ADAMTSL5 and CDH11: putative epigenetic markers for therapeutic resistance in acute lymphoblastic leukemia

Background and objectives: DNA hypermethylation has been linked to poor treatment outcome in childhood acute lymphoblastic leukemia (ALL). Genes differentially methylated in the chemoresponsive pre-B-ALL compared to chemoresistant pre-B-ALL cases provide potential prognostic markers.

Methods: DNA methylation profiles of five B-ALL childhood patients who achieved morphological complete remission (chemoresponsive) and five B-ALL patients who did not (chemoresistant) after induction treatments as well as four normal controls were compared on 27?000 CpG sites microarray chips. Subsequently, methylation-specific polymerase chain reaction (MSP) on selected hypermethylated genes was conducted on an additional 37 chemoresponsive and 9 chemoresistant B-ALL samples and 2 normal controls.

Results: Both methods were found to be highly correlated. Unsupervised principal component analysis showed that the chemotherapy-responsive and -resistant B-ALL patients could be segregated from one another. Selection of segregated genes at high stringency identified two potential genes (CDH11 and ADAMTSL5). MSP analysis on the larger cohort of samples (42 chemoresponsive, 14 chemoresistant B-ALL samples and 6 normal controls) revealed significantly higher rates of hypermethylation in chemoresistant samples for ADAMTSL5 (93 vs. 38%; p?=?0.0001) and CDH11 (79% vs. 40%, p?Conclusion: Chemoresistant B-ALL patients are associated with increased methylation in ADAMTSL5 and CDH11. These findings need to be validated in a larger group of patients, and the functional biological and prognostic significance of differential methylation needs to be studied further.     

Promoter hypermethylation of the CFTR gene and clinical/pathological features associated with non-small cell lung cancer

Background and objective: The exact role of the cystic fibrosis transmembrane conductance regulator (CFTR) in pathophysiology, and the mechanisms regulating its expression are poorly understood. The CFTR gene is known to be genetically or epigenetically associated with several cancers. In the present study, the methylation status of the promoter region of the CFTR gene and its expression in primary non‐small cell lung cancer (NSCLC) were investigated. Methods: The methylation status of the promoter region of the CFTR gene in NSCLC tissue was assessed by pyrosequencing and methylation‐specific PCR. Expression of the CFTR gene was analysed by real‐time PCR, and CFTR gene reactivation was investigated using 5‐aza‐2′‐deoxycytidine. The correlation between methylation of the CFTR gene and the clinical features of the patients was assessed. Results: Methylation of the CFTR gene in NSCLC was quantitatively high by pyrosequencing analysis and qualitatively frequent by methylation‐specific PCR analysis. Expression of the CFTR gene was significantly lower in NSCLC compared with normal lung tissue. In addition, the demethylating agent 5‐aza‐2′‐deoxycytidine increased CFTR gene expression. Methylation of the CFTR gene was significantly greater in squamous cell carcinomas than in adenocarcinomas. CFTR gene methylation was associated with significantly poorer survival in young patients, but not in elderly patients. Conclusions: These findings suggest that DNA methylation may be important for downregulation of CFTR gene expression in lung cancer. Promoter hypermethylation of the CFTR gene may be an important prognostic factor in younger patients with NSCLC.     

RUNX3 promoter hypermethylation is frequent in leukaemia cell lines and associated with acute myeloid leukaemia inv(16) subtype

Correlative and functional studies support the involvement of the RUNX gene family in haematological malignancies. To elucidate the role of epigenetics in RUNX inactivation, we evaluated promoter DNA methylation of RUNX1, 2, and 3 in 23 leukaemia cell lines and samples from acute myeloid leukaemia (AML), acute lymphocytic leukaemia (ALL) and myelodysplatic syndromes (MDS) patients. RUNX1 and RUNX2 gene promoters were mostly unmethylated in cell lines and clinical samples. Hypermethylation of RUNX3 was frequent among cell lines (74%) and highly variable among patient samples, with clear association to cytogenetic status. High frequency of RUNX3 hypermethylation (85% of the 20 studied cases) was found in AML patients with inv(16)(p13.1q22) compared to other AML subtypes (31% of the other 49 cases). RUNX3 hypermethylation was also frequent in ALL (100% of the six cases) but low in MDS (21%). In support of a functional role, hypermethylation of RUNX3 was correlated with low levels of protein, and treatment of cell lines with the DNA demethylating agent, decitabine, resulted in mRNA re‐expression. Furthermore, relapse‐free survival of non‐inv(16)(p13.1q22) AML patients without RUNX3 methylation was significantly better (P = 0·016) than that of methylated cases. These results suggest that RUNX3 silencing is an important event in inv(16)(p13.1q22) leukaemias.     

