Gene therapy holds transformative potential in treating a wide range of diseases鈥攆rom cancer and genetic disorders to infectious diseases. While there are just 14 gene therapy drugs currently on the market, in May 2025, GlobalData鈥檚 drugs database recorded over 2,000 drugs in development (discovery to pre-registration), as well as approximately 900 mRNA drugs and over 1600 antisense oligonucleotides in the pipeline.
These therapies are typically administered via injection and must be supplied as sterile products. However, their fill-finish processing presents a range of unique technical challenges due to the complexity and sensitivity of the drug substances involved.
These challenges include:
- Limited supply of drug substance (DS)
- Temperature sensitivity
- Risks of shear stress during compounding
- Ultra-low temperature storage needs
- Contamination control
This article discusses the drug product development and fill finish process for gene therapy products and offers solutions to the challenges listed above.
1. Limited supply of drug substance
Gene therapy products鈥攚hether DNA-based (plasmids, viral vectors) or RNA-based (mRNA, synthetic )鈥攁re often produced in limited quantities due to the substantial time and cost required to manufacture the drug substances. This is particularly true in the case of personalized medicines and rare disease treatments with small patient populations.
A CDMO can reduce loss through a systemic approach in process design, equipment, and operator training, including practices such as:
- Filtering into bioprocess bags versus other vessels
- Using fewer and smaller filters
- Reducing line purge requirements
- Performing non-destructive weight checks
- Performing fewer destructive weigh checks
- Lifting the bulk drug product at the end of a fill to allow for more product transfer
An innovative way to reduce drug product loss even further is to limit the amount of tubing used during the fill process. A CDMO can almost completely eliminate in the filling process by attaching the vessel containing the drug product directly to the filling needle. This can be achieved by removing the pump, but then a different method for accurate drug product dispensing is needed.
Peristaltic and piston pumps, commonly used in sterile filling, use suction to pull the solution in and mechanical force to push it out. In a pump-free setup, suction is unnecessary; instead, a force is needed to push the product out of the fill needle. This can be accomplished by pressurizing the filling vessel to a low pressure (~1 psi) with sterile gas, to provide the necessary force to push the product out.
To control dosing, a highly precise actuator can be attached to open and close a small port to the filling needle. By maintaining consistent pressure in the vessel, the actuator can set the dose volume by remaining open for a set duration when triggered. Smaller doses require the fill needle to be open for less time, while larger doses require it to be open longer.
Removing the pump eliminates several feet of tubing, which can save more than 40 mL of drug product typically lost in the process. The at Sharp Sterile Manufacturing (formerly Berkshire Sterile Manufacturing) uses only three inches of tubing to connect the fill vessel to the actuator and fill needle.
2. Temperature sensitivity: Time out of freezer constraints
Many gene therapy products have strict constraints on time out of ultra-low temperature storage, with even brief exposure potentially leading to degradation or aggregation. When manufacturers produce these exceptionally temperature-sensitive products in cleanrooms and filling lines that are at controlled room temperature, it is critical to understand the drug product and its specific limitations.
Partnering early with a CDMO will lead to a more comprehensive data package and understanding of the product鈥檚 sensitivity. It is important to run freeze-thaw and hold-time studies early; knowing how long the product can tolerate different temperatures allows for more robust downstream processes.
The ideal CDMO for a gene therapy project should have extensive experience designing fill-finish workflows that minimize processing time鈥攆rom thawing and compounding to filling and inspection鈥攚hile avoiding repeated freeze/thaw cycles. Every step needs to be thoughtfully scheduled to avoid fatigue or delays.
For more information on managing temperature-sensitive drug products, read our article, .
3. Sensitive compounding requirements: Shear sensitivity
The compounding stage must be carefully managed to prevent shear stress or degradation due to mixing, particularly with DNA-based therapies.
A standard fill finish project will use a stir bar or overhead mixer to mix the formulation, a peristaltic pump to push drug product through redundant sterile filters, and a peristaltic or piston pump to fill drug product. A CDMO should evaluate and select appropriate mixing technologies tailored to the product profile. Mixing technologies all produce shear forces that can damage and degrade LNP drug products. Shear testing can be performed to gauge the extent of the sensitivity and what changes need to be made in the process during mixing, filtering, and filling. For exceptionally shear-sensitive drug products, mixing can be slowed, or special low-shear mixing shafts and vessels can be employed. Filtration can also be slowed, or an alternate pump can be used, such as diaphragm pump, to reduce shear. And, finally, the sterile filling pump and its operation parameters can be optimized to reduce shear, or a time-pressure pump can be deployed to reduce shear.
RNA therapeutics can also encompass a wide range of compounding requirements, from straightforward buffer dissolutions to advanced lipid nanoparticle formulations. To learn more about lipid nanoparticles, read our article,
4. Ultra-low temperature storage
DNA therapy products often require ultra-low temperature storage, which poses unique challenges in primary packaging. Traditional glass vials may be prone to breakage at these temperatures. One solution is to use Crystal Zenith庐 (cyclic olefin polymer) vials鈥攁n increasingly preferred option for ultra-cold storage due to their durability. However, not all CDMOs have experience in handling and filling this type of vial.
5. Contamination control and sterility assurance
There are a number of reasons why contamination control and sterility assurance are absolutely critical when working with gene therapy products鈥攅ven more so than with many traditional biologics or small molecules. Many gene therapies鈥攅specially autologous therapies鈥攁re patient-specific. If a batch is contaminated, it’s not just a lost dose; it could mean no treatment at all for that individual. This makes preventing contamination a matter of therapeutic success or failure, not just regulatory compliance.
Gene therapy products often involve viral vectors (e.g., AAV, lentivirus) or nucleic acids (e.g., mRNA, plasmids), which are biologically active, fragile, and difficult to sterilize using terminal methods. That means the process must be aseptic from end to end鈥攅very transfer, every fill, and every closure must be contamination-free.
Maintaining sterility throughout fill-finish operations is paramount and can ideally be accomplished by filling in an isolator to minimize exposure to open environment. A CDMO filling gene therapy products must operate under stringent contamination control protocols, supported by a robust quality management system and a strong quality-driven culture.
Conclusion
Successfully navigating the technical challenges of gene therapy fill-finish operations is essential for bringing these groundbreaking treatments to patients. From managing limited drug substance supplies and preserving temperature-sensitive vectors to minimizing shear stress and maintaining ultra-low storage conditions, each step demands precision and expertise. Additionally, robust contamination control is critical to protect these highly sensitive, often life-changing therapies.
Partnering with a CDMO experienced in overcoming these complexities can be the difference between a promising therapy and a successful, life-saving treatment. With the right expertise, cutting-edge technologies, and a focus on quality, gene therapy developers can overcome these hurdles and deliver their innovations safely and effectively to the patients who need them most.
About Sharp Sterile
Sharp Sterile (formerly Berkshire Sterile Manufacturing) provides sterile manufacturing services with the highest level of sterility assurance and quality achievable through the use of the most modern technologies for sterile manufacturing, stringent quality standards, and highly trained employees. Sharp Sterile also provides ancillary support to their clients鈥� drug productions such as analytical method development and validation, stability studies and formulation scale up.
