Epigenetic markers of prostate cancer in plasma circulating DNA.

Epigenetic differences are a common feature of many diseases, including cancer, and disease-associated changes have even been detected in bodily fluids. DNA modification studies in circulating DNA (cirDNA) may lead to the development of specific non-invasive biomarkers. To test this hypothesis, we investigated cirDNA modifications in prostate cancer patients with locally confined disease (n = 19), in patients with benign prostate hyperplasias (n = 20) and in men without any known prostate disease (n = 20). This initial discovery screen identified 39 disease-associated changes in cirDNA modification, and seven of these were validated using the sodium bisulfite-based mapping of modified cytosines in both the discovery cohort and an independent 38-patient validation cohort. In particular, we showed that the DNA modification of regions adjacent to the gene encoding ring finger protein 219 distinguished prostate cancer from benign hyperplasias with good sensitivity (61%) and specificity (71%). We also showed that repetitive sequences detected in this study were meaningful, as they indicated a highly statistically significant loss of DNA at the pericentromeric region of chromosome 10 in prostate cancer patients (p = 1.8 × 10(-6)). Based on these strong univariate results, we applied machine-learning techniques to develop a multi-locus biomarker that correctly distinguished prostate cancer samples from unaffected controls with 72% accuracy. Lastly, we used systems biology techniques to integrate our data with publicly available DNA modification and transcriptomic data from primary prostate tumors, thereby prioritizing genes for further studies. These data suggest that cirDNA epigenomics are promising source for non-invasive biomarkers.

Tumor suppressor gene ZAC/PLAGL1: altered expression and loss of the nonimprinted allele in pheochromocytomas.

ZAC/PLAGL1 is a novel imprinted tumor suppressor gene encoding an important inducer of cell cycle arrest and apoptosis, and found to be lost during tumorigenesis. We analyzed the significance of ZAC in the development of a rare, usually benign tumor of the adrenal gland: pheochromocytoma (PCC). Twenty-four PCCs were analyzed for the loss of the active nonimprinted allele of ZAC, and nine of the twenty-four PCCs were also assayed for expression of the protein. In thirteen of the cases, a paired nonmalignant tissue was available for analysis. Methylation-specific polymerase chain reaction revealed frequent (15 of 23, 65%) loss of unmethylated DNA in the imprinting control region of ZAC. Immunohistochemistry identified reduced ZAC expression in 56% (5 of 9) of the subset cases. Four of the five PCC cases where reduced expression of ZAC was observed were also positive for the loss of the active ZAC allele. Additionally, the loss of ZAC expression was also found to be frequent in a series of capillary hemangioblastomas and gliomas (6 of 6, 100%, and 17 of 27, 63%, respectively) examined for comparison. In conclusion, our study suggests the involvement of the imprinted ZAC gene in the pathogenesis of PCC.