Selection and Application of Tissue microRNAs for Nonendoscopic Diagnosis of Barrett’s Esophagus

Abstract

Background & Aims MicroRNA (miRNA) is highly stable in biospecimens and provides tissue-specific profiles, making it a useful biomarker of carcinogenesis. We aimed to discover a set of miRNAs that could accurately discriminate Barrett’s esophagus (BE) from normal esophageal tissue and to test its diagnostic accuracy when applied to samples collected by a non-invasive esophageal cell sampling device. Methods We analyzed miRNA expression profiles of 2 independent sets of esophageal biopsy tissues collected during endoscopy from 38 patients with BE tissues and 90 patients with non-BE esophagus (controls) using Agilent microarray and Nanostring counter assays. Consistently upregulated miRNAs were quantified by real-time PCR in esophageal tissues collected by Cytosponge from patients with BE or without BE. miRNAs from plasmids and anti-sense oligonucleotides were expressed in NES normal esophageal squamous cells and effects on proliferation and gene expression patterns were analyzed. Results We identified 15 miRNAs that were significantly upregulated in BE vs control tissues. Of these, 11 (MIR215, MIR194, MIR 192, MIR196a, MIR199b, MIR10a, MIR145, MIR181a, MIR30a, MIR7, MIR199a) were validated in Cytosponge samples. The miRNAs with the greatest increases in BE tissues (7.9-fold increase inexpression or more, P<0.0001: MIR196a, MIR192, MIR194, and MIR215) each identified BE vs control tissues with area under the curve (AUC) values of 0.82 or more. We developed an optimized multivariable logistic regression model based on expression levels of 6 miRNAs (MIR7, MIR30a, MIR181a, MIR192, MIR196a, and MIR199a) that identified patients with BE with an AUC value of 0.89, 86.2% sensitivity, and 91.6% specificity. Expression level of MIR192, MIR196a, MIR199a, combined with Trefoil Factor 3 (TFF3), identified patients with BE with an AUC of 0.93, 93.1% sensitivity, and 93.7% specificity. Hypo-methylation was observed in the promoter region of the highly upregulated cluster MIR192-194. Overexpression of these miRNAs in NES cells increased their proliferation, via GRHL3 and PTEN signaling. Conclusions In analyses of miRNA expression patterns of BE vs non-BE tissues, we identified a profile that can identify Cytosponge samples from patients with BE with an AUC of 0.93. Expression of MIR194 is increased in BE samples via epigenetic mechanisms that might be involved in BE pathogenesis.

Role of TFF3 as an adjunct in the diagnosis of Barrett's esophagus using a minimally invasive esophageal sampling device—The CytospongeTM

“…19,[26][27][28] Modeling has shown the Cytosponge TM to have an acceptable associated cost as a first-line screening tool in populations at increased risk of BE 29,30 with a predicted 25-27% cost reduction compared to standard endoscopy and an incremental cost-effectiveness ratio (ICER) of $26 358-33 307 compared to no screening. 19,[26][27][28] Modeling has shown the Cytosponge TM to have an acceptable associated cost as a first-line screening tool in populations at increased risk of BE 29,30 with a predicted 25-27% cost reduction compared to standard endoscopy and an incremental cost-effectiveness ratio (ICER) of $26 358-33 307 compared to no screening.…”

“…Additional biomarkers could also be added to the Cytosponge TM -TFF3 test to further increase its sensitivity and specificity for detecting BE, a panel of three miRNAs or alternatively a methylation panel have shown potential in a pilot study and require further validation 27,28 The Cytosponge TM -TFF3 test has been developed to screen for BE in Western populations where EAC is the dominant histological subtype of esophageal carcinoma. Validation in a large cohort would be required to confirm that AI assessment of negative cases had a sufficiently high negative predictive value for these cases not to be screened by a pathologist.…”

“…Step 4-sections are cut from the paraffin block and stained for assessment by a pathologist cases of BE on a range of tissue sample types including miRNAs, methylation, protein expression and the presence of specific mutations. 19,[26][27][28] Modeling has shown the Cytosponge TM to have an acceptable associated cost as a first-line screening tool in populations at increased risk of BE 29,30 with a predicted 25-27% cost reduction compared to standard endoscopy and an incremental cost-effectiveness ratio (ICER) of $26 358-33 307 compared to no screening. 29 Microsimulation studies have also suggested a greater reduction in the incidence of symptomatic EACs in the at-risk population using Cytosponge TM based screening compared to endoscopic screening, 19% vs 17%, due to a higher predicted uptake of the Cytosponge TM test due to its increased convenience and acceptability compared to a standard endoscopy.…”

“…Validation in a large cohort would be required to confirm that AI assessment of negative cases had a sufficiently high negative predictive value for these cases not to be screened by a pathologist. Additional biomarkers could also be added to the Cytosponge TM -TFF3 test to further increase its sensitivity and specificity for detecting BE, a panel of three miRNAs or alternatively a methylation panel have shown potential in a pilot study and require further validation 27,28 The Cytosponge TM -TFF3 test has been developed to screen for BE in Western populations where EAC is the dominant histological subtype of esophageal carcinoma. Squamous neoplasia was not identified in any of the BEST series of studies reflecting its very low incidence in the targeted patient populations.…”

Accurate Nonendoscopic Detection of Barrett's Esophagus by Methylated DNA Markers: A Multisite Case Control Study

“…Nonendoscopic methods to detect BE are being developed using esophageal cell capture devices in combination with biomarkers. Investigators have targeted a protein marker (trefoil factor 3) alone ( 14 ), or in combination with other markers such as microRNAs ( 15 ). Others ( 16 , 17 ) have shown promising early results using methylated DNA markers (MDMs) on samples obtained via a capsule sponge or inflatable balloon devices in smaller studies.…”