Three-tiered risk stratification model to predict progression in Barrett's esophagus using epigenetic and clinical features

Background

Barrett''s esophagus predisposes to esophageal adenocarcinoma. However, the value of endoscopic surveillance in Barrett''s esophagus has been debated because of the low incidence of esophageal adenocarcinoma in Barrett''s esophagus. Moreover, high inter-observer and sampling-dependent variation in the histologic staging of dysplasia make clinical risk assessment problematic. In this study, we developed a 3-tiered risk stratification strategy, based on systematically selected epigenetic and clinical parameters, to improve Barrett''s esophagus surveillance efficiency.

Methods and Findings

We defined high-grade dysplasia as endpoint of progression, and Barrett''s esophagus progressor patients as Barrett''s esophagus patients with either no dysplasia or low-grade dysplasia who later developed high-grade dysplasia or esophageal adenocarcinoma. We analyzed 4 epigenetic and 3 clinical parameters in 118 Barrett''s esophagus tissues obtained from 35 progressor and 27 non-progressor Barrett''s esophagus patients from Baltimore Veterans Affairs Maryland Health Care Systems and Mayo Clinic. Based on 2-year and 4-year prediction models using linear discriminant analysis (area under the receiver-operator characteristic (ROC) curve: 0.8386 and 0.7910, respectively), Barrett''s esophagus specimens were stratified into high-risk (HR), intermediate-risk (IR), or low-risk (LR) groups. This 3-tiered stratification method retained both the high specificity of the 2-year model and the high sensitivity of the 4-year model. Progression-free survivals differed significantly among the 3 risk groups, with p = 0.0022 (HR vs. IR) and p<0.0001 (HR or IR vs. LR). Incremental value analyses demonstrated that the number of methylated genes contributed most influentially to prediction accuracy.

Conclusions

This 3-tiered risk stratification strategy has the potential to exert a profound impact on Barrett''s esophagus surveillance accuracy and efficiency.     

Classification of Early Stages of Esophageal Cancer Using Transfer Learning

ObjectivesEsophageal Cancer is the sixth most common cancer with a high fatality rate. Early prognosis of esophageal abnormalities can improve the survival rate of the patients. The sequence of the progress of the esophageal cancer is from esophagitis to non-dysplasia Barrett's esophagus to dysplasia Barrett's esophagus to esophageal adenocarcinoma (EAC). Many studies revealed a 5-fold increase in EAC patients diagnosed with esophagitis, and those diagnosed with Barrett's esophagus have a greater risk of EAC.Material and methodsConvolutional Neural Network (CNN) with efficient feature extractors enable better prognosis of the pre cancerous stage, Barrett's esophagus and esophagitis. The transfer learning techniques with CNN can extract more relevant features for the automated classification of Barrett's esophagus and esophagitis. This paper presents a study on the classification of the esophagitis and Barrett's esophagus (BE) using Deep Convolution Neural Networks (DCNN).ResultsIn the first experiment, the DCNN models perform as a feature extractor, and standard classifiers do the classification. The performance analysis shows that the CNN model ResNet50 with Support Vector Machine (SVM) has an accuracy of 93.5%, recall 93.5%, precision 93.4%, f score 93.5%, AUC 89.8%. In the second experiment, the DCNN classification models perform the classification with Transfer Learning and fine-tuning. The ResNet50 model has improved accuracy of 94.46%, precision 94.46%, f score 94.46%, AUC 96.20%.ConclusionThe ResNet50 model with transfer learning and fine-tuning gives a better performance than the ResNet50 model with SVM classifier. Our experiments show that the DCNN is effective for diagnosing EAC, both as feature extractors and classification models with transfer learning and fine-tuning.     

Alcohol Consumption and the Neoplastic Progression in Barrett's Esophagus: A Systematic Review and Meta-Analysis

Purpose

In the developed countries, the incidence of esophageal adenocarcinoma (EAC) is increasing over recent decades. The purpose of this meta-analysis was to arrive at quantitative conclusions about the contribution of alcohol intakes and the progression of Barrett''s esophagus.

Methods

A comprehensive, systematic bibliographic search of medical literature published up to Oct 2013 was conducted to identify relevant studies. A meta-analysis was conducted for alcohol consumption on the Barrett''s esophagus progression.

