Best Practices for Cell & Gene Therapy Process Development

July 26, 2021 Javier Cardenas, PhD
Best Practices for Cell & Gene Therapy Process Development Teaser

In 2019, the U.S Food and Drug Administration (FDA) forecasted that by the year 2025, between 10 and 20 cell and gene therapy (CGT) solutions would be approved per year in the United States. Since then, additional therapies have gone to market, while over 150 late stage (Phase 3) trials are ongoing with an estimated 8 approvals expected for 2021. Nonetheless, although there is much promise in this area, new challenges are also emerging.

We have already seen the CMC (Chemistry, Manufacturing, and Control) bar raised by regulators in recent years, leading to unforeseen delays for many of these advanced therapies. While these roadblocks are likely to be resolved over the coming years, it is critical to keep in mind points to consider early in the development process which will streamline the path to commercial success.

A major factor in the development for this class of advanced therapies is that there are a so many moving parts all at once. There can be instances where the timeline is so fast and consolidated that your organization can be both trying to qualify the process while also working to administer early or even first doses to patients in the clinic. It is therefore extremely important to have as much knowledge ahead of time as is possible. Specifically, there are a few focus areas that should be considered:

  1. Ensuring there are well defined assays that can hold up to cGMP requirements. These assays should use validated methods as well and are essential in avoiding comparability. If validated methods at an early stage are not feasible, bear this in mind and establish a strategy upfront on how best to tackle. Ideally these are qualified ahead of or during Phase I, with some cases waiting until Phase II at the latest. It can be helpful then to prepare and having the option to perform comparability when needed. This might include the capability of maintaining retain samples for those purposes, which are ideal for head-to-head analysis.


  1. The sourcing of reagents and other raw materials might not appear to be critical elements of a control strategy, but lack of assessing these can lead to significant setbacks. In fact, supply chain needs should be defined with commercial manufacture in mind very early in the development lifecycle. In the case of novel cell and gene therapies, understanding exactly what attributes lead to efficacious outcomes may not come to light until after some iterations of change, or later in the clinical path. Therefore understanding the limitations, and giving consideration as needed to changes such as reagents coming from an alternative site or supplier that may not be GMP grade, you can avoid risks to the product and process (i.e. potency assay issues, or repeat qualifications).


  1. Processing equipment can be very specific to the product (i.e. viral / non-viral vectors versus autologous or allogeneic donor-based cell therapies), and many times can be designed for small scale studies for laboratories. In these cases, consideration should be given to increased understanding of the capabilities but also the limitations. In this way, training personnel on proper handling and maintenance of the equipment can help with operations and guide the support systems which may be required for your specific application. In addition, rather than starting with off the shelf options without looking at your specific needs, having strong process knowledge can help in selecting the right equipment which will be fit for purpose. This can alleviate the strain of scaling up or out, and provide flexibility in seamlessly using or transferring similar technology into your cGMP manufacture.


  1. In some cases, the early-stage process concept is done using laboratory/clinical equipment, which can be sufficient for making a few batches, but is not ideal for large scale and routine cGMP manufacture. It is therefore helps to have some compliance knowledge upfront. Not only does this help alleviate challenges when transitioning to a different process, but it also forces you to understand your product, and what really matters in the context of SISPQ (Safety, Integrity, Strength, Purity, and Quality). A shortfall of using lab equipment is that although it may be a readily available option, if not careful you can find yourself constraining the process to around equipment that is suboptimal. This can feel like a shortcut at first, but can lead to many pain points during manufacturing (i.e. difficult to repair, limited “blackbox” proprietary nature of hardware/software).


