Epigenetic inactivation of the tissue inhibitor of metalloproteinase-2 (TIMP-2) gene in human prostate tumors

Gene silencing via CpG island methylation in the promoter region is one of the mechanisms by which tumor suppressor genes are inactivated in human cancers. Previous studies have shown that the tissue inhibitors of metalloproteinases (TIMP)-2 gene, which is an endogenous inhibitor of matrix metalloproteinases involved in cell invasion and tumorigenesis, is downregulated or silenced in a variety of human cancer cell lines. Here, we investigated the mechanism underlying TIMP-2 expression in prostate cancer cell lines and primary prostate tumor samples. We observed a strong correlation between promoter hypermethylation and lost expression of TIMP-2 gene, which was supported by other results demonstrating that promoter demethylation by 5-aza-2'-deoxycytidine and trichostatin A reactivated TIMP-2 and restored its expression in TIMP-2-silenced metastatic prostate cell lines. These results were further substantiated by a chromatin immunoprecipitation assay, showing the preferential binding of MeCP2 to methylated CpG island in TIMP-2-silenced metastatic prostate cell lines. In vitro Matrigel invasion assays showed that re-expression of TIMP-2 after a combined treatment with 5-aza and trichostatin-A in metastatic prostate cells resulted in a significant reduction of tumor cell invasion. Furthermore, CpG methylation of TIMP-2 promoter was also shown in primary prostate tumors that expressed decreased TIMP-2 protein levels. These results suggest that the downregulation of the TIMP-2 gene is associated with promoter methylation and that this may play an important role in prostate cancer progression during the invasive and metastatic stages of the disease.     

Deletion, methylation, and expression of the NKX3.1 suppressor gene in primary human prostate cancer

NKX3.1 is a prostate-specific homeoprotein and tumor suppressor that is affected by the loss of 8p21 in prostate cancer. In mice, Nkx3.1 haploinsufficiency results in prostatic dysplasia and complements cancer formation induced by loss of other suppressor genes. However, NKX3.1 expression can be immunohistochemically detected in most primary prostate cancers. We examined the relationship between suppressor gene haploinsufficiency, methylation, and quantitative NKX3.1 expression levels in primary prostate cancer. NKX3.1 gene copy number was assessed by microsatellite analysis, fluorescence in situ hybridization, and quantitative PCR. NKX3.1 gene methylation was determined in prostate cancer cell lines and we thereby identified potential CpG methylation sites for methylation-specific PCR analysis in tissues. We validated and then applied an internally controlled fluorescence immunomicroscopic assay for NKX3.1 protein expression in 48 primary prostate cancer specimens from radical prostatectomies. NKX3.1 loss of heterozygosity was found in 27 of 43 tissues tested. Classic CpG island methylation of the NKX3.1 gene was not found in either prostate cancer cell lines or tissues. However, in 33 of 40 samples tested, CpG sites at -921, -903, and -47 were methylated to a greater degree in malignant than in adjacent normal cells. In 43 of 48 samples, NKX3.1 protein expression was reduced from 0.34 to 0.90 compared with adjacent normal luminal epithelium (mean of all samples, 0.68; 95% confidence interval, 0.05). In 12 cases that also had high-grade prostatic intraepithelial neoplasia, NKX3.1 expression levels were similar in preinvasive and invasive cancer cells and significantly lower than adjacent normal cells. Even in the presence of allelic loss, NKX3.1 expression is reduced over a wide range in prostate cancer at the time of prostatectomy, suggesting that diverse factors influence expression. Samples with protein expression below the median level in cancer cells had both NKX3.1 deletion and selective CpG methylation.     

Candidate tumor suppressor gene SLC5A8 is frequently down-regulated by promoter hypermethylation in prostate tumor

Background

The prostate gland is the most common site of cancer and the third leading cause of cancer mortality in men. Solute carrier family 5 (iodide transporter), member 8 (SLC5A8) was proposed as a potential tumor suppressor gene which is silenced by epigenetic changes in various tumors. The aim of this study was to investigate the significance of DNA methylation in SLC5A8 expression in prostate tumors.

