IMP Healthcare Thought Leadership

Integrated Medical Partners Blog

July 24, 2020

The Role of Biomarkers In the Management of Barrett’s Esophagus

JULY 24, 2020  

The Role of Biomarkers In the Management of Barrett’s Esophagus  

Potential to optimize therapy, surveillance, and screening  


Ashton Ellison, MB ChB 

Department of Medicine
Baylor University Medical Center
Dallas, Texas 

Vani Konda, MD 

Department of Medicine
Baylor University Medical Center
Baylor Scott and White Center of Esophageal Diseases
Dallas, Texas 

Dr Ellison reported no relevant financial conflicts of interest. Dr Konda reported receiving grant support from Ironwood Pharmaceuticals. 


It is well established that selected patients with high-grade dysplasia (HGD)/esophageal adenocarcinoma (EAC) benefit from endoscopic therapy with an acceptable risk profile, but we have yet to develop selection criteria to determine which patients with Barrett’s esophagus and either no evidence of dysplasia or low-grade dysplasia (LGD) would benefit from treatment. 

It is plausible that a subset of these patients may benefit from therapy, whereas others may enjoy longer surveillance intervals. However, we lack the proper tools to confidently direct patients to a rigorous or a relaxed approach. In addition, current screening and surveillance approaches for Barrett’s esophagus are imperfect. Although it is not cost-effective to screen the entire population, the majority of patients who develop esophageal cancer are missed using the current standards. 

Clinicians have used clinical parameters to help risk-stratify patients with Barrett’s esophagus. For example, a clinical model that has been proposed for this purpose includes male sex, smoking, length of the lesion, and LGD at baseline (vs HGD or no dysplasia) to determine if patients are at low, intermediate, or high risk for progression.1 However, better tools are needed to improve risk stratification. For years, biomarkers in Barrett’s esophagus were enticing but remained on the horizon. The advent of recent work on many fronts now suggests that clinical incorporation of biomarkers is within our grasp and potentially allows us to tailor treatments, intervene at earlier stages, lengthen surveillance periods for those at low risk, and identify more patients at risk by offering broader population screening. 

Confirming the Promise of Prediction 

Common techniques to look for biomarkers in the laboratory include immunohistochemistry (IHC), which exploits antibodies binding to specific antigens in tissues, and fluorescence in situ hybridization, which highlights specific DNA/RNA sequences. Promising investigations also have demonstrated valuable information related to epigenetic events, with much attention recently focused on DNA methylation. 

This idea of a reliable biomarker already was proven and is in widespread use to aid in the early detection of other malignancies, such as breast and prostate cancers. Testing for the BRCA gene can help individuals understand their risk for breast cancer and guide preventive treatment plans, and prostate-specific antigen can help direct individual screening for prostate cancer. Metaplastic Barrett’s esophagus tissue specimens have been shown to acquire gene modifications that can lead to cancer even before demonstrating histologic features of dysplasia.2 Nondysplastic Barrett’s esophagus has a high frequency of somatic mutations, from 1.3 to 5.4 mutations per megabase of DNA, more than those found in cancers of the prostate and breast.3 This finding suggests that reliable biomarker(s) could help in the clinical management of Barrett’s esophagus that is nondysplastic, indefinite for dysplasia, or with LGD. 

Tumor suppressor genes are the cell’s mechanism to stop cell cycle replication. Mutations in these genes can lead to uncontrolled cell replication and, hence, cancer. Early promising biomarkers for progression in Barrett’s esophagus were alterations resulting in inactivation of 2 tumor suppressor genes, p16 and p53. Both genes have a role in arresting G1 cell cycle progression.3 However, only a minority of tumors progress along this pathway, which involved an accumulation of alterations in p53 and p16.4 The majority of Barrett’s esophagus–associated tumors (62.5%) develop through the genome-doubling pathway.3 This pathway starts with mutation in the p53 tumor suppressor gene, which is followed by a doubling of the cell’s whole genome, predisposing the cell to genomic instability and oncogene amplification.5 

Aberrations in p53 and their contribution to cancer progression in Barrett’s esophagus are well established. In a recent meta-analysis, Snyder et al showed that aberrant p53 (absent or increased expression) was significantly associated with risk for progression to HGD or EAC in patients with Barrett’s esophagus. The meta-analysis indicated that with p53 aberrancy, the odds ratio (OR) for Barrett’s esophagus to exhibit neoplastic progression was 3.84 (95% CI, 2.79-5.27; P<0.001) in 8 retrospective case-control studies, and the relative risk was 17.31 (95% CI, 9.35-32.08; P<0.001) in 7 cohort studies.6 

Despite the identification of these specific genetic aberrations, it is generally thought that a panel of several biomarkers will be the means to develop a clinically useful test. In a nested case-control study, LGD diagnosis, abnormal expression of p53, and abnormal expression of Aspergillus oryzae lectin were independent predictors for progression to HGD/EAC; when combined into a multivariate biomarker panel, they demonstrated an area under the receiver operating curve (AUC) of 0.73.7 In a Dutch surveillance cohort, a prediction model combined clinical factors including age, circumferential length of the Barrett’s segment, and clonicity features across chromosomes 7, 17, 20q, and c-MYC.8 This model resulted in an AUC of 0.88, a sensitivity of 0.91, and a specificity of 0.38. Additional aberrations, such as single nucleotide polymorphisms, or in microRNA, which functions primarily to inhibit gene expression, have been associated with progression in patients with Barrett’s esophagus and may be worthy of further study.9,10 

