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Molecular Oncology, Markers, Clinical Correlates |
Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, Missouri 65203 [H. Y., P. Y., T. H-M. H., H. S., C. W. C.]; Department of Life Sciences and Institute of Biomedicine, National Chung Hsing University, 402 Taichung, Taiwan [C-M. C.]; and Epigenomics, AG, Berlin D-10435, Germany [M. B., I. N., S. M., K. B.]
ABSTRACT
This investigation examined promoter DNA methylation of the androgen receptor (AR) gene in non-Hodgkins lymphoma (NHL) representing different stages of B-cell differentiation. Steroid hormones are important endocrine messengers with a broad range of physiological functions, including regulation of B-cell lymphopoiesis. Some of these effects are mediated via specific receptors such as AR that can act as a ligand-dependent transcription factor for other genes. DNA was isolated from 76 NHL specimens representing pregerminal center, germinal center, and postgerminal center states of differentiation. Initial methylation data were obtained from oligonucleotide microarrays and was confirmed and extended using methylation-specific PCR. Methylation of the AR gene promoter was present in a nonrandom pattern. Those tumors derived from pregerminal center or postgerminal center stages showed virtually no methylation and expressed AR mRNA. Cases of germinal center origin, mainly follicular lymphomas and some diffuse large B-cell lymphomas, showed hypermethylation. Studies with NHL cell lines revealed that demethylation or reversal of histone deacetylation partially restored AR expression but reversal of both simultaneously provided a synergistic release from suppression. Promoter methylation of AR occurs in a differentiation stage-selective manner; those cases arising in the germinal center are preferentially methylated. Full re-expression of AR requires both demethylation and reacetylation, a finding that may affect treatment decisions.
INTRODUCTION
The molecular pathophysiology of NHL2
is characterized by distinct genetic pathways that selectively associate with different clinicopathological categories of the disease and shows relationships to putative normal stages of B-cell differentiation (Fig. 1)
. After production in the bone marrow and migration of naïve, mature B cells in peripheral blood, additional differentiation in secondary lymphoid tissues can be divided into pregerminal center, germinal center, and postgerminal center phases. (1
, 2)
During the pregerminal center phase, selection and recombination of V(D)J genes occurs, as well as the insertion of nontemplated nucleotides within the V(D)J region. Later, in the germinal center phase, somatic hypermutations occur during V(D)J rearrangement, with or without antigen exposure. Those B cells not undergoing productive rearrangements and receiving appropriate survival signals are destined to undergo apoptotic cell death. Those cells successfully transiting the germinal center phase, then enter a postgerminal center phase whereby the cells have acquired memory and cease additional somatic hypermutations.
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Steroid hormones are important endocrine messengers with a broad range of physiological functions, including regulation of B-cell lymphopoiesis (4, 5, 6) . The effects of androgens are mediated via a specific AR belonging to the nuclear receptor family and acting as a ligand-dependent transcription factor for other genes containing AREs in their promoter or upstream regions (5) . In its inactive form, the receptor is complexed to heat shock proteins and located mainly in the cytoplasm. Upon ligand binding and activation, the receptor enters the nucleus, binds to its cognate ARE(s) as a homodimer, and stimulates gene transcription.
In normal cells, DNA methylation usually occurs by adding a methyl group to the fifth carbon position of cytosine within a 5'-CG-3' palindrome (CpG with p denoting the phosphate group) during DNA replication (7
, 8)
. Across the genome,
80% of CpG dinucleotides are heavily methylated but some remain unmethylated in specific GC-rich regions (G+C content: >5060%), called CpG islands (9)
. These 0.21-kb long DNA sequences are frequently located in the promoters and first exon regions of 4050% of all genes (8)
. The rest may be located in the intronic or other exonic regions of the genes or in regions containing no genes.
In cancer cells, patterns of DNA methylation are altered (7 , 10 , 11) . Promoter (including the first exon) CpG island hypermethylation is a frequent epigenetic event in many types of cancer, including NHLs (12, 13, 14) . This epigenetic mutation can result in gene silencing via alteration of local chromatin structure preventing normal interaction of the promoters with the transcriptional machinery (15) . If this occurs in genes critical to growth inhibition, the silencing event could promote tumor progression (7) .
Although androgens are involved in normal B-cell differentiation, the AR has not been studied extensively in NHL. McDonald et al. (16) reported promoter DNA methylation in 16 of 19 cases, mostly of follicular lymphomas. On the basis of data derived from microarray-based discovery experiments and the known relationships of B cells and NHL to sex steroid manipulation (16) , we additionally examined DNA methylation of AR as a potential epigenetic modifier in selected B-cell lines and subtypes of NHL that represent pregerminal center, germinal center, and postgerminal center stages of differentiation.
