Designing a biomarker plan for a clinical trial can be challenging due to the plethora of assays and advancing technologies that are now readily available. A well-defined biomarker plan sets the stage for success as it is designed to align the translational objectives with clinical study constraints. In this blog, we discuss factors that go into making the optimal choice of samples to collect, assays to perform, and analyses to undertake. Proper consideration of the options along with the constraints of the clinical study will help save not only time and money but also give you the best chance to answer the research questions you have during clinical development.
Defining your Translational Objectives
When designing a biomarker plan for the precision medicine components of a clinical trial or study, a key first step is to identify your translational objectives, or what you would like to learn from the study. With this approach you are designing the study to answer your research questions, rather than the classical approach of analyzing the data you have. The translational objectives should be clear and concise and based on the clinical development goals of the program. Depending on whether you are planning a first-in-class or an early versus late clinical trial will likely influence your translational objectives. Translational objectives may include selecting an optimal dose, identifying patients most likely to respond to your drug, differentiating your drug compared to competitors, demonstrating target engagement, or describing the mechanism of action of your drug. Identifying biomarkers is also a common translational objective, however it should be clearly stated what type of biomarker is of interest to identify–such as a prognostic, predictive, pharmacodynamic or response biomarker.
Selecting your Assays
Choosing the right assay is critical to achieving your translational objectives. This is becoming increasingly more challenging as technological advancements have given us the ability to measure more analytes at higher resolution and in more dimensions than ever before. With the launch of spatial transcriptomics you now have the ability to analyze the whole transcriptome at near single-cell resolution with spatial morphology of the tissue sample retained. This allows one to map and identify novel cell types, groups of cells of similar function, and changes in these cell types. However, this depth of information requires complex data analysis methods and may be cost-prohibitive to use in a large number of samples. At the other end of the spectrum is the tried-and-true ELISA assay, which measures the abundance of one protein in bulk samples with no cell or spatial resolution. Analysis is simple and cost is low. Somewhere in the middle is bulk transcriptomics analysis with RNA-seq, which evaluates the whole transcriptome in the absence of spatial and single cell resolution. To better support sponsors in biomarker planning, Alimentiv has worked with key opinion leaders in the IBD field to help define the appropriate use of transcriptomics in IBD clinical trials (Linggi et al; manuscript in progress) and has performed a meta-analysis to identify disease signatures that are common across multiple studies in Ulcerative Colitis (Linggi et al. Sci Rep. 2021).
There are pros and cons to all assays, with no one assay being better than the other. Assays should be considered as tools in your translational toolbox and selecting the right tool for the task needs to be carefully considered. The choice of which tool or assay to use comes back to the translational objectives. It’s useful to start with the translational objectives and imagine how the data will look when the study is completed. For example, do you picture a bar graph with error bars? What are the axes of the graph? Time or treatment group? Are there enough samples to determine statistical significance, or is the expectation to look for general trends in the data? How does the number of analytes being measured for a selected assay affect this calculation? Are samples from all of the patients and time points to be collected and analyzed, or just a subset? Are technical or biological replicates needed, and how will they be analyzed? As answers to these questions become clearer, it will be easier to determine which assay is the right tool to achieve your objectives.
Consider Clinical Study Constraints
In parallel to choosing your assays it is important to factor in clinical study constraints. Precision medicine/translational studies in a multi-site clinical study contend with many obstacles that are not typical in single-site or research laboratory settings. Identifying what instrumentation and skills are available at the study sites is a major consideration when developing a biomarker plan. For example, do your samples require experienced handling, such as isolation of peripheral blood mononuclear cells (PBMC) from blood samples? Alimentiv recently published a study that investigated when such approaches may be feasible taking into consideration the length of time it may take to transfer samples from clinical sites to a laboratory for processing (Linggi et al. J Immunol Methods. 2023).
Collecting, handling, and preserving clinical specimens/samples is an important aspect of clinical trials. In a UC or CD trial, invasive samples such as intestinal biopsies are usually collected for analysis of histological endpoints. Additional samples are often collected for exploratory biomarker analysis using a variety of methods. However, given the invasive nature of the procedure, a balance must always be taken between patient welfare and these analyses. Furthermore, optimizing the number (Battat et al. Aliment Pharmacol Ther. 2020) and location (Novak et al. Aliment Pharmacol Ther. 2019) of biopsies is critical when planning a study.
Even when considering non-invasive sample collection, such as blood or stool, patient compliance must be considered. While from an analysis point of view, densely sampled longitudinal collection of blood or serum may be optimal for the translational objectives, if such requirements appear as too burdensome for patients and decreases the recruitment rate or there is low compliance, other strategies may need to be considered.
The Value of the Biomarker Plan
The value (cost versus return) of Precision Medicine analysis is always some component of the discussion when planning a clinical trial. A well-designed study, biomarker plan and analysis strategy from the onset will give insights that otherwise would be left to chance and may help identify an optimal dose, give insight for a critical Go/No Go decision, identify unexpected effects, or even highlight other potential indications for the therapeutic agent. A poorly designed study, biomarker plan, and analysis strategy can lead to years of unnecessary sample storage costs, time spent deciphering the intended analysis, and at worst, lost/unusable/unidentifiable samples, uninterpretable data, or a combination of these.
Alimentiv weighs all these considerations for precision medicine/translational assays when supporting Sponsors in biomarker planning for clinical trials. There is by no means a one-size-fits-all solution to designing a biomarker plan, and our expert team can be your guide to obtaining valuable data and uncovering novel insights to tell the story of your compound.