistency and quality of products such as CAR-T cells while reducing manufacturing costs.^1–3

Innovations in viral vector manufacturing are also helping to address scale-up limitations. Stable producer cell lines and inducible producer cell line technologies are being developed to reduce dependence on transient transfection, improve manufacturing reproducibility, decrease raw material consumption, and increase vector yields for large-scale viral vector production. These approaches have the potential to improve process robustness while lowering manufacturing costs for commercial CGT production.^1,4,5

Get the Free PDF to Learn How Automation, Viral Vector Manufacturing, and Digital Quality Management Are Advancing Cell and Gene Therapies.

Regulatory and Quality Considerations

CGT manufacturing must comply with stringent regulatory requirements to ensure product safety, efficacy, and consistency. Researchers continue to improve batch consistency and traceability through procedural optimization, the use of good manufacturing practice (GMP)-compliant cell banks and manufacturing facilities, and advanced digital quality management systems. Skilled personnel are essential for maintaining documentation, process control, and compliance with phase-appropriate regulatory standards established by agencies such as the U.S. Food and Drug Administration (FDA) and the European Medicines Agency (EMA).^4,5

Quality control extends throughout the manufacturing process and encompasses cell processing, viral vector production, reagent preparation, and final product testing under aseptic conditions. Critical quality attributes include product identity, potency, purity, sterility, viability, vector genome concentration, residual host-cell DNA, residual proteins, viral contamination, and other release specifications that ensure product consistency and patient safety before clinical use.¹

As manufacturing processes evolve during clinical development and commercial scale-up, demonstrating comparability following process modifications becomes a major regulatory challenge. Manufacturers must validate that changes to production platforms, raw materials, equipment, manufacturing sites, or production scale do not adversely affect product quality, safety, potency, or clinical performance. Consequently, comparability studies remain a critical component of regulatory approval and lifecycle management for CGT products.¹

Future regulatory strategies increasingly emphasize integrated manufacturing models that combine production, testing, and product release at or near the point of care. These approaches aim to reduce transportation requirements, shorten vein-to-vein time for autologous therapies, simplify supply-chain logistics, and improve manufacturing efficiency while maintaining regulatory compliance and product quality.²

Future Outlook

Future advances in CGT manufacturing are expected to combine closed-system automation, decentralized or point-of-care manufacturing, artificial intelligence-assisted process control, standardized raw materials, stable producer cell technologies, and advanced analytics to improve scalability while maintaining consistent product quality.^1,2,4,5

Continued collaboration among academic institutions, manufacturers, technology developers, regulators, and funding organizations will be essential for expanding manufacturing capacity, developing a skilled workforce, reducing production costs, and accelerating patient access to life-changing cell and gene therapies.⁵

References

1. Lee, N. K., & Chang, J. W. (2024). Manufacturing Cell and Gene Therapies: Challenges in Clinical Translation. Annals of Laboratory Medicine, 44(4), 314. DOI:10.3343/alm.2023.0382, https://www.annlabmed.org/journal/view.html?doi=10.3343/alm.2023.0382
2. Harrison, R. P., Ruck, S., Medcalf, N., & Rafiq, Q. A. (2017). Decentralized manufacturing of cell and gene therapies: Overcoming challenges and identifying opportunities. Cytotherapy, 19(10), 1140-1151. DOI:10.1016/j.jcyt.2017.07.005, https://www.sciencedirect.com/science/article/pii/S1465324917306321
3. Challener, C. (2017). Cell and Gene Therapies Face Manufacturing Challenges, BioPharm International 30, 1, https://www.biopharminternational.com/view/cell-and-gene-therapies-face-manufacturing-challenges
4. Shupe, J., Zhang, A., Odenwelder, D. C., & Dobrowsky, T. (2022). Gene therapy: Challenges in cell culture scale-up. Current Opinion in Biotechnology, 75, 102721. DOI:10.1016/j.copbio.2022.102721, https://www.sciencedirect.com/science/article/pii/S0958166922000544?via%3Dihub
5. Fury, B., Bauer, G. (2025). GMP manufacturing of cell and gene therapy products: Challenges, opportunities, and pathways forward. Molecular Therapy; 33, 1886-1888, DOI:10.1016/j.ymthe.2025.02.022, https://www.cell.com/molecular-therapy-family/molecular-therapy/fulltext/S1525-0016(25)00111-X?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS152500162500111X%3Fshowall%3Dtrue

Further Reading

• All Gene Therapy Content
• What is Gene Therapy?
• Gene Therapy History
• Gene Therapy Issues
• Gene Therapy Types

Last Updated: Jun 30, 2026