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Priority Reports |
1 Genetics Branch and 2 Laboratory of Pathology, NIH/National Cancer Institute; 3 Pathology Department, Suburban Hospital, Bethesda, Maryland; 4 Illumina, Inc., San Diego, California; and 5 School of Medicine, University of California-San Francisco, San Francisco, California
Requests for reprints: Paul S. Meltzer, Room 6138, 37 Convent Drive, MSC 4265, Bethesda, MD 20892-4265. Phone: 301-496-5266; Fax: 301-480-3281; E-mail: pmeltzer{at}mail.nih.gov.
| Abstract |
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| Introduction |
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The current portrait of the cancer methylome is a composite derived from divergent sample types and methodologies. This portrait depicts a globally demethylated genome with locoregional promoter CGI hypermethylation. Many array-based methods of methylation profiling are biased toward detection of regions with high CpG density (3). Bisulfite sequencing and genotyping permit large-scale analysis of cancer tissue methylation, inclusive of high-density and low-density CpG genome space.
Archival formalin-fixed, paraffin-embedded (FFPE) specimens comprise the vast majority of human cancer tissues available for research studies and often may be the only available tissue source. FFPE archives have been used previously for genome-scale copy number profiling (4) and gene expression analysis (5). The demonstration of preserved DNA methylation signatures and a suitable method for their recovery would increase the value of FFPE archives for biomarker discovery.
The purposes of the present analysis are (a) to test the feasibility of differential-methylation profiling in FFPE samples compared with frozen samples; (b) to derive a balanced genomic profile of on-CGI and off-CGI differential methylation in a cancer, specifically follicular lymphoma (FL) relative to reactive lymph nodes selected for a predominance of follicular hyperplasia (FH); and (c) to investigate methylation–gene expression correlation in FL versus FH.
| Materials and Methods |
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Validation set. Eleven cases of FL grades 1 and 2 and 14 reactive lymph nodes, of ages 10 to 14 y, were analyzed. All anatomic pathology diagnoses were rendered by an expert hematopathologist according to WHO criteria (6).
Cells. Peripheral blood lymphocytes (PBL) were isolated from fresh commercial leukopaks (Blood Systems Research Institute). CD19+ B cells and CD4+ and CD8+ T cells were isolated from PBLs using immunomagnetic beads (Miltenyi). Lymphoblastoid B-cell DNA samples NA06999, NA07033, NA10923, and NA10924 were purchased from Coriell Institute for Medical Research.
DNA Methylation Profiling Using Bead Arrays
Tissue was scraped from entire 5-µm tissue sections from either FFPE unstained slides or frozen sections of cryopreserved tissue blocks (69 total tissue samples). Tissue lysis and DNA extraction were performed using proteinase K digestion (Qiagen). DNAs were bisulfite modified using the Zymo Methylation Gold kit. Bisulfite (250 ng)-modified DNA was used for the Illumina bead array methylation assay. Methylation detection for 1505 CpG sites was performed, as described previously (7), using the standard cancer panel according to the manufacturer's instructions. Image processing and intensity data extraction were performed with Illumina-supplied equipment. Each methylation data point is represented by fluorescent signals from the methylated (M) and unmethylated (U) alleles.
Gene Expression Profiling
RNA was isolated using Trizol reagent and subsequently purified over Qiagen columns. Complementary DNA was generated from total RNA by reverse transcription and linear amplifications (in vitro transcription) to generate biotinylated cRNA targets that were hybridized to Illumina Human Ref8 BeadChip arrays according to the manufacturer's protocols.
COBRA Assays
Differential methylation between FL and reactive hyperplasia was confirmed for numerous targets using COBRA (combined bisulfite restriction analysis; ref. 8) assays. Eight independent target CpG COBRA assays were developed (four hypomethylated and four hypermethylated targets in FL), which confirmed differential methylation in accordance with array analyses. Supplementary Table S3 provides target IDs and PCR primer sequences for COBRA assays. Figure 3 illustrates COBRA assays in representative cases of FL and reactive hyperplasia.
