From www.bloodjournal.org by guest on June 15, 2017. For personal use only. Blood First Edition Paper, prepublished online October 15, 2012; DOI 10.1182/blood-2012-04-423111 Reduced Ribosomal RNA Expression and Increased Ribosomal DNA Promoter Methylation in CD34+ Cells of Patients with Myelodysplastic Syndromes Aparna Raval1, Kunju J. Sridhar2, Shripa Patel3, Brit B. Turnbull4, Peter L. Greenberg2 and Beverly S. Mitchell1 Stanford Cancer Institute1, Division of Hematology2, Stanford Protein and Nucleic Acid Facility3 and Department of Health Research and Policy4, Stanford University, Stanford, CA 94305 Corresponding Author: Beverly S. Mitchell M.D. George E Becker Professor of Medicine Stanford Cancer Institute, LLSC Research Building (SIM1), 265 Campus Drive, Room G2167, Stanford, CA 94305-5458. Phone: 650-736-7716 Fax: 650-736-0607 E-mail: [email protected] 1 Copyright © 2012 American Society of Hematology From www.bloodjournal.org by guest on June 15, 2017. For personal use only. Abstract Myelodysplastic syndromes (MDS) are clonal disorders of hematopoietic stem cells characterized by ineffective hematopoiesis. The DNA hypomethylating agents 5-azacytidine (5AC) and 5-aza-2’-deoxycytidine (DAC) are effective treatments for patients with MDS, increasing time to progression to acute myelogenous leukemia and improving overall response rates. Although genome-wide increases in DNA methylation have been documented in bone marrow cells from MDS patients, the methylation signatures of specific gene promoters have not correlated with the clinical response to these therapies. Recently, attention has been drawn to the potential etiologic role of decreased expression of specific ribosomal proteins in MDS and in other bone marrow failure (BMF) states. We therefore asked whether ribosomal RNA (rRNA) expression is dysregulated in MDS. We found significantly decreased rRNA expression and increased rDNA promoter methylation in CD34+ hematopoietic progenitor cells (HPC) from the majority of MDS patients as compared to normal controls. Treatment of myeloid cell lines with DAC resulted in a significant decrease in the methylation of the rDNA promoter and an increase in rRNA levels. These observations suggest that an increase in rDNA promoter methylation can result in decreased rRNA synthesis that may contribute to defective hematopoiesis and BMF in some individuals with MDS. 2 From www.bloodjournal.org by guest on June 15, 2017. For personal use only. Introduction: The DNA hypomethylating drugs 5AC and DAC are in clinical use for the treatment of MDS 1,2 and have been shown to improve overall response rates and increase the time to progression to acute myelogenous leukemia (AML) as compared with best supportive care 3,4 . A number of studies have documented an increase in genome-wide promoter methylation in mononuclear cells as well as in CD34+ HPC derived from the bone marrows of MDS patients 5,6 . However, drug-induced differences in genome-wide promoter methylation signatures and in gene expression profiles have not correlated with the clinical response to hypomethylating agents 7. In addition, a correlation between changes in promoter methylation profiles and acquired resistance to 5AC or DAC has never been demonstrated 8 9 . Therefore, the role of DNA hypermethylation in the pathogenesis of MDS remains to be determined, as does the question of whether the therapeutic responses to 5AC and DAC result from the induction of gene-specific DNA hypomethylation as opposed to other sequelae such as the induction of a DNA damage response, the activation of an immune response, or the induction of senescence (7). The nucleolus contains clusters of genes that encode the 45S prerRNA precursor of ribosomal RNA that is subsequently processed to generate the 18S, 5.8S and 28S rRNA components 10,11. In human cells, there are ~400 copies of rDNA genes arranged as tandem repeats within nucleolar organizer regions located on chromosomes 13-15, 21 and 22, although not all of the genes are actively transcribed. Transcription of the rRNA genes depends on the chromatin structure