Researchers find unique epigenetic signature across five tumor types

A DNA molecule is methylated on both strands on the center cytosine. IMAGE COURTESY OF WIKIMEDIA USER CHRISTOPH BOCK

The epigenetic modification is the methylation of DNA at a cytosine base. In a recent study published in the Journal of Molecular Diagnostics, the NHGRI researchers showed that recurrent, aberrant methylation of DNA at ZNF154 CpG island can alter the expression of the gene containing the modification like a dimmer on a light switch.

“Finding the methylation signature was an incredibly arduous and valuable process,” said NHGRI Scientific Director Dan Kastner in an NIH press release. 

The study was led by Laura Elnitski, a computational biologist in the Division of Intramural Research at NHGRI. Elnitiski’s team was able to uncover the methylation mark in colon, lung, breast, stomach and endometrial cancers and they think the signature could exist in many more types of the disease.

Her group first discovered hypermethylation of the CpG island near human ZNF154 in 2013 by using arrays that detected methylation levels at select CpG sites. They found hypermethylation in 15 tumor types in 13 different organs, suggesting that this modification could be a universal cancer biomarker.

“No one in my group slept the night after that discovery,” says Elnitski in the press release. “We were so excited when we found this candidate biomarker. It’s the first of its kind to apply to so many types of cancer.”

A main challenge of cancer treatment has been the small number of reliable technologies that can detect the disease in early stages. By the time a tumor is visible on a scan, it often is advanced. But detection techniques that rely on next-generation sequencing, to find genomic signatures that distinguish cancer cells from normal cells have shown promise. The sequence reads are used to detect specific changes in DNA and infer patterns from a vast range of samples. These reads allow for early and consistent detection of mutations or modifications that are characteristic of cancer cells. For their diagnostic test, Elnitski’s group did not use next-generation sequencing on samples recovered from tumor biopsies but on other sources of tumor DNA that potentially can be detected before the tumor can be seen on a scan.

The first source was cell-free tumor DNA, which can be found in venous blood, buccal epithelium, saliva, urine, stools and bronchial aspirates. Venous blood also can contain circulating tumor cells, which is the second source of DNA. Both circulating cells and cell-free tumor DNA are sources from which DNA can be tested for common mutations and, as done in this study, genomic signatures such as hypermethylation of certain DNA segments.

Instead of scanning a large number of sites for modifications, the team used a more refined and cost-effective method to analyze cytosine methylation in CpG island modification. Elnitski and her team used polymerase chain reaction to identify modified versus unmodified cytosines from the DNA of healthy individuals and cancer patients in a high-throughput and easily quantifiable fashion. According to the journal article, this method provided greater resolution of the target area than in the 2013 study and showed patterns of DNA methylation in tumors that previously were unknown.

“Finding a distinctive methylation-based signature is like looking for a spruce tree in a pine forest,” Elnitski said. “It’s a technical challenge to identify.”

Elnitski and her team took on the challenge by developing computational tools that can characterize the methylated bases and by using computational simulation to show how these modification signatures can be used reliably to identify cancer. It was these techniques that helped the researchers find consistent elevation of ZNF154 CpG island methylation across the five different tumor types.

All the information to detect this specific CpG methylation signature can be gathered from a small amount of DNA, about the same amount contained in a basic blood sample. The next step is honing the methodology and developing a simple blood test that can be used in clinics for rapid and early cancer screening.

Aditi Dubey Aditi Dubey is a postdoctoral associate at New York University studying mechanisms of placode development in Xenopus.