Methods

DNA methylation status of the promoter region and expression of SLC5A8 were evaluated in prostate cancer cell lines, tumor and adjacent non-tumor prostate tissues from same prostate cancer patients, by using bisulphite-modified sequencing, RT-PCR and quantitative methylation-specific PCR (QMSP) analysis.

Results

The reduced or lost expression of SLC5A8 was observed in 70% of the tumor tissues. The bisulphite-modified sequencing analysis on the prostate cancer cell lines which do not express SLC5A8 detected the densely methylated SLC5A8 promoter region. SLC5A8 was reactivated by treatment with DNA methyl transferase inhibitor, 5-azacytidine but not by trichostatin A (TSA). Higher methylation at the promoter region of SLC5A8 in primary prostate tumor tissues was detected as compared with those in adjacent non-tumor tissues (7/10, 70%).

Conclusions

These data suggested that DNA methylation in the SLC5A8 promoter region suppressed the expression of SLC5A8 in prostate tumor.     

长链非编码RNA ZNF667-AS1在食管鳞状细胞癌组织中的表达及其DNA甲基化状态的研究

 目的 检测长链非编码RNA ZNF667-AS1在食管鳞状细胞癌（esophageal squamous cell carcinoma, ESCC）中的表达及甲基化状态。方法 应用qPCR和MSP法检测DNA甲基化转移酶抑制剂5-Aza-dC处理前后食管癌细胞系（Kyse170、Eca109、TE1和TE13）、ESCC及相应癌旁正常组织中ZNF667-AS1基因的表达,及其CpG岛三个区域的甲基化状态。结果 在5-Aza-dC处理后的四株细胞系中,ZNF667-AS1基因的表达均增高,且其CpG岛三个区域甲基化程度均降低。ZNF667-AS1基因在ESCC组织中的表达显著低于相应癌旁正常组织,且该基因CpG岛远端启动子区及第一外显子区甲基化率在ESCC与相应癌旁正常组织中的差异均具有统计学意义（均P<0.05）。ESCC组织中CpG岛近端启动子区甲基化率显著高于相应癌旁正常组织,并与组织分化程度、TNM分期密切相关,ZNF667-AS1基因CpG岛近端启动子区发生甲基化的ESCC组织中,低表达例数高于高表达例数,差异具有统计学意义。结论 ZNF667-AS1基因在食管癌细胞系和ESCC组织中的低表达与ESCC的发生发展密切相关,且其近端启动子区的高甲基化状态可能是导 致其表达沉默的机制之一。     

TMEM196基因在肺癌中的甲基化修饰与表达调控

目的:分析TMEM196基因在肺癌组织中的甲基化情况以及甲基化发生对TMEM196基因表达的影响。方法:采用MSP方法检测肺癌组织、癌旁正常对照组织及肺癌细胞株TMEM196基因甲基化率;用去甲基化药物5-氮-2'-脱氧胞苷(5-aza-dC)处理肺癌细胞后,采用RT-PCR法检测TMEM196 mRNA表达水平。 结果:肺癌组织中TMEM196基因甲基化发生率为57%(28/49),而正常对照组织中该基因甲基化发生率为0(0/20)。TMEM196基因甲基化与肿瘤的分化程度(P=0.012)和临床分期显著相关(P=0.007),而与患者的年龄、性别、吸烟以及肿瘤的病理分类无显著相关(P>0.05)。TMEM196基因在肺癌细胞株H1975和H1650中高甲基化且表达缺失,去甲基化药物(5-aza-dC)处理细胞后TMEM196 mRNA表达明显升高,说明TMEM196基因表达可能受甲基化调控。结论:TMEM196基因甲基化与肺癌的发生发展密切相关,推测该基因通过DNA甲基化失活参与了肿瘤的发生。     

S100A6 (Calcyclin) is a prostate basal cell marker absent in prostate cancer and its precursors

