Whether it’s mining the metabolome, probing for epigenetic hot spots, or dissecting tumor phenotypes, researchers are discovering new ways to advance biomarker identification and validation using modern tools.
Although the search for biomarkers presents many challenges, researchers persist because biomarkers have enormous potential for bringing new drugs to market, enhancing molecular diagnostics, and tailoring therapeutics for improved patient stratification and outcome.
Cancer is increasingly viewed as both a genetic and an epigenetic disease. “Aberrant DNA methylation is one of the most studied epigenetic mechanisms in colorectal cancer,” says Noel Doheny, CEO of Epigenomics, the U.S. subsidiary of the same-named German company. “Because aberrant methylation is an early-stage change, it can be used as a biomarker for cancer detection.”
If detected early, colorectal cancer is curable in 80% of cases. Yet it remains one of the highest causes of cancer-related death in the industrialized world. One reason the current tests, colonoscopy and fecal occult blood testing, fail to prevent more deaths, Doheny suggests, is that they have low patient compliance.
“We wanted to identify a blood-based biomarker that could serve as an in vitro screening diagnostic targeting the 40 million individuals who do not participate in current standard testing,” continues Doheny. “Our goal is not to replace colonoscopy, but rather to present a screening tool that, if positive, could be followed up with a colonoscopy.”
Epigenomics used genome-wide discovery methods to identify and characterize hundreds of DNA methylation-based biomarkers for colorectal cancer. Subsequently, the company identified its strongest biomarker candidate—the Septin9 gene. (This gene, which codes for a GTP-binding protein, has a promoter that is hypermethylated in colorectal cancer.) Finally, using this gene as a biomarker, the company developed a blood-based kit.
The test involves two steps. First, DNA is extracted from blood plasma and treated with bisulfite, which converts unmethylated cytosine residues to uracil. (Bisulfite is considered state-of-the art for sensitivity and throughput for molecular diagnostics.) Second, the bisulfite-converted DNA is assayed via duplex real-time PCR to detect if Septin9 DNA is methylated. The test is referred to as “duplex,” says Doheny, because it can support the simultaneous use of an internal control (beta-actin).
“When we used the test and compared it to colonoscopy in a large prospective trial of 8,000 average-risk individuals, we found 67% sensitivity and 88% specificity,” asserts Doheny “The Epi proColon® test is already available in Europe and undergoing FDA evaluation in the United States.”