Aberrant Gene Promoter Methylation of Tumor Suppressor Genes in Plasma Cell Disorders.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 2487-2487
Author(s):  
Carmen Stanganelli ◽  
Jorge Arbelbide ◽  
Juliana Zimerman ◽  
Dorotea Beatriz Fantl ◽  
Claudia Corrado ◽  
...  

Abstract There is increasing evidence that, in addition to genetic aberrations, epigenetic processes play a major role in carcinogenesis. Particularly, hypermethylation of CpG islands of the promoter regions of tumor suppressor genes (TSG) is now considered as an important epigenetic mechanism for gene inactivation. Multiple myeloma (MM) is characterized by neoplastic proliferation of monoclonal plasma cells. The natural course of disease may progress through monoclonal gammopathy of undetermined significance (MGUS) to MM. During this process, multiple genetic alterations are sequentially acquired and aberrant promoter hypermethylation might be one of the steps involved in this progression. In this study, we have evaluated methylation status of the following TSG: p15INK4b, p16INK4a, p14ARF, SOCS-1, p27KIP1, RASSF1A and p73 genes, in order to determine if they were involved in the evolution of MGUS to MM. Forty four MM (21 males; mean age 67.5 years; Durie-Salmon clinical stages: I: 20%, II:14% and III: 66%) and 21 MGUS patients (6 males; mean age 68 years) were study. All patients gave informed consent and the study was approved by the Ethics Committee of our Institution. Peripheral blood samples from 10 normal individuals and CpGenome Universal Methylated DNA (Chemicon International) were used as negative and positive controls, respectively. DNA was extracted from bone marrow cells of patients and peripheral blood lymphocytes of controls using phenol/chloroform method. Methylation status was performed using Methylation Specific PCR (MSP) technique. For statistical analysis, Student t and Fisher exact tests were used. The methylation index (MI; ratio between the number of genes methylated and the number of genes analyzed) was also calculated. SOCS-1 gene methylation was significantly more frequent in MM (52%) than in MGUS patients (14%) (p=0,006). Frequencies of methylation of p14ARF, p15INK4b, p16INK4a and RASSF1A were comparable in both entities: 29%, 32%, 7% and 2%, respectively, for MM; and 29%, 29%, 5% and 0%, respectively, for MGUS. TP73 gene showed a tendency of higher methylation in MM (45%) than in MGUS (33%). All patients lacked methylation at p27KIP1 gene. Whereas the percentage of MM with at least one gene methylated (84%) did not showed differences to that of MGUS (66%), the mean MI of MGUS was lower (0.16; range 0.14-0.43) than that of MM (0.24; range 0.14-0.71) (p<0.05). None of the target genes were methylated in normal samples. No statistical significant correlation with clinical characteristics: gender, age, isotype, level of M-component, type of light chain, stage of the disease, haemoglobin, serum albumin level, calcium, β2 microglobulin and LDH, were observed. To our knowledge, this is the first report of methylation in MM and MGUS from Argentina. The similar frequency of p14ARF, p15INK4b, p16INK4a and RASSF1A gene methylation observed in MM and MGUS would suggest that they are probably not involved in the progression of MGUS. However, SOCS1 gene methylation was significantly more frequent in MM than in MGUS suggesting that methylation of this gene might be involved in clonal evolution of MGUS to MM. SOCS1 is a negative regulator of cytokine signaling, being important in normal lymphocyte development and differentiation. Silencing of SOCS1 may result in greater responsiveness to cytokines, which may favour the neoplastic development.

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 4156-4156
Author(s):  
Christian Chena ◽  
Carmen Stanganelli ◽  
Guillermo Arrossagaray ◽  
Julio Cesar Sanchez Avalos ◽  
Irma Slavutsky