Furthermore, epigenetic events that affect regulation and expression of genes have been investigated as potential biomarkers in risk stratification in Barrett’s esophagus. There has been much interest in DNA methylation profiles, with certain profiles associated with progression.11,12 Biomarker panels also may be more promising with stratification along genomic, transcriptomic, and epigenetic profiles. Jammula et al demonstrated this potential by measuring DNA methylation data with genomic and transcriptomic information. They found 4 different subtypes in tissue samples of over 400 cases with Barrett’s esophagus and EAC; each subgroup was associated with different patient outcomes, dysplasia status, and grade.13 They went on to demonstrate in vitro how different subtypes may respond to specific therapeutic pathways and how biomarkers may help indicate specific types of targeted therapy for patients with esophageal cancer. 


 Figure. These images show molecular biomarkers that can be assessed in the context of the histology. This high-risk pattern was demonstrated in nondysplastic Barrett’s esophagus tissue in a patient who subsequently progressed to high-grade dysplasia.  

A. Overexpression of p53 (yellow) and AMACR (red) and loss of p16

B. Infiltration of lymphoctyes (red) and HIF-1 alpha-expressing cells (green). Nuclei are stained blue. 

The current guidelines from the American Gastroenterological Association, American College of Gastroenterology, and American Society for Gastrointestinal Endoscopy for the diagnosis and management of Barrett’s esophagus all suggest that biomarkers show promise but are not recommended for risk stratification.14-16 Although promising biomarkers and pathways have been identified, ultimately, these markers have to be feasible for clinical integration, provide reliably reproducible results, and be validated for meaningful clinical use. 

The TissueCypher Barrett’s Esophagus Assay (Cernostics) is an automated, quantitative assay that is well poised for consideration for clinical use. This commercially available assay uses formalin-fixed and paraffin-embedded tissue from endoscopic biopsies for multiplexed immunofluorescence for p53, p16, AMACR, HER2, cytokeratin-20, CD68, COX-2, HIF-1 alpha, and CD45RO and analyzes a scanned whole slide to extract data of 15 features. Risk scores are then compiled, assigning low, intermediate, and high risk for progression based on previous investigations.17,18 A recent independent, blinded study by Davison et al validated the performance of the prediction model for identifying patients with Barrett’s esophagus who have a higher risk for neoplastic progression.19 They assessed performance of the test in 210 nonprogressors and 58 progressors at 2 institutions and demonstrated predictive power independent of clinical variables. Among patients with nondysplastic Barrett’s esophagus, the positive predictive value for a high-risk score was 26%. The hazard ratio of high versus low risk by the assay test was 3.68 (95% CI, 1.67-8.11; P=0.0112); this result outperforms expert pathologic review, for which the diagnosis of LGD versus nondysplasia is 1.64 (95% CI, 0.68-3.95; P=0.27). This test suggested a similar probability of progression for patients who had nondysplastic Barrett’s esophagus on biopsy but scored as high risk and those who were diagnosed by expert pathologic review as having LGD. Additionally, the cost-effectiveness profile of such an assay recently was investigated in a hypothetical model. The model demonstrated the assay was cost-effective within 5 years, with a 16.6% reduction in endoscopies for low-risk patients, a 58.4% increase in endoscopic treatments for high-risk patients, and a theoretically decreased incidence of HGD and EAC.20 

On the Horizon for Screening: Nonendoscopic Methods  

The key to capturing more patients at risk for developing esophageal cancer is to include a broader population for testing. However, an endoscopic screening approach for the entire population is not cost-effective, worth the risk, or feasible.21 If there was a nonendoscopic screening device that could be administered in an office-based setting, it could enable identification of patients who would benefit from an endoscopy to assess for Barrett’s esophagus and associated neoplasia. 

A variety of nonendoscopic screening tools are under investigation that essentially employ a tethered device for a patient to ingest for collection of cells in the esophagus. In addition to cytology, these devices can acquire tissue for IHC and DNA methylation. 

