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Purpose: Current endoscopy-based screening and surveillance programs have not been proven effective at decreasing esophageal adenocarcinoma (EAC) mortality, creating an unmet need for effective molecular tests for early detection of this highly lethal cancer. We conducted a genome-wide methylation screen to identify novel methylation markers that distinguish EAC and high-grade dysplasia (HGD) from normal squamous epithelium (SQ) or nondysplastic Barrett's esophagus (NDBE). Experimental Design: DNA methylation profiling of samples from SQ, NDBE, HGD, and EAC was performed using HM450 methylation arrays (Illumina) and reduced-representation bisulfate sequencing. Ultrasensitive methylation-specific droplet digital PCR and next-generation sequencing (NGS)-based bisulfite-sequencing assays were developed to detect the methylation level of candidate CpGs in independent esophageal biopsy and endoscopic brushing samples. Results: Five candidate methylation markers were significantly hypermethylated in HGD/EAC samples compared with SQ or NDBE (P < 0.01) in both esophageal biopsy and endoscopic brushing samples. In an independent set of brushing samples used to construct biomarker panels, a four-marker panel (model 1) demonstrated sensitivity of 85.0% and 90.8% for HGD and EACs respectively, with 84.2% and 97.9% specificity for NDBE and SQ respectively. In a validation set of brushing samples, the panel achieved sensitivity of 80% and 82.5% for HGD and EAC respectively, at specificity of 67.6% and 96.3% for NDBE and SQ samples. Conclusions: A novel DNA methylation marker panel differentiates HGD/EAC from SQ/NDBE. DNA-methylation–based molecular assays hold promise for the detection of HGD/EAC using esophageal brushing samples.

Background: Risk factors contributing to more than tenfold increase in esophageal cancer in the last 50 years remain underexplored. We aim to examine the associations of sleep behaviors with esophageal adenocarcinoma (EAC) and squamous cell carcinoma (ESCC). Methods: We prospectively assessed the associations between sleep behaviors (chronotype, duration, daytime napping, daytime sleepiness, snoring, and insomnia) and EAC and ESCC risk in 393,114 participants in the UK Biobank (2006-2016). Participants with 0, 1, and ≥2 unhealthy behaviors, including sleep 9 h/day, daytime napping, and usual daytime sleepiness were classified as having a good, intermediate, and poor sleep. For EAC, we also examined interactions with polygenic risk score (PRS). Cox models were used to estimate hazard ratios (HRs) and 95% confidence intervals (CIs). Results: We documented 294 incident EAC and 95 ESCC. Sleep >9 h/day (HR=2.05, 95%CI: 1.18, 3.57) and sometimes daytime napping (HR=1.36, 95%CI: 1.06, 1.75) were individually associated with increased EAC risk. Compared with individuals with good sleep, those with intermediate sleep had a 47% (HR=1.47, 95%CI: 1.13, 1.91) increased EAC risk, and those with poor sleep showed a 87% (HR=1.87, 95%CI: 1.24, 2.82) higher risk (Ptrend

The joint linearity of the categorical covariates on the logit scale

Background: Barrett's esophagus is often asymptomatic and only a small portion of Barrett's esophagus patients are currently diagnosed and under surveillance. Therefore, it is important to develop risk prediction models to identify high-risk individuals with Barrett's esophagus. Familial aggregation of Barrett's esophagus and esophageal adenocarcinoma, and the increased risk of esophageal adenocarcinoma for individuals with a family history, raise the necessity of including genetic factors in the prediction model. Methods to determine risk prediction models using both risk covariates and ascertained family data are not well developed.Methods: We developed a Barrett's Esophagus Translational Research Network (BETRNet) risk prediction model from 787 singly ascertained Barrett's esophagus pedigrees and 92 multiplex Barrett's esophagus pedigrees, fitting a multivariate logistic model that incorporates family history and clinical risk factors. The eight risk factors, age, sex, education level, parental status, smoking, heartburn frequency, regurgitation frequency, and use of acid suppressant, were included in the model. The prediction accuracy was evaluated on the training dataset and an independent validation dataset of 643 multiplex Barrett's esophagus pedigrees.Results: Our results indicate family information helps to predict Barrett's esophagus risk, and predicting in families improves both prediction calibration and discrimination accuracy.Conclusions: Our model can predict Barrett's esophagus risk for anyone with family members known to have, or not have, had Barrett's esophagus. It can predict risk for unrelated individuals without knowing any relatives' information.Impact: Our prediction model will shed light on effectively identifying high-risk individuals for Barrett's esophagus screening and surveillance, consequently allowing intervention at an early stage, and reducing mortality from esophageal adenocarcinoma. Cancer Epidemiol Biomarkers Prev; 25(5); 727–35. ©2016 AACR.

