Abstract 4023: Genome-wide analysis of CpG island methylation identified OTX1, OSR1 and ONECUT2 as biomarkers for recurrent bladder cancer detection in voided urine

Cancers of the urinary bladder (BC) present as muscle-invasive (MIBC) or non-muscle invasive (NMIBC). Major problems with NMIBC are that 70% of the tumors will recur and 10-20% will eventually progress to MIBC. Therefore the patients are monitored by cystoscopy every 3-6 months after transurethral resection of the tumor in order to spot potential recurrences. DNA methylation has been shown to contribute to the pathogenesis cancer and may serve as useful biomarker. Recent studies showed promising urine methylation biomarkers for BC, but none of these were specifically tested for detection of recurrent BCs which are often smaller and hence more difficult to detect than primary tumors. Therefore we aimed to develop an assay specific for the diagnosis of recurrent bladder tumors in voided urine. From our earlier genome-wide study, we selected 8 candidate CGIs (CpG islands) methylated in BC to screen for the detection of recurrent bladder tumors in voided urine. We first screened these 8 CGIs on an independent set of 50 FFPE bladder tumors and 70 urines from age matched individuals without any history of BC as controls using BS-SNaPshot (Bisulfite specific single nucleotide primer extension assay). Subsequently, the 8 CGIs were investigated in a test set of 100 preTUR (before Trans Urethral Resection) urines associated with a concomitant recurrent tumor. We analyzed the sensitivity, specificity, AUC (area under the curve), PPV and NPV of all the individual markers and five best combinations. We then validated this on a separate cohort of 100 preTUR urines samples. Single marker OTX1 identified recurrent bladder tumors in voided urine with a sensitivity of 71% at a specificity of 90% with an AUC of 0.85 (CI: 0.80-0.91, P<0.0001). A 3 gene methylation panel OTX1, ONECUT2 and OSR1 showed a sensitivity of 73% at a specificity of 90% with an AUC of 0.86 (CI: 0.80-0.91, P< 0.0001). Combining this 3-gene panel methylation assay with FGFR3 (fibroblast growth factor receptor 3) mutation assay achieved a sensitivity of 78% at a specificity of 90% with an AUC of 0.87 (CI: 0.82-0.93, P< 0.0001). This panel of markers showed a sensitivity of 100% in detecting bladder tumor tissue DNA. These markers were also investigated on 40 urines collected from patients who are recurrence free for a period of longer than 6 months. A total of 9/40 (22%) urines were positive in these recurrence free patients. The lower specificity of these samples could be due to the anticipatory effect that has been attributed to urine tests, i.e. urines test sees the tumor earlier than cystocopy. We also observed that multiple tumors from a patient are highly concordant in their methylation percentage, which underlines the usefulness of the markers. In summary the panel biomarkers that are identified will be able to detect the recurrent bladder tumors in voided urine, thereby helping in surveillance of patients with bladder cancer.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4023. doi:1538-7445.AM2012-4023

Abstract 2259: Identifying causative genes and prognostic markers for bladder cancer

Upon presentation 70% of the bladder tumors are confined to the epithelial (stage pTa) and stromal layers (stage pT1) of the bladder. These non-muscle invasive tumors (NMI-BC) frequently recur and 10-15% will eventually invade the detrusor muscle and may cause metastases. The management of these tumors is characaterized by the difficult choice between transurethral resection (TURB) or total bladder removal by cystectomy. Our first objective was to identify DNA copy number changes as biomarkers predicting tumor progression in high grade NMI-BC to aid decision making. A set of 18 DNA samples isolated from fresh frozen high grade NMI-BC was hybridized on Illumina SNP arrays. Analysis of alterations was done with Nexus software. Hierarchical clustering of significantly differing SNPs showed that tumors that progressed and those that did not clustered separately. A comparison of the differential alterations between tumor groups resulted in many chromosomal locations encompassing chromosome 1p, 2-6, 8-10, 12p, 13q, 17q, 18p and 22q that were fit for inclusion in a validation assay. A custom Agilent 15K array was designed to include probes for these locations. We collected a retrospective series of 96 high grade NMI-BC paraffin embedded tumors with a median follow-up of 5 years. Half of these samples were from patients who developed a muscle-invasive tumor at a later time. Preliminary results show an interesting region on chromosome 8 with the best independent prognostic value. This region and the genes therein will be studied in more detail. This and other validated regions will be used to design a definitive prognostic assay.

Complex losses on chromosome 9 characterize bladder tumors regardless of stage. We hypothesized that the complex rearrangements on this chromosome in BC are the results of attempts of the tumor cell to loose tumor suppressor genes whilst struggling to retain other (onco)genes. Therefore, the second aim was to identify pivotal tumor suppressor and/or oncogenes on chromosome 9 for development of bladder cancer, with the aim to exploit these genes or the pathways in which they function as potential targets for therapy for tumors from all stage categories. A custom Agilent 44K array was designed, containing probes for all genes on chromosome 9 (and 8p). DNA from a series of 144 tumors from different stages was hybridized to the arrays. Analysis of alterations was done with Nexus software. We found many regions of loss as expected but also a region that appeared amplified in most tumors. Several candidate regions were validated of their copy number status with specific MLPA assays. Two potential candidate genes from chromosome 9 were selected for mutational and functional analysis. In one of those genes we found several mutations affecting protein function, suggesting that this gene is a new tumor suppressor gene for bladder cancer.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2259. doi:10.1158/1538-7445.AM2011-2259

In silico analysis of kinase expression identifies WEE1 as a gatekeeper against mitotic catastrophe in glioblastoma

Kinases execute pivotal cellular functions and are therefore widely investigated as potential targets in anticancer treatment. Here we analyze the kinase gene expression profiles of various tumor types and reveal the wee1 kinase to be overexpressed in glioblastomas. We demonstrate that WEE1 is a major regulator of the G(2) checkpoint in glioblastoma cells. Inhibition of WEE1 by siRNA or small molecular compound in cells exposed to DNA damaging agents results in abrogation of the G(2) arrest, premature termination of DNA repair, and cell death. Importantly, we show that the small-molecule inhibitor of WEE1 sensitizes glioblastoma to ionizing radiation in vivo. Our results suggest that inhibition of WEE1 kinase holds potential as a therapeutic approach in treatment of glioblastoma.