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Calculation of CpG target β. A nonlinear transformation was used to map the raw Cy3 and Cy5 BeadArray fluorescent intensities R,G to methylation β levels.
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FFPE versus frozen methylation profiles. Three of the 1,505 targets were identified by significance analysis of microarrays (SAM; ref. 9) as statistically different between the tissue-processing classes. However, in these three instances, the difference between frozen and FFPE classes was only 1% to 2% methylation. Further analysis showed that the identification of these three targets was most probably a mathematical artifact of the nonlinear transformation used to convert raw fluorescent intensities to methylation β levels.
Differentially methylated target identification: FL versus reactive hyperplasia. SAM (9) was used to identify CpG target methylation β values as statistically different between FL and reactive hyperplasia. The additional criterion group average target β difference between FL and reactive hyperplasia of >0.15 led to the exclusion of additional targets, resulting in the final list of 259 differentially methylated targets (DMT).
Classification accuracy: FL versus reactive hyperplasia. After exclusion of samples FL1 and FH9 (see text), the prediction analysis of microarrays (PAM) package was used to identify the most robust DMT classifiers of FL versus reactive hyperplasia.
Activity matrix. The methylation of targets in the reference (reactive hyperplasia) samples were categorized into unmethylated (β < 0.2), hemimethylated (0.2
β
0.8), and methylated (β > 0.8). The compartment (CGI or non-CGI) activity for hypermethylation in FL was then defined as
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Compartmental hypomethylation activity is correspondingly defined as
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Correlation of gene expression with DMTs. Differentially expressed genes between FL and reactive hyperplasia were ordered by t test value, and the DMT list was aligned to it. This analysis showed that DMTs were significantly enriched in those genes with low expression levels in both FL and reactive hyperplasia.
| Results and Discussion |
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Comparison of FFPE and frozen specimens. Precision and accuracy are two variables commonly used to characterize the quality of array measurements; precision estimates how close measured values are to their corresponding "true" values and is shifted by systematic biases, whereas accuracy reflects how well technical replicates agree and essentially captures stochastic noise (10). Because formalin fixation may alter DNA through fragmentation, sequence modification, and cross-linking, the methylomes of 20 surgical specimens (Table 1 )—parallel-processed with both FFPE and cryopreservation—were compared to identify potential random or systematic alterations.
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DNA methylation classifiers of FL are pervasive. Of the 1,505 targets (806 genes) analyzed, 259 targets distributed among 183 unique genes were identified as significantly differentially methylated between hyperplasia and FL (see Materials and Methods for DMT identification). Of the 259 DMTs, 184 were hypermethylated in FL (Supplementary Table S1), whereas 75 were hypomethylated (Supplementary Table S2; Figs. 1C and 2 ). Numerous DMTs were validated using the COBRA (8) assay, which showed correspondence with array analyses (Fig. 3 ). The PAM (11) software package was used to develop DMT classifiers discriminating FL and FH; it was found that these classifiers had perfect generalization properties (100% sensitivity and specificity) in PAM cross-validation tests. The PAM algorithm allows controlling the number of targets used in the final classifier by adjusting the threshold. By adjusting and reducing the target set size, it turned out that even very small sets of only two CpG targets were sufficient for perfect classification in the cross-validation tests. This excellent generalization property of the classifier was confirmed in a validation set of samples, as discussed in Materials and Methods. The successful classification of samples using a relatively small number of array CpG targets is promising for the future development of DMT-based assays for clinical molecular diagnostic application.
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Initially, two additional samples (FL1 and FH9) were included in the analysis that did not generalize well in the classification. In these two cases wherein the methylation profile conflicted with the group index of FL or reactive hyperplasia, further analysis of pathologic features explained these discrepancies. The sample labeled FL1 was a noncancerous lymph node obtained from a patient with a history of FL; microscopic FL was present in a lymph node adjacent to the one that was profiled (13). FH9 was an abnormal lymph node diagnosed as consistent with the plasma cell variant of multicentric Castleman's disease (MCD), negative for HHV-8. The idiopathic form of MCD is not well understood but is an immunosecretory disorder characterized by an excessive plasma cell proliferation in a background of reactive FH (14). These two samples were subsequently excluded from PAM identification of DMTs.