Results

A total of 882 cases in 6,867 individuals from 14 observational studies were indemnified in this meta-analysis. The result of this current meta-analysis, including 10 case-control and 4 cohort studies, indicated that alcohol consumption was not associated with the neoplastic progression in Barrett''s esophagus (RR, 1.17; 95% CI, 0.93–1.48). When stratified by the study designs, no significant association was detected in either high vs low group or ever vs never group.

Conclusions

Alcohol drinking is not associated with risk of neoplastic progression in Barrett''s esophagus. Further well designed studies are needed in this area.     

Malignant Transformation of Non-Neoplastic Barrett's Epithelial Cells through Well-Defined Genetic Manipulations

Background

Human Barrett''s cancer cell lines have numerous, poorly-characterized genetic abnormalities and, consequently, those lines have limited utility as models for studying the early molecular events in carcinogenesis. Cell lines with well-defined genetic lesions that recapitulate various stages of neoplastic progression in Barrett''s esophagus would be most useful for such studies.

Methodology/Principal Findings

To develop such model cell lines, we started with telomerase-immortalized, non-neoplastic Barrett''s epithelial (BAR-T) cells, which are spontaneously deficient in p16, and proceeded to knock down p53 using RNAi, to activate Ras by introducing oncogenic H-Ras^G12V, or both. BAR-T cells infected with either p53 RNAi or oncogenic H-Ras^G12V alone maintained cell-to-cell contact inhibition and did not exhibit anchorage-independent growth in soft agar. In contrast, the combination of p53 RNAi knockdown with expression of oncogenic H-Ras^G12V transformed the p16-deficient BAR-T cells, as evidenced by their loss of contact inhibition, by their formation of colonies in soft agar, and by their generation of tumors in immunodeficient mice.

Conclusions/Significance

Through these experiments, we have generated a number of transformed and non-transformed cell lines with well-characterized genetic abnormalities recapitulating various stages of carcinogenesis in Barrett''s esophagus. These lines should be useful models for the study of carcinogenesis in Barrett''s esophagus, and for testing the efficacy of chemopreventive and chemotherapeutic agents.     

Final results from 10 year cohort of patients undergoing surveillance for Barrett's oesophagus: observational study

ObjectivesTo review the benefit of an endoscopic surveillance programme for patients with Barrett''s oesophagus.DesignObservational study.SettingUniversity teaching hospital.Participants409 patients in whom Barrett''s oesophagus was identified during 1984-94; 143 were entered into the annual surveillance programme.ResultsThe average period of surveillance was 4.4 years; 55 patients were reassessed in 1994 but only eight remained in the programme in 1999, withdrawal being due to death (not from carcinoma of the oesophagus), illness, or frailty. Five of the patients who entered surveillance developed carcinoma of the oesophagus. Only one cancer was identified as a result of a surveillance endoscopy, the others being detected during endoscopy to investigate altered symptoms. Of the 266 patients who were not suitable for surveillance, one died from oesophageal cancer and 103 from other causes. Surveillance has resulted in 745 endoscopies and about 3000 biopsy specimens.ConclusionThe current surveillance strategy has limited value, and it may be appropriate to restrict surveillance to patients with additional risk factors such as stricture, ulcer, or long segment (>80 mm) Barrett''s oesophagus.     

Management of refractory and complicated reflux esophagitis.

Simple intermittent heartburn with minor or no esophagitis can be treated with simple measures including lifestyle changes and antacids as needed, or H2 receptor antagonists (H2RA), and has a good outcome. Problematic reflux includes resistance to therapy, stricture, Barrett''s esophagus and aspiration. Severe reflux esophagitis, often resistant to H2RA therapy, requires more potent treatment with potent acid suppression using proton pump inhibitors, often indefinitely. When complicated by stricture, dilatations with potent acid suppression are needed. Barrett''s esophagus is subject to esophagitis, which is no more difficult to treat than other cases of esophagitis. Reflux in Barrett''s esophagus should be treated on its own merits without regard to the presence of Barrett''s epithelium. Dysplasia leading to adenocarcinoma is a different problem, apparently not influenced by reduced exposure to acid. Indications for antireflux surgery are quite limited and should be carefully analyzed as a cost/risk/benefit problem.     

