An interview with Kelly Hunter, Chief Scientific Officer at Propath
Formalin-fixed paraffin-embedded (FFPE) tissue has played a major role in translational research. It supports many biomarker studies, gives access to important archived clinical samples, and is still the standard in clinical pathology. However, working with FFPE tissue can be challenging. Issues like RNA fragmentation, differences in tissue quality, and limited sample amounts all affect study design and the choice of analytical methods.
Before our webinar, we talked with Kelly Hunter, Chief Scientific Officer at Propath, about what it’s really like to work with difficult FFPE samples. He shared common misconceptions and practical lessons his team has learned while supporting translational research.
Rethinking what degraded RNA really means
Many researchers worry that a low RNA Integrity Number (RIN) means gene expression analysis is not possible. Kelly says this belief often causes valuable clinical samples to be discarded when they could still be useful.
"RNA fragmentation isn't something that happens by accident," he explains. "It's part of the preservation process. The important question isn't whether the RNA is degraded, but whether the technology you're using has been designed to work with fragmented RNA."
Traditional sequencing methods often have trouble with highly fragmented RNA, but some technologies made for FFPE tissue can analyse much shorter RNA pieces. Instead of seeing RNA quality as just pass or fail, researchers should check if their quality measures fit the technology they are using.
The technology should follow the biology
Kelly often gets asked whether researchers should use RNA sequencing, qPCR, or nCounter for their studies.
He rarely bases his answer on the technology alone.
"Start with the biological question," he says. "Every technology has strengths, but no single platform answers every research question."
RNA sequencing is still a strong choice for broad, exploratory studies, while qPCR works well for checking a few specific targets. For many FFPE studies, targeted gene expression methods offer a good balance between discovery and validation, especially when samples are limited or degraded.
The main point is to choose a method that matches both the biological question and the quality of the samples, instead of forcing the biology to fit a certain technology.
Why pathology still matters
Molecular data alone usually does not give the full picture.
Differences in gene expression might show real biological changes, but they can also come from differences in tissue makeup. For example, a sample with little tumor tissue will not give results that match a sample with a lot of tumor tissue.
Kelly sees pathology as more than just a quality control step. It is essential for understanding molecular results correctly.
"If you're comparing samples with different tissue composition, you're not always comparing like with like," he explains.
Looking at tissue structure, checking tumor content, and making sure the right areas are analyzed all help researchers better understand the biology and trust their results.
Getting more from every FFPE block
Clinical tissue samples are often scarce, so every section counts.
Luckily, with modern methods, one FFPE block can be used for more than one experiment. Researchers can do histology, immunohistochemistry, targeted gene expression, multiplex imaging, and spatial biology on nearby tissue sections.
This approach not only saves valuable material but also allows for multimodal analysis. Since all the data comes from the same tissue block, researchers can combine molecular and pathology information with more confidence than if they used separate samples.
"When your data comes from the same block, the biology is naturally much closer," Kelly says. "That makes multimodal integration much more meaningful."
Successful studies begin before the first assay
Many problems in gene expression analysis start well before any molecular tests are done.
Kelly suggests beginning with a careful check of the tissue. Before choosing an analysis method, researchers should look at pathology, tumor content, fixation quality, storage conditions, and RNA quality.
Often, small choices made early in a study can greatly affect the quality and usefulness of the final data.
"Understanding the tissue is every bit as important as understanding the technology," he says.
Five quick questions
- What's the biggest misconception about FFPE samples?
That degraded RNA automatically means gene expression analysis is no longer possible.
- What's the most common mistake researchers make?
Choosing an analytical technology before fully understanding the sample they are working with.
- What's the first thing every team should review?
The pathology. Knowing exactly what is present in the tissue provides the context for every downstream analysis.
- Can one FFPE block support multiple technologies?
Absolutely. With careful planning, a single block can support multiple complementary assays, making the most of valuable clinical material.
- What's the biggest opportunity in translational research today?
Bringing pathology, molecular biology and bioinformatics together to generate more complete biological insight from every sample.
Looking ahead
As biomarker research becomes increasingly multimodal, Kelly believes the focus should shift away from individual technologies and towards answering biological questions.
"Researchers don't just need more data," he says. "They need data that helps them understand the biology and supports better decisions throughout development."
This is what Propath’s upcoming webinar will cover. It will show how even difficult FFPE samples can produce strong gene expression data when the right technology, pathology skills, and analysis strategies are used together.
