FFPE: Friend or Foe to Chromatin Analysis?

August 4, 2010 It Seems like a no-brainer that chopping up proteins and denaturing DNA would have a dramatic effect on chromatin structure. Since so many cancer diagnoses, developmental studies, and examinations of chromatin structure in general rely on slices of wax-embedded tissue blocks, you’d think someone would take a comprehensive look at the effects of prepping those samples for analysis. Well, that’s exactly what Wendy Bickmore and colleagues from the University of Edinburgh did.

Bickmore's team put FFPE sections through the paces, looking at changes in gross features of chromatin and nuclear organization at each step in the FISH protocol. Different cell types were first treated with xylene and stained with DAPI, then sequentially nuked, treated with pepsin, and denatured with formamide. Here’s what happened to the samples:

• Microwaving increased the size of the nucleus, and nuclei became rounder, in some tissues.
• Some tissues responded to protease treatment by shrinking the nuclei along the y-axis. These same tissues’ cells shrank along the x-axis when subjected to formamide.
• DAPI staining tended to move toward the center of the nucleus as treatment progressed.
• Chromatin became less textured as treatment progressed.

All of these changes to FFPE samples point out that you'll want to pay special attention to the data that you get from them. Find out more about chromatin architecture in FFPE tissues at Chromosome Research, July 2010.