Researchers studying biomarkers linked to gastrointestinal cancers have successfully created a biomarker algorithm that, when paired with a noninvasive technique for collecting esophageal cells, may help doctors determine which patients have esophageal cancer or precancerous conditions like Barrett’s esophagus (BE) or high-grade dysplasia.
Researchers at the Johns Hopkins Kimmel Cancer Center and the Johns Hopkins University School of Medicine have crafted a biomarker algorithm by examining known biomarkers associated with gastrointestinal cancers. When used alongside a noninvasive method for gathering esophageal cells, this algorithm might assist clinicians in identifying patients with esophageal cancer or precancerous states such as Barrett’s esophagus (BE) or high-grade dysplasia. Ordinarily, these evaluations require an endoscopy, a more invasive procedure conducted under anesthesia.
If further studies validate this method, it could potentially serve as a preliminary test to determine which patients should undergo endoscopy for a conclusive diagnosis. The findings were published on January 17 in the American Journal of Gastroenterology.
According to Stephen Meltzer, M.D., a senior author of the study and a professor of medicine and oncology at the Johns Hopkins University School of Medicine, “Our study took a structured approach to pinpoint biomarkers, and we believe this is the first research to identify biomarkers for Barrett’s esophagus, esophageal adenocarcinoma, and high-grade dysplasia in this manner.” Meltzer, who is also a clinical research professor for the American Cancer Society, explained that their algorithm included the methylation of genes USP44, TBC1D30, and NELL1, which have been extensively studied as diagnostic markers in different cancers.
Methylation, a chemical modification, can influence gene expression and may contribute to cancer progression. Notably, USP44 has been previously identified as a marker for prostate, liver, and colorectal cancers. TBC1D30 has also shown significant methylation in colorectal cancer studies. NELL1 has been identified as a diagnostic marker for both Barrett’s esophagus and colorectal cancer, with its hypermethylation linked to the development of gastric, kidney, and lung cancers.
For this study, researchers analyzed six datasets from the Gene Expression Omnibus database to find biomarkers that were at least 30% methylated in BE and less than 5% in normal tissues, leading to the identification of 30 candidate biomarkers for additional research. Laboratory tests using a methylation-based polymerase chain reaction narrowed these down to 12 biomarkers that exhibited significantly higher methylation levels in BE compared to normal tissues.
From these 12 biomarkers, the team selected seven (GRAMD1B, USP44, HOXB13, A1BG, SPX, TBC1D30, and eg00720137) for further testing, along with five additional biomarkers (CDH13, FLT3, NELL1, TAC1, and SSTI) identified in earlier studies. Initially, they analyzed the biomarkers in 21 pairs of archived normal and Barrett’s tissue samples. Following that, they evaluated the biomarkers in 234 nonendoscopic esophageal sponge samples sourced from patients with BE and other patients undergoing endoscopy at Johns Hopkins, the Allegheny Health Network in Pittsburgh, and Erasmus University in the Netherlands. This group comprised 78 individuals with a normal esophagus, 77 with BE, 12 with high-grade dysplasia, five with low-grade dysplasia, one with indeterminate dysplasia, and 61 with esophageal adenocarcinoma.
To capture these samples, participants swallowed a small sponge encased in a gelatin capsule, which had a string attached. Once the capsule reached the bottom of the esophagus, the gelatin dissolved, allowing the sponge to expand. A clinician then gently pulled the string to retrieve the sponge, collecting cells from the esophagus as it was drawn back up.
The samples were gathered just before endoscopy or during a follow-up visit within three months post-endoscopy. All participants had a confirmed diagnosis of esophageal cancer, BE or high-grade dysplasia, or had undergone a biopsy that confirmed they did not have these conditions. The average age of participants was 65 years, with the majority being male (66%) and from the U.S. (82%).
The researchers divided the sponge samples into a training group of 199 samples and a testing group of 35 samples, evaluating all 12 biomarkers within the training group. Using the results obtained, they formulated a three-biomarker algorithm involving USP44, TBCD1D30, NELL1, alongside age and sex. This algorithm demonstrated an area under the curve (AUC) of nearly 0.97 when distinguishing between healthy tissue and cases of esophageal cancer and high-grade dysplasia, indicating strong performance. For differentiating healthy patients from those with Barrett’s esophagus and either high-grade dysplasia or esophageal cancer, the AUC was 0.86, which is also considered effective, according to Meltzer.
Meltzer, who leads the GI Early Detection Biomarkers Laboratory at Johns Hopkins, stated, “The purpose of this sponge-biomarker test is not to give a definitive diagnosis. Instead, it is to indicate to patients that they may require an endoscopy due to abnormal results in their methylation tests.”
He noted that the incidence of esophageal cancer has risen fivefold in the Western population over the last 40 years, making it the eighth most prevalent cancer and the sixth leading cause of cancer-related deaths worldwide. It’s estimated that around 5%-12% of patients with gastroesophageal reflux disease (GERD) develop BE, although the precise percentage is uncertain because many cases of BE remain undiagnosed.
With esophageal adenocarcinoma being the predominant type of esophageal cancer in the U.S., Meltzer emphasized the essential need for large-scale screening studies to evaluate whether these biomarkers can enhance the identification of Barrett’s esophagus and esophageal adenocarcinoma, ultimately improving patient survival rates.
The study also included contributions from coauthors Andrew Kalra, Ke Ma, Yulan Cheng, Leslie Cope, Yifan Yang, Simran Jit, Yousra Ahmed, Shayan Gheshlaghi, Vincent Castillo, Russell Hales, Vincent Lam, Kristin Marrone, Ken Hui, Michelle Ma, Robert Hughes, Venkata Akshintala, Kathy Bull-Henry, Jinny Ha, Karim Boudadi, Zachariah Foda, Richard Battafarano, Mouen Khashab, Eun Ji Shin, Olaya Brewer Gutierrez, and Saowanee Ngamruengphong from Johns Hopkins, along with researchers from the Allegheny Health Network, Thomas Jefferson University in Philadelphia, Jefferson Einstein Philadelphia Hospital, Eastern Virginia Medical School in Norfolk, and Previse in Baltimore, the manufacturer of the sponge test.