S100A6 (Calcyclin) is a calcium-binding protein that has been implicated in a variety of biological functions as well as tumorigenesis. The aim of our study was to investigate the involvement of S100A6 during prostate cancer development and progression. Using immunohistochemistry, the expression of S100A6 was examined in benign (n=66), premalignant (n=10), malignant (n=66) and metastatic prostate (n=5) tissues arranged in a tissue-microarray or whole sections as well as in prostate cancer cell lines. The S100A6 immunostaining pattern in tissues was compared with that of cytokeratin 5 (a basal cell marker) and 18 (a benign luminal cell marker). In all cases of benign epithelium, intense S100A6 expression was seen in the basal cell layer with absent staining in luminal cells. In all cases of prostatic adenocarcinoma (matched), metastatic lesions and 3/10 high-grade prostatic intraepithelial neoplasia lesions, an absence of S100A6 was seen. Western blotting and RT-PCR analysis of cell lines showed S100A6 expression to be absent in LNCaP, LNCaP-LN3 and LNCaP-Pro5 but present in Du145, PC3, PC-3M and PC-3M-LN4. LNCaP cells treated with 5-Azacytidine, caused re-expression of S100A6 mRNA. Sequencing of bisulphite modified DNA showed CpG methylation within the S100A6 promoter region and exon 1 of LNCaP, LNCaP-LN3 and LNCaP-Pro5 cell lines but not in Du145 cells. Our data suggest that loss of S100A6 protein expression is common in prostate cancer development and may occur at an early stage. The mechanism of loss of expression may involve hypermethylation of CpG sites. The finding of intense S100A6 expression in the basal cells of benign glands but loss of expression in cancer could be useful as a novel diagnostic marker for prostate cancer.     

ZNF185, an actin-cytoskeleton-associated growth inhibitory LIM protein in prostate cancer

We have recently identified ZNF185 as a gene that is downregulated in prostate cancer (PCa), in part via epigenetic alteration, and maybe associated with disease progression. In this study, we cloned the ZNF185 cDNA from normal human prostate tissues and investigated its biological function. We show that ZNF185 is a novel actin-cytoskeleton-associated Lin-l 1, Isl-1 and Mec-3 (LIM) domain-containing protein that localizes to F-actin structures, and is enriched at focal adhesions. We find that the NH(2)-terminal region, which we designate the actin-targeting domain, facilitates ZNF185 binding to actin in vitro and is both necessary and sufficient to mediate actin-cytoskeleton targeting of ZNF185, whereas the LIM domain, which is localized in the COOH-terminus is dispensable for this phenomenon. Interestingly, ectopic expression of full-length ZNF185, but not a mutant lacking the actin-targeting domain, could suppress proliferation and anchorage-independent growth of PCa cells. Together, our data suggest that ZNF185 may function as a tumor-suppressor protein by associating with the actin-cytoskeleton.     

Aberrant promoter methylation of laminin-5-encoding genes in prostate cancers and its relationship to clinicopathological features.

PURPOSE: Laminin-5 (LN5) is an essential component of the basement membrane (BM) and is composed of three chains that are the products of three distinct genes (LAMA3, LAMB3, and LAMC2). Differential expression of LN5 genes has been reported in prostate and other cancers. Recently, in lung cancers, we developed methylation-specific PCR assays for each gene and demonstrated that the aberrant methylation as the mechanism of inactivation of genes. In this study, we investigated the aberrant promoter methylation of LN5 genes in prostate cancers and correlated the data with clinicopathological features. EXPERIMENTAL DESIGN: Promoter methylation of LN5-encoding genes was analyzed in 101 prostate cancer samples by methylation-specific PCR assay. In addition, we analyzed 32 nonmalignant prostate tissue samples. The methylation index (MI) was determined as the methylated fraction of the genes examined. RESULTS: The frequencies of loss of expression for the LAMA3, LAMB3, and LAMC2 genes in six prostate cancer cell lines were 83, 67, and 50%, respectively, whereas the methylation frequencies were 83, 67, and 33%, respectively. The concordances between loss of expression and methylation for the three genes were 100, 100, and 83%, respectively. The frequency of methylation of LN5-encoding genes in prostate cancers and nonmalignant prostate tissues, respectively, were: 44 and 12% for LAMA3 (P = 0.001); 18 and 6% for LAMB3; and 41 and 9% for LAMC2 (P = 0.001). In addition, methylation frequencies of any one or two genes, frequencies of at least one-gene methylation and mean chain MI were significantly higher in prostate cancers than in nonmalignant prostate tissues. For clinicopathological correlations, the high Gleason score (GS) group, high preoperative serum prostate-specific antigen (PSA) group, and high stage group had significantly higher methylation frequencies of LAMA3 than their corresponding low groups. Methylation frequency of at least one gene and mean chain MI was significantly higher in the high PSA group and high-stage group than their respective low groups. There was significant correlation between MI and PSA. The high GS group had higher frequencies of at least one gene methylation and mean chain MI than the low GS group. CONCLUSIONS: Our results demonstrate frequent epigenetic silencing of LN5-encoding genes in prostate cancers and it correlates with clinicopathological features of poor prognosis. These findings are of biological interest and potentially of clinical importance.     