Purpose:Current endoscopy-based screening and surveillance programs have not been proven effective at decreasing esophageal adenocarcinoma (EAC) mortality, creating an unmet need for effective molecular tests for early detection of this highly lethal cancer. We conducted a genome-wide methylation screen to identify novel methylation markers that distinguish EAC and high-grade dysplasia (HGD) from normal squamous epithelium (SQ) or nondysplastic Barrett's esophagus (NDBE).Experimental Design:DNA methylation profiling of samples from SQ, NDBE, HGD, and EAC was performed using HM450 methylation arrays (Illumina) and reduced-representation bisulfate sequencing. Ultrasensitive methylation-specific droplet digital PCR and next-generation sequencing (NGS)-based bisulfite-sequencing assays were developed to detect the methylation level of candidate CpGs in independent esophageal biopsy and endoscopic brushing samples.Results:Five candidate methylation markers were significantly hypermethylated in HGD/EAC samples compared with SQ or NDBE (P < 0.01) in both esophageal biopsy and endoscopic brushing samples. In an independent set of brushing samples used to construct biomarker panels, a four-marker panel (model 1) demonstrated sensitivity of 85.0% and 90.8% for HGD and EACs respectively, with 84.2% and 97.9% specificity for NDBE and SQ respectively. In a validation set of brushing samples, the panel achieved sensitivity of 80% and 82.5% for HGD and EAC respectively, at specificity of 67.6% and 96.3% for NDBE and SQ samples.Conclusions:A novel DNA methylation marker panel differentiates HGD/EAC from SQ/NDBE. DNA-methylation–based molecular assays hold promise for the detection of HGD/EAC using esophageal brushing samples.

Supplementary Methods of imputation of age and estimating the parameters of the prediction model. Supplementary Table S1 Missing rates on the 8 covariates in the training and validation datasets. Supplementary Table S2 Stepwise removal of covariates in the MLM model on the basis of LRT tests and AIC. Supplementary Table S3. Description of the eight predictor covariates. Supplementary Table S4 Number of informative pedigrees without missing covariate data.

Esophageal adenocarcinoma is a deadly cancer with increasing incidence in the United States, but mechanisms underlying pathogenesis are still mostly elusive. In addressing this question, we assessed gene fusion landscapes by comprehensive RNA sequencing (RNAseq) of 55 pretreatment esophageal adenocarcinoma and 49 nonmalignant biopsy tissues from patients undergoing endoscopy for Barrett's esophagus. In this cohort, we identified 21 novel candidate esophageal adenocarcinoma–associated fusions occurring in 3.33% to 11.67% of esophageal adenocarcinomas. Two candidate fusions were selected for validation by PCR and Sanger sequencing in an independent set of pretreatment esophageal adenocarcinoma (N = 115) and nonmalignant (N = 183) biopsy tissues. In particular, we observed RPS6KB1–VMP1 gene fusion as a recurrent event occurring in approximately 10% of esophageal adenocarcinoma cases. Notably, esophageal adenocarcinoma cases harboring RPS6KB1–VMP1 fusions exhibited significantly poorer overall survival as compared with fusion-negative cases. Mechanistic investigations established that the RPS6KB1–VMP1 transcript coded for a fusion protein, which significantly enhanced the growth rate of nondysplastic Barrett's esophagus cells. Compared with the wild-type VMP1 protein, which mediates normal cellular autophagy, RPS6KB1–VMP1 fusion exhibited aberrant subcellular localization and was relatively ineffective in triggering autophagy. Overall, our findings identified RPS6KB1–VMP1 as a genetic fusion that promotes esophageal adenocarcinoma by modulating autophagy-related processes, offering new insights into the molecular pathogenesis of esophageal adenocarcinomas. Cancer Res; 76(19); 5628–33. ©2016 AACR.