DNA damage levels are raised in Barrett's oesophageal mucosa relative to the squamous epithelium of the oesophagus

Barrett's oesophagus (BE) is a pre-malignant metaplastic tissue predisposing to oesophageal adenocarcinoma (EC), and gastro-oesophageal reflux is a risk factor for both conditions. Reflux of acid and bile can cause mucosal injury and initiate chronic inflammation. These processes can induce DNA damage, possibly via an oxidative stress mechanism, thus increasing the likelihood of progression from Barrett's metaplasia to dysplasia and finally carcinoma. The comet assay was optimized for the detection of DNA damage (strand breaks and alkali-labile sites) in oesophageal biopsies, including incorporation of the DNA repair enzyme Fapy-DNA glycosylase (Fpg). Fpg allows the detection of 8-hydroxy-2-deoxyguanosine (8-OHdG) sites, a known pro-mutagenic DNA lesion. BE patients were recruited from BE surveillance clinics and oesophageal biopsies collected at endoscopy. Comet analysis revealed significantly increased (p<0.001) DNA damage in Barrett's epithelium compared with matched squamous epithelium, with median % tail DNA values of 25.1% (first to third quartile 21.7–29.6%) and 18.6% (first to third quartile 16.9–21.4%), respectively. The median % tail DNA was up to 70% higher in the matched BE tissue compared with squamous epithelium from the same patient. Fpg sensitive sites were demonstrated in both tissue types at similar levels. The raised level of DNA damage in the premalignant BE may contribute to the accumulation of genetic alterations occurring during progression to EC. Understanding these underlying mechanisms provides a basis for cancer prevention strategies in BE patients.     

Endoscopic OCT with forward‐looking probe: clinical studies in urology and gastroenterology

In the current paper we present results of application of endoscopic time‐domain OCT (EOCT) with lateral scanning by forward looking miniprobe. We analysed material of clinical studies of 554 patients: 164 patients with urinary bladder pathology, and 390 with gastrointestinal tract pathology. We reviewed the materials obtained in different clinics using the OCT device elaborated at the Institute of Applied Physics. We demonstrate results of EOCT application in detection of early cancer and surgery guidance, examples of combined use of OCT and fluorescence imaging. As a result, we show the diagnostic accuracy of EOCT in specific clinical tasks. The sensitivity of EOCT cancer determination in Barrett's esophagus is from 71% to 85% at different stages of neoplasia with specificity 68% for all stages. As for bladder carcinoma, the sensitivity and specificity are 85% and 68%, respectively. In colon dysplasia EOST demonstrates high efficacy: sensitivity 92% and specificity 84%. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Migration of the ductular elements of gut-associated glands gives clues to the histogenesis of structures associated with responses to acid hypersecretory state: the origins of "gastric metaplasia" in the duodenum of the specialized mucosa of barrett's esophagus and of pseudopyloric metaplasia.

This article suggests that cell lineages of defined phenotype arise within gastrointestinal epithelia exposed to acid hypersecretion-the ulcer-associated cell lineage (UACL), "gastric metaplasia" and that of Barrett''s esophagus. Detailed study of both the histogenesis and secretory peptide phenotype of the UACL and gastric metaplasia reveal an origin from newly-formed ducts and Brunner''s gland ducts, respectively. It is suggested that Barrett''s epithelium arises directly from the epithelium of the cardiac esophageal glands, and that these three ductal epithelia are the origins of these three important adaptive phenomena to gastric hypersecretion.     

Immunohistochemical analysis of selected molecular markers in esophagus precancerous,adenocarcinoma and squamous cell carcinoma in Iranian subjects

Background: The molecular and cellular mechanisms linking chronic inflammation and gastrointestinal malignancy are not known with certainty. Aim: To investigate changes in potential causative factors during progression of esophagus cancer in a population living in high-risk area in Iran. Subjects: Formalin-fixed, paraffin-embedded esophageal specimens (n = 87) from patients with gastroesophageal reflux disease (GERD), Barrett's metaplasia, adenocarcinoma (ADC) and squamous cells carcinoma (SCC) were collected based on their pathological diagnosis. Methods: Immunohistochemical (IHC) technique was used to study tissue accumulation of P53, P21, cyclooxygenase-2 (COX-2), glutathione S-transferase-P (GST-Pi) and nitrotyrosine (NT) in patients and controls. Results: P53 expression was not detected in esophageal tissues from normal and GERD samples, whereas it was found positive in Barrett's, ADC, and SCC samples. P21 positive sample was relatively higher in ADC patients as compared to that in SCC (ADC: 52.6%; SCC: 25%). GST-Pi expression was equally accumulated in all the samples. NT was predominantly expressed in ADC (72.7%). COX-2 expression was significantly higher in Barrett's (60.0%) and ADC (66.6%) as compared to that in GERD, SCC and normal. These data were further confirmed by detecting the scores of immunostainings in all the positive samples. Conclusion: The pathological changes in ADC and SCC samples which were associated with increasing frequency of NT and COX-2 provides further evidence for involvement of these inflammatory factors in progression of esophagus cancer.     

