Protein biomarkers are observable flags in a patient sample that correlate with important events or indicate specific states in a biological process, such as disease progression. Their importance lies in the fact that proteins are often easier to measure than the complex events they represent. Protein biomarkers are valuable at so many stages of the drug development process, that many pharmaceutical companies now have their own biomarker programs to develop these essential tools.
The uses of biomarkers are many, from understanding diseases and pathways, to identifying early diagnostic markers of disease, to finding novel drug targets and improving the designs of clinical trials. This article discusses the role of biomarkers in drug development, and how they facilitate bringing safe and effective therapeutics to hopeful patients.
Biomarkers for diagnosis and prediction
Pharma companies rely on protein biomarkers for their diagnostic, prognostic, and predictive power. Biomarkers are helping scientists to identify diagnostic markers for early-stage disease; predictive biomarkers can identify patients who might benefit from particular therapies; both can lead to earlier treatment for a better patient outcome. For example, there is increasing emphasis on the early use of biomarkers to detect cancer at a stage where it may still be treatable with a good prognosis.
In Alzheimer’s disease, definitive diagnosis occurs after death when amyloid plaques are observed during a brain autopsy, leaving physicians with complex and less concrete diagnostic tools. Specialized brain imaging can reveal diagnostic clues but is expensive and less accessible. Finding easier and cheaper biomarkers for Alzheimer’s disease can help researchers to understand disease progression and treatment response.
The Alzheimer's Drug Discovery Foundation (ADDF) invests in research to develop reliable biomarkers for diagnosing Alzheimer’s disease. Last year the ADDF partnered with pharma companies to create a biobank sharing program. The biobank includes Alzheimer’s patient specimens, such as blood and cerebral spinal fluid samples, used in clinical trials and taken at different stages of the disease.
This promises to be a valuable tool in the development of biomarkers for Alzheimer’s diagnosis, as recently demonstrated by the first blood test for Alzheimer’s disease. In late 2020, C2N Diagnostics released the PrecivityADTM blood test, which measures amyloid beta 40 and 42 protein levels, and detects isoforms of apolipoprotein E, by mass spectrometry. Test values can help a physician assess the likelihood that a patient’s brain contains amyloid plaques, and to advise appropriate action depending on other tests and clinical symptoms.
Biomarkers in clinical trials
Biomarkers are valuable tools for improving clinical trials of drug candidates during development. They can be used to monitor safety and efficacy over time and to stratify patients into subclasses according to symptoms or responses to the drug candidate. “Predictive markers are valuable for [the] inclusion or exclusion [of patients] in clinical trials, improving the outcome of the trials by allowing researchers to stratify patient populations and identify patients that will respond to the therapy,” says Brett Houser, Bio-Plex global product manager at Bio-Rad Laboratories.
Efficacy biomarkers are particularly valuable for saving time and resources during clinical trials. Efficacy biomarkers can be used as surrogate endpoints in clinical trials, indicators that signal how well the drug candidate is working. This has two benefits: if efficacy biomarkers are reached, companies can halt the successful trials earlier than the longer standard trial duration, and perhaps get the drugs to patients sooner. If efficacy biomarkers aren’t detected, companies can halt the trial to minimize time and resources lost on unsuccessful drug candidates, and move on to test another drug candidate.
Protein biomarker tools
Recent advances in multiplexing make it possible to monitor levels of multiple biomarkers in clinical trials. Houser says that Bio-Rad’s pharmaceutical clients use biomarkers in all stages of drug development, “from early cell-based efficacy markers to safety markers for preclinical and prognostic markers for clinical trial selections.” They start with an initial multiplex screening using as many potential biomarkers as possible, then look for a distinct set of informative biomarkers. “Pharmaceutical companies have shared with me the importance of finding a robust, smaller set of biomarkers early in the development [of a drug],” says Houser. “Ideally they prefer smaller plex levels after screening that allow them to scale up for high-throughput monitoring in preclinical and clinical trials.” Bio-Rad’s Bio-Plex System can detect up to 100 proteins simultaneously from one small sample by immunoassay using Luminex’s xMAP technology.
Incorporated into the protein biomarker programs of many pharma companies, Olink’s technology uses the Proximity Extension Assay (PEA), a dual-recognition immunoassay comprised of antibody pairs labeled with DNA oligonucleotides. When both antibodies bind to their protein biomarker target, the oligos hybridize to form a unique DNA barcode. In the Olink Explore 1536 platform, the DNA barcodes are read by next-generation sequencing on Illumina’s NovaSeq 6000 System. “This enables rapid interrogation of the low-abundant plasma proteome, where the richest store of knowledge related to dynamic biological changes in health and disease may be found, at an unprecedented scale,” says Ida Grundberg, chief scientific officer at Olink.
“PEA has been widely used in studies to identify protein biomarkers and signatures that can predict outcomes and responses, effectively stratify patient populations, and provide crucial new insights into the biology of disease.”
In a recent collaboration, a research team from Massachusetts General Hospital used the Olink Explore 1536 platform to profile over 1400 proteins from COVID-19 patients, looking for new biomarkers that can help to diagnose, treat, and prevent COVID-19 infection. “The extensive dataset, with over 1.3 million protein data points and essential clinical parameters from the study, is now freely available through the Olink website, to stimulate and facilitate further investigation of the pathways underlying severe disease that may be the basis for early diagnosis and clinical intervention,” says Grundberg.
Boosting biomarkers with genetic information
Grundberg notes that therapeutic programs based on both genetic and protein evidence are twice as likely to succeed in the clinic. As such, Olink’s technology will soon be used to measure plasma protein concentrations from 53,000 people from the UK Biobank, a large database of genetic and health information used by scientists researching the biology of diseases and therapies. “The project is funded by a consortium of ten biopharmaceutical companies, clearly signaling the importance they see in bringing in large-scale proteomics to their drug development programs,” says Grundberg.
According to Grundberg, another promising approach for novel drug target discovery involves combining protein data with large-scale genetic analysis, such as genome wide association studies to identify protein quantitative trait loci or pQTL. “These provide robust connections between a gene variant and the levels of a protein,” she says. “When combined with clinical data and analyzed by Mendelian randomization, these can provide extremely confident identification of proteins that are causal in disease and therefore represent promising new drug targets.”
Going forward, the combination of proteomics and genomics data will increase the chances of drug development success. “By combining proteomics with genomics data, pharmaceutical companies will be able to understand which potential therapeutic protein targets actually have a causal role in the specific disease of interest, which is obviously a critical step in any successful new drug program,” says Grundberg.
Biomarkers act as keys to open doors to actionable information at many stages of drug development. “Biomarkers can provide information about mechanism of action, efficacy and safety leading to faster decision making and saving companies money, while at the same time increasing their success rates,” says Houser. Increasingly, biomarkers are the keys to developing life-saving and life-changing therapeutics faster and cheaper than ever.