Abstract Aberrant methylation of CpG islands of the promoter regions of tumor suppressor genes (TSG) is now considered an important epigenetic mechanism for gene inactivation. Chronic lymphocytic leukemia (CLL) is the most frequent type of adult leukemia in the Western world, accounting for about 30% of all leukemic cases. It is characterized by a highly variable clinical course with survival times ranging from months to decades. Some patients have a more stable, indolent disease whereas others exhibit a progressive disease requiring early therapy. During this prolonged period of clinical history, different genetic alterations may be sequentially acquired, including aberrant promoter hypermethylation. In this study, we have evaluated methylation status of p15INK4b, p16INK4a, p14ARF, SOCS-1, p27KIP1, RASSF1A and TP73 (TAp73 isoform) genes in patients with CLL. Results were correlated with clinicopathologic characteristics of these patients. Thirty-three CLL patients (16 males; median age 65 years; Rai stage: 0: 9, I–II: 14 and III–IV: 10) were evaluated. All patients gave informed consent and the study was approved by the Ethics Committee of our Institution. Peripheral blood samples from 10 normal individuals and CpGenome Universal Methylated DNA (Chemicon International) were used as negative and positive controls, respectively. DNA was extracted from peripheral blood cells from patients and controls using phenol/chloroform method. Methylation status was performed using Methylation Specific PCR technique and DNA sequencing. For statistical analysis, Student’s t and Fisher’s exact tests were used. The methylation index (MI; ratio between the number of genes methylated and the number of genes analyzed) was also calculated. Cytogenetic and FISH (fluorescence in situ hybridization) analysis using specific DNA probes for CLL (LSI p53/ATM/13q14/13q34/CEP12, Vysis-Abbott) were also performed. The gene most frequently methylated was TP73 (70% of cases). Frequencies of p15INK4band p16INK4a gene methylation were 9% and 3%, respectively. A coexistence of p15INK4b and TP73 gene methylation was observed. No patient showed methylation in p14ARF, SOCS-1, p27KIP1 and RASSF1A genes. The methylation index ranged from 0 to 0.29 with a median of 0.14, corresponding to one gene/sample. No significant differences in the frequencies of cytogenetic (31,3% and 50%) and FISH genomic alterations (62% and 87,5%) between patients with and without aberrant methylation, respectively, were found. Similarly, the correlation with clinical characteristics: sex, age, Rai stage, lymphocytosis, β2 microglobulin, LDH, and treatment free survival in both groups of patients did not reach statistical significance. Our findings suggest that aberrant methylation of TP73 gene is a frequent event in this pathology. TAp73 isoform is involved in cell cycle arrest and apoptosis. Thus, its silencing could be important for CLL cells survival. Simultaneously, our data would confirm that, in Caucasian population, the methylation of p15INK4band p16INK4a gene promoters can be detected in a small subset of CLL patients.


Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 2780-2780
Author(s):  
Ana Valencia ◽  
Jose Cervera ◽  
Esperanza Such ◽  
Esther Gamero ◽  
Mariam Ibañez ◽  
...  

Abstract Abstract 2780 Poster Board II-756 Patients with refractory anemia with ring sideroblasts (RARS) are considered to have good prognosis and anemia is usually managed with best supportive care and erythroid stimulating agents. Nowadays, no specific molecular marker related to outcome and disease progression has been identified. Several genes involved in cell cycle and apoptosis that may become inactivated by aberrant hypermethylation have been identified in patients with myelodysplastic syndromes (MDS) but the significance of a methylation profile (studying several genes at the same time) in RARS is unknown, mainly because the number of patients with RARS in published reports is rather low. To assess the implication of aberrant methylation in RARS, we studied the methylation status of 25 sequences of a set of tumor suppressor genes in 40 patients (median age 70 yr, 25 male gender) with RARS according to FAB criteria [WHO classification, RARS in 22 patients (55%); refractory citopenia with multilineage dysplasia and ring sideroblasts, 18 (45%)] by means of methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) assay. The MS-MLPA procedure (SALSA MLPA kit ME001, MRC-Holland, Amsterdam, The Netherlands) has been developed for detecting in a semi-quantitative manner changes in the methylation status of 25 tumor suppressor genes in a single experiment. Briefly, approximately 50 ng of DNA were denatured and hybridized with MLPA probes. Subsequently, the probes were ligated in half of every sample, whereas for the rest of the sample, ligation was combined with an endonuclease HhaI digestion resulting in ligation of the methylated sequences only. PCR was performed as described by the manufacturer, and then separated by capillary gel electrophoresis and quantified using the Genemapper software (ABI 310, Applied Biosystems, Foster City, CA). Quantification of the methylation status was done by dividing the peak area with the combined areas of the control probes lacking the target sequence of the HhaI. Finally, the relative peak area of each target probe from the digested sample was compared with those obtained from the undigested sample. Aberrant methylation was scored when the calculated methylation percentage was >10%. To validate the MS-MLPA method the methylation status of CDKN2B was also analyzed by methylation-specific PCR (MSP). Actuarial curves of OS were built by Kaplan-Meier method and differences between curves compared with log-rank tests. Small numbers precluded the use of multivariate methodology. The MS-MLPA analysis detected methylation of at least one gene in 17 patients (42.5%). The genes aberrantly methylated were CDKN2B (n = 8, 20%), RASSF1 (n = 7, 17%), RARB (n = 3, 7.5%), CDH13 (n = 3, 7.5%) and FHIT (n = 2; 5%). Of the 17 patients, five (12%) presented methylation in two genes (RASSF1-FHIT in 2, RASSF1-RARB in 1, RASSF1-CDH13 in 1, and CDKN2B-CDH13 in 1, who was the only patient who progressed to AML). The presence of aberrant gene methylation was not significantly associated with any clinical or biological characteristic or WHO morphological subtype. Patients with aberrant gene methylation had a significantly shorter overall survival (OS) than patients without methylated genes (median OS, 72 mo vs 114 mo, respectively; P = 0.03). Patients with hemoglobin level below 10 g/dL and platelet count below 150 ×109/L also had a significantly poorer OS (P= 0.01 and P= 0.02, respectively). As the majority of probes used in the MS-MPLA method detect methylation in only one CpG pair, the results of CDKN2B methylation were validated by MSP, which yielded the same methylation results than with MS-MPLA methodology. The 8 patients with methylated CDKN2B show a trend for a shorter survival than the remaining 32 with unmethylated CDKN2B (median 72 mo vs 114 mo, P = 0.08). The results of this study indicate that aberrant methylation of several tumor suppressor genes is observed in a substantial proportion of patients with RARS. As occurs in patients with high-risk MDS, our results suggest that aberrant gene methylation confers a poor prognosis in RARS, but these data and their potential independent value require confirmation in larger series that employ multivariate methods. Finally, these findings provide a strong rationale for the use of hypomethylating agents (e.g., azacitidine or decitabine) in patients with RARS. This work has been partially supported by ISCIII grants RD06/0020/0031 and CA08/00141. Disclosures: No relevant conflicts of interest to declare.


Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 4487-4487
Author(s):  
Jose M Paz-Carreira ◽  
Raquel Losada ◽  
Arantxa Garcia-Rivero ◽  
Augusto Alvarez ◽  
Fernando Bal ◽  
...  

Abstract INTRODUCTION. Germinal centers (GC) are unique sites in peripheral lymphoid tissue where clonal selection of B cells takes place. This occurs as a response to stimulation by various antigens originating, sometimes, follicular hyperplasia (FH). GC have been known as a major source of B-cell lymphomas including follicular (FL) and diffuse large cell (DLCL). DNA methylation of tumor-suppressor genes is a mechanism of gene silencing involved in the pathogenesis of FL and DLCL. Much less is known about the role of methylation in FH. We determined the methylation status of 6 tumor-suppressor genes in 43 patients with FH, 18 patients with FL and 49 patients with DLCL in order to see the differential implication of this epigenetic mechanism in the pathological and the physiological development of GC. MATERIAL AND METHODS. Genomic DNA extracted from paraffin-embedded samples of 43 FH, 18 FL and 49 DLCL after being treated with EZ DNA-Methylation Kit (Zymo Research) with the manufacturer’s instructions, were analyzed by methylation-specific polymerase chain-reaction to determine promoter hypermethylation of DAP-k, SHP1, Rarβ, p14, SHP1, MGMT and PDRM1. All samples were obtained mostly from lymph nodes and tonsils. Diagnosis was based on morphology and immunohistochemistry analysis. All cases were matched for age, sex and ethnic origin. RESULTS: DAP-k promoter methylation occurred with higher frequency in FL(89%) than in DLCL(78%) and FH(40%). SHP1 was methylated in 61% of FL, 58% of FH and 23% of DLCL. RARb was methylated in 67% of FL patients, 30% of DLCL and only 12% of FH. Eight (44%) FL, seventeen (35%) DLCL and four (10%) BFH patients showed MGMT methylation. Promoter hypermethylation of p14 was detected only in 5 (12%) FH, 2 (4%) DLCL and none FL patients. Methylation of PRMD1 was present only in 1 (6%) FL, 2 (6%) DLCL and 1 (4%) FH samples. CONCLUSIONS. Inactivacion of DAP-K and SHP1 is present in B-cell malignancies, DLCL and FL, and BFH. Therefore, it may represent a physiologic event conferring a temporal survival advantage necessary for a GC hyperplastic response. Inactivation of the retinoic acid response through the methylation of Rarâ is significantly more frequent in lymphomas than in FH. As reported in other tumors methylation of MGMT is more frequent in lymphomas than in FH. With our data methylation of Cyclin dependent kinase inhibitors p14 is not a differential pathogenic event in lymphomas of GC origin, in fact it is more frequent in FH. Promoter Methylation of PDRM1 is not the mechanism involved in lymphomagenesis in FL and DLCL, the two FH positive deserve further follow-up to determine its significance.