Finally, the cosegregation in the hierarchical cluster of a greater number of FFPE/frozen pairs of FL than FH samples (Fig. 2A) is consistent with a greater overall uniformity in the FH than FL group. In other words, the DMT profiles of FL lymph nodes are more individualized. Correlation of such individual variations in DMT profile in FL patients with clinical phenotype is warranted in future studies.
Validation set of FL and FH tissue samples. The matched FFPE and frozen samples included in the initial analysis were <3 years old. Because additional DNA damage may occur during routine archiving of FFPE specimens (e.g., oxidative damage), 25 additional FFPE samples including one B5-mercury fixed specimen, archived from 10 to 14 years (Supplementary Table S5), were subsequently analyzed. The additional cases included 11 FL and 14 FH and yielded comparable signal intensities and phenotype-dependent methylation profiles to the matched FFPE/frozen samples. The array methylation β values from this additional set were subjected to the PAM classifier, which resulted in correct classification of 24/25 (96%). This result indicates excellent generalizability of a DNA methylation–based PAM classifier. Additionally, unsupervised hierarchical clustering of the validation set based on the original 259 DMT profile (Supplementary Tables S1 and S2) resulted in correct segregation of all 25 samples according to pathologic status of FL versus FH (Supplementary Fig. S1).
Pattern of differential methylation in FL is divergent from normal lymphoid populations. Analysis of appropriate reference groups is an important consideration for comparative epigenetic research. In our study, we considered the possibility that FL DMTs could originate from enrichment for wild-type lineage-dependent epigenetic markings of the cell type of origin of the cancer, namely B cells. The FL DMT profile was, therefore, compared with that of purified populations of PBL B and T cells and transformed B-lymphoblastoid cell lines to assess for pathologic divergence of methylation as opposed to shifts in B-cell and T-cell composition. Pursuantly, the CGI hypermethylations observed in FL were absent in the B-cell and EBV-transformed B-cell line populations (Fig. 2B). Of further note, only 10 (<5%) of the 259 DMTs in FL versus FH show a significant difference in methylation between normal B and T cells, although 97 array targets are highly differentially methylated (
β >0.35; Supplementary Table S3) between B and T cells. Thus, the preponderance of hypomethylated and hypermethylated DMTs in FL represents epigenetic divergences from the wild-type lymphoid lineages analyzed and are not shifts in proportions of background T and B cells between FL and reactive lymph nodes. The analysis further showed that follicular lymphomagenesis and B-cell immortalization via EBV transformation are two largely distinct epigenetic processes. Whereas several hypomethylations were shared by FL and EBV-transformed B cells, the majority of hypomethylations and nearly all hypermethylations in FL relative to FH are absent from B cells immortalized by EBV.
It is likely that the hypermethylations that distinguish FL from reactive hyperplasia are also divergences from bone marrow stem cells (BMSC). Bibikova and colleagues (15) recently reported a DNA methylation analysis of BMSC, differentiated somatic lineages and tissues, embryonic stem cells, and cancer cell lines. Globally, of the 370 genes profiled in their study, BMSC methylation was comparable with that of B-cell lines, and these two groups clustered together in an unsupervised analysis that included ES cells and numerous cancer cell lines. Roughly, 80% of the genes profiled in that study were also profiled in this study, albeit not at identical CpG target loci. Thus, comparison of the two data sets implies that the FL profile is largely divergent from BMSC.