Purpose: Recent microarray and RNA-sequencing studies have uncovered aberrantly expressed microRNAs (miRNA) in Barrett's esophagus–associated esophageal adenocarcinoma. The functional significance of these miRNAs in esophageal adenocarcinoma initiation and progression is largely unknown.Experimental Design: Expression levels of miR-199a/b-3p, -199a-5p, -199b-5p, -200b, -200c, -223, and -375 were determined in microdissected tissues from cardiac mucosa, Barrett's esophagus, dysplastic Barrett's esophagus, and esophageal adenocarcinoma using quantitative real-time PCR. miR-223 expression was validated in precursors and esophageal adenocarcinomas from 95 patients with esophageal adenocarcinoma by in situ hybridization (ISH). miR-223 was transfected into two esophageal adenocarcinoma cell lines, and in vitro assays were conducted. Target genes were identified using Illumina microarray, and results were validated in cell lines and human specimens.Results: miR-199 family members and miR-223 were significantly overexpressed in esophageal adenocarcinoma, however, only miR-223 showed a stepwise increase during esophageal adenocarcinoma carcinogenesis. A similar trend was observed by ISH, which additionally showed that miR-223 is exclusively expressed by the epithelial compartment. miR-223–overexpressing cells had statistically significantly more migratory and invasive potential than scramble sequence–transfected cells. PARP1 was identified as a direct target gene of miR-223 in esophageal adenocarcinoma cells. Increased sensitivity to chemotherapy was observed in cells with enforced miR-223 expression and reduced PARP1.Conclusions: miR-223 is significantly upregulated during the Barrett's esophagus–dysplasia–esophageal adenocarcinoma sequence. Although high miR-223 levels might contribute to an aggressive phenotype, our results also suggest that patients with esophageal adenocarcinoma with high miR-223 levels might benefit from treatment with DNA-damaging agents. Clin Cancer Res; 19(15); 4067–78. ©2013 AACR.

Supplementary Tables - PDF file 55K, This file contains supplementary tables S1, S2 and S3. Table S1: Literature‐based miR selection for qRT‐PCR validation in a chemo‐radiation na�ve EAC cohort. Two types of miRs were chosen; miRs that may play a role in the development of BE‐ND (BE‐miRs) and miRs that may be involved in the neoplastic progression of BE (Neo‐miRs). Table S2: Quantitative real‐time PCR primers used for the validation of the Illumina microarray results. Table S3: this table contains the microarray results on two biological replicate experiments in OE33 cells. Only the genes that were more than 1.5 fold lower expressed upon miR-223 transfection are listed in this table.

Supplementary Data from Novel DNA Methylation Biomarker Panel for Detection of Esophageal Adenocarcinoma and High-Grade Dysplasia

Contains Supplementary Figures 1-3 as follows: Supplementary Figure 1: Full-length sequence and protein domains of RPS6KB1-VMP1 and OSBPL1A-LAMA3 fusion transcripts identified in EACs Supplementary Figure 2: Somatic copy-number aberrations in the RPS6KB1 and VMP1 genomic locus Supplementary Figure 3: NIH/3T3 transformation assay

Supplementary Figure S1 - PDF file 28K, This file contains supplementary figure S1. An overview of the study design for miR validation using FFPE and frozen specimens is provided in this flowchart

Excel file containing Supplementary Tables 1-7 as follows: Supplementary Table 1 - Sample distribution in the discovery RNAseq cohort Supplementary Table 2 - Fusion transcripts detected in EACs in the discovery RNAseq cohort Supplementary Table 3 - Fusion transcripts detected in non-malignant samples in the discovery RNAseq cohort Supplementary Table 4 - Candidate fusion transcripts in EACs in the discovery RNAseq cohort Supplementary Table 5 - Sample distribution in the validation cohort Supplementary Table 6 - Candidate fusion frequencies in EACs in the discovery and validation cohorts Supplementary Table 7 - Candidate fusions found in both EAC and matched normal SQ tissues in the discovery cohort

