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PITX2 Methylation Biomarker Test Validated on Prostate Cancer Tissue Biopsies


NEW YORK (GenomeWeb) – Researchers in Germany have found that a PCR-based method to detect methylation of a biomarker gene found in biopsy samples could anticipate prostate cancer recurrence and be used to prevent unneeded radical treatments. 

The assay detects methylation of the PITX2 gene, and was shown to discriminate between cancer and non-cancerous tissue as well as to predict biochemical recurrence after surgery. Importantly, the researchers also found the assay was sensitive enough that it could yield results even with small core needle biopsy samples.

A study describing the work, published yesterday in The Journal of Molecular Diagnostics, is purportedly the first to determine whether PITX2 methylation can be used for individualized risk assessment of prostate cancer using core biopsy tissue.

Glen Kristiansen, the corresponding author on the study and the director of the Institute of Pathology at the University Hospital Bonn, told GenomeWeb his research team took the initial steps to identify PITX2 methylation as a marker of prostate cancer about 10 years ago. 

The group was part of a scientific collaboration with Berlin-based Epigenomics at the time. In 2006, that firm took initial steps to bring a PITX2-based test through US Food and Drug Administration clearance process, and a few years later it was seeking diagnostics partners for the test and contemplating the US market. But instead, the firm's Epi ProColon blood based colorectal cancer test became the firm's first FDA-approved test in 2016. 

Kristiansen noted that Therawis Diagnostics is currently developing a test for PITX2 as a marker to predict effectiveness of anthracycline treatment in patients with triple negative and other high-risk breast cancers, and that the firm has entered a co-development partnership with Qiagen.

The partnership may ultimately allow the test to become "widely available in standardized workflows for routine diagnostics" and potentially become part of clinical routine globally, Kristiansen said.

Meantime, Kristiansen and his colleagues developed a qPCR-based workflow to detect methylation in the PITX2 gene, specifically in degraded formalin-fixed and paraffin-embedded samples.

The method is based on proprietary technology from Epigenomics called HeavyMethyl, which uses real-time PCR along with blockers and probes that ensure methylation-specific amplification and detection, according to Epigenomics' website. The method is also suited to detecting small amounts of circulating tumor DNA in patient blood samples.

The JMD study tested the method on three different cohorts. First, it examined matched samples of neoplastic and non-neoplastic tissue from 24 patients with prostate cancer, concluding the assay can reliably differentiate the two. Then it examined 300 patients who had undergone radical prostatectomy, finding that the assay could predict an increased risk of biochemical recurrence. 

Finally, the study examined a cohort of 720 fine needle biopsies from 63 patients with and without cancer, and determined that methylation levels were assessable in 95 percent of the samples.

"Prior studies ... had used tissues from radical prostatectomy specimens, which provide ample material for analysis," Kristiansen said, while the JMD research, "Is the first to demonstrate the applicability of our assay to the minute amounts of tissue that can be retrieved from the paraffin block of a prostate biopsy."

In the research, the group also used a DNA extraction and bisulfite conversion kit optimized for FFPE samples from Analytik Jena that Kristiansen said his group also helped to develop, called innuConvert.

Kristiansen was recently part of a team that found methylation status of PITX2 and an adjacent long non-coding RNA could be independent predictors for overall survival in patients with squamous cell carcinoma of the head and neck region. That study concluded that tissue-based methylation testing could potentially be used to identify patients requiring more radical treatments.

Although Epigenomics owns patents on PITX2 methylation as a prognostic and predictive biomarker and has previously developed a diagnostic test for outcome prediction in prostate cancer patients, that test "is not suitable for biopsies at the moment," Kristiansen said.

However, "We feel that further validation on a larger biopsy cohort is the next step to take before considering the development of a [commercially available] diagnostic test," he said.

Nevertheless, overtreatment of prostate cancer patients "is a fundamental problem," Kristiansen said, and there is an unmet need for a test that can be used before surgical resection of the prostate.

"Only a test that works on biopsies is suited to identify patients who will not benefit from a radical treatment and who do not need a surgical tumor resection," he said.

When it comes down to it, "The question now for every clinician caring for a patient with newly diagnosed prostate cancer, is whom not to treat actively but to leave on active surveillance," he said, adding, "PITX2 is a promising candidate biomarker that will need to be evaluated for this indication."