BackgroundMany men develop a rising PSA after initial therapy for prostate cancer. While some of these men will develop a local or metastatic recurrence that warrants further therapy, others will have no evidence of disease progression. We hypothesized that an expression biomarker panel can predict which men with a rising PSA would benefit from further therapy.Methodology/Principal FindingsA case-control design was used to test the association of gene expression with outcome. Systemic (SYS) progression cases were men post-prostatectomy who developed systemic progression within 5 years after PSA recurrence. PSA progression controls were matched men post-prostatectomy with PSA recurrence but no evidence of clinical progression within 5 years. Using expression arrays optimized for paraffin-embedded tissue RNA, 1021 cancer-related genes were evaluated–including 570 genes implicated in prostate cancer progression. Genes from 8 previously reported marker panels were included. A systemic progression model containing 17 genes was developed. This model generated an AUC of 0.88 (95% CI: 0.84–0.92). Similar AUCs were generated using 3 previously reported panels. In secondary analyses, the model predicted the endpoints of prostate cancer death (in SYS cases) and systemic progression beyond 5 years (in PSA controls) with hazard ratios 2.5 and 4.7, respectively (log-rank p-values of 0.0007 and 0.0005). Genes mapped to 8q24 were significantly enriched in the model.Conclusions/SignificanceSpecific gene expression patterns are significantly associated with systemic progression after PSA recurrence. The measurement of gene expression pattern may be useful for determining which men may benefit from additional therapy after PSA recurrence.

We evaluated the significance of aberrant DNA methyltransferase 1 (DNMT1) protein expression during gastric carcinogenesis. The protein expression of DNMT1, Muc2, human gastric mucin, E-cadherin, and proliferating cell nuclear antigen was examined immunohistochemically in gastric cancers and corresponding noncancerous mucosae from 134 patients. The DNA methylation status of the CpG islands of the p16, human MutL homologue 1 (hMLH1), E-cadherin, and thrombospondin-1 (THBS-1) genes and the methylated in tumor (MINT)-1, -2, -12, and -31 clones was examined by methylation-specific polymerase chain reaction and combined bisulfite restriction enzyme analysis. Epstein-Barr virus (EBV) infection was detected by in situ hybridization. Nuclear immunoreactivity for DNMT1 was not detected in any of the noncancerous epithelia, except in proliferative zones (positive internal control), but was found in 97 (72%) of the gastric cancers. DNMT1 overexpression correlated significantly with poorer tumor differentiation (P < 0.001), but not with the phenotype (gastric type versus intestinal type) of the cancer cells. It also correlated significantly with DNA hypermethylation of the CpG islands of the hMLH1 (P ‫؍‬ 0.024) and THBS-1 genes (P ‫؍‬ 0.043), and with the CpG island methylator phenotype in the gastric cancers (P ‫؍‬ 0.007). Reduced E-cadherin expression correlated significantly with poorer tumor differentiation (P ‫؍‬ 0.002), DNA hypermethylation of the E-cadherin gene (P < 0.001) and DNMT1 overexpression (P ‫؍‬ 0.014). DNMT1 overexpression was also associated with EBV infection (a potential etiological factor in gastric car- DNA methylation plays an important role in transcriptional regulation and chromatin remodeling in mammalian cells.1 Both overall DNA hypomethylation and more regional DNA hypermethylation have been well documented in various cancers.1-8 Aberrant DNA methylation may be involved in carcinogenesis as a result of 1) increased gene mutagenicity because of deamination of 5-methylcytosine to thymine; 2) a possible association of aberrant DNA methylation with allelic loss; and 3) repression of gene transcription through methylation of CpG islands in regulatory regions of specific genes, including tumor-suppressor genes.

