Survey of Differentially Methylated Promoters in Prostate Cancer Cell Lines

Sidney Kimmel Cancer Center, 10835 Road to the Cure, San Diego, CA 92121, USA.
Neoplasia (Impact Factor: 4.25). 09/2005; 7(8):748-60. DOI: 10.1593/neo.05289
Source: PubMed


DNA methylation and copy number in the genomes of three immortalized prostate epithelial and five cancer cell lines (LNCaP, PC3, PC3M, PC3M-Pro4, and PC3M-LN4) were compared using a microarray-based technique. Genomic DNA is cut with a methylation-sensitive enzyme HpaII, followed by linker ligation, polymerase chain reaction (PCR) amplification, labeling, and hybridization to an array of promoter sequences. Only those parts of the genomic DNA that have unmethylated restriction sites within a few hundred base pairs generate PCR products detectable on an array. Of 2732 promoter sequences on a test array, 504 (18.5%) showed differential hybridization between immortalized prostate epithelial and cancer cell lines. Among candidate hypermethylated genes in cancer-derived lines, there were eight (CD44, CDKN1A, ESR1, PLAU, RARB, SFN, TNFRSF6, and TSPY) previously observed in prostate cancer and 13 previously known methylation targets in other cancers (ARHI, bcl-2, BRCA1, CDKN2C, GADD45A, MTAP, PGR, SLC26A4, SPARC, SYK, TJP2, UCHL1, and WIT-1). The majority of genes that appear to be both differentially methylated and differentially regulated between prostate epithelial and cancer cell lines are novel methylation targets, including PAK6, RAD50, TLX3, PIR51, MAP2K5, INSR, FBN1, and GG2-1, representing a rich new source of candidate genes used to study the role of DNA methylation in prostate tumors.

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    • "In particular, our analysis focused on gene promoters at specific sites of CpG islands with high mutation rates in cancer tissue (Albany et al., 2011). No significant differences were observed between the parental line and the antiandrogen-resistant subclone, even in RASSF1, GSTP1 and RARB gene promoters whose methylation status is frequently altered in prostate cancer (Meiers et al., 2007; Hesson et al., 2007; Wang et al., 2005). Ultrastructural alterations in mitochondrial morphology that support the hypothesis of metabolic hyperactivity and evidence from the literature highlighting the role of mtDNA alterations in cancer progression led us to investigate the potential involvement of mtDNA alterations behind the switch to antiandrogen resistance of the subline LNCaP-Rbic (Wheater et al., 2007; Prince, 1999). "
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    ABSTRACT: Advanced prostate cancers, initially sensitive to androgen deprivation therapy, frequently progress to the castration-resistant prostate cancer phenotype (CRPC) through mechanisms not yet fully understood. In this study we investigated mitochondrial involvement in the establishment of refractoriness to hormone therapy. Two human prostate cancer cell lines were used, the parental LNCaP and the resistant LNCaP-Rbic, the latter generated after continuous exposure to 20 μM of (R)-bicalutamide, the active enantiomer of Casodex®. We observed a significant decrease in mtDNA content and a lower expression of 8 mitochondria-encoded gene transcripts involved in respiratory chain complexes in both cell lines. We also found that (R)-bicalutamide differentially modulated dynamin-related protein (Drp-1) expression in LNCaP and LNCaP-Rbic cells. These data seem to indicate that the androgen-independent phenotype in our experimental model was due, at least in part, to alterations in mitochondrial dynamics and to a breakdown in the Drp-1-mediated mitochondrial network.
    Molecular and Cellular Endocrinology 01/2014; 382(1):314–324. DOI:10.1016/j.mce.2013.10.022 · 4.41 Impact Factor
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    • "Its role in tumorigenesis, TSG or oncogene, seems to be dependent on the tumor type [47], [48]. UCHL1 methylation has been reported in multiple tumors [49], such as esophageal [50], gastric [36], [51], renal [52], prostate [53], head and neck squamous [47], ovarian [54], hepatocellular and colorectal cancers [49], [55]. Some studies even suggested the use of UCHL1 methylation as a biomarker for diagnosis and prognosis of certain tumors [50], [55], [56]. "
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    ABSTRACT: Epigenetic regulation of tumor suppressor genes (TSGs) has been shown to play a central role in melanomagenesis. By integrating gene expression and methylation array analysis we identified novel candidate genes frequently methylated in melanoma. We validated the methylation status of the most promising genes using highly sensitive Sequenom Epityper assays in a large panel of melanoma cell lines and resected melanomas, and compared the findings with those from cultured melanocytes. We found transcript levels of UCHL1, COL1A2, THBS1 and TNFRSF10D were inversely correlated with promoter methylation. For THBS1 and UCHL1 the effect of this methylation on expression was confirmed at the protein level. Identification of these candidate TSGs and future research designed to understand how their silencing is related to melanoma development will increase our understanding of the etiology of this cancer and may provide tools for its early diagnosis.
    PLoS ONE 10/2011; 6(10):e26121. DOI:10.1371/journal.pone.0026121 · 3.23 Impact Factor
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    • "Interestingly, mutations in FBN1, which is a member of the fibrillin family, are associated with the Marfan syndrome [49]. FBN1 methylation has previously been identified in prostate cancer cell lines [50] and the gene has also been shown to be epigenetically silenced in tumor endothelial cells [51]. Functional validation by RNA interference in endothelial cells pinpointed FBN1 as a negative regulator of cell growth and angiogenesis [51]. "
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    ABSTRACT: The presence of cancer-specific DNA methylation patterns in epithelial colorectal cells in human feces provides the prospect of a simple, non-invasive screening test for colorectal cancer and its precursor, the adenoma. This study investigates a panel of epigenetic markers for the detection of colorectal cancer and adenomas. Candidate biomarkers were subjected to quantitative methylation analysis in test sets of tissue samples from colorectal cancers, adenomas, and normal colonic mucosa. All findings were verified in independent clinical validation series. A total of 523 human samples were included in the study. Receiver operating characteristic (ROC) curve analysis was used to evaluate the performance of the biomarker panel. Promoter hypermethylation of the genes CNRIP1, FBN1, INA, MAL, SNCA, and SPG20 was frequent in both colorectal cancers (65-94%) and adenomas (35-91%), whereas normal mucosa samples were rarely (0-5%) methylated. The combined sensitivity of at least two positives among the six markers was 94% for colorectal cancers and 93% for adenoma samples, with a specificity of 98%. The resulting areas under the ROC curve were 0.984 for cancers and 0.968 for adenomas versus normal mucosa. The novel epigenetic marker panel shows very high sensitivity and specificity for both colorectal cancers and adenomas. Our findings suggest this biomarker panel to be highly suitable for early tumor detection.
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