of the promoter region 12-14. Promoters of active rRNA genes are devoid of CpG methylation and are associated with acetylated 3 From www.bloodjournal.org by guest on June 15, 2017. For personal use only. histones, while the reverse is found for silenced genes methyltransferase 1 (DNMT1) controls rDNA gene transcription 15 . DNA 16 and also regulates the nucleolar architecture by maintaining the heterochromatin state within intergeneic repetitive sequences 17,18. A number of recent observations have suggested that ribosomal protein synthesis is an essential component of normal hematopoietic stem cell function. Haploinsufficiency of the ribosomal gene RPS14 in 5q- syndrome 19,20 , the presence of RPS19 mutations in Diamond-Blackfan anemia 21, and the aberrant expression of multiple ribosomal proteins in MDS 22-24 all suggest that altered ribosome biogenesis could play a major role in the pathogenesis of bone marrow failure syndromes. To determine whether rRNA synthesis might be altered in HPC from a broader spectrum of MDS patients, we have compared the level of rRNA expression and the extent of rDNA promoter methylation in CD34+ cells derived from bone marrows of MDS patients to those in normal CD34+ cells. Our data demonstrate that rRNA expression is decreased in MDS hematopoietic progenitors while methylation within the rDNA upstream regulatory region is increased. We show that rRNA expression and rDNA methylation are inversely correlated in our combined data obtained from healthy controls and MDS patients. In addition, treatment of human myeloid leukemia cell lines with DAC resulted in both a decrease in promoter methylation and an increase in rRNA expression. We suggest that disruption of ribosomal biogenesis resulting from alterations in rRNA synthesis may also underlie hematopoietic progenitor cell dysfunction in some MDS patients. 4 From www.bloodjournal.org by guest on June 15, 2017. For personal use only. Materials and Methods MDS Patient samples CD34+ mononuclear cells were enriched from freshly obtained bone marrow from 22 MDS patients and 11 healthy donors by magnetic bead separation (Miltenyi Biotec). CD34+ purity was greater than 90% as assessed by flow cytometry. Cells were immediately snap-frozen and stored at -80C until use. Bone marrow samples were obtained from patients after informed consent per the Declaration of Helsinki and according to an IRB-approved protocol. Cell Culture Experiments: The THP1, Mono Mac6 and ML-2 (human myelomonocytoc leukemia cell lines) were incubated (37°C and 5% CO2) in RPMI 1640 supplemented with 10% FBS (HyClone Laboratories, Logan, UT), 100 U/ml penicillin, and 100 μg/ml streptomycin (Invitrogen, Carlsbad CA). Cells were treated with 0.1μM DAC (Sigma-Aldrich, St. Louis MO) for a maximum of 3 days and drug was added daily. Cells were harvested after three days of treatment and DNA and RNA were extracted according to manufacturer’s instructions (Qiagen, Valencia, CA). Quantitative RT-PCR Total RNA was extracted from cell lines and bone marrow-derived CD34+ cells using the RNAeasy micro kit (Qiagen, Valencia, CA). Total RNA was treated with DNAse (Ambion, Life Technologies, Carlsbad, CA) according to the manufacturer’s instructions and reverse transcription was performed with random hexamer primers using the SUPERSCRIPT First-Strand Synthesis kit (Invitrogen). PCR primers were located within the 5’ Externally Transcriped Sequence of the rDNA gene and pre-rRNA expression was measured by 5 From www.bloodjournal.org by guest on June 15, 2017. For personal use only. quantitative RT-PCR carried out in triplicates using SYBR Green Master Mix (Applied Biosystems, Foster City, CA). cDNA was amplified using primers within the rDNA promoter and the absence of PCR product confirmed the lack of rDNA amplification. The RT-PCR primers used were: pre-rRNA: forward primer 5'- gaacggtggtgtgtcgttc -3', reverse primer 5'- gcgtctcgtctcgtctcact -3' (Murayama A et al Cell 2008); GAPDH: forward primer 5'-ccccttcattgacctcaactacat-3', reverse primer 5'-cgctcctggaagatggtga3’. Quantitative DNA Methylation using Pyrosequencing: