Imagine that you could go back in time and analyze the DNA methylation profiles of long-ago cancer samples (not to mention recession-proof your investment portfolio). EpiGenie can’t help with the latter because our time machine is on the fritz, but we can tell you about a new study in which researchers profiled the methylomes of archival follicular lymphoma tissues.
The results revealed that formalin-fixed, paraffin-embedded (FFPE) cancer specimens can be a rich source of preserved DNA methylation signatures, and that follicular lymphoma shows a distinct methylation profile compared with reactive hyperplasia or with normal lymphoid populations.
DNA damage resulting from formalin fixation and long-term storage is a major concern for the analysis of FFPE cancer specimens. However, with a sensitive bead array methylation assay, the research team determined the methylation profiles of FFPE lymph node samples archived for 14 years. Paul Meltzer of the National Cancer Institute, the lead author of the study, says, “We are very excited about the potential of using archives of FFPE blocks as a resource to explore the cancer epigenome.”
Meltzer and co-workers identified 259 CpG targets that were differentially methylated in follicular lymphoma compared with reactive hyperplasia, many of which are novel potential biomarkers for tumor classification. According to Meltzer, “Our analysis led to the surprising discovery of highly pervasive genomic methylation reprogramming during carcinogenesis that extends beyond an oncogene/tumor suppressor genecentric process.” See for yourself at Cancer Research, January 2009.