Pan-CDK inhibition augments cisplatin lethality in nasopharyngeal carcinoma cell lines and xenograft models.

In addition to their canonical roles in regulating cell cycle transition and transcription, cyclin-dependent kinases (CDKs) have been shown to coordinate DNA damage response pathways, suggesting a rational pairing of CDK inhibitors with genotoxic chemotherapeutic agents in the treatment of human malignancies. Here, we report that roniciclib (BAY1000394), a potent pan-CDK inhibitor, displays promising anti-neoplastic activity as a single agent and potentiates cisplatin lethality in preclinical nasopharyngeal carcinoma (NPC) models. Proliferation of the NPC cell lines HONE-1, CNE-2, C666-1, and HK-1 was effectively curbed by roniciclib treatment, with IC50 values between 11 and 38 nmol/L. These anticancer effects were mediated by pleiotropic mechanisms consistent with successful blockade of cell cycle CDKs 1, 2, 3, and 4 and transcriptional CDKs 7 and 9, ultimately resulting in arrest at G1/S and G2/M, downregulation of the transcriptional apparatus, and repression of anti-apoptotic proteins. Considerably enhanced tumor cell apoptosis was achieved following combined treatment with 10 nmol/L roniciclib and 2.0 µmol/L cisplatin; this combination therapy achieved a response over 250% greater than either drug alone. Although roniciclib chemosensitized NPC cells to cisplatin, it did not sensitize untransformed (NP69) cells. The administration of 0.5 mg/kg roniciclib to BALB/c xenograft mice was well tolerated and effectively restrained tumor growth comparable to treatment with 6 mg/kg cisplatin, whereas combining these two agents produced far greater tumor suppression than either of the monotherapies. In summary, these data demonstrate that roniciclib has strong anti-NPC activity and synergizes with cisplatin chemotherapy at clinically relevant doses, thus justifying further evaluation of this combinatorial approach in clinical settings.

DNA methylation subgroups and the CpG island methylator phenotype in gastric cancer: a comprehensive profiling approach.

BACKGROUND: Methylation-induced silencing of promoter CpG islands in tumor suppressor genes plays an important role in human carcinogenesis. In colorectal cancer, the CpG island methylator phenotype (CIMP) is defined as widespread and elevated levels of DNA methylation and CIMP+ tumors have distinctive clinicopathological and molecular features. In contrast, the existence of a comparable CIMP subtype in gastric cancer (GC) has not been clearly established. To further investigate this issue, in the present study we performed comprehensive DNA methylation profiling of a well-characterised series of primary GC. METHODS: The methylation status of 1,421 autosomal CpG sites located within 768 cancer-related genes was investigated using the Illumina GoldenGate Methylation Panel I assay on DNA extracted from 60 gastric tumors and matched tumor-adjacent gastric tissue pairs. Methylation data was analysed using a recursively partitioned mixture model and investigated for associations with clinicopathological and molecular features including age, Helicobacter pylori status, tumor site, patient survival, microsatellite instability and BRAF and KRAS mutations. RESULTS: A total of 147 genes were differentially methylated between tumor and matched tumor-adjacent gastric tissue, with HOXA5 and hedgehog signalling being the top-ranked gene and signalling pathway, respectively. Unsupervised clustering of methylation data revealed the existence of 6 subgroups under two main clusters, referred to as L (low methylation; 28% of cases) and H (high methylation; 72%). Female patients were over-represented in the H tumor group compared to L group (36% vs 6%; P = 0.024), however no other significant differences in clinicopathological or molecular features were apparent. CpG sites that were hypermethylated in group H were more frequently located in CpG islands and marked for polycomb occupancy. CONCLUSIONS: High-throughput methylation analysis implicates genes involved in embryonic development and hedgehog signaling in gastric tumorigenesis. GC is comprised of two major methylation subtypes, with the highly methylated group showing some features consistent with a CpG island methylator phenotype.

Diagnostic and prognostic utility of a DNA hypermethylated gene signature in prostate cancer.