MATERIALS AND METHODS
Tissue Samples.
Tissue samples were obtained from patients after diagnostic evaluation for suspected lymphoma at the Ellis Fischel Cancer Center (Columbia, MO) in compliance with our local Institutional Review Board. DNA was isolated from a total of 76 specimens; 14 from patients with B-CLL/SLL, 14 from FLI, 12 FLII, 14 MCL, 14 DLBCL, 4 LPL, and 4 MM were examined. All cases of B-CLL/SLL had peripheral blood and bone marrow involvement, and thus were technically categorized as CLL. These are all referred to as B-CLL/SLL in this article. On the basis of CD38 expression, 8 of 14 (57.2%) cases were pregerminal center tumors, and the remaining 6 (42.8%) were postgerminal center. For the DLBCL group, 6 of 14 (42.8%) were CD10+, a finding usually associated with DLBCL of a germinal center type. All specimens contained a minimum of 80% neoplastic cells, as determined by flow cytometry (data not shown). Total RNA was isolated using RNeasy Total RNA System (Qiagen, Valencia, CA). Enrichment of B cells from nonneoplastic lymph nodes was accomplished by immunoseparation into CD19+ B cells and CD19-lymph node cells. Cell suspensions (
1 x 107/ml in RPMI 1640) were incubated with CD19-conjugated immunomagnetic beads (Dynal, Lake Success, NY) at 4°C for 30 min, washed twice in PBS containing FCS (0.5%), and released with Detach-a-Bead (Dynal). This method routinely yields >95% purity and >85% recovery in our laboratory (data not shown).
Bisulfite Treatment and PCR Amplification for Microarray Hybridizations.
Bisulfite treatment of genomic DNA was performed with minor modifications as described previously (17)
. For the PCR amplification of the bisulfite-treated sense strand of the genes used for class prediction and discovery, the primers were designed according to the guidelines of Clark et al. (18)
, ensuring preferred amplification of DNA fragments with complete bisulfite conversion. Note that primers were designed to hybridize to DNA fragments containing no CpG dinucleotides, thus allowing unbiased amplification of methylated and unmethylated alleles. For the methylation profiling of lymphoma samples, CpG sites from regulatory regions of the genes listed in Table 1
were analyzed. Seven or eight fragments were amplified in parallel using multiplex PCR. The following protocol was used for multiplex PCR reactions: 10 ng of bisulfite-treated DNA as template, 2 pmol of each primer (seven or eight primer pairs), 1.6 mM deoxynucleoside triphosphates, and 1 unit of Taq polymerase (HotStarTaq; Qiagen, Hilden, Germany) in reaction buffer supplied with the enzyme with 3.5 mM MgCl2 were incubated in 25 µl of total volume. After activation of the enzyme (15 min, 96°C), the incubation times and temperatures were 95°C for 1 min followed by 39 cycles (95°C for 1 min, 55°C for 45 s, and 65°C for 75 s) and 65°C for 10 min.
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Cell Lines and Treatments.
Four NHL cell lines were studied for methylation and gene expression. The germinal center cell line RL is a follicular lymphoma derived from a male patient with the t(14,18) gene rearrangement (21)
, and the CD77+ Burkitt lymphoma-derived Daudi cell line is often used as a model of germinal center function (22)
. The postgerminal center cell line DB is a DLBCL cell line that has undergone isotype switching (21)
, and Raji cells are of germinal center derivation (23)
. All four of these cell lines expressed surface CD10 (data not shown), thus suggesting a germinal center relationship. These were obtained from the American Type Culture Collection and all were maintained in RPMI 1640. Cells were harvested and RNA, and DNA were extracted for reverse transcriptase-PCR expression analysis and for MSP.
For some experiments, RL cells were treated during the log phase of growth with TSA, 5-Aza, or both. Cells were seeded at 5 x 106/ml in RPMI 1640 with 10% calf serum. Control cell received no additives, whereas 5-Aza was added at 2.5 µM for 60 h of incubation, TSA (100 ng/ml) was added for 12 h, and the culture that received both was first incubated for 48 h with 5-Aza followed by an additional 12 h with TSA included in the culture. Cells were harvested and RNA and DNA were extracted for reverse transcriptase-PCR expression analysis and for MSP.
MSP.
For MSP, 2 µg of genomic DNA were treated with Na-bisulfite according to the manufactures recommendations (CpGenome; Intergen, Purchase, NY), and 100 ng of bisulfite-treated DNA were used for each assay. The following primers designed for the AR promoter region were; unmethylated (5'-TAGTGTGGTGGTTTTGAAGTTGTTGTTT-3' and 5'-CAAACTAACAACACTAAACCAACAAAAACA-3') and methylated (5'-GCGGCGGTTTCGAAGTCGTCGTTC-3' and 5'-CGCTAAACCGACGAAAACGAAAAAACG-3').