Alteration of DNA methylation is one of the most consistent epigenetic changes in human cancers. DNA methyltransferase (DNMT) 1 is a major enzyme involved in establishing genomic methylation patterns. Most of the studies concerning DNMT1 expression in human cancers have been performed only at the mRNA level. To directly examine DNMT1 protein expression levels during human hepatocarcinogenesis, 16 histologically normal liver tissues, 51 noncancerous liver tissues exhibiting chronic hepatitis or cirrhosis, which are considered to be precancerous conditions, and 53 hepatocellular carcinomas (HCCs) were subjected to immunohistochemic examination. If more than 20% of the cells exhibited nuclear DNMT1 staining, the tissue sample was considered to be DNMT1-positive. DNMT1 immunoreactivity was observed in 23 (43%) of the HCCs, but in none (0%) of the histologically normal liver or noncancerous liver tissues exhibiting chronic hepatitis or cirrhosis. The incidence of increased DNMT1 protein expression in HCCs correlated significantly with poor tumor differentiation (p ‫؍‬ 0.0006) and portal vein involvement (p ‫؍‬ 0.0002). Moreover, the recurrence-free (p ‫؍‬ 0.0001) and overall (p < 0.0001) survival rates of patients with HCCs exhibiting increased DNMT1 protein expression were significantly lower than those of patients with HCCs that did not exhibit increased expression. Increased DNMT1 protein expression may play a critical role in the malignant progression of HCCs and be a biologic predictor of both HCC recurrence and a poor prognosis in HCC patients. © 2003 Wiley-Liss, Inc. Key words: DNA methylation, chronic hepatitis, liver cirrhosis, hepatocarcinogenesisAberrant DNA methylation is one of the most consistent epigenetic changes in human cancers. [1][2][3][4] Generally, the overall DNA methylation level is lower in cancers than in normal tissues. 5 However, some loci tend to exhibit increased DNA methylation in cancers, 6 -8 whereas others are often hypomethylated. 9 DNA methylation may play a role in carcinogenesis by virtue of 3 mechanisms: (i) DNA cytosine methylation facilitates gene mutation, as 5-methylcytosine is deaminated to thymine; 10 (ii) aberrant DNA methylation may be associated with allelic loss 9,11-13 and (iii) DNA methylation occurs frequently in CpG islands near regulatory regions of genes and affects the transcription of specific genes. [1][2][3][4] To date, 3 enzymes that possess DNA methyltransferase (DNMT) activity-DNMT1, 14 DNMT3a and DNMT3b, 15 -have been confirmed. Of these, DNMT1 is the major and best known. As DNMT1 has a preference for hemimethylated, rather than unmethylated, substrates in vitro 16 and targets replication foci by binding to proliferating cell nuclear antigen (PCNA), 17 it was recognized as the "maintenance" DNMT that copies methylation patterns after DNA replication. However, some researchers have proposed that DNMT1 possesses both maintenance and de novo DNA methylation activity in vivo, regardless of its preference for substrates in vitro. 4,18 Moreover, recent studies...

To clarify the significance of DNA methylation alterations during renal carcinogenesis, methylome analysis using single-CpG-resolution Infinium array was performed on 29 normal renal cortex tissue (C) samples, 107 non-cancerous renal cortex tissue (N) samples obtained from patients with clear cell renal cell carcinomas (RCCs) and 109 tumorous tissue (T) samples. DNA methylation levels at 4830 CpG sites were already altered in N samples compared with C samples. Unsupervised hierarchical clustering analysis based on DNA methylation levels at the 801 CpG sites, where DNA methylation alterations had occurred in N samples and were inherited by and strengthened in T samples, clustered clear cell RCCs into Cluster A (n = 90) and Cluster B (n = 14). Clinicopathologically aggressive tumors were accumulated in Cluster B, and the cancer-free and overall survival rates of patients in this cluster were significantly lower than those of patients in Cluster A. Clear cell RCCs in Cluster B were characterized by accumulation of DNA hypermethylation on CpG islands and considered to be CpG island methylator phenotype (CIMP)-positive cancers. DNA hypermethylation of the CpG sites on the FAM150A, GRM6, ZNF540, ZFP42, ZNF154, RIMS4, PCDHAC1, KHDRBS2, ASCL2, KCNQ1, PRAC, WNT3A, TRH, FAM78A, ZNF671, SLC13A5 and NKX6-2 genes became hallmarks of CIMP in RCCs. On the other hand, Cluster A was characterized by genome-wide DNA hypomethylation. These data indicated that DNA methylation alterations at precancerous stages may determine tumor aggressiveness and patient outcome. Accumulation of DNA hypermethylation on CpG islands and genome-wide DNA hypomethylation may each underlie distinct pathways of renal carcinogenesis. Abbreviations:BAMCAbacterial artificial chromosome array-based methylated CpG island amplificationCnormal renal cortex tissue obtained from patients without any primary renal tumorCIMPCpG island methylator phenotypeHCChepatocellular carcinomaNnon-cancerous renal cortex tissue obtained from patients with clear cell renal cell carcinomasNCBINational Center for Biotechnology InformationRCCrenal cell carcinomaTtumorous tissueTNMTumor-Node-Metastasis

No abstract