Review: Helicobacter pylori and non‐malignant upper gastrointestinal diseases

This review covers recent publications investigating the relationship between Helicobacter pylori infection and gastroesophageal reflux disease, Barrett's esophagus, eosinophilic esophagitis, peptic ulcer disease (PUD), H pylori gastritis, and functional dyspepsia. In the area of gastroesophageal reflux disease, new data suggest that reflux may have a role in the transmission of H pylori infection. In addition to several observational studies, data on alterations in esophageal physiology in patients with H pylori infection are presented. Further evidence for the inverse relationship between H pylori infection and Barrett's esophagus is available in the form of a meta‐analysis from the North American Barrett's and Esophageal Carcinoma Consortium. The relationship between H pylori infection and eosinophilic esophagitis remains uncertain. Although new data do not indicate a significantly lower prevalence of H pylori among patients with eosinophilic esophagitis, a meta‐analysis showed a 37% reduced risk of eosinophilic esophagitis among H pylori‐infected patients. Novel data are presented on the genetic variability of bacterial virulence factors and their relationship with PUD. We also report data on plasma biomarkers, which may detect progression to gastric cancer in H pylori‐associated PUD. A new meta‐analysis was published, which assessed the risk of PUD in low‐dose aspirin users with H pylori infection. Finally, we report on the ongoing attempts to stratify patients with gastritis using endoscopic methods when compared to standard biopsy examination.     

Evaluation of a Minimally Invasive Cell Sampling Device Coupled with Assessment of Trefoil Factor 3 Expression for Diagnosing Barrett's Esophagus: A Multi-Center Case–Control Study

BackgroundBarrett''s esophagus (BE) is a commonly undiagnosed condition that predisposes to esophageal adenocarcinoma. Routine endoscopic screening for BE is not recommended because of the burden this would impose on the health care system. The objective of this study was to determine whether a novel approach using a minimally invasive cell sampling device, the Cytosponge, coupled with immunohistochemical staining for the biomarker Trefoil Factor 3 (TFF3), could be used to identify patients who warrant endoscopy to diagnose BE.ConclusionsThe Cytosponge-TFF3 test is safe and acceptable, and has accuracy comparable to other screening tests. This test may be a simple and inexpensive approach to identify patients with reflux symptoms who warrant endoscopy to diagnose BE.     

Superficial photothermal laser ablation of ex vivo sheep esophagus using a cone‐shaped optical fiber tip

Superficial photothermal laser ablation (SPLA) may be useful as a therapeutic approach producing a depth of injury that is sufficient to eliminate mucosal lesion but not deep enough to induce thermal effects in deeper tissue layers. The purpose of this preliminary study is twofold: (a) to describe design steps of a fiber probe capable of delivering a tightly focused laser beam, including Monte‐Carlo‐based simulations, and (b) to complete the initial testing of the probe in a sheep esophagus model, ex vivo. The cone‐shaped (tapered) fiber tip was obtained by chemical etching of the optical fiber. A 1505 nm diode laser providing power up to 500 mW was operated in continuous wave. The successful SPLA of the sheep mucosa layer was demonstrated for various speed‐power combinations, including 300 mW laser power at a surface scanning rate of 0.5 mm/s and 450 mW laser power at a surface scanning rate of 2.0 mm/s. Upon further development, this probe may be useful for endoscopic photothermal laser ablation of the mucosa layer using relatively low laser power.     

Wide‐field optical property mapping and structured light imaging of the esophagus with spatial frequency domain imaging

As the incidence of esophageal adenocarcinoma continues to rise, there is a need for improved imaging technologies with contrast to abnormal esophageal tissues. To inform the design of optical technologies that meet this need, we characterize the spatial distribution of the scattering and absorption properties from 471 to 851 nm of eight resected human esophagi tissues using Spatial Frequency Domain Imaging. Histopathology was used to categorize tissue types, including normal, inflammation, fibrotic, ulceration, Barrett's Esophagus and squamous cell carcinoma. Average absorption and reduced scattering coefficients of normal tissues were 0.211 ± 0.051 and 1.20 ± 0.18 mm^?1, respectively at 471 nm, and both values decreased monotonically with increasing wavelength. Fibrotic tissue exhibited at least 68% larger scattering signal across all wavelengths, while squamous cell carcinoma exhibited a 36% decrease in scattering at 471 nm. We additionally image the esophagus with high spatial frequencies up to 0.5 mm^?1 and show strong reflectance contrast to tissue treated with radiation. Lastly, we observe that esophageal absorption and scattering values change by an average of 9.4% and 2.7% respectively over a 30 minute duration post‐resection. These results may guide system design for the diagnosis, prevention and monitoring of esophageal pathologies.      