Epigenetic landscape of the TERT promoter: a potential biomarker for high risk AML/MDS

Although recent observations implicate the importance of telomerase activity in acute myeloid leukaemia (AML), the roles of epigenetic regulations of the TERT gene in leukaemogenesis, drug resistance and clinical prognosis in AML are not fully understood. We developed a quantitative pyrosequencing‐based methylation assay covering the TERT proximal promoter and a partial exon 1 (TERTpro/Ex1) region and tested both cell lines and primary leukaemia cells derived from AML and AML with preceding myelodysplastic syndrome (AML/MDS) patients (n = 43). Prognostic impact of methylation status of the upstream TERT promoter region was assessed by the Kaplan–Meier method. The activity of the telomerase inhibitor, imetelstat, was measured using leukaemia cell lines. The TERTpro/Ex1 region was highly methylated in all cell lines and primary leukaemia cells showed diverse methylation profiles. Most cases showed hypermethylated regions at the upstream TERTpro/Ex1 region, which were associated with inferior patient survival. TERTpro/Ex1 methylation status was correlated with the cytotoxicity to imetelstat and its combination with hypomethylating agent enhanced the cytotoxicity of imetelstat. AML cell lines and primary blasts harbour distinct TERTpro/Ex1 methylation profiles that could serve as a prognostic biomarker of AML. However, validation in a large cohort of patients is necessary to confirm our findings.     

Promoter methylation and loss of coding exons of the fragile histidine triad (FHIT) gene in intrahepatic cholangiocarcinomas.

AIMS: About 10-30% of primary liver cancers represent intrahepatic cholangiocarcinomas (IHCC). Since chromosomal losses of 3p are detectable in about 40% of cholangiocarcinomas our study aimed at the identification of mechanisms leading to functional deletion of tumor suppressor genes in this region. Our efforts focussed on genomic losses and epigenetic inactivation of two tumor suppressor genes, the fragile histidine triad (FHIT) and the ras association domain family 1 (RASSF1A) genes, both located on the short arm of chromosome 3. METHODS: Methylation-specific PCR (MSP) and combined bisulfite-dependent restriction analysis (COBRA) were applied to detect epigenetic silencing of gene promoters. Genomic duplex PCR was used to identify exon losses of the FHIT gene. Nineteen paraffin-embedded samples of intrahepatic cholangiocarcinomas were studied. RESULTS: Here we report for the first time that in addition to frequent losses of the exons 5 and 6, hypermethylation of the FHIT promoter occured in a significant portion of IHCC. Methylation specific PCR (MSP) detected epigenetic inactivation of the FHIT/FRA3B locus in 8 of 19 (42%) cases. Combined bisulfite restriction analysis (COBRA) revealed that high levels of methylated FHIT promoter sequences were present in 6 of the 8 methylation positive samples. In agreement with previous reports MSP identified hypermethylation of the RASSF1A gene in 13 of 19 (68%) IHCC specimens examined. CONCLUSIONS: Epigenetic silencing of the FHIT tumor suppressor gene is a novel inactivation mechanism to be considered in the development of intrahepatic cholangiocarcinomas. However, a statistically significant inverse correlation between K-Ras activation and RASSF1A inactivation was not found.     

Folate levels in mucosal tissue but not methylenetetrahydrofolate reductase polymorphisms are associated with gastric carcinogenesis

INTRODUCTION Methylation of gene regulatory elements is a well-documented epigenetic change that can lead to gene inactivation. Human gastric carcinogenesis is suggested to be associated with the decrease of total genomic DNA methylation, hypomethylation …     