食管鳞癌中DACT2基因表达及甲基化状态研究

[目的]检测食管鳞状细胞癌(ESCC)中DACT2基因表达及启动子区甲基化状态,探讨DACT2基因在食管鳞癌发生发展中的作用.[方法]分别应用逆转录—聚合酶链反应(RTPCR)以及甲基化特异性PCR(MSP)的方法检测DNA甲基转移酶抑制剂5-氮杂-2'-脱氧胞苷(5-aza-dC)处理前后的食管癌细胞系(TE1、TE13、T.Tn、Eca109)以及食管鳞癌组织及相应癌旁组织中DACT2 mRNA表达情况及启动子区甲基化状态.[结果]经5-aza-dC处理后4种食管癌细胞系中DACT2基因的表达均增高.4种未经5-aza-dC处理的食管癌细胞系中DACT2基因呈高甲基化状态.应用5-aza-dC处理后,DACT2基因在4种细胞系中均呈非甲基化状态.DACT2基因在食管鳞癌组织中的表达显著低于癌旁组织(0.66±0.53 vs 0.95±0.64,t=-2.43,P=0.018),并与淋巴结转移密切相关(t=-2.030,P=0.048).食管鳞癌组织中DACT2基因的启动子区甲基化率显著高于癌旁组织(50.0％ vs 21.1％,x2=9.439,P=0.002),并与TNM分期、组织学分化程度和淋巴结转移密切相关(P均＜0.05).发生DACT2基因甲基化的食管鳞癌组织中DACT2基因的表达量显著低于未发生甲基化的食管鳞癌组织(0.46±0.32 vs 0.78±0.61,t=-2.341,P=0.023).[结论]DA CT2基因在食管鳞癌中的异常低表达与食管鳞癌的发生、发展密切相关,且其启动子区甲基化可能是导致其表达沉默的机制之一.     

5' CpG island methylation of the FHIT gene is correlated with loss of gene expression in lung and breast cancer

Allele loss and loss of expression of fragile histidine triad (FHIT), a putative tumor suppressor gene located in chromosome region 3p14.2, are frequent in several types of cancers. Tumor-acquired methylation of promoter region CpG islands is one method for silencing tumor suppressor genes. We investigated 5' CpG island methylation of the FHIT gene in 107 primary non-small cell lung cancer (NSCLC) samples and corresponding nonmalignant lung tissues, 39 primary breast carcinomas, as well as in 49 lung and 22 breast cancer cell lines by a methylation-specific PCR assay. In addition, we analyzed brushes from the bronchial epithelium of 35 heavy smokers without cancer. FHIT methylation was detected in 37% of primary NSCLCs, 31% of primary breast cancers, and 65% of lung and 86% of breast cancer cell lines. The frequency of methylation in small cell and NSCLC cell lines were identical. Methylation was found in 9% of the corresponding nonmalignant lung tissues and in 17% of bronchial brushes from heavy cigarette smokers. FHIT methylation was significantly correlated with loss of FHIT mRNA expression by Northern blot analysis in lung cancer cell lines and with loss of Fhit expression in NSCLC and breast tumors by immunostaining. We conclude that methylation of FHIT is a frequent event in NSCLC and breast cancers and is an important mechanism for loss of expression of this gene. Methylation of FHIT commences during lung cancer pathogenesis and may represent a marker for risk assessment.     