Macrophage-specific RAM11 monoclonal antibody cross-reacts with basal cells of stratified squamous epithelia

RAM11 is a mouse monoclonal anti-rabbit macrophage antibody recognizing connective tissue and vascular (atheromatous tissue) macrophages. This study demonstrates a cross-reaction of RAM11 with an unknown antigen in rabbit normal epithelial cells. Formalin-fixed, paraffin sections of the New Zealand White rabbit normal skin, oral mucosa, esophagus, small intestine and lung were immunostained with RAM11 antibody followed by goat anti-mouse Cy-3-conjugated antiglobulin. RAM11-positive immunofluorescence was observed in basal layer cells of stratified squamous epithelia (skin, oral mucosa, esophagus). No RAM11 immunostaining was found in any cells of simple (intestinal, bronchial) epithelia. These findings show that basal cells of stratified squamous keratinized and non-keratinized epithelia of the rabbit express an antigenic epitope which is common with that of macrophage antigen recognized by RAM11 monoclonal antibody.     

Bioinformatic analyses of microRNA-targeted genes and microarray-identified genes correlated with Barrett's esophagus

Barrett's esophagus (BE) is defined as a metaplasia condition in the distal esophagus, in which the native squamous epithelium lining is replaced by a columnar epithelium with or without intestinal metaplasia. It is commonly accepted that BE is a precancerous lesion for esophageal adenocarcinoma. The aim of this study was to investigate the aberrant microRNAs (miRNAs) and differentially expressed genes (DEGs) associated with BE based on online microarray datasets. One miRNA and five gene expression profiling datasets were retrieved from the Gene Expression Omnibus Database. Aberrant microRNAs and DEGs were obtained using R/Bioconductor statistical analysis language and software. 23 dysregulated miRNAs and 632 DEGs demonstrating consistent expression tendencies in the five gene microarrays were identified in BE. Moreover, 1962 target genes of aberrant miRNAs were predicted using three bioinformatic tools, namely TargetScan, RNA22-HSA and miRDB. Ultimately, 93 target DEGs were obtained, after which functional annotation was performed on DAVID Bioinformatics Resources. Among Gene Ontology (GO) biological processes, digestive tract development and epithelial cell differentiation have demonstrated significant associations with BE pathogenesis. In addition, analysis of the KEGG pathways has revealed associations with cancer. To enable further study, one miRNA-target DEGs regulatory network was constructed using Cytoscape. 6 target DEGs demonstrated higher-degree distributions in the network, and ROC analysis indicated that FNDC3B may be the best potential biomarker for BE diagnosis. The data presented herein may provide new perspectives for exploring BE pathogenesis and may offer hits with regard to potential biomarkers in BE diagnosis, prediction and therapeutic evaluation.     

ATM mRNA在食管癌组织中的表达及其临床意义

目的探讨共济失调性毛细血管扩张症突变基因(Ataxia-telangiectasia mutated,ATM)mRNA在食管鳞状细胞癌组织中的表达及其临床意义。方法应用原位分子杂交方法检测52例食管正常黏膜、45例食管上皮内瘤变组织及63例食管癌组织ATM mRNA的表达。结果食管正常黏膜、食管上皮内瘤变及食管癌组织中ATM mRNA表达率分别为26.9%(14/52)、44.4%(20/45)及63.5%(40/63),食管癌组织中ATM mRNA表达率明显高于正常黏膜及上皮内瘤变(P≤0.05),ATM mRNA表达率与食管癌组织分级呈负相关(r=-0.312,P=0.013);食管正常黏膜和食管上皮内瘤变ATM mRNA表达率无明显差异(P=0.07),食管癌组织中ATM mRNA表达与患者年龄、性别、肿瘤浸润深度、淋巴结转移、临床分期及其它临床病理因素无关(P0.05)。结果 ATM mRNA在食管癌组织中异常表达,有望成为食管癌治疗的新靶点。