Dana-Farber researchers detect early kidney cancer with DNA methylation-screening blood test

Using a DNA-sequencing blood test, researchers at Dana-Farber Cancer Institute found they were able to spot some of the earliest signs of kidney cancer, a potentially fatal disease that currently lacks a broad screening exam.

In early studies, the test was nearly 100% accurate at identifying people with kidney cancer based on their blood samples, using a combination of high-throughput sequencing and analyses of DNA methylation—the chemical process that tags certain sequences of genetic code with additional molecules that alter their function.

It’s a different method than other DNA-based liquid biopsy tests, which may read through the code itself to search for specific mutations linked to different cancers. Instead, the test hunts for DNA released by cancer cells into the bloodstream marked with abnormal methylation patterns compared to DNA from healthy cells, which can be used as clearer evidence of the disease.

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These tactics have underpinned the development of blood tests for other types of cancer, but kidney cancer has always served as an obstacle.

The disease “is one of the hardest tumors to detect, because it doesn't shed as much DNA as other tumors," said Matthew Freedman, M.D., a medical oncologist at Dana-Farber and co-senior author of the study, which was published in Nature Medicine. By identifying these patterns in small amounts of DNA, the researchers’ findings are “a proof of principle that early stage disease is detectable," Freedman added.

Dubbed cfMeDIP-seq, for cell-free methylated DNA immunoprecipitation, the researchers also believe their method could be used on urine samples as an even less invasive testing method. However, it is currently less accurate than using blood. They said they think its performance could be improved and potentially validated through expanded clinical trials.

"Hopefully we can scale this to a much larger level and detect cancer earlier so we can act earlier," said co-senior author Toni Choueiri, director of Dana-Farber’s Lank Center for Genitourinary Oncology.

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In blood samples from 99 patients with early and advanced kidney cancer—as well as 15 with metastatic bladder cancer and 28 cancer-free participants acting as a control—the test was able to detect small, localized kidney tumors that can be curable.

These early cancers typically do not cause symptoms, with many being discovered during abdominal scans ordered for other medical reasons. However, there is no early imaging or kidney screening test currently recommended for the general population, according to Dana-Farber, with about one-third of cancers being diagnosed after they have grown and spread beyond the kidney.

To start, a diagnostic test based on this method may be used to first screen people with a family history of kidney cancer or those previously had kidney cancer, said Choueiri. "We need to be specific first, before making it totally mainstream.”