Abstract 168: Genome-wide survey of CpG methylation across the spectrum of B-cell lymphomas
Authors: Taylor Kristen H. , Shaknovich Rita , Martin-Subero Jose , Arthur Gerald , Bennett Lynda , Ammerpohl Ole , Richter Julia , Siebert Reiner , Melnick Ari , Caldwell Charles 
Published: February 2011

Abstract
Introduction: An international consortium was established to create comprehensive methylomes of B-cell lymphoma cell lines representing multiple stages of B-cell differentiation. One of the consortium's long-term goals is to identify genes and pathways that are perturbed by methylation in these cell lines either individually, or wholly, so that this information may be utilized to identify novel targets of aberrant methylation in patient samples.
Experimental procedures: The B-cell derived tumor cell lines included in this study represent the spectrum of B-cell development: chronic lymphocytic leukemia (Mec1); mantle cell lymphoma (Granta); diffuse large B-cell lymphoma (Val and Ly10); follicular lymphoma (RL); Burkitt's lymphoma (Raji); and multiple myeloma (U266B1).
Three methods were employed in this study: 1) Methylated CpG island amplification (MCA) and Agilent CpG island arrays; 2) HpaII tiny fragment enrichment by ligation-mediated PCR (HELP) and Agilent CpG island arrays; and 3) Bisulfite treatment in conjunction with the Illumina Infinium Methylation BeadChip.
Data summary: Comprehensive genome-wide methylation profiles were constructed for each tumor cell line using the data generated from three different methods. The number of detected differentially methylated probes, genes and gene promoters differed for each method. The number of unique methylated genes identified ranged from 25 for Granta to more than 200 for U266B1. Recurrent aberrant methylation was detected in ∼100 genes in all seven cell lines included in this study. Methylation of key miRNAs was identified in each of the cell lines.
Gene lists that included genes with promoter methylation were submitted to the database for annotation, visualization and integrated discovery (DAVID) to identify enriched functional-related gene groups. Cell differentiation, transcription factor activity and HOX were among the top three functionally enriched gene groups in all cell lines. Genes associated with the Wnt, MAPK and Hedgehog pathways were also enriched in select cell lines.
Conclusions: All approaches suffer from limitations in their ability to detect methylated sequences. The probes assayed on the Agilent CpG island array are limited to sequences that are contained within the restriction fragments produced in the MCA and HELP assays. The MCA method relies on the co-hybridization of a sample of interest to a “normal control” which may introduce biases if the “proper” control is not used. Finally, the Illumina Infinium BeadChip assays, on average, only 2 probes per gene and is the least informative of the detection assays. Despite these shortcomings, the combination of the data generated by each method has allowed the identification of novel genes and pathways that can be used to design screening assays for large numbers of patient samples.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 168.