Genomic DNA from CD34+ cells from 14 MDS and 11 normal samples (100-200 ng) and from myeloid cell lines (1 mg) was treated with sodium bisulfite using the EZ DNA methylation kit (Zymo Research, Orange, CA). For 13/14 MDS and 8/11 control samples used for promoter methylation analysis, pre-rRNA expression was also studied by quantitative RT-PCR. Quantitative DNA methylation analysis was performed by pyrosequencing as described 25 . Methylation of specific CpGs by pyrosequencing was evaluated using the published human rDNA repeat sequence (accession number U13369). A 247 bp rDNA promoter region was amplified using rDNA specific primers; forward: 5'-GTGTTTTTGGGTTGATTAGAGG-3' and reverse: 5'-biotin CATCCCAAAACCCAACCTCTCC-3'. Three different primers (P1: 5'GGTTGATTAGAGGGATT-3'; P2 : 5'-TTTTGGGGATAGGTG-3' and P3 : 5'-TTYGGGGGAGGTATATTTT-3') were annealed to the purified singlestranded 247 bp PCR product and pyrosequencing was performed using PyroMark Q24 (Qiagen). Determining the ratio of cytosine to thymidine incorporation during pyrosequencing allows quantitation of the degree of methylation of target CpG sequences. Data were analyzed using the 6 From www.bloodjournal.org by guest on June 15, 2017. For personal use only. PyroMark Q24 software. Of the 29 CpGs present within the 247bp amplified PCR product, six were not included in the analysis because the observed to expected methylation ratios (as compared to in vitro methylated standard DNA) was not linear. Bisulfite Sequencing: The bisulfite treated DNA from CD34+ normal and MDS samples were amplified using specific rDNA primers, as outlined above. The 247 bp PCR products were purified from a 1.5% agarose gel using the Qiagen Gel Extraction kit (Qiagen) and subcloned using the TOPO TA-Cloning kit (Invitrogen). Five clones were sequenced from each samples and methylation at 26 CpGs per clone was analyzed using SeqMan Pro software (DNASTAR). Statistical Analysis: The Mann-Whitney test with two-sided alpha-level 0.05 was used to compare level of rRNA expression and average percent promoter methylation between control and MDS samples. To examine the relationship between rRNA expression and promoter methylation at each individual CpG, Pearson correlation estimates were calculated with confidence intervals approximated using Fisher’s Z transform. To examine the relationship between rRNA expression and average percent promoter methylation, the Pearson correlation estimate was calculated, and a linear model was fit, controlling for disease status. In multiple hypothesis testing, significance was determined by using the Bonferroni correction to control family-wise error-rate at 0.05. 7 From www.bloodjournal.org by guest on June 15, 2017. For personal use only. Results: Expression of pre-rRNA in MDS samples: The level of expression of 48S precursor rRNA in CD34+ HPCs was determined by measuring the abundance of the transcript processed at externally transcribed regions, as described in Materials and Methods. Results from a representative experiment (Figure 1A) showed that pre-rRNA expression was significantly reduced (p value < 0.01) in CD34+ HPC from 6 MDS patients compared to that in cells from 5 normal controls. Overall, prerRNA expression was studied in CD34+ HPC from 22 MDS samples and 11 controls. The cumulative data from repetitive quantitative RT-PCR determinations revealed that pre-rRNA expression was significantly decreased (p value < 0.001) in 22 MDS samples as compared to control samples (Figure 1B). These data demonstrate that rRNA synthesis is reduced in bone marrow progenitor cells from the majority of MDS patients studied. Methylation of the rDNA promoter in MDS CD34+ cells The rRNA gene promoter is highly enriched in CpG dinucleotides 26-28 . We postulated that reduced rRNA levels in MDS could result from promoter hypermethylation. PCR amplification of sodium bisulfite-treated DNA and subsequent pyrosequencing of the PCR products was used to quantitate methylation at 23/29 CpG sites within the rDNA promoter. Six of the 29 CpGs were not included in the analysis as the observed to