The large number of both CGI-positive and CGI-negative gene promoters profiled in our study permitted evaluation for a pathologic CGI bias in target hypermethylation in FL. Preliminary analysis suggested such a bias: 74% (136 of 184) of the hypermethylated targets were located inside CGI, significantly more than their fraction of targets on the entire array (43%, n = 649). However, rather than being specifically targeted for methylation, it is possible that CGI hypermethylation in FL is a mere reflection of the underlying kinetics. In noncancerous lymph nodes, CpGs manifest lower methylation states inside CGI; therefore, more targets can be further methylated. Inversely, there is a greater methylation "preload" for off-CGI targets, so comparatively fewer of these targets can be hypermethylated. The "activity coefficients" introduced in this study (see Materials and Methods) take these kinetic factors into account. Even with this correction, the methylation activity inside CGIs is twice that found at off-CGI targets. However, the most pronounced difference between on-CGI and off-CGI targets is not in their hypermethylation activity but in demethylation; hypomethylation activity is over one order of magnitude lower inside CGIs (Fig. 4 ).
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Correlation of gene expression and differential methylation. Emerging information from genome-wide DNA methylation profiling studies reveals widespread cancer CGI hypermethylation that involves numerous genes not implicated in cell growth or tumorigenesis (16). To explore the relationship in FL between gene expression and differential methylation, gene expression analysis was performed on a subset of the cryopreserved lymphoma (n = 8) and hyperplasia (n = 5) samples for which sufficient RNA could be extracted (data are available; GEO accession number GSE14214). Two different tests were used to determine the correlation between differential methylation and differential expression for proximate genes. No agreement was observed between the differentially expressed genes and the differential methylation state, as assessed by Pearson's correlation coefficients and gene set enrichment analyses. By contrast, hypermethylated DMTs preferentially link to genes showing the least differential expression. The absence of differences was in part driven by the fact that differentially methylated genes were expressed at lower levels than unaffected genes, regardless of pathologic state. A random permutation test revealed not a single instance of differential expression (P < 0.01) between the median expression of the differentially methylated genes and the median expression of 100,000 randomly selected gene sets of the same size.
An important aspect of cancer epigenetics is the elucidation of how DNA methylation changes contribute to the malignant phenotype, including the consequences for the transcription of biologically critical genes. Remarkably, integration of the methylation data with gene expression analysis found not a single randomly selected set of differentially expressed genes that correlated with differential DNA methylation in FL. In large part, DMT neighbor genes are weakly expressed in both FL and reactive hyperplasia. In a recent study of diffuse large B-cell lymphoma, Pike and colleagues made a similar observation (17). In addition, comparable with our findings, Keshet and colleagues found that CGI hypermethylation in cancer occurs frequently at genes that are already repressed (16). The present analysis of FL further reveals that preferential hypermethylation of weakly expressed genes is not related to CGI status. The uniformity of the DMT profile among FL cases and the significant enrichment for nonexpressed/nonlymphoid genes among the DMTs argue against a purely random process of pathologic methylation. At the same time, the results underscore the emerging concept in cancer tissue epigenetics that differential methylation can operate at the genomic level and may not correlate with a change in gene expression for individual targets.
To summarize the portrait of the FL methylome that emerges from these analyses, (a) FL manifests a pervasive shift in genomic DNA methylation relative to reactive hyperplasia, T cells, B cells, or bone marrow stem cells; (b) FL does not show any significant hypomethylation of CGI targets, despite the presence of numerous normally methylated CGI in reactive hyperplasia and B cells; (c) in contrast, non-CGI genome space contains significant pathologic DMTs, including a relatively large hypomethylation activity; (d) microanatomic B-cell compositional enrichment in FL does not contribute substantially to the identified DMT profile; (e) hypermethylated targets in an unselected FL cohort are those with minimal or no expression at baseline in benign lymph nodes and include numerous nonlymphoid genes; and finally, (f) the ability to analyze complex genomic patterns of differential methylation in archival FFPE pathology specimens will be a useful tool for biomarker discovery.
| Disclosure of Potential Conflicts of Interest |
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| Acknowledgments |
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The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
We thank Marbin Pineda, Theresa Davies-Hill, and Dr. Lynn Sorbara for technical assistance; Julie Stewart for help with figures; and Art Glatfelter, Shannon Harmon, Shyam Kalavar CT, Rachel Dove HT, Marie Mueller CTR, and Dr. Gene Passamani for facilitating pathology archive research.
| Footnotes |
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Received 8/ 1/08. Revised 11/12/08. Accepted 12/ 9/08.
| References |
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