Semiquantitative Reverse Transcriptase-PCR.
First strand cDNA was synthesized using SuperscriptII reverse transcriptase (Invitrogen, Carlsbad, CA). Reverse transcriptase-PCR was conducted (30 cycles) using primers 5'-CCTGGCTTCCGCAACTTACAC-3' and 5'-GATTTTTCAGCCCATCCACTGG-3' for AR cDNA amplification. The levels of AR mRNA were normalized with the level of ß-actin mRNA as described previously (24)
.
RESULTS
Microarray-based Discovery in Gene Methylation.
Fig. 3
illustrates comparative DNA methylation data from a single locus of AR interrogation from both genders (top panel) and also separated into male-only cases (bottom panel) to examine any bias because of the influence of methylation-associated X chromosomal inactivation in the analyzed gene set (16)
.
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1:1000 positive cells, we conclude there is no detectable AR methylation in males, but both methylated and unmethylated alleles are present in females. We also tested gender separation on the basis of AR methylation across all NHL classes (female, n = 18; male, n = 49) specifically with the same four loci of AR and three loci from ELK1 and found statistical separation at Ps shown in Table 3
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When only female cases of B-CLL/SLL (n = 4) were compared with FLI/FLII/DLBCL (n = 4), the first locus of AR differed with P = 0.00379, whereas the other three loci all had P > 0.05. This may be a limitation of the few cases examined. Fig. 4
shows female cases of B-CLL/SLL and FLI/FLII methylation patterns. Virtually all cases demonstrate both methylated and unmethylated bands as expected in normal female cells, but additionally, the cases of FLI/FLII demonstrate stronger methylated:unmethylated band densities compared those of B-CLL/SLL. Thus, in this group, there is promoter DNA methylation beyond that expected from the X chromosomal inactivation process. A comparison of the ratios of methylated to unmethylated alleles in B-CLL/SLL (where virtually no methylation of AR occurs in male patients) to cases of FLI/FLII demonstrates an increase in methylation in the latter. In fact, it would be quite surprising if tumor-related DNA methylation were gender specific. Nevertheless, this pattern differs from that of male patients with B-CLL/SLL and FLI/FLII (Fig. 5)
.
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Some of the samples examined by MSP were cases that were previously examined by microarray (for confirmation). As examples, Fig. 5
illustrates MSP patterns from NHL cases of pregerminal center (MCL and B-CLL/SLL) germinal center (FLI, FLII, and DLBCL) or postgerminal center B cells (LPL and MM). Cases of DLBCL are included as germinal center cases, although it is recognized that some are likely of postgerminal center stage (2)
. In fact, 42.8% of our cases of DLBCL showed AR methylation, but the number of cases is too low for statistical validation. Virtually all cases of FLI (10 of 10 male, 4 of 4 female) and FLII (5 of 6 male, 6 of 6 female) and 35.7% of the DLBCL cases (5 of the 6 CD10+ cases) revealed methylation within the promoter region. Thus, there was concordance with the microarray methylation data, but in addition, we demonstrated lack of promoter methylation of AR in the additional de novo cases of NHL of pregerminal center and postgerminal center stages of differentiation.
Relationship of Methylation to Gene Silencing in NHL Cell Lines.
In an analogous manner, we examined promoter DNA methylation of four NHL cell lines and demonstrate that all show evidence of promoter DNA methylation (Fig. 6A)
. We also investigated whether AR gene expression might be altered in conjunction with promoter CpG island methylation from these same NHL cell lines (Figs. 6B)
. Semiquantitative reverse transcriptase-PCR was performed using ß-actin as an internal control. Lymph node cells from 1 male subject were included as an unmethylated control. As shown, methylation was present in all cell lines, but reciprocal down-regulation or ablation of mRNA expression was variable. For instance, although RL (follicular lymphoma) was methylated and had no detectable mRNA, Daudi showed methylation but also strong mRNA expression. It is known that methylation works in concert with acetylation with respect to AR expression (26)
, so this is not totally unexpected.
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DISCUSSION
This study provides important new information regarding AR in NHL. However, it should also be noted that a brief report on 26 cases of FLI/FLII and 14 cases of MCL were previously examined, and it was noted that CDKN1C (20) was hypermethylated in MCL but not FLI/FLII, but the AR gene promoter was methylated in FLI/FLII but not MCL. Gene expression for AR was inversely correlated with methylation (20) . First, B-cell NHL is associated with promoter DNA methylation of AR in a differentiation stage-selective manner; those cases arising in the germinal center (FLI/FLII/DLBCL) are preferentially methylated. The pregerminal center and postgerminal center tumors do not show the same methylation pattern. Second, these methylation patterns hold across both genders, although a normal pattern of X chromosomal inactivation via methylation is present in women. Third, although demethylating agents can potentially reverse the methylation, full re-expression of AR requires both demethylation and reacetylation. Thus, examination of AR methylation in NHL has provided provocative data and new mechanistic insights, but the overall effect of AR silencing in NHL is not clear because it potentially affects numerous other genes.