expected methylation ratios observed by in vitro methylated standard DNA was not linear. A 247 bp DNA segment was amplified using rRNA promoter-specific primers that overlapped the upstream core element and the core promoter as illustrated in Figure 2. This amplicon served as a template for analyzing the degree of promoter methylation at 23 CpGs spanning rDNA promoter region 8 From www.bloodjournal.org by guest on June 15, 2017. For personal use only. (-195 to +52) using the primers P1 to P3. The heat map shown is a schematic representation of the percent DNA methylation at each of these 23 CpGs. The extent of methylation varies from 100% methylation (dark blue) to no methylation (white) in CD34+ HPCs from normal controls (upper panel) and 14 MDS samples (lower panel). Densely methylated CpGs were present across the 247 bp rDNA promoter in MDS samples. The percent methylation at each CpG was significantly greater than that in control samples at 22/23 CpGs (p value < 0.05), (Supplementary Figure 1A-D). Bisulfite sequencing was used to determine whether rDNA promoter methylation varied within individual PCR clones obtained from three normal and four MDS CD34+ samples. As shown in Figure 3, sequencing of clones from control samples showed that the majority of clones were either unmethylated or methylated at low frequency. In contrast, the frequency of methylated CpGs per clone in MDS samples was high in the majority of clones analyzed. None of the clones obtained from patient samples was methylated at every CpGs and two clones were unmethylation. These data further confirm the increased rDNA promoter methylation observed in patient samples obtained using pyrosequencing and also suggest that the number of transcriptionally active rDNA genes may be significantly fewer in MDS CD34+ cells. rDNA promoter methylation quantitated by pyrosequencing was then correlated with rRNA expression levels in 8 controls and 13 MDS samples (8/11 control and 13/22 MDS samples shown in Figure 1B). The average of the percent methylation across 23 CpGs in CD34+ HPC was significantly increased (p-value < 0.0001) in MDS samples as shown in Figure 4A and the pre-rRNA expression levels were significantly decreased (Figure 4B) in the same patient samples. When MDS and control samples are combined, the 9 From www.bloodjournal.org by guest on June 15, 2017. For personal use only. average percent methylation and expression is inversely correlated with a pvalue < 0.01. The Pearson correlation coefficient estimate is -0.6, with 95% confidence interval (-0.2, -0.8). The relationship between the three variables (average percent methylation, rRNA expression, and disease status) is shown in Figure 5A. The estimates of correlation, with 95% confidence intervals, between expression and methylation at each individual CpG (among the 13 MDS samples and 8 control samples) are shown in Figure 5B. All point estimates are negative, suggesting inverse correlation across the 23 CpG’s, although we cannot declare significance at individual CpG’s when correcting for multiple hypothesis testing. These data are concordant with studies that have shown an increase in overall methylation in MDS samples but are the first to address specific methylation changes in the rDNA promoter region. Effect of DAC treatment on pre-rRNA expression and promoter methylation To address the question of whether DAC treatment would decrease rDNA promoter methylation and concordantly increase rRNA synthesis, we treated leukemic cell lines with the drug. Cells treated with 0.1 μΜ DAC for five days resulted in a gradual increase in pre-rRNA expression over days 2 to 5 as compared to control cells treated with DMSO over the same interval. Increasing the DAC concentration from 0.1 to 0.5μM did not further increase rRNA expression (data not shown), suggesting that 0.1μM DAC is the optimal dose. We then treated three different myelomonocytic leukemia cell lines, THP1, Mono Mac 6 and ML2, with 0.1μM DAC for 3 days and observed an increase in pre-rRNA expression and a decrease in promoter methylation as measured by pyrosequencing