Analysis of Methylated Genes in Peritoneal Fluids of Ovarian Cancer Patients: A New Prognostic Tool

Müller, Hannes M.; Millinger, Simone; Fiegl, Heidi; Goebel, Georg; Ivarsson, Lennart; Widschwendter, Andreas; Müller‐Holzner, Elisabeth; Marth, Christian; Widschwendter, Martin

doi:10.1373/clinchem.2004.034090

Cited by 30 publications

(17 citation statements)

References 23 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Methylated DNA can be detected in various body fluids from patients with neoplasia and the methylation status of individual as well as panels of genes can potentially be used for risk assessment [48]. DNA methylation has previously been identified in both serum and peritoneal fluid from ovarian cancer patients [49,50]. In the present study, we find high methylation frequencies of HOXA9 and RASSF1A in tumours from this patient group.…”

Section: Discussionsupporting

confidence: 67%

DNA methylation profiling of ovarian carcinomas and their in vitro models identifies HOXA9, HOXB5, SCGB3A1, and CRABP1 as novel targets

et al. 2007

View full text Add to dashboard Cite

Background The epigenetics of ovarian carcinogenesis remains poorly described. We have in the present study investigated the promoter methylation status of 13 genes in primary ovarian carcinomas (n = 52) and their in vitro models (n = 4; ES-2, OV-90, OVCAR-3, and SKOV-3) by methylation-specific polymerase chain reaction (MSP). Direct bisulphite sequencing analysis was used to confirm the methylation status of individual genes. The MSP results were compared with clinico- pathological features. Results Eight out of the 13 genes were hypermethylated among the ovarian carcinomas, and altogether 40 of 52 tumours were methylated in one or more genes. Promoter hypermethylation of HOXA9, RASSF1A, APC, CDH13, HOXB5, SCGB3A1 (HIN-1), CRABP1, and MLH1 was found in 51% (26/51), 49% (23/47), 24% (12/51), 20% (10/51), 12% (6/52), 10% (5/52), 4% (2/48), and 2% (1/51) of the carcinomas, respectively, whereas ADAMTS1, MGMT, NR3C1, p14 ARF , and p16 INK 4a were unmethylated in all samples. The methylation frequencies of HOXA9 and SCGB3A1 were higher among relatively early-stage carcinomas (FIGO I-II) than among carcinomas of later stages (FIGO III-IV; P = 0.002, P = 0.020, respectively). The majority of the early-stage carcinomas were of the endometrioid histotype. Additionally, HOXA9 hypermethylation was more common in tumours from patients older than 60 years of age (15/21) than among those of younger age (11/30; P = 0.023). Finally, there was a significant difference in HOXA9 methylation frequency among the histological types (P = 0.007). Conclusion DNA hypermethylation of tumour suppressor genes seems to play an important role in ovarian carcinogenesis and HOXA9, HOXB5, SCGB3A1, and CRABP1 are identified as novel hypermethylated target genes in this tumour type.

show abstract

Section: Discussionsupporting

confidence: 67%

DNA methylation profiling of ovarian carcinomas and their in vitro models identifies HOXA9, HOXB5, SCGB3A1, and CRABP1 as novel targets

et al. 2007

View full text Add to dashboard Cite

show abstract

“…Assays to measure DNA methylation may be potentially very useful in clinical practice, because many tumor suppressor genes have been shown to be methylated and functionally silenced in a variety of human neoplasias. 2,3 DNA methylation may be a useful marker for predicting prognosis and monitoring efficacy of adjuvant therapy in cancer patients 10,11 and for evaluating risks for tumor recurrence in surveillance of high-or low-risk individuals. 8,9,12 A variety of assays to measure DNA methylation have been developed for paraffin-embedded tissue, and many of these methods rely on sodium bisulfite treatment of genomic DNA from tumor tissue.…”

Section: Discussionmentioning

confidence: 99%

“…6 DNA methylation may be a useful marker for cancer diagnosis, screening, surveillance in high-risk individuals, monitoring of minimal residual disease, and determining optimal therapeutic options. 2,[7][8][9][10][11][12] Therefore, there are increasing demands for reliable assays to measure DNA methylation, particularly for formalin-fixed paraffin-embedded tissue.…”

mentioning

confidence: 99%

Precision and Performance Characteristics of Bisulfite Conversion and Real-Time PCR (MethyLight) for Quantitative DNA Methylation Analysis

