Derisking the Road to Commercially Viable Stem-Cell Therapies


Pluripotent stem cell (PSC) therapies enable developers to address some of the most difficult diseases and injuries. Accordingly, interest in such therapies is growing rapidly. The number of PSC-therapy clinical trials conducted around the world increased from 12 in 2015 to more than 90 in 2020 (1). A Mordor Intelligence study suggests that, by 2028, the induced pluripotent stem cell (iPSC) therapy market could be worth ~US$2 billion — up sharply from 2023’s ~$1.2 billion valuation (2).

Despite growing interest from drug companies, traditional approaches to PSC development often rely on short-term strategies that are replete with risks that hinder many promising therapies from reaching the market. Unaddressed risks in PSC-therapy development can have downstream consequences that threaten even the most promising programs. Scientists need a new developmental framework to realize the potential of PSC therapies.

Planning for Success

Sourcing Suitable Cell Lines: Challenges with PSC development can begin when developers choose their cellular starting materials. Many startup companies and academic laboratories use research-grade cell lines established in their own research and development (R&D) laboratories for early process- and analytical-development work. But to progress to clinical production, companies must use starting material that is generated in accordance with current good manufacturing practices (CGMPs). Doing so usually requires scientists who work with research-grade material to change cell lines. Critically, a GMP-grade cell line may not perform well with a manufacturing protocol that was developed for the original research-grade cell line. The new cell lines even could produce entirely different products and necessitate a costly return to preclinical exploration.

Aside from cell-line switching, development-milestone expenses for a GMP-grade cell lines often are cost-prohibitive for startup companies. Moreover, eligibility criteria for cell-line donors can differ significantly among geographical regions. For example, among other requirements, US approval typically requires that donors hail from countries without incidence of transmissible spongiform encephalopathies. Companies often fail to explore such eligibility criteria, limiting their cell lines’ market access to specific geographical regions. At worst, uninformed cell-line selection can force some companies to return to early development work after significant time and resource investment — and many simply cannot afford to do that.

Raw Material Challenges: Generating PSC lines and manufacturing therapeutic products can involve reagents of complex composition, some of which contain proteins such as cytokines and animal-derived materials such as fetal bovine serum. Animal-derived components are inherently variable in their biological properties and can pose a risk to human health by introducing adventitious agents into manufacturing processes.

Consequently, companies that use such reagents are at high risk of process-reproducibility challenges, which can have knock-on effects on drug-product quality, safety, and even mode of action. Exposure to adventitious agents in animal-derived components requires developers to assess risk diligently and screen both their raw materials and final products to ensure that they are safe for humans. Doing so is time and resource intensive and drives up the cost of goods (CoG).

Aside from the inherent challenges posed by reagents are risks associated with maintaining supplies. Many companies source each reagent from a single supplier, but if that supplier’s operational continuity is compromised (e.g., because of a natural disaster), then developers could face costly manufacturing delays or be forced to reimagine their production processes.

Difficulty From Cellular Diversity: To produce a PSC therapy successfully, developers must have means for guiding the differentiation of cellular starting material. But they often face low differentiation efficiency with large variation among batches. PSCs give rise to a diversity of cell types, but only some types are desired. Variation occurs for two reasons.

First, the natural signaling that drives stem-cell differentiation is poorly understood, so it is difficult to recapitulate that faithfully and consistently in a Petri dish or bioreactor. The complex cocktail of reagents needed to induce signaling also can be inconsistent, amplifying reproducibility and efficiency problems. Second, PSCs can exhibit an inherent bias for differentiating back into their source-tissue cell types rather than to a desired target type, which further hampers efforts to ensure process consistency.

In practice, switching cell lines or starting material often is required for developers facing differentiation-efficiency challenges. Making such a change, however, can entail a great amount of rework and significantly raise costs in delaying a development program.

Labor-Intensive Manufacturing Processes: Traditional manufacturing processes are labor intensive, and that also can threaten a PSC-therapy program’s viability. For many differentiation protocols, skilled operators must change cell-culture media and other reagents daily. For clinical production, daily operations must take place in a cleanroom environment, where detailed process traceability is mandatory. Such factors will complicate manufacturing process further.

Quality assessments depend heavily on visual observation of cell morphology. It is an inherently time-intensive process that requires highly trained, technically competent staff who can be expensive to source and difficult to train in house. By relying on subjective human judgment for quality assessment, companies run the risk of making errors — for example, operators could miss subtle indications of suboptimal batch quality — which can lead to late and costly batch failure. The cumbersome, lengthy, and more error-prone nature of traditional PSC-therapy manufacturing drives CoG higher, jeopardizing commercial viability.

Scaled Manufacturing and Comparability Challenges: PSC therapies differ greatly in their dosages and target-population sizes, which means that required manufacturing scales — and therefore culturing methods — also can differ significantly. For example, a monolayer cell culture using conventional cell-culture flasks may be suitable for commercial production of small-dose therapies with small target populations. However, larger-scale production of higher-dose therapies may demand suspension culture in bioreactors.

