title: Large-scale profiling of archival lymph nodes reveals pervasive remodeling of the follicular lymphoma methylome.
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.
authors.affiliation: Genetics Branch, Laboratory of Pathology, NIH/National Cancer Institute, Bethesda, Maryland, USA.
authors.forename: J Keith
authors.initials: JK
authors.lastname: Killian
authors.forename: Sven
authors.initials: S
authors.lastname: Bilke
authors.forename: Sean
authors.initials: S
authors.lastname: Davis
authors.forename: Robert L
authors.initials: RL
authors.lastname: Walker
authors.forename: M Scott
authors.initials: MS
authors.lastname: Killian
authors.forename: Erich B
authors.initials: EB
authors.lastname: Jaeger
authors.forename: Yidong
authors.initials: Y
authors.lastname: Chen
authors.forename: Jason
authors.initials: J
authors.lastname: Hipp
authors.forename: Stefania
authors.initials: S
authors.lastname: Pittaluga
authors.forename: Mark
authors.initials: M
authors.lastname: Raffeld
authors.forename: Robert
authors.initials: R
authors.lastname: Cornelison
authors.forename: William I
authors.initials: WI
authors.lastname: Smith
authors.forename: Marina
authors.initials: M
authors.lastname: Bibikova
authors.forename: Jian-Bing
authors.initials: JB
authors.lastname: Fan
authors.forename: Michael R
authors.initials: MR
authors.lastname: Emmert-Buck
authors.forename: Elaine S
authors.initials: ES
authors.lastname: Jaffe
authors.forename: Paul S
authors.initials: PS
authors.lastname: Meltzer
mesh_terms: D018899:CpG Islands; D019175:DNA Methylation; D004273:DNA, Neoplasm / Q000235:genetics / Q000302:isolation & purification; D005557:Formaldehyde; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008198:Lymph Nodes / Q000473:pathology*; D008224:Lymphoma, Follicular / Q000235:genetics* / Q000473:pathology*; D016612:Paraffin Embedding; D015203:Reproducibility of Results; D016707:Tissue Fixation
chemical_list: D004273:DNA, Neoplasm; D005557:Formaldehyde