Contains detailed experimental methods

Supplementary Figure from Novel DNA Methylation Biomarker Panel for Detection of Esophageal Adenocarcinoma and High-Grade Dysplasia

As of 2022, only 51% of active eligible state employees in Missouri have been screened for colorectal cancer and 67% for breast cancer, despite having state-sponsored health insurance. In fall 2020, the Missouri Department of Health and Senior Services Comprehensive Cancer Program partnered with the Missouri Cancer Consortium to create a strategy to improve cancer screening rates among state employees. The project was designed to include 3 phases: 1) a colorectal cancer education phase, 2) an expanded education phase that included additional cancers, and 3) a proposed intervention phase that will include screening events. In the first phase, in 2020, colorectal cancer educational materials were sent to all state employees. In the second phase, in 2022, educational resources were expanded to include additional cancers and screening tools. In both initiatives, educational materials and information on current screening recommendations were distributed to approximately 40,000 state employees. A database of screening rates was developed to monitor screening rates and challenge state employees to complete screenings. Evidence-informed interventions were implemented with a focus on health equity. We used a regional approach to identify geographic areas with the greatest need. These efforts will support the next phase of the project, which involves planning breast and colorectal cancer screening events. Policy changes will be encouraged to remove systems-level barriers that discourage employees from being screened for cancer. Recommended tools and strategies can be adopted by similar organizations with complex, multitier employee structures.

INTRODUCTION Up to 89% of physicians who routinely perform endoscopy experience some type of musculoskeletal pain. In this study, we sought to quantitatively analyze provider factors that influence ergonomic strain during live endoscopic procedures. METHODS Surface electromyography (sEMG) was used to measure ergonomic strain on physicians while performing upper and lower endoscopies. EMG data were normalized to a maximal voluntary contraction (MVC) recording for each muscle group, yielding a %MVC value. Subgroup analyses were performed based on glove size, physician training level, specialty, and handedness. RESULTS A total of 165 upper (n = 68) and lower (n = 97) endoscopies were recorded. Endoscopists with small hand sizes had significantly higher ergonomic strain in the left anterior and posterior forearm muscle compartments as compared to endoscopists with medium or large hands (%MVC L-anterior: small: 9.1 ± 1.1; medium: 6.4 ± 1.2; large: 5.9 ± 1.6; p

The identification of hereditary cancer genes for esophageal adenocarcinoma (EAC) and its precursor, Barrett’s esophagus (BE), may prove critical for the development of novel prevention and treatment strategies. Specifically, efforts for detecting BE and EAC susceptibility genes have focused on families with three or more affected members, since these individuals have an earlier age onset compared to non-familial individuals. Given that the use of BE may overestimate the likelihood of disease heritability, we evaluated the age of diagnosis in kindreds with a restricted definition including only confirmed high-grade dysplasia (HGD) or EAC. The Familial Barrett’s Esophagus Consortium database was used to identify individuals with HGD and EAC. These individuals were subsequently split into three kindred groups: non-familial—a single affected family member, duplex—two affected family members, and multiplex—three or more affected family members. Age of cancer diagnosis and other risk factors were compared between individuals in these groups. The study included 441 non-familial, 46 duplex, and 13 multiplex individuals. There was a statistically significant difference for age of diagnosis for individuals in the multiplex families compared to the non-familial and duplex families (56.0 versus 64.3, 63.5; p = 0.049). There was no significant difference between demographic factors and other cancer risk factors between family types. The results of this study support a genetic basis for familial Barrett’s associated neoplasia and evaluation of the genetic susceptibility to this disease should continue to focus on families with multiple (three or more) affected members.

