Large-Scale Profiling of Archival Lymph Nodes Reveals Pervasive Remodeling of the Follicular Lymphoma Methylome

^{1 1}Genetics Branch and ²Laboratory of Pathology, NIH/National Cancer Institute; ³Pathology Department, Suburban Hospital, Bethesda, Maryland; ⁴Illumina, Inc., San Diego, California; and ⁵School of Medicine, University of California-San Francisco, San Francisco, California

^* To whom correspondence should be addressed. E-mail: pmeltzer{at}mail.nih.gov.

	Abstract

Emerging technologies allow broad profiling of the cancer genome for differential DNA methylation relative to benign cells. Herein, bisulfite-modified DNA from lymph nodes with either reactive hyperplasia or follicular lymphoma (FL) were analyzed using a commercial C/UpG genotyping assay. Two hundred fifty-nine differentially methylated targets (DMT) distributed among 183 unique genes were identified in FL. Comparison of matched formalin-fixed, paraffin-embedded and frozen surgical pathology replicates showed the complete preservation of the cancer methylome among differently archived tissue specimens. Analysis of the DMT profile is consistent with a pervasive epigenomic remodeling process in FL that affects predominantly nonlymphoid genes. [Cancer Res 2009;69(3):758–64]

Key Words: follicular lymphoma, methylation profiling, epigenetics, FFPE, pathology

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