at CpGs 7-23 in each cell lines 10 From www.bloodjournal.org by guest on June 15, 2017. For personal use only. (Figure 6A-F). Due to limited number of cells obtained from the bone marrow aspirates, we were unable to perform rRNA expression and promoter methylation analysis in CD34+ enriched populations from MDS patients. Discussion The requirement for ribosomal biogenesis reflects the overall demand for cellular protein synthesis. Formation of the mature 80S ribosome requires coordinated expression of four rRNAs and approximately 80 ribosomal proteins and perturbation at any stage of ribosomal biogenesis or assembly would be expected to impair cellular proliferation 29 . Our data demonstrate decreased rRNA levels that inversely correlate with rDNA promoter methylation in control and MDS CD34+ hematopoietic progenitors. The high throughput array-based published reports for gene expression (Affymetrix gene-chip arrays) 7,30,31 or promoter methylation (Nimblegen oligonucleotide arrays or Illumina bead arrays) 5,6 in MDS used arrays that lack probes for rRNA or rDNA, respectively. Therefore, this is the first report to specifically examine rRNA gene expression and rDNA promoter methylation in MDS. Our results suggest that the increase in methylation of this CpG-rich promoter is at least one of the mechanisms resulting in decreased rRNA gene expression, potentially altering the synthesis of ribosomal proteins 32 , thus hampering ribosomal biogenesis. Impairment of ribosome biogenesis characterizes several BMF syndromes 33 . Multiple mouse models have demonstrated that mutation of genes including those encoding Rps19, Rps14 and Rps6 result in defective hematopoiesis. Haploinsufficiency of Rps6 or of the Cd74-Nid67 region that contains 6 genes including Rps14 results in macrocytic anemia, erythroid 11 From www.bloodjournal.org by guest on June 15, 2017. For personal use only. hypoplasia, megakaryocytic dysplasia and reduced number of hematopoietic stem/progenitor cells, all of which are characteristic features of 5q- syndrome 20,24 . Similarly, conditional expression of mutant Rps19 or its haploinsufficiency in mice results in anemia, exhaustion of HSC and bone marrow failure 34,35 . Bone marrows from these mice have high levels of p53 protein expression and increased apoptosis, while breeding them with p53deficient animals rescues the phenotype. A number of studies have demonstrated that the release of specific ribosomal proteins, including RPL5 and RPL11, from the nucleolus increases p53 levels through an interaction with the MDM2 ubiquitin ligase, resulting in increased levels of p53 36,37 . Decreased expression of RPS19 or RPS14 causes selective activation of the p53 pathway in erythroid progenitors, further establishing the sensitivity of hematopoietic precursors to disruptions in ribosome biogenesis 38 . Thus, a common mechanism underlying bone marrow failure states appears to be the up-regulation of p53 through alterations in ribosome assembly. Increased p53 stability also occurs when rRNA synthesis is decreased, either through down-regulation of the catalytic subunit of RNA Polymerase I 39 or through knock-out of TIF-1A, a protein required for rRNA transcription 40 . The increase in p53 expression results in enhanced apoptosis as well as in disruption of nucleolar architecture. The chromatin status of rRNA genes maintains the appropriate ratio of expression among genes that are actively transcribed and those that are not, thereby regulating cellular proliferation 12. The nucleolar remodeling complex (NoRC), an ATP-dependent chromatin remodeling complex that regulates rRNA gene silencing, interacts both with DNA methyltransferase 1 (DNMT1) and with the histone deacetylase HDAC1 26,41 . Our data raise the possibility that alterations in rRNA 12 From www.bloodjournal.org by guest on June 15, 2017. For personal use only. expression may underlie the up-regulation of p53 and apoptosis of bone marrow progenitor cells in MDS patients. Further characterization of the epigenetic events regulating nucleolar rRNA gene expression, including both the