Epigenetic silencing of LRRC3B in colorectal cancer

Objective. Tumor suppressor gene silencing via promoter hypermethylation is an important event in the pathogenesis of colorectal cancer (CRC). Some aberrant DNA hypermethylation has high tumor specificity, so it may contribute to early diagnosis of CRC. The objective of this study was to establish novel therapeutic and diagnostic strategies against CRC by identifying the novel methylation-related genes. Material andmethods. Two microarray-based approaches were used to identify novel methylation-related genes in CRC. We identified methylation-sensitive genes in colon cancer cell line SW1116 by comparing differential expression genes after treatment with the methylation inhibiting drug, 5-aza-2'-deoxycitidine (5-aza-dC) using gene expression microarray. Promoter microarray analysis was performed to identify cancer-specific, methylation-related genes in two patients with CRC. Gene promoter methylation was identified by methylation-specific polymerase chain reaction (PCR) (MSP) in primary CRC. Gene expression level was assessed using real-time PCR analysis. Results. By using gene expression microarray, up-regulation of 253 genes was detected in the CRC cell line, SW1116, after treatment with 5-aza-dC. Of the 253 genes identified by gene expression microarray analysis, LRRC3B (leucine-rich repeat containing 3B) was isolated as a potential methylation-specific gene by promoter microarray analysis. MSP analysis showed frequent methylation of LRRC3B in primary CRC (24/31 cases, 77%). In addition, the LRRC3B methylation intensity was significantly higher in cancer tissues than in the corresponding non-cancerous tissues. Decreased LRRC3B expression (17/31, 55%) was observed in the cancer tissues by real-time PCR. Conclusions.LRRC3B may be a novel methylation-sensitive tumor suppressor gene in CRC. LRRC3B methylation has significant tumor specificity and may be a biomarker of CRC.     

Promoter hypermethylation of p15INK4B, HIC1, CDH1, and ER is frequent in myelodysplastic syndrome and predicts poor prognosis in early-stage patients

The propensity of myelodysplastic syndrome (MDS) to transform into acute myeloid leukemia (AML) suggests the existence of common pathogenic components for these malignancies. Here, four genes implicated in the development of AML were examined for promoter CpG island hypermethylation in cells from 37 patients with different stages of MDS. Aberrant methylation was detected by polymerase chain reaction amplification of bisulfite-treated DNA followed by denaturing gradient gel electrophoresis. The highest rate of methylation was found for p15INK4B (51%), followed by HIC1 (32%), CDH1 (27%), and ER (19%). Concurrent hypermethylation of > or = 3 genes was more frequent in advanced compared with early-stage MDS (P < or = 0.05), and hypermethylation of p15INK4B was associated with leukemic transformation in early MDS (P < or = 0.05). The median overall survival was 17 months for cases showing hypermethylation of > or = 1 genes vs. 67 months for cases without hypermethylation (P = 0.002). Specifically, promoter hypermethylation identified a subgroup of early MDS with a particularly poor prognosis (median overall survival 20 months vs. 102 months; P = 0.004). In multivariate analysis including stage and thrombocyte count, hypermethylation of > or = 1 genes was an independent negative prognostic factor (P < 0.05). These data suggest that hypermethylation of p15INK4B, HIC1, CDH1, and ER contribute to the development and outcome of MDS.     

Correlation between promoter methylation of glutathione-S-tranferase P1 and oxidative stress in acute-on-chronic hepatitis B liver failure

Summary. Promoter methylation of glutathione‐S‐transferase P1 (GSTP1) may be involved in liver damage caused by oxidative stress in acute‐on‐chronic hepatitis B‐induced liver failure (ACHBLF). This study aimed to explore GSTP1 promoter methylation status and oxidative stress in such patients. DNA was extracted from peripheral blood mononuclear cells (PBMCs) of patients with acute‐on‐chronic liver hepatitis B‐induced liver failure, chronic hepatitis B (CHB) and normal controls, followed by sodium‐bisulfite treatment and methylation‐specific PCR (MSP) analysis. Plasma malondialdehyde (MDA) adducts levels were detected by enzyme‐linked immunosorbent assay as oxidative stress marker. Model for end‐stage liver disease (MELD) score was employed to estimate the severity of the liver failure. Eleven of 35 patients with acute‐on‐chronic liver failure and 3 of 35 patients with stab le hepatitis B displayed GSTP1 promoter methylation, and the difference was significant (χ² = 5.71, P = 0.02). No differences in standard liver function tests were found in patients with acute‐on‐chronic liver failure with and without GSTP1 promoter methylation although the levels of total bilirubin were greater in those with methylation. The levels of MDA adducts were significantly higher in patients with liver failure when compared to those with CHB (12.44 ± 5.38 pmol/mg vs 8.42 ± 5.49 pmol/mg, P < 0.01), and in the patients with liver failure who had promoter methylation the levels were higher than in those who did not (15.2 ± 4.68 pmol/mg vs 11.17 ± 5.29 pmol/mg, P < 0.01). The MELD score was not significantly different between methylated and unmethylated patients with liver failure (P > 0.05), although MDA adducts were correlated with MELD scores in patients with acute‐on‐chronic liver failure (r = 0.579, P < 0.01). GSTP1 promoter methylation may facilitate oxidative stress–associated liver damage in ACHBLF, and oxidative stress is correlated with ACHBLF severity.     

