Developing new drugs is a complex and multifaceted process that demands precise, targeted approaches to ensure safety, efficacy, and successful regulatory approval. One of the most critical tools in modern drug development is biomarker testing. Biomarkers are measurable indicators that provide vital information about biological processes, diseases, and responses to treatment. They play an essential role at every stage of drug development, from early discovery to clinical trials and beyond. Various types of biomarkers are used in drug development, including protein biomarkers, genetic biomarkers, phosphobiomarkers, epigenetic biomarkers, expression biomarkers, and cell markers. In this context, we will explore the methods used to test these biomarkers, highlighting advanced techniques like Next-Generation Sequencing (NGS) and quantitative PCR (qPCR/dPCR), as well as emphasizing the critical importance of assay validation and Good Clinical Laboratory Practice (GCLP) compliance.
The primary role of biomarkers is to provide measurable data that can inform decisions throughout the drug development process. Biomarkers can be classified into several categories, each playing a unique role:
Diagnostic biomarkers: These biomarkers are used to identify and diagnose diseases early, allowing for more targeted drug development by pinpointing the presence or absence of a condition.
Prognostic biomarkers: These indicators help predict the likely course of a disease, including the potential for recovery, progression, or recurrence, which is invaluable in designing clinical trials and selecting patient populations.
Predictive biomarkers: By predicting how a patient will respond to a particular treatment, predictive biomarkers enable personalized therapy, ensuring patients receive the most effective drugs based on their unique biological makeup.
Pharmacodynamic biomarkers: These markers provide insights into the biological response to a drug, helping researchers understand the mechanism of action and optimize dosing strategies.
Safety biomarkers: By monitoring for potential toxic effects, safety biomarkers help in identifying and mitigating adverse effects early in the drug development process.
Biomarker testing across drug development phases
Biomarkers influence every stage of the drug development pipeline, from early discovery to post-market surveillance:
Early-stage drug discovery: In the initial phases, biomarkers are used to identify promising drug targets and to understand the underlying mechanisms of diseases. For example, genetic biomarkers can reveal mutations that drive cancer, guiding researchers toward specific molecular targets. This targeted approach reduces the trial-and-error nature of drug discovery, leading to more focused and efficient research efforts.
Preclinical development: During preclinical testing, biomarkers are employed to assess the safety and efficacy of drug candidates in laboratory models. Pharmacodynamic biomarkers can provide early indications of a drug’s therapeutic potential, allowing researchers to refine and optimize drug candidates before they enter clinical trials.
Clinical trials: Biomarkers play a pivotal role in designing and conducting clinical trials. Using predictive biomarkers, researchers can stratify patients based on their likelihood of responding to treatment, leading to more targeted and efficient trials. This approach improves the chances of success and reduces the time and cost associated with bringing a drug to market. Additionally, safety biomarkers help monitor adverse effects in real time, ensuring patient safety and identifying risks that might not have been evident in earlier stages.
Regulatory approval: Including validated biomarkers in the drug development process can expedite regulatory approval. Regulatory agencies, such as the FDA, increasingly recognize the value of biomarkers in demonstrating a drug’s safety and efficacy. Biomarker data can provide compelling evidence that a drug works as intended, speeding up the review process and facilitating faster patient access to new therapies.
Post-market surveillance: Even after a drug is approved, biomarkers continue to monitor its safety and effectiveness in the general population. Post-market studies often rely on biomarkers to detect rare or long-term side effects, ensuring ongoing patient safety and informing potential future improvements in treatment protocols.
The impact of biomarkers on drug development speed and success
The integration of biomarkers into drug development will lead to several key benefits:
Increased precision: Biomarkers enable more precise targeting of therapies, reducing the likelihood of failure in clinical trials and increasing the chances of regulatory approval.
Cost-effectiveness: By improving patient selection and reducing trial sizes, biomarkers help lower the overall cost of drug development.
Reduced time to market: Biomarkers accelerate various stages of drug development, from discovery through clinical trials, resulting in faster patient access to new treatments.
Personalized medicine: Biomarkers are the cornerstone of personalized medicine, allowing treatments to be tailored to individual patients based on their unique biological characteristics.
Biomarker testing platforms
Protein biomarkers are among the most common due to their role as functional molecules in enzymatic activities, signal transduction, and structural functions. These biomarkers are traditionally measured using immunohistochemistry (IHC), enzyme-linked immunosorbent assays (ELISA), and mass spectrometry. New technologies have emerged, using antibodies coupled with oligonucleotides to achieve high selectivity, with readouts via qPCR or NGS technologies that provide high sensitivity. For example, Olink offers various protein panels that measure multiple proteins simultaneously in microliters of donor plasma or blood.
In advanced therapies, such as cell and gene therapies, pharmacodynamic (PD) readouts often involve RNA rather than protein due to the extremly low protein concentrations generated and the higher sensitivity of molecular analysis platforms like qPCR and dPCR. This approach allows for easier discrimination between endogenous and transgene expression.
Genetic biomarkers include genes with polymorphisms, copy number alterations, or chromosomal abnormalities. These biomarkers are crucial for understanding genetic predispositions to diseases and for developing targeted therapies based on individual genetic profiles. In oncology, genetic biomarker testing can provide insights into clonal evolution in tumors, detect secondary mutations correlated with therapy response, and monitor minimal residual disease (MDR) or circulating tumor DNA (ctDNA) from liquid biopsies.
Expression biomarkers are measured as mRNA or non-coding RNA, such as microRNAs (miRNAs), which provide information about gene activity and regulation. These biomarkers are critical for understanding disease mechanisms and drug responses. Technologies like NGS can quantify total RNA gene expression levels, while qPCR or dPCR is more straightforward for analyzing specific gene expressions.
Short nucleic acid targets such as siRNA, miRNA, and small nucleolar RNAs (snoRNAs) have traditionally been challenging to analyze using qPCR/dPCR workflows because they are too short to be amplified by regular PCR. However, there are many benefits to using a PCR workflow, including lower costs, faster turnaround times, and higher sample throughput. To enable the amplification of short targets, they need to be elongated, which can be done using either the inflexible but easily designed stem-loop approach or the more flexible Two-Tail PCR probe, which relies on two-site binding for increased sensitivity and selectivity.
Phosphobiomarkers and epigenetic biomarkers represent additional layers of biological regulation, crucial for understanding signaling pathways and epigenetic modifications that influence gene expression.
Conclusion
Biomarker testing is not just a tool but a cornerstone of modern drug development, driving innovation and precision in the way we approach disease treatment. As technologies advance, the ability to accurately measure and interpret biomarkers will continue to enhance our understanding of complex diseases, leading to more effective, personalized therapies and ultimately improving patient outcomes. The future of drug development is inseparably linked to the evolution of biomarker testing, ensuring that new treatments are effective and tailored to each patient’s individual needs.