Background: Barrett’s esophagus (BE) is a precancerous condition defined as replacement of the normal esophageal squamous epithelium with metaplastic columnar intestinal epithelium caused by chronic gastroesophageal reflux disease. Importantly, BE confers the strongest predisposition to developing esophageal adenocarcinoma. There is a deficiency of knowledge regarding the molecular pathogenesis of BE development. To this end, a thorough elucidation of the development context by which BE develops will uncover novel avenues to detect BE and revert it back to normal esophagus to ultimately halt the development of cancer. Spatial specification of the developing digestive tract occurs through a series of regulated transcriptional cascades. At embryonic day 9, the dorsal foregut is marked by expression of SOX2, a transcription factor of the Sry-like HMG box family, which is required for esophageal development. SOX2 continues to be expressed in the esophageal epithelium throughout adulthood as an important homeostatic maintenance factor. I hypothesize that SOX2 functions to maintain foregut squamous epithelial identity, and its loss is a critical step during BE development. Methods/Results: Here, we show using human BE tissue microarrays that SOX2 is expressed in the normal squamous epithelium and its expression is significantly decreased during BE development. To assay the molecular effects of SOX2 expression changes, we have conducted a series of novel complementary experiments involving a foregut-specific inducible Sox2 knockout mouse model and a biobank of human BE derived organoids. Using the murine model, Krt5CreER/+; Sox2flox/flox; ROSA26LSLTdTomato/+, we have assessed the histologic and transcriptional effects of SOX2 loss on squamous epithelium homeostasis. In addition, we have conducted a series of experiments involving a wholly novel biobank of human Barrett’s esophagus derived organoids. We have been able to expand, cryopreserve, and genetically manipulate these primary cells, and here we characterize these organoids and show that they recapitulate key pathohistologic and molecular features of BE. Using the human BE organoid biobank, we have established BE organoids that have forced expression of SOX2, and we are developing a high-throughput screening system using a SOX2 luciferase promoter reporter assay to identify novel compounds and drugs that induce SOX2 expression. Immediate future avenues will involve defining the direct transcriptional targets of SOX2, and interactions with the intestinal transcription factor CDX2. Conclusions: In summary, it is possible that in BE there is a stepwise transcriptional progression towards a more posterior phenotype with loss of SOX2 expression being an important initial step. Together, these experiments will elucidate novel molecular pathways involved in BE maintenance and may reveal novel therapeutic avenues to treat BE and prevent esophageal cancer. Citation Format: Ramon U. Jin, Toni M. Nittolo, Jean S. Wang, Jason C. Mills, Qing K. Li. The role of SOX2 in Barrett's esophagus development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2430.

Up to 89% of physicians who routinely perform endoscopy experience some type of musculoskeletal pain. In this study, we sought to quantitatively analyze provider factors that influence ergonomic strain during live endoscopic procedures.Surface electromyography (sEMG) was used to measure ergonomic strain on physicians while performing upper and lower endoscopies. EMG data were normalized to a maximal voluntary contraction (MVC) recording for each muscle group, yielding a %MVC value. Subgroup analyses were performed based on glove size, physician training level, specialty, and handedness.A total of 165 upper (n = 68) and lower (n = 97) endoscopies were recorded. Endoscopists with small hand sizes had significantly higher ergonomic strain in the left anterior and posterior forearm muscle compartments as compared to endoscopists with medium or large hands (%MVC L-anterior: small: 9.1 ± 1.1; medium: 6.4 ± 1.2; large: 5.9 ± 1.6; p 0.001); (%MVC L-posterior: small: 12.0 ± 0.8; medium: 9.4 ± 1.3; large: 8.8 ± 1.4; p 0.001). Additionally, upper body muscle groups had significantly higher ergonomic strain in endoscopists with less lifetime endoscopic experience (%MVC R-trapezius: expert: 8.4 ± 1.2; novice: 9.3 ± 1.2; p 0.05); (%MVC R-deltoid: expert: 6.1 ± 1.4; novice: 8.5 ± 1.3; p 0.001). There were no significant ergonomic differences between surgeons or gastroenterologists and no differences between right- and left-handed dominant individuals.Endoscopists with small hands experienced great ergonomic strain in their left forearm. Our data support the widely held belief that "one size does not fit all" and will hopefully spark change in the design of future endoscopes by device manufacturers. Our data also support that the experience level of the endoscopist contributed significantly to ergonomic performance, likely due to postural differences leading to decreased upper body strain. Therefore, it remains critically important to educate young proceduralists on strategies for ergonomic relief early in his or her endoscopic training program that can ameliorate ergonomic strain that accrues over the lifetime of a physician's career.