老年肺癌病人痰标本中p16基因异常甲基化的研究

目的分析老年肺癌病人痰标本中p16基因启动子区域异常高甲基化的改变情况,评价该指标作为肺癌辅助诊断分子标记物的价值。方法运用半巢式甲基化特异性聚合酶链反应技术,检测94例老年原发性肺癌病人痰标本和部分对应肿瘤组织,以及10例慢性肺炎病例痰标本中p16基因启动子区域的甲基化改变。结果74%的肺癌病人痰标本中检测到了p16基因异常高甲基化,与传统细胞学(46.8%)相比,痰标本中p16基因异常高甲基化对肿瘤的检出率(74.5%)灵敏度更高(P<0.01);痰细胞中p16甲基化检测和细胞学相结合,对肿瘤的检出率可达86.17%(81/94)。如果痰标本中p16基因启动子区域发生高甲基化,其对应的肿瘤组织中p16基因亦为高甲基化。10例慢性肺炎病人痰标本中仅3例检测出p16基因甲基化。结论痰标本中p16基因甲基化是临床肺癌辅助诊断的有效分子生物标记物之一。     

Epigenetic inactivation of INK4/CDK/RB cell cycle pathway in acute leukemias

Dysregulation of cell cycle is important in oncogenesis. We analyzed the inactivation of the INK4 family CKI/CDK/RB pathway by gene promoter hypermethylation in leukemogenesis. The methylation-specific polymerase chain reaction (MSP) with primers for methylated (M-MSP) and unmethylated (U-MSP) alleles of the p15, p16, p18, and RB genes was used to study five leukemic cell lines, 50 acute myeloid leukemia (AML) and 25 acute lymphoblastic leukemia (ALL) samples. None of the leukemic cell lines showed p18 and RB methylation. p15 was methylated in Raji, while p16 was methylated in U937 and Raji. In NB4 and Jurkat, both alleles of p15 and p16 appeared to be deleted. At diagnosis, p15 methylation occurred in 29 (58%) AML patients, and 10 (40.0%) ALL patients. p16 methylation occurred in two (4%) AML and two (8%) ALL patients. Only one each of AML and ALL patients had concurrent p15 and p16 methylation. None of the patients had methylation of p18 or RB. In AML, p15 methylation was associated with M2 subtype (p=0.018). Patients with and without p15 methylation had similar complete remission (CR) rates and projected 5-year overall survival (OS) or disease-free survival (DFS). Therefore, methylation inactivation of the INK4/CDK/RB pathway in leukemia involved primarily p15 and occasionally p16, but not p18 or RB. In AML, p15 gene methylation was associated with the M2 subtype, but was not prognostic for CR, OS, or DFS.     

Epigenetic analysis of the IFNλ3 gene identifies a novel marker for response to therapy in HCV‐infected subjects

Chronic hepatitis C virus (HCV) infection is characterized by high interindividual variability in response to pegylated interferon and ribavirin. A genetic polymorphism on chromosome 19 (rs12979860) upstream of interferon‐λ3 (IFNλ3) is associated with a twofold change in sustained virologic response rate after 48 weeks of treatment with pegylated interferon/ribavirin in HCV genotype 1 (GT1) treatment‐naïve patients. We conducted epigenetic analysis on the IFNλ3 promoter to investigate whether DNA methylation is associated with response to HCV therapy. DNA samples from HCV GT1‐infected subjects receiving an interferon‐free paritaprevir‐containing combination regimen (N=540) and from HCV‐uninfected, healthy controls (N=124) were analysed for IFNλ3 methylation levels. Methylation was strongly associated with rs12979860 allele status whether adjusting for HCV status (r=65.0%, 95% CI: [60.2%, 69.5%]), or not (r=64.4%), both with P<2.2×10^?16. In HCV GT1‐infected subjects, C/C genotypes had significantly lower methylation levels relative to C/T or T/T genotypes (P<1×10^?14), with each T allele resulting in a nine‐unit increase in mean methylation level. Methylation levels did not correlate with response in subjects treated for 12 or 24 weeks. However, non‐C/C subjects with higher methylation levels were more likely to relapse when treatment duration was 8 weeks. This analysis suggests that methylation status of the IFNλ3 promoter region may be a useful parameter that identifies patients more likely to relapse following HCV therapy; however, continuing therapy for a sufficient duration can overcome this difference. These findings may provide mechanistic insight into the role of IFNλ3 genetic variants in HCV treatment response.