Large-scale profiling of archival lymph nodes reveals pervasive remodeling of the follicular lymphoma methylome.
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.
Killian
J Keith
JK
Genetics Branch, Laboratory of Pathology, NIH/National Cancer Institute, Bethesda, Maryland, USA.
Bilke
Sven
S
Davis
Sean
S
Walker
Robert L
RL
Killian
M Scott
MS
Jaeger
Erich B
EB
Chen
Yidong
Y
Hipp
Jason
J
Pittaluga
Stefania
S
Raffeld
Mark
M
Cornelison
Robert
R
Smith
William I
WI
Bibikova
Marina
M
Fan
Jian-Bing
JB
Emmert-Buck
Michael R
MR
Jaffe
Elaine S
ES
Meltzer
Paul S
PS
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
D004273:DNA, Neoplasm; D005557:Formaldehyde