For decades, formalin-fixed paraffin-embedded (FFPE) tissue has been the cornerstone of pathology and clinical research. From cancer biopsies to rare disease samples, FFPE blocks are the standard way to preserve tissues, creating archives that span back decades and number in the millions worldwide.
These collections represent an invaluable record of human biology, yet until recently, their utility in advanced molecular profiling has been limited. Genomics and transcriptomics have made strides in extracting information from FFPE, and proteomics is steadily advancing. But one critical dimension of biology has remained largely inaccessible in FFPE tissue: metabolomics. This all changes with Panome Bio’s TissueBridge™ FFPE Metabolomics offerings.
The Untapped Potential of FFPE Archives
Metabolites — the small molecules that reflect cellular processes, drug responses, and disease states — provide a direct snapshot of phenotype. Unlike genes or transcripts, which show what could happen, metabolites capture what is happening in the tissue. This makes metabolomics uniquely powerful for biomarker discovery, since metabolic signatures can be directly associated with disease progression or treatment response. It also offers tremendous value in drug development, where metabolic profiling can be used to validate mechanisms of action or identify predictive response markers. Perhaps most importantly, metabolomics enables retrospective analysis, allowing researchers to link clinical outcomes with molecular data in patient cohorts that have already been extensively studied.
The problem has been that traditional preservation methods used in FFPE processing distort or degrade metabolites, leaving most archives untapped for this type of analysis.
Why This Matters Now
Pharma and biotech researchers are often sitting on extensive FFPE collections from clinical trials, translational research programs, and collaborations with biobanks. These samples capture critical patient populations, often with rich annotation and long-term outcomes. Being able to add metabolomics to these existing collections eliminates the need for fresh sample acquisition, which can be both costly and logistically challenging. It also provides access to hard-to-replicate cohorts, such as rare diseases, early-phase clinical trial material, or discontinued drug studies. Most importantly, it makes it possible to generate new biological insights from existing, already paid-for materials. In other words, metabolomics on FFPE unlocks value from samples that organizations already own.
Making Metabolomics Possible in FFPE
While the technical challenges of working with FFPE-preserved tissues have long limited metabolomic analysis, Panome Bio’s TissueBridge Metabolomics advanced sample preparation and analytical workflows have successfully overcome these barriers. With our Next Generation Metabolomics platform, researchers can now generate reliable, reproducible metabolomic data from archived FFPE tissues. This breakthrough enables scientists to explore questions and uncover insights that were previously inaccessible, unlocking the full potential of these valuable tissue archives.
Impact on Research and Development
With metabolomics now feasible in FFPE (click here to read our Application Note), research and development organizations gain a powerful new tool. They can re-examine past clinical studies with a new lens, potentially revealing why some patients responded differently than others. They can expand translational research by integrating metabolic insights with genomic, transcriptomic, or proteomic data already obtained from FFPE. They can also accelerate discovery by mining existing collections instead of waiting years to recruit new patient cohorts. The result is faster insight, broader discovery, and the ability to capitalize on resources that are already in hand.
Conclusion
FFPE archives represent decades of patient samples, and until now, a significant portion of their biological information remained locked away. By enabling metabolomics from FFPE tissues, researchers can finally access that missing dimension — creating opportunities for biomarker discovery, drug development, and retrospective analyses that simply weren’t possible before.
At Panome Bio, we’re excited to make this new capability available to pharmaceutical and biotechnology partners in the form of our new service: TissueBridge Metabolomics. If your team has archived FFPE tissues and is interested in exploring their metabolic profiles, we’d be glad to discuss how this service can help advance your research.
Learn more about TissueBridge metabolomicsRead the full data reportLearn more about FFPE