Colorectal cancer (CRC) is one of the most common types of cancer with a high mortality rate. Colonoscopy is the preferred procedure for CRC screening and has proven to be effective in reducing CRC mortality. Thus, a reliable computer-aided polyp detection and classification system can significantly increase the effectiveness of colonoscopy. In this paper, we create an endoscopic dataset collected from various sources and annotate the ground truth of polyp location and classification results with the help of experienced gastroenterologists. The dataset can serve as a benchmark platform to train and evaluate the machine learning models for polyp classification. We have also compared the performance of eight state-of-the-art deep learning-based object detection models. The results demonstrate that deep CNN models are promising in CRC screening. This work can serve as a baseline for future research in polyp detection and classification.

BACKGROUND AND AIM The standard for classifying Barrett's metaplasia on endoscopy, the Prague C&M criteria, ignores all islands of metaplastic-appearing tissue. The aims of the present study were to measure the prevalence of columnar islands, quantify their impact on metaplasia extent, and determine if they harbor advanced dysplasia. METHODS Data from two prospective patient cohorts were retrospectively analyzed. They included adults who underwent upper endoscopy to evaluate for gastroesophageal reflux disease, Barrett's esophagus (BE), dysplasia, or adenocarcinoma between 2003 and 2012 at tertiary care centers in the USA and Germany. The BE pattern, location, and pathology were examined. The extent of BE as defined by the Prague criteria (disregarding the location of islands) was compared with the complete maximal extent of BE (incorporating the location of islands). RESULTS A total of 555 patients underwent endoscopy (mean age 60.1 years, 67.2% male, 91.9% white). Among those patients, 191 (34.4%) showed metaplastic-appearing mucosa in islands. Endoscopically, in 101 (52.9%) cases, islands were proximal to the farthest segment of BE as defined by the Prague M location. Histologically, intestinal metaplasia was confirmed in 60 (58.8%) of the 102 esophagogastroduodenoscopies (EGDs) where islands were biopsied. In 41 (40.2%) cases, the histologically confirmed BE islands extended farther than the maximal segment based on the Prague criteria. Pathology from biopsies of islands either changed the diagnosis or worsened the BE dysplasia grade in 16 (15.7%) of the 102 patients. CONCLUSIONS Columnar islands are commonly seen on EGD. The Prague C&M criteria may underestimate the maximal extent of BE and overlook the area of highest dysplasia grade.

BACKGROUND & AIMS: Aneuploidy has been proposed as a tool to assess progression in patients with Barrett’s Esophagus (BE), but has heretofore required multiple biopsies. We assessed whether a single esophageal brushing that widely sampled the esophagus could be combined with massively parallel sequencing to characterize aneuploidy and identify patients with disease progression to dysplasia or cancer. METHODS: Esophageal brushings were obtained from patients without BE, with non-dysplastic BE (NDBE), low-grade dysplasia (LGD), high grade dysplasia (HGD), or adenocarcinoma (EAC). To assess aneuploidy, we employed RealSeqS, a technique that uses a single primer pair to interrogate ∼350,000 genome-spanning regions and identify specific chromosome arm alterations. A classifier to distinguish NDBE from EAC was trained on results from 79 patients. An independent validation cohort of 268 subjects was used to test the classifier at distinguishing patients at successive phases of BE progression. RESULTS: Aneuploidy progression was associated with gains of 1q, 12p, and 20q and losses on 9p and 17p. The entire chromosome 8q was often gained in NDBE, whereas focal gain of 8q24 was identified only when there was dysplasia. Among validation subjects, a classifier incorporating these features with a global measure of aneuploidy scored positive in 96% of EAC, 68% of HGD, but only 7% of NDBE. CONCLUSIONS: RealSeqS analysis of esophageal brushings provides a practical and sensitive method to determine aneuploidy in BE patients. It identifies specific chromosome changes that occur early in NDBE and others that occur late and mark progression to dysplasia. The clinical implications of this approach can now be tested in prospective trials.

