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Carcinogenesis Advance Access published online on June 14, 2006
Carcinogenesis, doi:10.1093/carcin/bgl092
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© The Author 2006. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org
Received January 6, 2006
Revised May 18, 2006
Accepted May 19, 2006

CANCER BIOLOGY

Discovery of novel epigenetic markers in non-Hodgkin's lymphoma

Huidong Shi 1, Juyuan Guo 1, Deiter J. Duff 1, Farahnaz Rahmatpanah 1, Rebecca Chitima-Matsiga 1, Mufadhal Al-Kuhlani 1, Kristen H. Taylor 1, Ozy Sjahputera 1, Melinda Andreski 2, James E. Wooldridge 2, and Charles W. Caldwell 1 *

1 Department of Pathology and Anatomical Sciences, Ellis Fischel Cancer Center, University of Missouri School of Medicine, Columbia, Missouri 65203
2 Department of Internal Medicine, Holden Comprehensive Cancer Center at University of Iowa, Iowa City, Iowa, 52242

* To whom correspondence should be addressed.
Charles W. Caldwell, E-mail: caldwellc{at}health.missouri.edu


  Abstract

Non-Hodgkin's lymphoma (NHL) is a group of malignancies with heterogeneous genetic and epigenetic alterations. Discovery of molecular markers that better define NHL should improve diagnosis, prognosis, and understanding of the biology. We developed a CpG island DNA microarray for discovery of aberrant methylation targets in cancer, and now apply this method to examine NHL cell lines and primary tumors. This methylation profiling revealed differential patterns in 6 cell lines originating from different sub-types of NHL. We identified 30 hypermethylated genes in these cell lines and independently confirmed 10 of them. Methylation of 6 of these genes was then further examined in 75 primary NHL specimens comprised of four subtypes representing different stages of maturation. Each gene (DLC-1, PCDHGB7, CYP27B1, EFNA5, CCND1 and RAR{beta}2) was frequently hypermethylated in these NHLs (87 %, 78%, 61%, 53%, 40%, and 38% respectively), but not in benign follicular hyperplasia. While some genes such as DLC-1 and PCDHGB7 were methylated in the vast majority of NHLs, others were differentially methylated in specific subtypes. The methylation of the candidate tumor suppressor gene DLC-1 was detected in a high proportion of primary tumor and plasma DNA samples by using quantitative methylation specific PCR analysis. This promoter hypermethylation inversely correlated with DLC-1 gene expression in primary NHL samples. Thus, this CpG island microarray is a powerful discovery tool to identify novel methylated genes for further studies of their relevant molecular pathways in NHLs and identification of potential epigenetic biomarkers of disease.

Keywords: CpG island Microarray; DNA Methylation; Non-Hodgkin's Lymphoma.
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