Aberrant methylation of trail decoy receptor genes is frequent in multiple tumor types

TNF-related apoptosis-inducing ligand (TRAIL) selectively induces programmed cell death (apoptosis) in various cancer cells but not in normal cells. TRAIL is known to bind to 4 different receptors, 2 proapoptotic (DR4 and DR5), and 2 potentially antiapoptotic receptors lacking death domains (DcR1 and DcR2). Aberrant promoter methylation and resultant silencing of tumor suppressor genes play an important role in the pathogenesis of many tumor types. Recently aberrant methylation of TRAIL decoy receptors was reported in pediatric tumor cell lines and neuroblastomas. We examined the methylation and expression status of TRAIL receptor genes in cancers of breast, lung, mesothelioma, prostate, bladder, cervix, ovary, brain and in hematopoietic malignancies. Aberrant methylation of DcR1 or DcR2 was present in 70% of primary breast cancers, 31% of primary lung cancers, in 63% of primary malignant mesothelioma (MM), in 60% of prostate cancer, in 42% of bladder cancer, in 100% of cervical cancer, in 43% of ovarian cancer, in 41% of lymphoma, in 26% of leukemia and in 56% of multiple myeloma. Methylation of DR4 and DR5 was rare in all the tumor types examined. Methylation of all the 4 receptors was rare in non malignant tissues. In cell lines, aberrant methylation of DcR1 was present in 11 of 23 (48%) breast, 10 of 27 (37%) lung and 3 of 7 (43%) MM, whereas aberrant methylation of DcR2 was present in 17 of 23 (74%) breast, 13 of 27 (48%) lung and 5 of 7 (71%) MM. The concordance between loss of gene expression and aberrant methylation ranged from 70-100%. Treatment with 5-aza-2'-deoxycytidine restored DcR1 and DcR2 expression in 9 methylated cell lines confirming that aberrant methylation was the cause for silencing of DcR1 and DcR2 expression. Our results demonstrate that DcR1 and DcR2 genes are frequently methylated in various tumor types, and that the role of decoy receptors in tumor pathogenesis needs to be re-evaluated.     

Methylation and expression of p16INK4 tumor suppressor gene in primary colorectal cancer tissues

It is known that p16(INK4) tumor suppressor gene expression in colon cancer cells is repressed by methylation at the CpG island of promoter, but in vivo silencing of p16 gene is not fully understood. Some studies showed that primary colorectal cancer (CRC) tissues often overexpress the p16 protein, while others showed the high incidence of p16 methylation. The aim of this study was to clarify p16 gene regulation in vivo. We used real-time methylation-specific PCR (MSP) to examine density of p16 methylation, and immunohistochemistry, Western blot analysis to determine p16 protein expression. Methylation was detected in 5 CRC cell lines tested and 9 of 21 (42.9%) CRCs. Four of 5 CRC cell lines did not express p16 mRNA, but 6 of 9 CRCs did express p16 mRNA even with methylation. Real-time MSP showed that CRC tissues had a wide variety in methylation density (methylation index: 0.28-0.91) and that highly methylated CRC tissues displayed significantly lower p16 mRNA expression than those with no-methylation or low-methylation. Immunohistochemistry showed that the majority of CRCs (53 of 55: 96.4%) overexpressed the p16 protein. Low p16 expression was associated with lymph node metastasis (p=0.003) and large tumor size (p=0.048). Western blot in a subset of non-tumor and tumor samples showed a consistent overexpression of the p16 protein. These results showed that CRC tissues displayed variable methylation density, which may be characteristics of p16 gene methylation in vivo. Our data suggest that a low p16 expression due to methylation may contribute to tumor enlargement and expansion of CRC.