New technology to study DNA in archived tissue samples


Researchers at IGP have developed a technology that allows studies of DNA profiles in archived tissue samples. The technology permits investigators to better understand regulation of gene activity in cancer and precision medicine.

In human cells, the DNA is wound around proteins to form a complex called chromatin. Parts of the chromatin where the DNA is less tightly wound contain genes that are active, i.e they can be transcribed and translated into proteins. To study human diseases, it is important to be able to determine which parts of the chromatin are accessible for transcription.

Previously, researchers have developed a technology called ATAC-seq that can be used to study chromatin profiles to see where it is accessible. In the new study, the IGP scientists have adjusted the ATAC-seq method to be used on formalin-fixed paraffin-embedded tissue samples, and called this technology FFPE-ATAC.

“Tissue samples are often preserved by treating them with the chemical formalin, followed by embedding them in paraffin. There is a very large number of such samples that researchers could study but the formalin treatment damages the DNA in the tissues. In such cases, the ATAC-seq method doesn’t work optimally. We have now adjusted the standard ATAC-seq method and established FFPE-ATAC, which can be used on formalin-fixed paraffin-embedded material,” says Xingqi Chen who has led the study.

Using the FFPE-ATAC, the researchers found the same profile of accessible chromatin as in frozen tissue samples. They could also see that the method was sensitive enough to study the chromatin profile in as little as 500 cell nuclei, prepared from single sections of formalin-fixed paraffin embedded tissue.

“We also examined formalin-fixed paraffin-embedded tissue samples from colorectal cancer patients that had been stored up to ten years and we could detect disease-associated chromatin profiles. This makes the new FFPE-ATAC a powerful tool for use in preclinical studies and in research on precision medicine,” says Xingqi Chen.

The study involved several research groups at IGP and has been published in the scientific journal Genome Research

More information:
Paper in Genome Research
Xingqi Chen’s research
Fredrik Swartling’s research
Tobias Sjöblom’s research

Last modified: 2022-01-26