extent of DNA methylation and the nature of histone modifications, may help to further our understanding of BMF syndromes. Reversal of DNA methylation by DNMT inhibitors has constituted a major rationale for treating MDS patients with these drugs. Although clinically significant responses occur in MDS patients treated with both 5AC and DAC 3,4,42,43 and although both drugs cause global DNA hypomethylation 31,44-46 , specific methylation changes have not been identified that predict the clinical response 2,7-9 . In addition, most patients ultimately develop resistance to 5AC or DAC 8,9. Our in vitro data with cell lines suggest that the response to hypomethylating agents could involve an increase in rRNA transcription, resulting in decreased apoptosis. This supposition is supported by recent data demonstrating that upregulation of rRNA expression increases ribosome biogenesis and ubiquitination of p53, thereby reducing p53 levels 39. It will be of interest to obtain clinical data on the response of rRNA expression in CD34+ cells of patients receiving hypomethylating agents in relation to the durability of their response to this intervention. 13 From www.bloodjournal.org by guest on June 15, 2017. For personal use only. Acknowledgements: This study was supported by a Leukemia and Lymphoma Society SCOR and translational grant award to B.S. Mitchell. Authorship Contributions: Planning experiment: A.R., P.L.G and B.S.M. Executing experiment: A.R., K.S. and S.P. Analyzing experiment: A.R., B.B.T and B.S.M. Writing Manuscript: A.R., B.B.T and B.S.M. Disclosure of Conflicts of Interest: The authors declare no competing financial interests. Corresponding Author: Beverly S. Mitchell M.D. George E Becker Professor of Medicine Stanford Cancer Institute, LLSC Research Building (SIM1), 265 Campus Drive, Room G2167, Stanford, CA 94305-5458. Phone: 650-736-7716 Fax: 650-736-0607 E-mail: [email protected] 14 From www.bloodjournal.org by guest on June 15, 2017. For personal use only. References: 1. Kroger N. Epigenetic modulation and other options to improve outcome of stem cell transplantation in MDS. 2. Hematology Am Soc Hematol Educ Program. 2008:60-67. Shen L, Kantarjian H, Guo Y, et al. DNA methylation predicts survival and Journal of clinical oncology : official journal of the American Society of Clinical Oncology. response to therapy in patients with myelodysplastic syndromes. 3. Feb 1 2010;28(4):605-613. Kantarjian H, Oki Y, Garcia-Manero G, et al. Results of a randomized study of 3 schedules of low-dose decitabine in higher-risk myelodysplastic syndrome 4. and chronic myelomonocytic leukemia. Musolino C, Sant'antonio myelodysplastic 5. 7. Blood. Penna G, Jan 1 2007;109(1):52-57. et al. Epigenetic therapy European journal of haematology. syndromes. in Jun 2010;84(6):463-473. Jiang Y, Dunbar A, Gondek LP, et al. 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Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of 17. rRNA genes. Genes & development. Oct 15 2010;24(20):2264-2269. Gagnon-Kugler T, Langlois F, Stefanovsky V, Lessard F, Moss T. Loss of human ribosomal gene CpG methylation enhances cryptic transcription and disrupts ribosomal RNA processing. 18. 20. 22. and nucleolar architecture Nucleic Acids Res. deficient cells. in DNA methyltransferase 1 (Dnmt1) 2007;35(7):2191-2198. Ebert BL, Pretz J, Bosco J, et al. Identification of RPS14 as a 5q- syndrome gene by RNA interference screen. Barlow JL, Drynan Nature medicine. Campagnoli LF, Hewett anemia Nature. DR, in a Jan 17 2008;451(7176):335-339. et al. mouse A p53-dependent model of human mechanism 5q- syndrome. Jan 2010;16(1):59-66. MF, Ramenghi U, Armiraglio M, et al. Hum Mutat. patients with Diamond-Blackfan anemia. RPS19 mutations in Jul 2008;29(7):911-920. Sridhar K, Ross DT, Tibshirani R, Butte AJ, Greenberg PL. 