  1. It is also worthwhile to explore risk management practices at an early stage:
  • Due to the fast-paced path to commercialization, there must be a handoff of methods or processes to and from vendors. Having risk management principles in place allows you to look at the important information which helps mitigate potential issues. For example, a vendor may use slightly different raw materials from a different supplier than your small-scale studies, and even different impurities or grade could have a negative impact on the process or product. Understanding that risk can facilitate the need to potentially lock down a particular supplier to avoid issues down the road.
  • A QbD (Quality by Design) approach is critical to: (1) Define the Quality Target Product Profile (QTPP) as early as possible, (2) Define critical quality attributes (CQAs) based on the risks while maintaining the QTPP, (3) Define the critical process parameters (CPPs) that are needed to ensure CQAs are satisfied – we can use design of experiments (DoE) studies to help develop this knowledge and create a control strategy where Multifactorial DoE studies can analyze the data exhaustively.
  1. For a facility handling multiple therapy platforms, cross contamination control is important:
  • Many contract organizations have diverse client portfolios, requiring significant cross contamination control. The Azzur Cleanrooms on Demand™ facilities are designed to mitigate risk, especially for viral vector vs. cell therapy processes. It is important to have a partnership with an organization that understands these risks and has procedures in place to address accordingly. A recent example of what can go wrong occurred when a mix-up of viral vector materials at a contract facility forced 15 million doses of COVID-19 vaccines to be discarded.
  1. Speed is most important to developers right now, and to support this the use of rapid characterization techniques are very important. A few examples of promising options are listed below:
  • Light scattering (DLS, SEC-MALS, FFF-MALS)
  • In-line technologies (i.e. Raman spectroscopy)
  • Droplet digital PCR (ddPCR)
  • Rapid microbiological testing (i.e. BacT, Rapid qPCR mycoplasma)
  1. The use of new technologies is also beneficial to the organization since:
  • Robust methods will mean more data can be generated, while also requiring less material inputs. This leads to both better efficiency and reduced costs.
  • Traditional technologies while often sufficient for the purpose, are not future proof from the perspective of scalability options, for example, using hollow fiber bioreactor processes to scale up a cell bank.
  • Advanced downstream processing can consolidate multiple processing steps into a single or fewer steps, which translates to better product recovery. One example would be the use of alternating tangential flow technology to combine clarification and buffer exchange activities leading to reduced product loss. A similar case is presented when comparing membrane versus resin-based chromatography, again emphasizing less process steps for improved productivity.
  1. Defining comparability early on in the product lifecycle is important:
  • Usually, you need to have predefined CQAs to perform comparability, but sometimes you may not have the full picture, as it is too early in the development phase. Comparability can inform you of them if you are unable to show comparability and you identify additional aspects that may need to be considered part of the QTPP.
  • Comparability is only as robust as the assays. Unreliable assays with variability can make it very difficult to establish comparability (head-to-head testing is important in this scenario to bridge IND to BLA). Ideally you have quantitative assays in place, or other advanced analytics with fast turnaround.
  • Consider establishing/understanding coverage of the process before and after a change is made. You want to ensure that new versus old process will not have an impact on other processes (example – upstream process change leads to new impurities, and these impurities make it challenging to process and analyze downstream).
  • An alternative is to minimize the need for comparability by:
  • Getting into materials and processes that are easily translatable.
  • Using equivalent GMP grade as research grade.
  • Consider incorporating regulatory needs early on, as the early stage is often performed in research labs where GMP consideration may not have been made. Committing to a path early without this vision leads to significant process changes which can be hard to implement, or materials that cannot be utilized in late-stage process development/qualifications.

At the rate that innovation is coming to the CGT space, this is undoubtedly an exciting time for the industry to extend its reach to patients.

As the technologies become more advanced and transformative, regulations are going to evolve and adapt as well to address the biggest risks to the patient. Regardless of size, CGT developers have many challenges to tackle and to get their product to market. As interest continues to grow over the next five years, competition will drive changes that will only expedite timelines further. Nonetheless, there are numerous resources available to support these organizations, including CDMOs or Cleanrooms on Demand (CoD), as well as highly skilled consultants to navigate the ever-changing regulatory landscape.

Javier Cardenas, PhD Headshot

Javier Cardenas, PhD

Javier Cardenas, Ph.D. is a Senior Consultant at Azzur Group. In this role, Dr. Cardenas facilitates increased compliance of sterile injectables, medical devices, and biologics manufacturing facilities through Commissioning, Qualification, and Validation (CQV) efforts in the Southern California region. Having received his graduate degree in Molecular Biotechnology at the University of California – Irvine, his passion is driving technical advancements and knowledge in the Cell & Gene Therapy space.
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