The race to make life-changing cell and gene therapies (CGTs) more accessible remains hindered due to the lack of innovative approach adoption to ensure quality and safety in time. When examining critical quality attributes of CGT products, replacing current assays with a comprehensive NGS assay would not only preserve biological material and reduce costs but also accelerate investigational new drug (IND) applications and ultimately treatment availability.
While we have the potential to reverse currently incurable diseases with cell and gene therapies, the challenge to guarantee their safety limits this from truly becoming a reality. Cell therapies such as Tecartus and gene therapies including Luxturna have had remarkable outcomes1 yet there have been multiple cases where other therapeutics have led to life-threatening unforeseen outcomes and clinical holds.2,3 A likely cause? The companies developing these treatments are under pressure to deliver safe biological material under tight timelines. To avoid unexpected outcomes and guarantee that the intended therapeutic is developed, in-process testing is required to ensure these therapeutics maintain critical quality attributes (CQAs). Regulatory authorities such as the FDA and the EMA also request detailed documentation regarding CQAs when companies apply for an IND. Establishing and monitoring these attributes throughout development and manufacturing can help to ensure the product developed is safe and fit for its purpose. For this, a streamlined assay portfolio and the right technology that allows determining multiple attributes of a therapeutic simultaneously would be highly beneficial.
What Are CQAs and How Do They Differ for Cell or Gene Therapies?
A Critical Quality Attribute has been defined as a physical, chemical, biological or microbiological property or characteristic that should be within an appropriate limit, range, or distribution to ensure the desired product quality.4
For cell therapies prone to impact by the starting material origin (patient/donor characteristics such as age, genetic makeup, etc.) and their external environment, CQAs include identity, potency, and safety.
Identity: the product contains the intended cellular components
Potency: the product has the biological function relevant to treating the clinical indication
Safety: the product does not contain viable adventitious agents (e.g., mycoplasma, bacteria, viruses) and foreign matter (e.g., endotoxins, proteins, vectors, DNA, unwanted cells or culture reagents )
Safety can be further separated into Sterility, which focuses only on contaminating microorganisms, and Purity which refers to process impurities. Depending on the type of cell therapy (e.g., pluripotent, multipotent, and unipotent stem cells), specific assays are used to establish CQAs, however, the expanding number and diversity of cell therapies means a lack of standardization between organizations.5 This variation makes it even more essential to perform in-process testing and characterization but presents challenges when it comes to ensuring consistency and assessment by regulatory authorities.
For gene therapies, the genetic material is packaged within a vector delivery system (e.g., viruses), therefore the identity is known. However, integrity, potency, and safety remain just as important to confirm. According to the FDA, the method used to confirm potency in-vivo must reflect the products’ biological properties.5 This includes the ability of the vector to transfer the gene and the biological effect of the expressed genetic sequence.
How Can NGS Help to Monitor CQAs of CGT?
Next-Generation Sequencing (NGS) is an advanced technique that enables in-depth characterization of biotherapeutics using a range of innovative approaches. For example, single-cell RNA-Seq is an NGS-based approach that allows examining heterogeneity in a sample of cells – this can be extremely valuable to confirm the identity, potency, and purity of cell and gene therapy products. NGS is also useful for biosafety testing to detect the presence of adventitious agents allowing safety confirmation. The NGS-based approach known as targeted locus amplification (TLA), a Cergentis-developed technology, allows for verification of gene integration sites, determination of the copy number of genes inserted into cell therapy products, or analysis of the potential for insertional mutagenesis, and many more. In short, NGS is now the multi-attribute method for CGT products as it eliminates the need for implementing several different assays to determine CQAs by streamlining multiple assays. The vast amount of useful information obtained from NGS makes it easier, faster, and more cost-efficient to answer the questions:
Is my product what I think it is? (Identity)
Is my product able to fulfill its intended purpose? (Potency)
Is my product contaminated with other organisms? (Safety)
Moreover, NGS is gaining increasing interest as a widely used technique for CQA establishment and monitoring. It is no surprise that the European Medicines Agency requested the developers of Zolgensma, the gene therapy for spinal muscular atrophy, to perform NGS to assure vector genome integrity.6
However, working with NGS data can be complex if a company does not have the resources to automate the processing and insight generation from the wealth of data produced. Without this, data-informed Go/No-Go decision-making is delayed during development and manufacturing.
Overcoming the Complexity of NGS with Genedata Selector®
Genedata Selector empowers biopharma companies to accelerate the development of safe cell and gene therapy products by accurately confirming identity, potency, sterility, and purity. With Playbooks, the enterprise software platform simplifies and automates NGS data analysis for any user no matter their level of bioinformatics experience. This allows leveraging the comprehensive insights that can be gained from NGS-based assays throughout the CGT development and manufacturing process. For cell therapy, Genedata Selector automates the analysis and visualization of data from scRNA-sequencing, CRISPR events, and TLA analysis, to confirm identity and monitor cell characteristics after genetic manipulation. For gene therapy, besides allowing safety confirmation through adventitious agent detection (e.g., viral contamination, wrongly packed nucleic acids), the software facilitates the generation of mutation profiles to assess potency. Built to streamline submission to regulatory authorities, the future-proof platform tracks all sample information including genomic and phenotypic information and generates automated detailed reports.
While there has been a lot of focus on CGT development technologies and manufacturing processes, innovative methods for maintaining in-process critical quality attributes are lacking. Also, the wide diversity of therapeutics has led to discrepancies between developing organizations and an increasing number of assays being used to establish CQAs. By leveraging the full power of NGS using Genedata Selector, rather than performing 20 assays, biopharma companies can significantly reduce this to approximately 4 assays allowing standardization and automation for GMP compliant in-house processes. The software simplifies not only the data management, processing, analysis, and visualization, but also the conversion of data into actionable results that support Go/No-Go decisions from assay definition and development to standardization and automation. By choosing Genedata Selector, companies can ensure well-documented, transparent, and seamless cross-collaboration with internal and external partners while benefitting from interactive communication tools all within a single point of truth. This facilitates efficient collaborative confirmation of CQA products that serve their intended purpose while maintaining patient safety.