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Blood. like patients with Diamond- Dec 1 2011;118(23):6087-6096. Dai MS, Zeng SX, Jin Y, Sun XX, David L, Lu H. Ribosomal protein L23 activates p53 by inhibiting MDM2 function in response to ribosomal perturbation but not 37. to translation 2004;24(17):7654-7668. MDM2 checkpoint pathway. and mediates a p53-dependent Molecular and cellular biology. ribosomal-stress Dec 2003;23(23):8902- 8912. Dutt S, Narla A, Lin K, et al. Haploinsufficiency for ribosomal protein genes causes selective activation of p53 in human erythroid progenitor cells. 39. Sep Zhang Y, Wolf GW, Bhat K, et al. Ribosomal protein L11 negatively regulates oncoprotein 38. Molecular and cellular biology. inhibition. Blood. Mar 3 2011;117(9):2567-2576. Donati G, Bertoni S, Brighenti E, et al. The balance between rRNA and ribosomal protein synthesis up- and downregulates the tumour suppressor 40. p53 in mammalian cells. factor 41. TIF-IA leads mediated apoptosis. Santoro R, temporal 42. Oncogene. Jul 21 2011;30(29):3274-3288. Yuan X, Zhou Y, Casanova E, et al. Genetic inactivation of the transcription to Grummt order nucleolar Mol Cell. I. of Epigenetic H, Issa JP, cell mechanism NoRC-mediated remodeling, and DNA methylation. Kantarjian disruption, cycle arrest, and p53- Jul 1 2005;19(1):77-87. Rosenfeld histone Mol Cell Biol. CS, et al. of rRNA gene modification, silencing: chromatin Apr 2005;25(7):2539-2546. Decitabine improves patient outcomes in myelodysplastic syndromes: results of a phase III randomized 43. study. Lyons Cancer. RM, Apr 15 2006;106(8):1794-1803. Cosgriff TM, Modi SS, et al. Hematologic response to three alternative dosing schedules of azacitidine in patients with myelodysplastic Journal of clinical oncology : official journal of the American Society of Clinical Oncology. syndromes. Apr 10 2009;27(11):1850-1856. 17 From www.bloodjournal.org by guest on June 15, 2017. For personal use only. 44. Aoki E, Ohashi H, Uchida T, Murate T, Saito H, Kinoshita T. Expression levels of DNA methyltransferase genes do not correlate with p15INK4B gene Leukemia : official journal of the Leukemia Society of America, Leukemia Research Fund, U.K. methylation in myelodysplastic syndromes. Sep 45. 2003;17(9):1903-1904. Mund C, Hackanson B, Stresemann C, Lubbert M, Lyko F. Characterization of DNA demethylation effects induced with myelodysplastic syndrome. 46. by 5-Aza-2'-deoxycytidine Cancer research. in patients Aug 15 2005;65(16):7086- 7090. Yang AS, Doshi KD, Choi SW, et al. DNA methylation changes after 5-aza-2'deoxycytidine therapy in patients with leukemia. Cancer research. May 15 2006;66(10):5495-5503. 18 From www.bloodjournal.org by guest on June 15, 2017. For personal use only. Figure Legends Figure 1. Pre-rRNA expression in CD34+ cells from normal and MDS bone marrow. A. Levels of pre-rRNA expression were determined in CD34+ cells from 5 normal individuals and 6 patients with MDS in a single representative experiment. GAPDH was used as the internal control and samples were run in triplicates represented by circles in controls and squares in patients. B. Cumulative data showing levels of pre-rRNA in CD34+ cells from 10 normal control and 22 MDS samples. GAPDH was used as the internal control. The ends of the whiskers represent minimum and maximum values while the bar indicates the median value (50th percentile). Significance was determined using the Mann-Whitney test. Figure 2. Methylation of the rDNA promoter in MDS CD34+ cells using pyrosequencing. Heat map representation of the extent of rDNA gene promoter methylation at individual CpGs across the upstream core element and the core promoter region. A 247 bp DNA segment (blue line) was amplified and the extent of methylation at each of 23/29 CpG sites (-195 to +52 bp) was determined by pyrosequencing using primers P1 to P3. Each square represents a single CpG and each row represents a sample. The extent of methylation is represented over the range of 0% (white) to 100% (dark blue). The heat map was constructed using R software. 