Background Familial aggregation and segregation analysis studies have provided evidence of a genetic basis for esophageal adenocarcinoma (EAC) and its premalignant precursor, Barrett's esophagus (BE). We aim to demonstrate the utility of linkage analysis to identify the genomic regions that might contain the genetic variants that predispose individuals to this complex trait (BE and EAC). Methods We genotyped 144 individuals in 42 multiplex pedigrees chosen from 1000 singly ascertained BE/EAC pedigrees, and performed both model-based and model-free linkage analyses, using S.A.G.E. and other software. Segregation models were fitted, from the data on both the 42 pedigrees and the 1000 pedigrees, to determine parameters for performing model-based linkage analysis. Model-based and model-free linkage analyses were conducted in two sets of pedigrees: the 42 pedigrees and a subset of 18 pedigrees with female affected members that are expected to be more genetically homogeneous. Genome-wide associations were also tested in these families. Results Linkage analyses on the 42 pedigrees identified several regions consistently suggestive of linkage by different linkage analysis methods on chromosomes 2q31, 12q23, and 4p14. A linkage on 15q26 is the only consistent linkage region identified in the 18 female-affected pedigrees, in which the linkage signal is higher than in the 42 pedigrees. Other tentative linkage signals are also reported. Conclusion Our linkage study of BE/EAC pedigrees identified linkage regions on chromosomes 2, 4, 12, and 15, with some reported associations located within our linkage peaks. Our linkage results can help prioritize association tests to delineate the genetic determinants underlying susceptibility to BE and EAC.

Barrett's esophagus (BE) is the only known precursor to esophageal adenocarcinoma (EAC). Based on striking aggregation of breast cancer and BE/EAC within families as well as shared risk factors and molecular mechanisms of carcinogenesis, we hypothesized that BE may be associated with breast cancer. Pedigree analysis of families identified prospectively at multiple academic centers as part of the Familial Barrett's Esophagus Consortium (FBEC) was reviewed and families with aggregation of BE/EAC and breast cancer are reported. Additionally, using a matched case-control study design, we compared newly diagnosed BE cases in Caucasian females with breast cancer (cases) to Caucasian females without breast cancer (controls) who had undergone upper endoscopy (EGD). Two familial pedigrees, meeting a stringent inclusion criterion, manifested familial aggregation of BE/EAC and breast cancer in an autosomal dominant inheritance pattern with incomplete penetrance. From January 2008 to October 2016, 2812 breast cancer patient charts were identified, of which 213 were Caucasian females who underwent EGD. Six of 213 (2.82%) patients with breast cancer had pathology-confirmed BE, compared to 1 of 241 (0.41%) controls (P-value

We report a biomarker-based non-endoscopic method for detecting Barrett’s esophagus (BE), based on detecting methylated DNAs retrieved via a swallowable balloon-based esophageal sampling device. BE is the precursor of, and a major recognized risk factor for, developing esophageal adenocarcinoma (EAC). Endoscopy, the current standard for BE detection, is not cost-effective for population screening. We performed genome-wide screening to ascertain regions targeted for recurrent aberrant cytosine methylation in BE, identifying high-frequency methylation within the CCNA1 locus. We tested CCNA1 DNA methylation as a BE biomarker in cytology brushings of the distal esophagus from 173 individuals with or without BE. CCNA1 DNA methylation demonstrated an area under the curve (AUC)=0.95 for discriminating BE-related metaplasia and neoplasia cases versus normal individuals, performing identically to methylation of VIM DNA, an established BE biomarker. When combined, the resulting two biomarker panel was 95% sensitive and 91% specific. These results were replicated in an independent validation cohort of 149 individuals, who were assayed using the same cutoff values for test positivity established in the training population. To progress toward non-endoscopic esophageal screening, we engineered a well-tolerated, swallowable, encapsulated balloon device able to selectively sample the distal esophagus within 5 minutes. In balloon samples from 86 individuals, tests of CCNA1 plus VIM DNA methylation detected BE metaplasia with 90.3% sensitivity and 91.7% specificity. Combining the balloon sampling device with molecular assays of CCNA1 plus VIM DNA methylation enables an efficient, well-tolerated, sensitive, and specific method of screening at-risk populations for BE.

