Gene Sequencing, Esophageal Brushings May Identify Patients With Barrett’s Esophagus at Risk for Cancer Progression

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A combination of esophageal brushing and extensive genetic sequencing of the sample collected may detect chromosome alterations in people with Barrett’s esophagus, identifying patients at risk for progressing to esophageal cancer. These findings were published by Douville et al in Gastroenterology.

In Barrett’s esophagus, chronic acid reflux from the stomach damages the cells lining the lower esophagus, causing them to become more like cells of the lower digestive system. Cells in the lower esophagus progress through several precancerous stages before sometimes developing into esophageal adenocarcinoma, a cancer with a 5-year survival rate below 20%. Barrett’s esophagus is the only known precursor to esophageal adenocarcinoma.

Role of Aneuploidy

Clinicians can detect these progressive states in patients with Barrett’s esophagus by looking for chromosomal alterations known as aneuploidy—a common feature in most cancer cells—but until now, the process has involved multiple biopsies.

A single esophageal brushing paired with the sequencing technique called RealSeqS is sensitive and specific enough to identify aneuploidy at several stages of Barrett’s esophagus progression and can even match specific types of aneuploidy with specific stages of the disease, the researchers said.

“Aneuploidy has long been implicated in the development, initiation, or progression of esophageal cancer, but the assays or experimental methods to detect this have not been as easily achieved or as high throughput as we would have wanted to allow for clinical implementation,” said senior study author Chetan Bettegowda, MD, PhD, Jennison and Novak Families Professor of Neurosurgery at the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University.

The method could help clinicians identify people at higher risk of having Barrett’s esophagus progress to esophageal adenocarcinoma, “instituting more intensive follow-up for those patients or instituting treatments at earlier stages of the disease,” said Dr. Bettegowda.

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Esophageal Brushing and RealSeqS

Esophageal brushing uses a soft brush attachment for an endoscope to collect cells from the esophageal lining. The method can sample cells from a larger surface area of the esophagus than a usual biopsy. Endoscopy, often with brushing, “is part of the standard of care for people who have Barrett’s,” said Dr. Bettegowda, so incorporating the aneuploidy detection method would not substantially change clinical practice.

Only a few cells out of hundreds sampled through brushing may demonstrate aneuploidy, however, so combining brushing with massively parallel sequencing is key to finding these cells. The researchers used a technique called RealSeqS to look across more than 350,000 regions of the genome to identify specific chromosome arm alterations. RealSeqS can typically detect aneuploidy at the level of about 1 in 200 cells, which is necessary when large portions of the esophageal brushing are derived from normal cells, said study lead author Christopher Douville, PhD, the Kimmel Center researcher who designed RealSeqS.

“The method is quick and can process hundreds of samples cost effectively, making it an ideal choice for Barrett’s esophagus research,” said Dr. Douville.

The researchers obtained esophageal brushings from patients without Barrett’s esophagus; with Barrett’s esophagus and no abnormal cells; with Barrett’s esophagus and either low-grade or high-grade cell abnormalities; and patients with esophageal adenocarcinoma. They trained their identification system to distinguish brushings from patients with Barrett’s esophagus without cell abnormalities from those with adenocarcinoma using samples from 79 patients. The research team then looked at samples from 268 patients to test whether the method could distinguish different stages of Barrett’s esophagus progression.

Study Findings

The team identified a threshold of aneuploidy that distinguished patients with high-grade cell abnormalities and adenocarcinoma from patients with Barrett’s esophagus and no cell abnormalities. At this threshold, the method identified 232 high-risk patients, or 86.7% of cases.

The method also identified specific chromosomal arm changes at each stage of Barrett’s esophagus progression toward adenocarcinoma. Some of these specific changes have already been linked to disease stages by previous research, “but they were not comprehensive enough to be used in some diagnostic or prognostic way,” said Dr. Douville.

The researchers used these changes to develop an assessment tool they called BAD (Barrett’s Aneuploidy Decision) for distinguishing stages of Barrett’s esophagus progression. The tool could be especially useful for identifying high-risk individuals when cell biopsies look benign, because the BAD tool points out molecular changes that are linked to more aggressive disease, said Dr. Bettegowda.

“Aneuploidy is as universal a biomarker as we can find at the moment for cancer, so we are excited to see how we can employ this technology for a multitude of cancers,” he concluded. “We are optimistic that given the versatility of the RealSeqS assay, we could study other disease processes, other cancer types, and potentially find other ways to intervene earlier.”

Disclosure: The work was supported by the National Institutes of Health; the Burroughs Wellcome Career Award for Medical Scientists; Earlier Detection of Cancers Using Non-Plasma Liquid Biopsies; The Virginia and D.K. Ludwig Fund for Cancer Research; The Sol Goldman Sequencing Facility at Johns Hopkins; and The Conrad R. Hilton Foundation. For full disclosures of the study authors, visit

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