Cell-Based Bioassays for Potency Testing: From Assay Design to GMP Readiness

Cell-based bioassays (CBBAs) have become a cornerstone of modern pharmaceutical development. As therapies grow more complex—particularly in biologics, cell therapies, and gene therapies—demonstrating potency, consistency, and safety increasingly depends on assays that can reflect real biological function. Unlike purely physicochemical methods, CBBAs operate in living cells, preserving the complexity of biological systems and providing data that is far more physiologically relevant.

This article distills key insights from Solvias’ recent CBBA e-book into a practical, high-level guide for developers navigating assay design, regulatory expectations, and the transition from R&D to GMP.

What Is a Cell-Based Bioassay?

A cell-based bioassay is any assay performed in a living cell system to measure a biological response to a drug or therapeutic candidate. Because these assays preserve cellular context, they are particularly valuable for evaluating drug potency, mechanism of action, and functional activity—critical quality attributes (CQAs) that underpin regulatory approval and patient safety.

While the applications of CBBAs are broad, successful assay development consistently relies on four foundational elements:

• A clearly defined biological question or goal
• A relevant and well-characterized cell model
• Carefully selected biological endpoints
• An appropriate analytical readout to convert biology into data

Each of these steps introduces complexity, and misalignment at any stage can compromise assay robustness or regulatory acceptability.

Common Types of Cell-Based Bioassay

CBBAs can be designed to interrogate many aspects of cellular behavior. Some of the most widely used formats include:

Cell Viability and Cell Death Assays

These assays provide complementary perspectives on how a therapy affects cell health. Viability assays assess metabolic activity or cellular function, while cell death (cytotoxicity or apoptosis) assays capture loss of membrane integrity, enzyme activation, or DNA fragmentation. Measuring both live and dead cell signals together improves confidence in potency conclusions and reduces the risk of false interpretation.

Binding Assays

Binding assays evaluate whether a drug interacts with its intended target and how strong or specific that interaction is. They are commonly used in oncology and immunotherapy, for example to assess whether checkpoint inhibitors successfully disrupt PD-1/PD-L1 interactions and restore immune activity.

Reporter Assays

Reporter assays link a measurable signal—such as fluorescence or luminescence—to gene expression or pathway activation. They are particularly useful for monitoring transcriptional activity, dose-response relationships, and pathway modulation in a controlled cellular context.

Cell Signaling Assays

These assays measure activation or inhibition of intracellular signaling pathways, often through second messengers such as calcium or cAMP. They are especially important for drugs targeting membrane receptors like GPCRs, helping developers confirm that binding translates into functional signaling.

Proliferation Assays

Proliferation assays track cell growth and division over time and are critical in oncology, regenerative medicine, and toxicity testing. Techniques such as BrdU incorporation allow direct measurement of DNA synthesis as a marker of cell division.

Turning Cellular Responses into Reliable Data

Biological responses must ultimately be translated into quantitative, reproducible data. Common CBBA readout technologies include:

• Flow cytometry, enabling high-resolution, single-cell analysis
• qPCR, for sensitive detection of gene expression changes
• ELISA, widely used for protein and cytokine quantification
• Capillary electrophoresis (CE), for separation and analysis of charged biomolecules
• Mass spectrometry (MS), offering antibody-independent, multiplexed protein quantification
• High-performance liquid chromatography (HPLC), for separating and quantifying drugs and metabolites

No single readout technology is sufficient for every application. In practice, combining orthogonal methods often provides the most robust understanding of potency and mechanism of action.

Why Are Cell-Based Bioassays So Challenging?

Despite their value, CBBAs are among the most challenging assays to develop and validate.

Biological Variability

Living cells introduce inherent variability. Differences in donor material, culture conditions, genetic stability, and phenotypic drift can all impact assay performance. This variability is particularly pronounced in advanced therapy medicinal products (ATMPs).

Autologous Therapy Constraints

For autologous cell therapies, each batch is patient-specific, with limited material and short shelf life. Testing timelines must align with product viability, leaving little margin for error.

Capturing Complex Mechanisms of Action

Many advanced therapies act through multifactorial and dynamic biological pathways. Reliance on a single potency assay has repeatedly proven insufficient and, in some cases, has delayed regulatory approval.

Scaling from R&D to GMP

Transferring a CBBA from research into a GMP-compliant environment requires careful timing. Premature over-validation can lead to costly rework, while under-investment increases the risk of regulatory delays, failed inspections, or clinical holds.

Reducing Variability Through Advanced QC Strategies

Given the central role of cellular variability, genomic tools are increasingly used to strengthen CBBA robustness. Targeted Locus Amplification (TLA), for example, enables deep characterization of genetic modifications in engineered cell lines and vectors. When integrated early, such tools improve control over critical variables and support both assay development and final product quality control.

Navigating the Regulatory Landscape

Regulatory expectations for CBBAs—particularly potency assays—continue to evolve. Developers often face uncertainty around how many assays are required, which are critical, and when validation should occur. Regulatory agencies increasingly encourage early evaluation of multiple assay approaches, followed by phase-appropriate selection and validation.

Importantly, potency assay deficiencies remain a leading cause of clinical holds in cell and gene therapy programs. Early investment in a clear potency assurance strategy can significantly reduce risk, protect timelines, and support smoother progression from IND to commercialization.

Partnering for Confidence and Compliance

Developing robust, GMP-ready CBBAs requires deep biological expertise, regulatory insight, and operational excellence. At Solvias, we support developers across the full product lifecycle—rapidly developing, transferring, and validating cell-based bioassays tailored to product modality and development stage.

With dedicated CBBA centers of excellence in Europe and the United States, Solvias combines global consistency with local scientific expertise to help clients navigate complexity, reduce risk, and accelerate time to market.

Final Thoughts

Cell-based bioassays are essential for demonstrating the potency, safety, and consistency of today’s most advanced therapies. While inherently complex, thoughtfully designed CBBAs—supported by the right mix of technologies, quality systems, and expertise—can transform biological variability into actionable, regulator-ready data.

By investing early and partnering strategically, developers can move from complexity to confidence, bringing innovative therapies to patients faster and with greater assurance.