2017 ◽  
Vol 35 (1) ◽  
pp. 122-131 ◽  
Author(s):  
Agnieszka Bukowska-Damska ◽  
Edyta Reszka ◽  
Pawel Kaluzny ◽  
Edyta Wieczorek ◽  
Monika Przybek ◽  
...  

2010 ◽  
Vol 55 (12) ◽  
pp. 3449-3457 ◽  
Author(s):  
Tomomitsu Tahara ◽  
Tomoyuki Shibata ◽  
Masakatsu Nakamura ◽  
Hiromi Yamashita ◽  
Daisuke Yoshioka ◽  
...  

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. e16197-e16197
Author(s):  
Oleg I. Kit ◽  
Vladimir S. Trifanov ◽  
Natalya N. Timoshkina ◽  
Dmitry Yu. Gvaldin ◽  
Milana Yu. Mesheryakova ◽  
...  

e16197 Background: Aberrant DNA methylation is a characteristic feature of cancer, affecting gene expression and tumor phenotype. In this study, we quantified the methylation of promoters of eight tumor suppressor genes in pancreatic neuroendocrine tumors (Pan-NET). Methods: The method of pyrosequencing was used to quantity level (Met,%) of methylation of gene promoters - tumor suppressors AHRR, APC1A, DAPK, MGMT, MLH1, P16, RASSF1A, RUNX3 in tumor samples from 55 patients with pancreatic NET (G1-G3) and in the blood of 10 healthy donors. Met for each sample was calculated as the median methylation of CpG sites in triplicate. Results: Hypermethylation was observed for AHRR (75%), APC1A (25%), RASSF1A (30%). In contrast, DAPK, MGMT, MLH1, P16, RUNX3 had low methylation levels ( < 20%). The median of methylation in the blood of healthy donors for AHRR was 91% (76-98); for all other loci it did not exceed 6%. A high incidence of methylation in excess of blood levels in healthy donors was identified for RASSF1A (0.96); AHRR (0.75); MGMT (0.65); RUNX3 (0.41), APC1A (0.25). For tumor suppressor P16, only one case of increased methylation was recorded (Met = 15%), despite the fact that this phenomenon is not uncommon for NETs of other localizations. In 66% of pancreatic NET cases, hypermethylation of more than two promoters of tumor suppressor genes was noted. An association tendency was found between the presence of MEN1 mutations and the RASSF1A methylation level (p = 0.08). Correlation analysis revealed a significant level of negative association between changes in methylation of MLH1 and AHRR (p < 0.01); for the latter, the prognostic value of a high methylation status and a better prognosis for many malignant neoplasms were described. Conclusions: In the present study, significant methylation of the promoters of the APC1A, DAPK, MGMT, RASSF1A, and RUNX3 genes in well-differentiated pancreatic NETs was identified with a high frequency. At the same time, isolated cases of hypermethylation were noted for the well-known tumor suppressors MLH1 and P16.


2022 ◽  
Vol 12 ◽  
Author(s):  
Ritu Raina ◽  
Abdulmajeed G. Almutary ◽  
Sali Abubaker Bagabir ◽  
Nazia Afroze ◽  
Sharmila Fagoonee ◽  
...  

Purpose: Plant-derived phytochemicals have shown epigenetic modulatory effect in different types of cancer by reversing the pattern of DNA methylation and chromatin modulation, thereby restoring the function of silenced tumor-suppressor genes. In the present study, attempts have been made to explore chrysin-mediated epigenetic alterations in HeLa cells.Methods: Colony formation and migration assays followed by methylation-specific PCR for examining the methylation status of CpG promoters of various tumor-suppressor genes (TSGs) and the expression of these TSGs at the transcript and protein levels were performed. Furthermore, global DNA methylation; biochemical activities of DNA methyltransferases (DNMTs), histone methyl transferases (HMTs), histone deacetylases (HDACs), and histone acetyl transferases (HATs) along with the expression analysis of chromatin-modifying enzymes; and H3 and H4 histone modification marks analyses were performed after chrysin treatment.Results: The experimental analyses revealed that chrysin treatment encourages cytostatic behavior as well as inhibits the migration capacity of HeLa cells in a time- and dose-dependent manner. Chrysin reduces the methylation of various tumor-suppressor genes, leading to their reactivation at mRNA and protein levels. The expression levels of various chromatin-modifying enzymes viz DNMTs, HMTs, HDACs, and HATS were found to be decreased, and H3 and H4 histone modification marks were modulated too. Also, reduced global DNA methylation was observed following the treatment of chrysin.Conclusion: This study concludes that chrysin can be used as a potential epigenetic modifier for cancer treatment and warrants for further experimental validation.