Background: Colorectal cancer (CRC) is the second most common cancer in the US. Despite evidence that screening reduces CRC incidence and mortality, screening rates are sub-optimal with disparities by race/ethnicity, income, and geography. Rural-urban differences in CRC screening are understudied even though approximately one-fifth of the US population lives in rural areas. This focus on urban populations limits the generalizability and dissemination potential of screening interventions. Methods: Using community-based participatory research (CBPR) principles, we designed a cluster-randomized trial, adaptable to a range of settings, including rural and urban health centers. We enrolled 483 participants across 11 health centers representing 2 separate networks. Both networks serve medically-underserved communities; however one is primarily rural and one primarily urban. Results: Our goal in this analysis is to describe baseline characteristics of participants and examine setting-level differences. CBPR was a critical for recruiting networks to the trial. Patient respondents were predominately female (61.3%), African-American (66.5%), and earned

BACKGROUND Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC) are far more prevalent in European Americans than in African Americans. Hypothesizing that this racial disparity in prevalence might represent a genetic susceptibility, we used an admixture mapping approach to interrogate disease association with genomic differences between European and African ancestry. METHODS Formalin fixed paraffin embedded samples were identified from 54 African Americans with BE or EAC through review of surgical pathology databases at participating Barrett's Esophagus Translational Research Network (BETRNet) institutions. DNA was extracted from normal tissue, and genotyped on the Illumina OmniQuad SNP chip. Case-only admixture mapping analysis was performed on the data from both all 54 cases and also on a subset of 28 cases with high genotyping quality. Haplotype phases were inferred with Beagle 3.3.2, and local African and European ancestries were inferred with SABER plus. Disease association was tested by estimating and testing excess European ancestry and contrasting it to excess African ancestry. RESULTS Both datasets, the 54 cases and the 28 cases, identified two admixture regions. An association of excess European ancestry on chromosome 11p reached a 5% genome-wide significance threshold, corresponding to -log10(P) = 4.28. A second peak on chromosome 8q reached -log10(P) = 2.73. The converse analysis examining excess African ancestry found no genetic regions with significant excess African ancestry associated with BE and EAC. On average, the regions on chromosomes 8q and 11p showed excess European ancestry of 15% and 20%, respectively. CONCLUSIONS Chromosomal regions on 11p15 and 8q22-24 are associated with excess European ancestry in African Americans with BE and EAC. Because GWAS have not reported any variants in these two regions, low frequency and/or rare disease associated variants that confer susceptibility to developing BE and EAC may be driving the observed European ancestry association evidence.

Intestinal metaplasia (IM), a premalignant lesion, is associated with an increased risk of gastric cancer. Although estrogen exposure, including tamoxifen, has been studied in correlation with gastric cancer, little has been investigated about its effects on IM.Therefore, we investigated whether chronic tamoxifen use was associated with the risk of IM in human stomach.We evaluated 512 gastric biopsies from 433 female breast cancer patients that underwent endoscopic gastroduodenoscopy (EGD) ≥6 months after breast surgery. Histopathological findings were scored according to the updated Sydney classification. Demographic and clinical characteristics were also included to identify predictive factors for IM.In a multivariate logistic regression analysis, age at EGD (odds ratio [OR], 1.04; P = 0.002), biopsies from antrum (OR 2.08; P0.001), and Helicobacter pylori positivity (OR 1.68; P = 0.016) were significantly associated with an increased risk of IM, whereas chronic tamoxifen use (≥3 months) was associated with a decreased risk of IM (OR 0.59; P = 0.025). After stratifying by biopsy site, association between tamoxifen use and IM persisted for corpus (OR 0.42; P = 0.026) but not for antrum (OR 0.74; P = 0.327). In analysis limited to patients with follow-up EGD, chronic tamoxifen use also correlated with improved IM score compared to no tamoxifen use (improved, 77.8 vs. 22.2%; no change, 65.4 vs. 34.6%; worsened, 30.0 vs. 70.0%; P = 0.019).This study suggests that chronic tamoxifen use can decrease the risk of IM in human stomach. The effect of tamoxifen is predominantly observed in the corpus.