The Cytosponge (Medtronic) is an encapsulated tethered sponge that can be swallowed, released from the capsule, and then withdrawn to collect cells from the esophagogastric junction and esophagus. These cells can be stained for Trefoil factor 3, which identifies the presence of intestinal metaplasia. In a case-control study across 11 sites and 1,110 subjects (647 with Barrett’s esophagus, the rest with dyspepsia or reflux), 93.9% of the subjects swallowed the device successfully.22 Sensitivity for the diagnosis of Barrett’s esophagus was 79.9% (95% CI, 76.4%-83.0%). Sensitivity increased for patients with long segments of Barrett’s esophagus (≥3 cm) to 87.2% (95% CI, 83.0%-90.6%). A randomized controlled trial in the primary care setting is underway to assess whether centers that offer the Cytosponge will be able to detect more cases of Barrett’s esophagus than the usual care practice.23 

There is the opportunity to incorporate additional biomarkers, such as hypermethylation of TFPI2, TWIST1, ZNF345, and ZNF569, which also have shown potential on cytology-based samples obtained from Cytosponge in the diagnosis of Barrett’s esophagus.24 A model analyzing Cytosponge samples followed by endoscopic confirmation showed it is a cost-effective strategy.25 

Another sponge on a string device under investigation, EsophaCap (Capnostics), serves as a vehicle to examine DNA methylation markers. One study looking at discriminant DNA methylation markers found a 2-marker panel (VAV3 plus ZNF682) that demonstrated the ability to detect Barrett’s esophagus (AUC, 1).26 Another study looked at methylation markers p16, HPP1, NELL1, TAC1, and AKAP12 with high accuracy for Barrett’s esophagus and found an AUC of 0.929 (95% CI, 0.810-1.0; P<0.001).27 

Another study used a balloon-based device (EsoCheck/EsoGuard, Lucid Diagnostics) that examined molecular assays of CCNA1 plus VIM DNA methylation on cytologic specimens and detected Barrett’s esophagus metaplasia with 90.3% sensitivity and 91.7% specificity.28 

An even less invasive platform is being investigated with an electronic nose device, Aeonose (The eNose Company), which uses a breath test for volatile organic compound signatures to screen for Barrett’s esophagus and esophageal cancer.29 A recent study in 402 patients was able to identify volatile organic compounds associated with Barrett’s esophagus, with a sensitivity of 91% and specificity of 74%.30 


There is an unmet need to identify which patients may benefit from endoscopic therapy, closer surveillance intervals, or a screening endoscopy. Although additional larger validation studies are required, recent activity in the development and validation of biomarkers is paving the way from the laboratory setting to the clinical arena. This promising body of data demonstrates that biomarker panels have the potential to be clinically integrated in an accessible and acceptable manner into treatment, surveillance, and screening paradigms for Barrett’s esophagus. 


  1. Parasa S, et al. Gastroenterology. 2018;154(5):1282-1289.e2.  
  2. Souza RF, et al. CA Cancer J Clin. 2005;55(6):334-351. 
  3. Stachler MD, et al. Nat Genet. 2015;47(9):1047-1055. 
  4. Souza RF, et al. Aliment Pharmacol Ther. 2001;15(8):1087-1100. 
  5. Nones K, et al. Nat Commun. 2014;5:5224. 
  6. Snyder P, et al. Dig Dis Sci. 2019;64(5):1089-1097. 
  7. Duits LC, et al. Dis Esophagus. 2019;32(1):doy102. 
  8. Hoefnagel SJM, et al. PLoS One. 2020;15(4):e0231419. 
  9. Sepulveda JL, et al. Int J Cancer. 2019;145(10):2754-2766. 
  10. Craig MP, et al. Clin Transl Gastroenterol. 2020;11(1):e00125. 
  11. Nieto T, et al. BMJ Open. 2018;8(6):e020427. 
  12. Dilworth MP, et al. Ann Surg. 2019;269(3):479-485. 
  13. Jammula S, et al. Gastroenterology. 2020;158(6):1682-1697. 
  14. Shaheen N, et al. Am J Gastroenterol. 2016;111(1):30-50. 
  15. American Gastroenterological Association, et al. Gastroenterology. 2011;140(3):1084-1091. 
  16. ASGE Standards of Practice Committee, et al. Gastrointest Endosc. 2019;90(3):335-359. 
  17. Critchley-Thorne RJ, et al. Cancer Epidemiol Biomark Prev. 2016;25(6):958-968. 
  18. Critchley-Thorne RJ, et al. Cancer Epidemiol Biomark Prev. 2017;26(2):240-248. 
  19. Davison JM, -et al. Am J Gastroenterol. 2020 Feb 18. [Epub ahead of print]. doi: 10.14309/ajg.0000000000000556. 
  20. Hao J, et al. Clinicoecon Outcomes Res. 2019;11:623-635. 
  21. Inadomi JM, et al. Dig Dis Sci. 2018;63(8):2094-2104. 
  22. Ross-Innes CS, et al. PLoS Med. 2015;12(1):e1001780. 
  23. Offman J, et al. BMC Cancer. 2018;18(1):784. 
  24. Chettouh H, et al. Gut. 2018;67(11):1942-1949. 
  25. Heberle CR, et al. Clin Gastroenterol Hepatol. 2017;15(9):1397-1404.e7. 
  26. Iyer PG, et al. Am J Gastroenterol. 2018;113(8):1156-1166. 
  27. Wang Z, et al. Clin Cancer Res. 2019;25(7):2127-2135. 
  28. Moinova HR, et al. Sci Transl Med. 2018;10(424):eaao5848. 
  29. Chan DK, et al. Gastroenterology. 2017;152(1):24-26. 
  30. Peters Y, et al. Gut. 2020 Feb 25. [Epub ahead of print]