Cancers ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 850 ◽  
Author(s):  
Mohammed I. Y. Elmallah ◽  
Olivier Micheau

One of the main characteristics of carcinogenesis relies on genetic alterations in DNA and epigenetic changes in histone and non-histone proteins. At the chromatin level, gene expression is tightly controlled by DNA methyl transferases, histone acetyltransferases (HATs), histone deacetylases (HDACs), and acetyl-binding proteins. In particular, the expression level and function of several tumor suppressor genes, or oncogenes such as c-Myc, p53 or TRAIL, have been found to be regulated by acetylation. For example, HATs are a group of enzymes, which are responsible for the acetylation of histone proteins, resulting in chromatin relaxation and transcriptional activation, whereas HDACs by deacetylating histones lead to chromatin compaction and the subsequent transcriptional repression of tumor suppressor genes. Direct acetylation of suppressor genes or oncogenes can affect their stability or function. Histone deacetylase inhibitors (HDACi) have thus been developed as a promising therapeutic target in oncology. While these inhibitors display anticancer properties in preclinical models, and despite the fact that some of them have been approved by the FDA, HDACi still have limited therapeutic efficacy in clinical terms. Nonetheless, combined with a wide range of structurally and functionally diverse chemical compounds or immune therapies, HDACi have been reported to work in synergy to induce tumor regression. In this review, the role of HDACs in cancer etiology and recent advances in the development of HDACi will be presented and put into perspective as potential drugs synergizing with TRAIL’s pro-apoptotic potential.


Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 2473-2473
Author(s):  
Brian A. Walker ◽  
Matthew W. Jenner ◽  
Poala E. Leone ◽  
Nicholas J. Dickens ◽  
David C. Johnson ◽  
...  

Abstract We have shown that loss of heterozygosity (LOH) at 16q is an adverse prognostic marker when it occurs in combination with either t(4;14) translocation or del(17p). Using 500K Affymetrix mapping arrays we found that 16q was involved in translocations with the IgH locus, deleted, or had uniparental disomy (UPD). The deletion patterns led us to 2 regions at 16q12.1 and 16q21-q24.1, which contains 5 genes and is the location of the t(14;16) translocation. By integrating mapping and expression profiling data from presenting myeloma cases we were able to identify WWOX and CYLD as key genes deregulated in these regions. Both WWOX and CYLD are known tumor suppressor genes. WWOX is known to have a pro-apoptotic effect by participating in the TNF apoptotic pathway and via the direct physical interaction with p53 and p73. CYLD functions as a negative regulator of the NF-κB pathway as well as blocking the activation of cyclin D. WWOX is found to be methylated in other cancer tissues, whereas CYLD is frequently mutated. To determine mode of action of these genes in samples with LOH we performed mutation and methylation analysis on myeloma cell lines and pre-treatment patient samples. Variant transcripts of WWOX, which may act as dominant negatives to block the function of WWOX have been reported so we also determined the nature of these in the samples. Exons from WWOX and CYLD were PCR amplified from samples with LOH, as well as from samples with retention of heterozygosity, and sequenced directly. All differences to the consensus were checked against databases for known SNPs and mutations. Mutations in the tumor sample were confirmed by a repeat PCR, and mutations were also checked against peripheral blood DNA from the same patient to determine if these were acquired in the tumor. LOH of 16q was found in 2 out of 9 myeloma cell lines and additionally homozygous deletion of WWOX exons 5-8 in KMS11 cells was observed. cDNA analysis from these cell lines showed that KMS11 cells expressed variant 3, as could be expected, whereas the dominant transcript in other cell lines is variant 1. However, 2 cell lines also expressed an additional transcript (variant 4), which has previously been shown to act as a dominant-negative transcript. All pretreatment samples expressed the variant 1 transcript. 16 pretreatment samples with LOH were screened for mutations revealing 2 mutations in exon 9, one of which was non-synonymous. Methylation analysis of the WWOX locus is underway. Analysis of CYLD showed frequent mutation in cell lines with many synonymous and non-synonymous mutations, including several frame-shifts resulting in truncated products. Screening of 14 pretreatment samples with LOH at the CYLD locus revealed 2 mutations including a C&gt;TT mutation in exon 11, which results in a frameshift and premature termination of translation. Alternative transcripts of CYLD are formed through splicing of exons 3 and 7. Both exon 3 variants were present but only the variant lacking exon 7 was present in myeloma cell lines. These data suggest that dysregulation of both WWOX and CYLD may be important in the pathogenesis of myeloma and contribute to the effect of del(16q) on patient survival.


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