We aimed to identify a prostate cancer DNA hypermethylation microarray signature (denoted as PHYMA) that differentiates prostate cancer from benign prostate hyperplasia (BPH), high from low-grade and lethal from non-lethal cancers. This is a non-randomized retrospective study in 111 local Asian men (87 prostate cancers and 24 BPH) treated from 1995 to 2009 in our institution. Archival prostate epithelia were laser-capture microdissected and genomic DNA extracted and bisulfite-converted. Samples were profiled using Illumina GoldenGate Methylation microarray, with raw data processed by GenomeStudio. A classification model was generated using support vector machine, consisting of a 55-probe DNA methylation signature of 46 genes. The model was independently validated on an internal testing dataset which yielded cancer detection sensitivity and specificity of 95.3% and 100% respectively, with overall accuracy of 96.4%. Second validation on another independent western cohort yielded 89.8% sensitivity and 66.7% specificity, with overall accuracy of 88.7%. A PHYMA score was developed for each sample based on the state of methylation in the PHYMA signature. Increasing PHYMA score was significantly associated with higher Gleason score and Gleason primary grade. Men with higher PHYMA scores have poorer survival on univariate (p = 0.0038, HR = 3.89) and multivariate analyses when controlled for (i) clinical stage (p = 0.055, HR = 2.57), and (ii) clinical stage and Gleason score (p = 0.043, HR = 2.61). We further performed bisulfite genomic sequencing on 2 relatively unknown genes to demonstrate robustness of the assay results. PHYMA is thus a signature with high sensitivity and specificity for discriminating tumors from BPH, and has a potential role in early detection and in predicting survival.

The topography of DNA methylation in the non-neoplastic colonic mucosa surrounding colorectal cancers.

The degree of gene hypermethylation in non-neoplastic colonic mucosa (NNCM) is a potentially important event in the development of colorectal cancer (CRC), particularly for the subgroup with a CpG island methylator phenotype (CIMP). In this study, we aimed to use an unbiased and high-throughput approach to evaluate the topography of DNA methylation in the non-neoplastic colonic mucosa (NNCM) surrounding colorectal cancer (CRC). A total of 61 tissue samples comprising 53 NNCM and 8 tumor samples were obtained from hemicolectomy specimens of two CRC patients (Cases 1 and 2). NNCM was stripped from the underlying colonic wall and samples taken at varying distances from the tumor. The level of DNA methylation in NNCM and tumor tissues was assessed at 1,505 CpG sites in 807 cancer-related genes using Illumina GoldenGate® methylation arrays. Case 1 tumor showed significantly higher levels of methylation compared to surrounding NNCM samples (P < 0.001). The average level of methylation in NNCM decreased with increasing distance from the tumor (r = -0.418; P = 0.017), however this was not continuous and "patches" with higher levels of methylation were observed. Case 2 tumor was less methylated than Case 1 tumor (average ß-value 0.181 vs. 0.415) and no significant difference in the level of methylation was observed in comparison to the surrounding NNCM. No evidence was found for a diminishing gradient of methylation in the NNCM surrounding CRC with a high level of methylation. Further work is required to determine whether CIMP+ CRC develop from within "patches" of NCCM that display high levels of methylation.

Chlorin e6-polyvinylpyrrolidone mediated photodynamic therapy--A potential bladder sparing option for high risk non-muscle invasive bladder cancer.

BACKGROUND: Bladder sparing treatment options for high risk non-muscle invasive blader cancer (NMIBC) after intravesical Bacillus Calmette-Guerin (BCG) failure are limited. OBJECTIVE: To evaluate photodynamic therapy (PDT) using chlorin e6-polyvinylpyrrolidone (Ce6-PVP) as a bladder sparing therapy for NMIBC refractory to intravesical BCG therapy. MATERIALS AND METHODS: Between July 2004 and June 2009, patients with recurrent NMIBC after induction intravesical BCG therapy were treated with PDT performed with a 665nm laser and light dosimetry of 10-24J/cm(2). The patients underwent cystoscopic surveillance for tumour recurrence post PDT. Post treatment lower urinary tract symptoms and bladder capacity were also monitored. Serum and urine samples were collected for spectrometric quantification of photosensitizer levels. RESULTS: Five patients underwent PDT, with a total of seven treatments performed. One patient received intravenous Ce6-PVP, while the rest received intravesical Ce6-PVP.The median age was 80 years (mean 79 years, range 72-88 years). There were three patients with primary CIS of the bladder and two with T1 high grade TCC and CIS of the bladder. At a median follow-up of 29 months (mean 25 months, range 6-36 months), two patients were disease free, two patients developed recurrence and one patient progressed to muscle invasive disease. There were no immediate adverse effects. The patient receiving intravenous Ce6-PVP developed an enterovesical fistula 16 months post PDT. CONCLUSIONS: Despite being a small pilot study, intravesical Ce6-PVP mediated PDT is a feasible bladder sparing treatment option for recurrent high risk non-muscle invasive bladder carcinoma in selected individuals.

Impact of sample heterogeneity on methylation analysis.