It is crucial for developers to know which culture systems and methods are appropriate for their products because manufacturing in a bioreactor is more complex and expensive than culturing in static flasks. The process is so different that changing a culture approach from flask to bioreactor can produce a noncomparable product or render manufacturing commercially unviable.

During early development, companies rarely explore dosing or batch size requirements for different phases of a product cycle. And that means they have little knowledge of the manufacturing scale and approaches that they need and whether the associated plans make commercial sense. Companies sometimes select a cell-culturing approach without considering the needs of later, scaled-up production, and that can lead to costly changes in development. When companies do require a change, they often don’t have an adequate comparability strategy for accurately ascertaining whether their newly produced product will be the same as that produced at smaller scales. In most such cases, companies must return to early testing to verify the identity, safety, and efficacy of the new cell-therapy products.

Too Little, Too Late: PSC-therapy development can be difficult and convoluted. But traditional PSC-therapy development is risky not simply because difficulties exist; it’s risky because some companies explore and attempt to mitigate difficulties only when they arise, which can be too late in a clinical-development program. Developers don’t always pay attention to early exploratory research data, or they extensively and continually monitor their products and processes throughout development. When companies fail to begin development with a commercial end-goal in mind, the consequences can be hard to overcome.

For organizations taking a reactive approach to risk mitigation, problem-solving becomes slow, disruptive, and financially costly. It even can result in late program failure, which is detrimental to the company and its investors. But there is a better way to approach PSC-therapy development.

Derisking Development for a Greater Chance of Success

At Alder Therapeutics, we have improved upon the traditional approach to PSC-therapy development. At the core of our development programs, we build a meticulously planned framework that prioritizes risk mitigation and commercial strategy. Doing so enables us to anticipate and address challenges at the earliest stages of research and discovery and achieve our goals by coordinating efforts and activities toward producing a commercially viable product.

We begin by defining an early iteration of a quality target product profile (QTPP), which acts as a compass for continued product and process development. We define version 1 of the product’s critical quality attributes (CQAs) through extensive analytical testing and by drawing early on exploratory scientific data. We continue to use an array of multidisciplinary sciences and analytical tools throughout development for continuous improvement of our understanding about product quality and the manufacturing process.

After gaining product and process insight early in development, we can set criteria for batch success and failure. We then develop strategies for in-process monitoring and control to track the evolution of product identity, safety, and potency throughout a development cycle. With early CQA information, we also have the knowledge to support thorough and accurate comparability assessments, which better prepares us to identify critical process parameters (CPPs) for scaled manufacturing. We also can alter steps or unit operations of our manufacturing process more easily.

Dosing, Formulation, and Delivery: We conduct dose-range studies early in development to build out a continually updating a QTPP. That gives us a clear idea of the required scale of manufacturing and whether we can achieve the same therapeutic efficacy with fewer cells per dose to reduce the CoG.

It is important to understand end-product formulation, preparation, and handling requirements, so we can use that information to guide our development decisions. For example, we ensure that early formulations and preparation steps for preclinical test batches use only excipients and ingredients that will be suitable for humans. That enables us to reduce the handling and preparation steps required for a drug product when it reaches a clinical site, thereby minimizing contamination risk, improving safety, reducing costs, and standardizing administration.

Starting Cellular Materials: Developers can use a number of strategies to address key challenges and curtail risks when selecting a cell line. For example, Alder Therapeutics uses research-grade cell lines established from CGMP-grade seed banks. That reduces early costs and eases the transition to GMP-grade cell lines for clinical production. When the early source material is the same as the GMP-grade cell lines, significant alterations won’t be necessary during transition.

To prevent donor eligibility issues later, we consider eligibility requirements and select cell lines that adhere to the legislature in regions where we are seeking phase 1 and 2 clinical trials. Ideally, companies should try to meet regulatory requirements for as many countries as possible to minimize barriers during clinical or commercial manufacture.

Carefully considering your choice of cell line also can help to minimize differentiation-efficiency challenges. We test and compare several cell lines early in development using our differentiation protocol, progressing with the option that offers the best efficiency. That enables us to prevent late cell-line changes and potentially minimize the scale of manufacturing, which ultimately reduces CoG.

No Stone Unturned: Early in development, we interrogate new manufacturing processes to unearth sources of risk or potential failure that could disrupt a program. First, we comprehensively map the early manufacturing process in detail, creating a breakdown of every action in that process. Once we have a detailed map of the inputs, steps, outputs, and time taken — overall and for each unit operation — we group information into process modules, explore elements that pose risk, categorize those risks, and then rank them based on their criticality. Several tools help facilitate this effort. For example, we use Ishikawa diagrams, risk analysis and mitigation matrices, and failure mode, effects, and criticality analysis (FMECA).

Once risk analysis is complete, we use it to compose a list of priority actions that balance ease of implementation and process benefit. Then, we take actions that help maximize our chance of process success. That methodology is widely applicable to cell therapies manufactured from iPSCs , including an established manufacturing process for therapeutic megakaryocytes (3).

