Prostate cancer is the third most commonly diagnosed cancer in men worldwide, and in the United States, this cancer claims the number three spot on the list of leading causes of cancer death among men. Phosphatase with TENsin homology (PTEN) is a tumor suppressor gene that regulates cell growth; germline mutations and somatic deletion of PTEN have been implicated in many different types of cancer, including that of the prostate. Furthermore, several studies have reported that loss of PTEN is associated with more aggressive tumors and poorer patient outcomes. “However, the underlying molecular alterations that drive prostate cancer progression in men with PTEN deleted tumors are not well characterized,” says Dr. Janet Stanford in the Division of Public Health Sciences at Fred Hutch. To address these gaps, the Stanford group conducted and recently published a study in Oncotarget on the role of PTEN loss in recurrence of prostate cancer and primary tumor DNA methylation profiles.
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The authors conducted a prospective cohort study that included 471 men diagnosed with localized prostate cancer with a mean follow-up period of approximately eight years. Tumor samples obtained at radical prostatectomy were used to assess both PTEN status and genome-wide tumor DNA methylation. First, the authors assessed the extent to which PTEN status was associated with recurrence-free survival (see Figure). Compared to patients with intact PTEN, loss of one PTEN copy (hemizygous) was not associated with cancer recurrence. However, loss of both copies (homozygous) was associated with a 2.8-fold increased risk of recurrence. Dr. Milan Geybels, the lead author of the paper, emphasized the importance of these results, “we confirmed the association of PTEN loss with prostate cancer recurrence in an additional large prospective patient cohort, and our results therefore add significantly to the existing evidence.”
DNA methylation of CpG sites across the genome plays a major role in the regulation of gene expression. Changes in DNA methylation levels, with hyper- or hypomethylated CpG regions, and altered gene expression are common characteristics of tumors that likely influence tumor aggressiveness, yet whether prostate tumor DNA methylation profiles are differentially altered according to PTEN status had not previously been investigated. To assess this relationship, the authors conducted epigenome-wide methylation profiling of purified tumor DNA. These analyses revealed that loss of PTEN was associated with extensive differences in methylation. Stanford summarized the results, “Epigenetic profiling of PTEN deleted (any loss) and PTEN intact tumors identified more than 4,200 differentially methylated CpG sites between tumor subtypes, and 46% of these were hypermethylated in the PTEN deleted tumors. We found a panel of CpG sites that when combined into a DNA methylation signature could distinguish between PTEN deleted vs. PTEN intact tumors.” This methylation signature included eighteen CpG sites over a total of thirteen genes. To confirm the robustness of the signature, the authors tested it using The Cancer Genome Atlas (TCGA) prostate cancer dataset, a publically-available resource. Consistent with the initial finding, any loss of PTEN was associated with significantly higher levels of the DNA methylation signature relative to intact PTEN.
These results are novel and advance our understanding of the impact of PTEN loss at the molecular level in prostate cancer. Says Geybels, “This is the first large study of prostate cancer to identify and then confirm in an independent dataset a DNA methylation signature that is uniquely associated with PTEN loss. Prostate tumors with PTEN loss are more aggressive, and these findings therefore provide evidence that aberrant DNA methylation may mediate disease progression in men with PTEN deleted tumors.”
The results from this study have also generated several new questions that may be addressed in future work. Follow-up studies focused on the thirteen genes that comprise the methylation signature may advance our understanding at the molecular level of how or why prostate tumors are more aggressive with loss of PTEN. When asked about the next steps, Stanford stated, “In addition to PTEN loss, other somatic alterations in primary prostate tumors may identify subtypes of the disease with different molecular profiles and patient outcomes. An important goal is to understand the mechanisms and pathways through which these somatic events may alter tumor biology and mediate its aggressiveness. Future studies of DNA methylation profiling may define other unique signatures that can improve classification of disease subtypes and provide novel insights that can be used to improve patient outcomes.”
Also contributing to this project from the Fred Hutch were Drs. Min Fang, Jonathan Wright, Xiaoyu Qu, and Peter Nelson.
Geybels MS, Fang M, Wright JL, Qu X, Bibikova M, Klotzle B, Fan J-B, Feng Z, Ostrander EA, Nelson PS, Stanford JL. 2017. PTEN loss is associated with prostate cancer recurrence and alterations in tumor DNA methylation profiles. Oncotarget. 8(48):84338-84348.
Funding for this study was provided by the National Institutes of Health and Fred Hutch.