19 From www.bloodjournal.org by guest on June 15, 2017. For personal use only. Figure 3. rRNA promoter methylation by bisulfite sequencing DNA derived from CD34+ normal and MDS samples were treated with bisulfite, PCR amplified, cloned and sequenced. Each row represents an individual clone. The open squares represent unmethylated CpGs and closed squares represent methylated CpGs. Grey squares indicate that data were not obtained. One of the CpGs (CpG # 6 in Figure 2) reported in the published rDNA sequence (accession number U13369) was found to be missing when individual clones were sequenced. Figure 4: Hypermethylation of the rDNA promoter and decreased rRNA expression in MDS CD34+ cells. A. The average percent DNA methylation across the 23CpGs of the rDNA promoter is higher (p-value < 0.0001) and B. the pre-rRNA expression level is lower (p-value < 0.01) in 13 MDS samples compared to 8 controls. The ends of the whiskers represent minimum and maximum values while the bar indicates the median value (50th percentile). Significance was determined using the Mann-Whitney test. Figure 5. rRNA expression correlates with the extent of rDNA promoter methylation. A. As MDS samples have higher average percent DNA methylation and lower rRNA expression, among all data these variables are inversely correlated (p-value < 0.01). B. Pearson correlation estimates between prerRNA expression and rDNA promoter methylation at 23CpGs in 8 control 20 From www.bloodjournal.org by guest on June 15, 2017. For personal use only. samples and 13 MDS samples are shown. Vertical lines represent 95% confidence intervals. Figure 6. Effect of DAC on rRNA expression and rDNA promoter methylation in myeloid leukemia cell lines. A-C. THP1, Mono Mac 6 and ML2 cells were treated with DMSO or 0.1 μM DAC for 3 days. The level of expression of pre-rRNA is shown relative to that in DMSO-treated cells. GAPDH was used as an internal control and the samples were run in triplicates. D-F The cells were treated with DMSO or 0.1 μM DAC for 3 days and the extent of CpG methylation was determined by pyrosequencing at CpGs 7-23 spanning the rDNA upstream core element and the core promoter. 21 A Pre-rRNA/GAPDH mRNA 1 2 3 4 CD34+ Normal Ct B Pre-rRNA/GAPDH mRNA Figure 1 5 M1 M2 M3 M4 M5 M6 CD34+ MDS Samples Upstream Control Element Core Promoter A2 A3 CD34+ Normal Controls A1 +1 CD34+ MDS Samples Figure 2 100% 0% CH3 CD34+ Normal Controls Figure 3 1 2 3 CD34+ MDS Samples 1 2 3 Unmethylated CpG Methylated CpG 4 NA A Pre-rRNA/GAPDH mRNA Figure 4 B Figure 5 A B Expression vs. Average Methylation By Disease Status Correlation Between rDNA Promoter Methylation And rRNA Expression: Estimates with 95% CI Figure 6 D % Methylation A 120 THP1 Control 100 THP1 DAC 80 60 40 20 0 CpGs 7-23 E 120 % Methylation B F MM6 Control MM6 DAC 80 60 40 20 0 120 % Methylation C 100 100 80 60 40 20 0 ML2 Control ML2 DAC From www.bloodjournal.org by guest on June 15, 2017. For personal use only. Prepublished online October 15, 2012; doi:10.1182/blood-2012-04-423111 Reduced ribosomal RNA expression and increased ribosomal DNA promoter methylation in CD34+ cells of patients with myelodysplastic syndromes Aparna Raval, Kunju J. Sridhar, Shripa Patel, Brit B. Turnbull, Peter L. Greenberg and Beverly S. Mitchell Information about reproducing this article in parts or in its entirety may be found online at: http://www.bloodjournal.org/site/misc/rights.xhtml#repub_requests Information about ordering reprints may be found online at: http://www.bloodjournal.org/site/misc/rights.xhtml#reprints Information about subscriptions and ASH membership may be found online at: http://www.bloodjournal.org/site/subscriptions/index.xhtml Advance online articles have been peer reviewed and accepted for publication but have not yet appeared in the paper journal (edited, typeset versions may be posted when available prior to final publication). Advance online articles are citable and establish publication priority; they are indexed by PubMed from initial publication. Citations to Advance online articles must include digital object identifier (DOIs) and date of initial publication. Blood (print ISSN 0006-4971, online ISSN 1528-0020), is published weekly by the American Society of Hematology, 2021 L St, NW, Suite 900, Washington DC 20036. Copyright 2011 by The American Society of Hematology; all rights reserved.
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