Ogino

Kawasaki

Brahmandam

et al. 2006

The Journal of Molecular Diagnostics

372

425

View full text Add to dashboard Cite

Assays to measure DNA methylation, which are important in epigenetic research and clinical diagnostics, typically rely on conversion of unmethylated cytosine to uracil by sodium bisulfite. However, no study has comprehensively evaluated the precision and performance characteristics of sodium bisulfite conversion and subsequent quantitative methylation assay. We developed quantitative real-time polymerase chain reaction (MethyLight) to measure percentage of methylated reference (PMR, ie, degree of methylation) for the MGMT, MLH1, and CDKN2A (p16) promoters. To measure the precision of bisulfite conversion, we bisulfite-treated seven different aliquots of DNA from each of four paraffin-embedded colon cancer samples. To assess run-to-run variation, we repeated MethyLight five times. Bisulfite-to-bisulfite coefficient of variation (CV) of PMR ranged from 0.10 to 0.38 (mean, 0.21), and run-to-run CV of PMR ranged from 0.046 to 0.60 (mean, 0.31). Interclass correlation coefficients were 0.74 to 0.84 for the three loci, indicating good reproducibility. DNA mixing study with methylated and unmethylated DNA showed good linearity of the assay. Of 272 colorectal cancers evaluated, most showed PMR either <1 or >10, and promoter methylation (PMR >4) was tightly associated with loss of respective protein expression (P < 10 ؊16 ). In conclusion, sodium bisulfite conversion and quantitative MethyLight assays have good precision and linearity and can be effectively used for high-throughput DNA methylation analysis on paraffin-embedded tissue.

show abstract

“…Assays to measure DNA methylation may be potentially very useful in clinical practice. 10 DNA methylation may be a useful marker for predicting prognosis and monitoring efficacy of adjuvant therapy in cancer patients 38 and for risk assessment in surveillance of high-or low-risk individuals. 39,40 In the current study, the use of quantitative DNA methylation assays as well as relatively unbiased, population-based samples of colorectal cancer from two large prospective cohorts has enabled us to precisely estimate the frequency of colorectal cancers with specific molecular features (such as CIMP-high, MSI-H, p27 loss, etc.)…”

Section: Discussionmentioning

confidence: 99%

Loss of nuclear p27 (CDKN1B/KIP1) in colorectal cancer is correlated with microsatellite instability and CIMP

et al. 2007

View full text Add to dashboard Cite

Downregulation of p27 (cyclin-dependent kinase inhibitor-1B, CDKN1B or KIP1) is caused by increased ubiquitin-mediated proteasomal degradation in colorectal cancer, and has been associated with poor prognosis. CpG island methylator phenotype (CIMP) is a phenotype of colorectal cancer with extensive promoter methylation, and associated with high degree of microsatellite instability (MSI-H) and BRAF mutations. We have recently shown that both CIMP and MSI-H are inversely associated with downregulation of p21 (CDKN1A or CIP1), another cyclin-dependent kinase inhibitor. However, no study to date has examined relationship between p27 and CIMP status in colorectal cancer. Using MethyLight assays, we measured DNA methylation in five CIMP-specific gene promoters {CACNA1G, CDKN2A (p16), CRABP1, MLH1 and NEUROG1} in 706 colorectal cancer samples obtained from two large prospective cohorts. Among the 706 tumors, 112 (16%) were CIMP-high tumors with Z4/5 methylated promoters. We assessed p27 and p53 expressions by immunohistochemistry. Loss of nuclear p27 expression {observed in 231 tumors (33%)} was significantly associated with CIMP-high, MSI-H and BRAF mutations, and these associations were much more pronounced among p53-negative tumors than p53-positive tumors. When CIMP-high and non-CIMP-high tumors were stratified by MSI status (or KRAS and BRAF status), CIMP-high and MSI-H (but not BRAF mutations) were still significantly associated with nuclear p27 loss. Nuclear p27 loss did not appear to be directly related to CDKN2A (p16) methylation. We conclude that downregulation of nuclear p27 is associated with CIMP-high and MSI-H in colorectal cancer. These associations are stronger among p53 wild-type tumors, implying important interplay of p27 and p53 functions (or dysfunctions) in the development of various molecular subtypes of colorectal cancer. Modern Pathology (2007) 20, 15-22.

show abstract

Analysis of Methylated Genes in Peritoneal Fluids of Ovarian Cancer Patients: A New Prognostic Tool

Cited by 30 publications

References 23 publications

DNA methylation profiling of ovarian carcinomas and their in vitro models identifies HOXA9, HOXB5, SCGB3A1, and CRABP1 as novel targets

DNA methylation profiling of ovarian carcinomas and their in vitro models identifies HOXA9, HOXB5, SCGB3A1, and CRABP1 as novel targets

Precision and Performance Characteristics of Bisulfite Conversion and Real-Time PCR (MethyLight) for Quantitative DNA Methylation Analysis

Loss of nuclear p27 (CDKN1B/KIP1) in colorectal cancer is correlated with microsatellite instability and CIMP

Contact Info

Product

Resources

About