Diagnosis of Bladder Cancer Recurrence Based on Urinary Levels of <em>EOMES</em>, <em>HOXA9</em>, <em>POU4F2</em>, <em>TWIST1</em>, <em>VIM,</em> and <em>ZNF154</em> Hypermethylation

<div><h3>Background</h3><p>Non muscle invasive bladder cancer (NMIBC) has the highest recurrence rate of any malignancy and as many as 70% of patients experience relapse. Aberrant DNA methylation is present in all bladder tumors and can be detected in urine specimens. Previous studies have identified DNA methylation markers that showed significant diagnostic value. We evaluated the significance of the biomarkers for early detection of tumor recurrence in urine.</p> <h3>Methodology/Principal Findings</h3><p>The methylation levels of <em>EOMES</em>, <em>HOXA9</em>, <em>POU4F2</em>, <em>TWIST1</em>, <em>VIM,</em> and <em>ZNF154</em> in urine specimens were measured by real-time PCR (MethyLight). We analyzed 390 urine sediments from 184 patients diagnosed with NMIBC. Urine from 35 age-matched control individuals was used to determine the methylation baseline levels. Recurrence was diagnosed by cystoscopy and verified by histology. Initially, we compared urine from bladder cancer patients and healthy individuals and detected significant hypermethylation of all six markers (P<0.0001) achieving sensitivity in the range 82%–89% and specificity in the range 94%–100%. Following, we validated the urinary hypermethylation for use in recurrence surveillance and found sensitivities of 88–94% and specificities of 43–67%. <em>EOMES</em>, <em>POU4F2</em>, <em>VIM</em> and <em>ZNF154</em> were more frequently methylated in urine from patients with higher grade tumors (P≤0.08). Univariate Cox regression analysis showed that five markers were significantly associated with disease recurrence; <em>HOXA9</em> (HR = 7.8, P = 0.006), <em>POU4F2</em> (HR = 8.5, P = 0.001), <em>TWIST1</em> (HR = 12.0, P = 0.015), <em>VIM</em> (HR = 8.0, P = 0.001), and <em>ZNF154</em> (HR = 13.9, P<0.001). Interestingly, for one group of patients (n = 15) we found that hypermethylation was consistently present in the urine samples despite the lack of tumor recurrences, indicating the presence of a field defect.</p> <h3>Conclusion/Significance</h3><p>Methylation levels of <em>EOMES</em>, <em>HOXA9</em>, <em>POU4F2</em>, <em>TWIST1</em>, <em>VIM,</em> and <em>ZNF154</em> in urine specimens are promising diagnostic biomarkers for bladder cancer recurrence surveillance.</p>