Detailed modularization and evaluation of a manufacturing process often flags raw-material composition as a key source of risk, because of the inherent variability and safety concerns that such materials can pose. When possible, we eliminate animal-derived ingredients from all our manufacturing processes early in development. As an example, for ALD01 (our gene-agnostic candidate cell therapy for retinitis pigmentosa), we developed a manufacturing process in the discovery stage that uses only xeno- and serum-free reagents, enabling us to ensure more reproducible cell differentiation, minimize regulatory challenges, and speed up the transition to GMP manufacturing.

Optimizing Manufacturing: Given the problems posed by drawn-out, labor-intensive manufacturing protocols, we seek to shorten and simplify processes and remove human subjectivity whenever possible. We have implemented advanced tools for quality assessment in cell culturing that leverage artificial intelligence (AI) and machine learning (ML) algorithms to automate analysis of both cell microscopy imagery and flow cytometry data. That strategy has eliminated visual inspection of our cell cultures and manual gating of cell populations. The approach also enables us to minimize human error and expedite assessment to drive greater throughput and increase process robustness, which ultimately translates into reduced production costs.

Transitioning to larger and more complex cell-culture methods during development can slow progress significantly and even compromise the financial viability of a program. We seek to eliminate those problems by maximizing PSC differentiation efficiency. Doing so can increase our dose-per-lot ratio, so we can minimize required production batch volumes. With ALD01, we’ve taken two steps to maximize differentiation efficiency. First, we’ve selected the cell line (produced under CGMP standards) that most reliably differentiates into our target therapeutic cells. Second, we use a retinal-tissue–specific laminin (laminin 523) as the substrate for our starting cells — as opposed to nonspecific recombinant extracellular matrix proteins. Using laminin 523 provides conditions for more controlled differentiation toward the target cell (4).

The greater number of dosages per batch — considering the fact that dose sizes for retinal cell therapies are inherently low — enables us to use two-dimensional adherent cell-culture methods to deliver our batch needs through to commercial production. Compared with more complex suspension methods, the adherent method used for ALD01 manufacturing requires fewer manual handling and processing steps, enabling a 3–5× faster manufacturing run. That ensures a healthy difference between the CoG and the projected reimbursement price.

Exploring Market Potential: We investigate up front whether our product is commercially viable. To get a reliable answer, we collect several critical pieces of information, about the factors below.

Epidemiology: We seek a solid grasp of the eligible patient population size for a candidate therapy.

Competitor Landscape: We explore the number of current and potential competitor therapies — along with their upstream processes, projected costs, and so on — to compare our offering with those in the market.

Projected Market Size: We estimate the market size for a target indication at the point of anticipated commercialization and consider the estimated market share captured by competitors.

Dosage and Batch Requirements: We understand that how many doses we’ll need to produce to meet market demand is key in helping us plan our production method and scale.

Manufacturing Costs: Finally, we draft the manufacturing processes for phase 1 through to commercial production, using technologies that are available today (rather than those predicted to exist later) to gain a clear understanding of the CoG and produce a preliminary reimbursement strategy.

By integrating and analyzing that and other information, we piece together an early picture of whether a market opportunity exists for a given therapy and begin to understand the potential return on investment. If the commercial case for a therapy is strong, then we proceed with development.

Engaging with Regulators Early: Cell-therapy sponsors should engage in informal discussions with regulators early in development to prevent difficulties when optimizing processes or implementing novel systems or approaches. By sharing ideas with regulators at that point, companies can receive critical feedback and better determine whether their proposed approaches are likely to be accepted. With such insight, companies can keep from investing resources into strategies that might be rejected and then focus on exploring suitable alternatives.

Carving Out a Confident Path to Cell Therapy Success

Although PSC therapies are new, their promise has helped to establish a market that is predicted to grow significantly. However, the path to safe, effective, and commercially viable therapies is paved with challenges and risks. Failing to address those problems early can lead to program failures.

By taking a new approach to development, one that prioritizes risk reduction and keeps the commercial end-product in mind from the start, cell-therapy sponsors can increase their chances of success and speed their product’s path to market. Ultimately, the remarkable benefits of PSC therapies could reach patients more quickly.


1 Ilic D, Ogilvie C. Pluripotent Stem Cells in Clinical Setting — New Developments and Overview of Current Status. Stem Cells 40(9) 2022: 791–801;

2 Induced Pluripotent Stem Cells Production Market Size & Share Analysis — Growth Trends & Forecasts (2024–2029). Mordor Intelligence: Hyderabad, India, 2024;

3 Lawrence M, et al. Process Analysis of Pluripotent Stem Cell Differentiation to Megakaryocytes To Make Platelets Applying European GMP. npj Regen. Med. 6(27) 2021;

4 Tay HG, et al. Photoreceptor Laminin Drives Differentiation of Human Pluripotent Stem Cells to Photoreceptor Progenitors That Partially Restore Retina Function. Mol. Ther. 31(3) 2023: 825–846;

Ricardo Baptista, PhD, is chief technology officer; Stijn Heessen, PhD, is chief operations officer; and Kristian Tryggvason, PhD, is chief executive officer, all at Alder Therapeutics in Solna Sweden; 46-0-70-743-22-33. Thomas Hope, BSc, is senior science writer at BioStrata. Please direct inquiries to Jean-Pierre Joubert at [email protected].

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