New Method Unlocks RNA Data from Decades-Old FFPE Samples

For over a century, hospitals and labs worldwide have preserved human tissue by fixing it in formalin and embedding it in paraffin wax, allowing scientists and clinicians to slice, stain and examine it under a microscope. That preservation method has created enormous archives of patient samples, but newer sequencing technologies have largely been unable to make use of them. A new method from the lab of Ken Lau, from Vanderbilt University, is changing that.

One such technology, single-cell RNA sequencing (scRNA-seq), has reshaped scientists’ understanding of tissue heterogeneity by showing that individual cells within the same tissue express different kinds and levels of RNA, the molecule that carries out DNA’s genetic instructions. Applying scRNA-seq to formalin-fixed, paraffin-embedded (FFPE) archives has been difficult, though, because the preservation process can damage the molecular information researchers are trying to recover, according to Lau lab graduate student James Evans, first author of the study published in Cellular and Molecular Gastroenterology and Hepatalogy.

Earlier techniques managed to isolate cell nuclei from FFPE samples, but doing so discards the rest of the cell, and with it a significant amount of RNA and other biological information. The new method was developed to recover more whole, intact cells rather than nuclei alone.

“By recovering whole cells instead of only their nuclei, our method captures more of the biological information contained within each cell. This could make the enormous collections of patient samples already stored in hospitals a source of rich molecular data,” Evans said. The approach also recovered cell types that other methods typically capture in low numbers, producing a fuller picture of the cell populations present in a given tissue.

The team tested the method on colon and thymus tissue and found the whole-cell recovery advantage was much stronger in colon tissue, with limited benefit in thymus. “Our results suggest that recovering whole cells may be especially useful in tissues containing larger cells that have more material outside the nucleus, such as the cells that line the colon, compared to the smaller immune cells in the thymus,” Evans said.

Evans hopes the method encourages other scientists to draw on decades of stored patient samples, particularly tissue linked to known patient histories and outcomes. “Researchers could examine an archived tumor and investigate how the individual cells within that tumor differed between patients who responded differently to treatment or experienced different outcomes,” he said. “Studies like these could eventually help researchers better understand how diseases develop and progress, identify biological features associated with patient outcomes, and discover new markers or potential targets for treatment.”