The recent emergence of high-throughput arrays for methylation analysis has made the influence of tumor content on the interpretation of methylation levels increasingly pertinent. However, to what degree does tumor content have an influence, and what degree of tumor content makes a specimen acceptable for accurate analysis remains unclear. Taking a systematic approach, we analyzed 98 unselected formalin-fixed and paraffin-embedded gastric tumors and matched normal tissue samples using the Illumina GoldenGate methylation assay. Unsupervised hierarchical clustering showed 2 separate clusters with a significant difference in average tumor content levels. The probes identified to be significantly differentially methylated between the tumors and normals also differed according to the tumor content of the samples included, with the sensitivity of identifying the "top" candidate probes significantly reduced when including samples below 70% tumor content. We also tested whether the removal of the probes featuring single nucleotide polymorphisms and/or DNA repetitive elements, reportedly present in GoldenGate arrays, would significantly affect the study's findings, and found little change in the results with their omission. Our findings suggest that tumor content significantly influences the interpretation of methylation levels and candidate gene identification, and that 70% tumor content may be a suitable threshold for selecting samples for methylation studies.

Comprehensive profiling of DNA methylation in colorectal cancer reveals subgroups with distinct clinicopathological and molecular features.

BACKGROUND: Most previous studies of the CpG island methylator phenotype (CIMP) in colorectal cancer (CRC) have been conducted on a relatively small numbers of CpG sites. In the present study we performed comprehensive DNA methylation profiling of CRC with the aim of characterizing CIMP subgroups. METHODS: DNA methylation at 1,505 CpG sites in 807 cancer-related genes was evaluated using the Illumina GoldenGate methylation array in 28 normal colonic mucosa and 91 consecutive CRC samples. Methylation data was analyzed using unsupervised hierarchical clustering. CIMP subgroups were compared for various clinicopathological and molecular features including patient age, tumor site, microsatellite instability (MSI), methylation at a consensus panel of CpG islands and mutations in BRAF and KRAS. RESULTS: A total of 202 CpG sites were differentially methylated between tumor and normal tissue. Unsupervised hierarchical clustering of methylation data from these sites revealed the existence of three CRC subgroups referred to as CIMP-low (CIMP-L, 21% of cases), CIMP-mid (CIMP-M, 14%) and CIMP-high (CIMP-H, 65%). In comparison to CIMP-L tumors, CIMP-H tumors were more often located in the proximal colon and showed more frequent mutation of KRAS and BRAF (P<0.001). CONCLUSIONS: Comprehensive DNA methylation profiling identified three CRC subgroups with distinctive clinicopathological and molecular features. This study suggests that both KRAS and BRAF mutations are involved with the CIMP-H pathway of CRC rather than with distinct CIMP subgroups.

Shorter CAG repeats in androgen receptor and non-GG genotypes in prostate-specific antigen loci are associated with decreased risk of benign prostatic hyperplasia and prostate cancer.

The age-adjusted risk of prostate cancer (PC) has increased in Singapore since 1968. We investigated the relationship between polymorphisms in four genes, androgen receptor (AR), prostate-specific antigen (PSA), 5alpha-reductase type II (SRD5A2) and cytochrome P450c17alpha (CYP17) and PC and benign prostatic hyperplasia (BPH). Men with shorter CAG repeats in AR and above 69 years at diagnosis showed a trend of decreased PC risk (OR=0.28, 95% CI=0.08-1.03; p=0.05). Shorter CAG repeats and non-GG genotypes in the AR and PSA loci, respectively, showed a trend of decreased PC risk (OR=0.25, 95% CI=0.06-1.03; p=0.06) and a significantly decreased BPH risk (OR=0.38, 95% CI=0.15-0.94; p=0.04). The results indicate that allelic variation in PSA promoter activity may be androgen dependent and interaction of genes in androgen pathway may influence the risk of BPH and PC in Singapore males.

Membrane transport enhancement of chlorin e6-polyvinylpyrrolidone and its photodynamic efficacy on the chick chorioallantoic model.

We have determined the influences of polyvinylpyrrolidone (PVP) on the topical delivery of chlorin e6 (Ce6) in malignant bladder cells. The chick chorioallantoic membrane (CAM) was used to model the tumor spheroids that resemble small residual bladder tumors prior to vascularization. Macroscopic fluorescence imaging showed that Ce6-PVP-induced fluorescence had a higher sensitivity and specificity for delineating tumor from the adjacent normal CAM compared to Ce6 alone. Nonlinear regression analyses have shown that Ce6-PVP has a longer half-life in the tumor compared to Ce6. The uptake ratio of Ce6-PVP was found to have a 2-fold increase across the CAM when compared to that of Ce6, indicating that PVP was able to facilitate diffusion of Ce6 across the membrane. Confocal laser scanning microscopy further confirmed that Ce6-PVP has better penetration in the CAM as well as in the tumor cells compared to Ce6. The present work contributes to our understanding of the Ce6-PVP drug-polymer system by demonstrating for the first time that the presence of PVP facilitates the transport of Ce6 across the chorioallantoic membrane.