Hand in Hand: How Proteomics Can Support Companion Diagnostic Development

As the pace of precision medicine accelerates, developing targeted therapies and companion diagnostics in tandem is becoming increasingly common. Nearly fifty companion diagnostics have currently been approved by the FDA, mostly in oncology and hematology, and the field is developing rapidly.

Companion diagnostics rely on the use of biomarkers to predict the likely response or toxicity of a drug in specific individuals. They also accelerate timelines, reduce cost, and increase the chances of regulatory approval, effectively de-risking the drug development process.

Recently, there has been an increasing focus on developing companion diagnostics that provide comprehensive testing for multiple clinically relevant biomarkers.

For example, gene-based companion diagnostics use next-generation sequencing to test for the presence of a number of specific mutations in tumor samples, helping to guide the selection of the most appropriate therapy. Pan-cancer, histology-independent, and tumor agnostic companion diagnostics are also emerging.

The best biomarkers for use in companion diagnostics are those that most accurately predict how a patient will respond to therapy. Although gene-based companion diagnostics are becoming increasingly common, relying on genomic data alone risks missing vital information about what’s really going on within tissues and tumors.

Here’s how Biognosys’ cutting-edge technology and expertise in large-scale mass spectrometry proteomics are supporting the development and commercialization of companion diagnostics in the era of precision medicine.

Going Beyond Genomics for Companion Diagnostic Development

It is now widely recognized that without reliable biomarkers and companion diagnostics, targeted drugs lose their value.

However, biomarker discovery can be challenging, especially if there is limited information about a disease or the mechanism of action of a drug is not well understood. And once an appropriate biomarker has been identified, there are often further challenges with validation and developing commercially viable diagnostic tools.

It’s becoming increasingly clear that there is a complex relationship between genotype and phenotype. Genomic biomarkers therefore cannot fully capture the rich complexity and dynamic nature of the resulting disease phenotype, limiting the predictive power of this information.

For example, there may be epigenetic, post-transcriptional or post-translational effects at work, which cannot be captured through genome sequencing. In turn, this limits the effectiveness and commercial potential of gene-based companion diagnostics.

Protein biomarkers can be a more sensitive and accurate representation of a patient’s phenotype, therefore providing better predictive qualities. But, until recently, the limitations of proteomics technologies have restricted the development and commercialization of protein-based companion diagnostics.

This has now changed, thanks to advances in mass spectrometry pioneered by Biognosys. Unbiased, reproducible high-throughput proteomics is now a reality, supporting the discovery, development, and commercialization of companion diagnostics for a wide range of diseases.

Next-generation Technologies are Opening up the Proteome for Biomarker Discovery

Biognosys combines unmatched depth of proteome analysis with reproducible and precise quantification to identify and validate the most promising protein biomarkers for companion diagnostic development.

Our data-independent acquisition mass spectrometry (DIA-MS) platform enables unbiased analysis with unprecedented depth, identifying and quantifying tens of thousands of proteins within a sample for true biomarker discovery. And our Hyper Reaction Monitoring (HRM™) technology allows high-throughput DIA-MS in large-scale studies involving thousands of clinically relevant samples.

Easy-to-follow workflows ensure reproducible results over hundreds or even thousands of samples from a range of tissues or biofluids in any organism and at multiple time points.

Biognosys’ plasma depletion technology also overcomes the challenge of the large dynamic range of different proteins within samples, bringing the sensitivity needed to identify and measure low abundance proteins that may be clinically relevant biomarkers.

Unlike affinity-based proteomics approaches based on panels of antibodies or aptamers against specified targets, mass spectrometry proteomics provides an unbiased readout of all the proteins present in any sample, enabling true discovery research.

And because it can be used across all organisms and sample types, mass spectrometry proteomics can be applied across all stages of the companion diagnostic development journey from bench to bedside, providing an end-to-end research tool.

A Smoother Ride to Companion Diagnostic Commercialization

Accurate and reliable biomarkers mean a smoother road from discovery through to companion diagnostic commercialization.

Unbiased discovery proteomics technologies can uncover novel reproducible, predictive biomarkers based on the underlying biology of disease to take forward for clinical validation and further development.

This includes biomarkers based on post-translational protein modifications or structural changes, which cannot be detected through genomic or transcriptomic approaches.

The depth and scale of today’s proteomics technologies also allow the identification of protein signatures that are relevant across multiple diseases, therapies, and sample types, bringing pan-cancer and histology-independent therapies closer to reality.

Bridging the Gap from Biomarker Discovery to Companion Diagnostics

Moving from the initial discovery of a predictive biomarker through to a commercial diagnostic tool requires coordination and support across all aspects of the development journey.

We’ve now teamed up with Siemens Healthineers to make this a seamless reality for our customers. We’re combining the power of our proprietary discovery proteomics technologies with Siemens Healthineers’ diagnostic assay development and commercial expertise for the discovery and development of novel diagnostic biomarkers.

Together, we can help you accelerate the progress of your companion diagnostics from the initial stages of discovery through to assay development and successful commercialization.

Explore our website to discover how our large-scale proteomics technology can support your work in companion diagnostics, or get in touch with one of our expert advisors to find out more.