Pan Cancer Epigenetic Signature Readable in Circulating Tumor DNA

    If cancer has a signature, the dotted line may be a gene called ZNF154, say scientists at the National Institutes of Health. Although the scientists don’t know exactly what the gene does, they do know that it may carry distinctive methylation marks, and that these marks have been associated with multiple types of cancer. In their most recent work, the scientists have evaluated whether these marks might serve as a universal cancer biomarker.

    The team, led by Laura Elnitski, Ph.D., a computational biologist at the NIH’s National Human Genome Research Institute, previously identified hypermethylation around the ZNF154 gene in 15 solid epithelial tumor types from 13 different organs. In their current work, which was described February 5 in the Journal of Molecular Diagnostics, these scientists are going further. They are testing whether ZNF154 hypermethylation can distinguish tumor samples from normal tissue samples. What’s more, the scientists are running computer simulations to evaluate whether the tiny amounts of tumor DNA that end up circulating in blood can be detected on the basis of ZNF hypermethylation.

    The results of this work led the scientists to conclude that ZNF hypermethylation is a relevant biomarker for identifying solid tumor DNA. Moreover, the scientists say that it “may have utility as a generalizable biomarker for circulating tumor DNA.”

    Details appeared in the Journal of Molecular Diagnostics article (“Robust Detection of DNA Hypermethylation of ZNF154 as a Pan-Cancer Locus with in Silico Modeling for Blood-Based Diagnostic Development”), which described how the magnitude and pattern of ZNF hypermethylation across colon, lung, breast, stomach, and endometrial tumor samples were measured using next-generation bisulfite amplicon sequencing.

    “To evaluate this site as a possible pan-cancer marker, we compare the ability of several sequence analysis methods to distinguish the five tumor types (184 tumor samples) from normal tissue samples (n = 34),” wrote the authors. “The classification performance for the strongest method, measured by the area under (the receiver operating characteristic) curve (AUC), is 0.96, close to a perfect value of 1. Furthermore, in a computational simulation of circulating tumor DNA, we were able to detect limited amounts of tumor DNA diluted with normal DNA.”

    Even when the scientists reduced the amount of methylated molecules by 99%, the computer could still detect the cancer-related methylation marks in the mixture. Knowing that tumors often shed DNA into the bloodstream, the scientists calculated the proportions of circulating tumor DNA that could be found in the blood.

    Going forward, Dr. Elnitski’s group will begin screening blood samples from patients with bladder, breast, colon, pancreatic, and prostate cancers to determine the accuracy of detection at low levels of circulating DNA. Tumor DNA in a person with cancer typically constitutes 1–10% of all DNA circulating in the bloodstream. The group noted that when 10% of the circulating DNA contains the tumor signature, their detection rate is quite good. Because the methylation could be detected at such low levels, it should be adequate to detect advanced cancer as well as some intermediate and early tumors, depending on the type.

    Dr. Elnitski’s group will also collaborate with Christina Annunziata, M.D., Ph.D., an investigator at the National Cancer Institute (NCI). The scientists will test blood samples from women with ovarian cancer to validate the process over the course of treatment and to determine if this type of analysis leads to improved detection of a recurrence and, ultimately, improved outcomes.

    Current blood tests are specific to a known tumor type. In other words, clinicians must first find the tumor, remove a sample of it and determine its genome sequence. Once the tumor-specific mutations are known, they can be tracked for appearance in the blood. The potential of the new approach is that no prior knowledge of cancer is required, it would be less intrusive than other screening approaches like colonoscopies and mammograms and it could be used to follow individuals at high risk for cancer or to monitor the activity of a tumor during treatment.

    “Finding a distinctive methylation-based signature is…a technical challenge, but we found an elevated methylation signature around the gene known as ZNF154 that is unique to tumors,” declared Dr. Elnitski. “We have laid the groundwork for developing a diagnostic test, which offers the hope of catching cancer earlier and dramatically improving the survival rate of people with many types of cancer.”