Although speculative, the reason(s) for this may relate to the unique activities that take place in the germinal center reaction. The state of methylation has been correlated with immunoglobulin gene regulation; both the µ heavy chain and
light chain gene are hypermethylated in cells in which they are not recombined (30)
. Concomitant with V(D)J rearrangement, these loci become unmethylated and transcriptionally active. Regulated demethylation is thought to control the specificity of the V(D)J recombinase (31)
. Furthermore, it has been shown that Pax5, a gene expressed in normal B cells until plasmacytic differentiation, is under control of DNA methylation (32)
.
How AR might function with respect to germinal center NHL is also speculative. One of the hallmarks of FLI/FLII is surface expression of CD10 or NEP, an enzyme thought to identify lymphoid cells with specific cycling and apoptotic abilities (33) . An interesting relationship between AR and the NEP gene has been reported previously (34) . In prostate cell lines, steroid regulation of NEP involves at least two elements, including a typical ARE that binds receptors for androgen, progesterone, and glucocorticoids, and a unique androgen-responsive region that only binds AR. Thus, it is tempting to speculate on the possible impact of AR methylation silencing and NEP expression. Although NEP expression in lymphoid cells relates to specific cycling and apoptotic abilities, the t(14,18) translocation that is characteristic of FLI/FLII leads to high levels of bcl-2 protein and may protect cells from apoptosis (35) . Both bcl-2 and c-myc interact in progression of follicular lymphomas (36) and c-myc increases transcription of a large number of genes in B cells that are necessary for acceleration of G1 progression. Also, c-myc is an AR-regulated gene in some tumors, with a reciprocal relationship between AR mRNA levels and c-myc overexpression (37 , 38) .
The loss of AR expression in prostate cancer may be an important event in tumor progression, moving from a hormone-dependent to a hormone-independent condition that appears to be dependent on the acquisition of autocrine pathways (39)
. It is possible that NHL with silenced AR might be more susceptible to the activities of other autocrine mechanisms such as IL-6 signaling. Cross-talk between the IL-6 and AR signal transduction pathways has been reported in which IL-6 induced several ARE-driven reporters that are dependent on AR and functioned via the mitogen-activated protein kinase and signal transducers and activators of transcription 3 pathways (40)
. IL-6 also regulates the human DNA methyltranferase-1 gene promoter and resultant enzyme activity, which requires transcriptional activation by the Fli-1 transcription factor via signal transducers and activators of transcription 3 (41
, 42) . A convincing role for IL-6 in plasmacytic differentiation of B-cells and autocrine tumor growth has been demonstrated, but an even more convincing link involves a murine model of extraosseous plasmacytoma (43)
. Upon stimulation with pristane, all of the transgenic mice carrying a widely expressed IL-6 transgene developed lymphoplasmacytic tumors. Unexpectedly,
30% of these developed follicular lymphomas or DLBCL, thus demonstrating a connection between IL-6 dysregulation of an inflammatory response and development of germinal center lymphomas. Thus, it is conceivable that interactions between IL-6, AR methylation and silencing, and potentially IL-6-driven override of the silenced AR may be involved in development of FLI/FLII and DLBCL. However, at this time, any definitive mechanism(s) is speculative, but the data presented create many opportunities for additional exploration of the role(s) of AR in NHL.
FOOTNOTES
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.
1 To whom requests for reprints should be addressed, at Department of Pathology and Anatomical Sciences, Ellis Fischel Cancer Center, University of Missouri School of Medicine, 115 Business Loop 70 West, Columbia, MO 65203. Phone: (573) 882-1283; E-mail: caldwellc{at}health.missouri.edu ![]()
2 The abbreviations used are: NHL, non-Hodgkins lymphoma; MCL, mantle cell lymphoma; FLI, grade I follicular lymphoma; FLII, grade II follicular lymphoma; ARE, androgen response element; AR, androgen receptor; DLBCL, diffuse large B-cell lymphoma; LPL, lymphoplasmacytic lymphoma; MM, multiple myeloma; B-CLL/SLL, B-cell chronic lymphocytic leukemia/small lymphocytic lymphoma; MSP, methylation-specific PCR; TSA, trichostatin A; 5-Aza, 5-azacytidine; HDAC, histone deacetylase; NEP, neutral endopeptidase 24.11; IL, interleukin. ![]()
Received 1/ 3/03; revised 5/16/03; accepted 5/16/03.
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