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Cell-free transcriptome of Barrett’s Esophagus and Esophageal Cancer [Nanopore - long read]

ABSTRACT: Esophageal adenocarcinoma (EAD) benefits from a large improvement in five-year survival when detected in early stages, therefore, early detection strategies are paramount to mitigating disease. Those diagnosed with Barrett’s Esophagus (BE) are at higher risk for EAD, though there exists no routine screening for EAD. Recent advances in cell-free RNA sequencing aim to create minimally-invasive diagnostic modalities. We present short and long read data from plasma of BE, EAD, and Healthy patients for biomarker discovery.

ORGANISM(S): Homo sapiens

PROVIDER: GSE271389 | GEO | 2025/12/08

REPOSITORIES: GEO

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Cell-free transcriptome of Barrett’s Esophagus and Esophageal Cancer [Illumina - short read]

Project description:Esophageal adenocarcinoma (EAD) benefits from a large improvement in five-year survival when detected in early stages, therefore, early detection strategies are paramount to mitigating disease. Those diagnosed with Barrett’s Esophagus (BE) are at higher risk for EAD, though there exists no routine screening for EAD. Recent advances in cell-free RNA sequencing aim to create minimally-invasive diagnostic modalities. We present short and long read data from plasma of BE, EAD, and Healthy patients for biomarker discovery.

2025-12-08 | GSE271390 | GEO

HOXA13 in etiology and oncogenic potential of Barrett’s esophagus [EPC2]

Project description:Barrett’s esophagus in gastrointestinal reflux patients constitutes a columnar epithelium with distal characteristics, prone to progress to esophageal adenocarcinoma. HOX genes are known mediators of position-dependent morphology. Here we show HOX collinearity in the adult gut while Barrett’s esophagus shows high HOXA13 expression in stem cells and their progeny. HOXA13 overexpression appears sufficient to explain both the phenotype (through downregulation of the epidermal differentiation complex) and the oncogenic potential of Barrett’s esophagus. Intriguingly, employing a mouse model that contains a reporter coupled to the HOXA13 promotor we identify single HOXA13-positive cells distally from the physiological esophagus, which is mirrored in human physiology, but increased in BE. Additionally, we observe that HOXA13 expression confers a competitive advantage to cells. We thus propose that Barrett’s esophagus and associated esophageal adenocarcinoma is the consequence of expansion of this gastro-esophageal HOXA13-expressing compartment following epithelial injury.

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Comprehensive analysis of transcriptome-wide N6-methyladenosine methylomes in the rat Barrett’s esophagus

Project description:To investigate the mRNA m6A modification pattern in Barrett’s esophagus,we performed transcriptome-wide maps of m6A methylation，foreseeing a molecular mechanism of m6A-mediated gene in Barrett’s esophagus.

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Cloning Barrett’s esophagus stem cells

Project description:Barrett’s esophagus is a precancerous lesion that confers a significant risk of esophageal adenocarcinoma. Strategies for selective eradication of Barrett’s have been stymied by our inability to identify the Barrett’s stem cell. Here we employ novel technologies to clone patient-matched stem cells of Barrett’s, gastric, and esophageal epithelium. Genomic analyses of Barrett’s stem cells reveal a patient-specific mutational spectrum ranging from low somatic variation similar to patient-matched gastric epithelial stem cells to ones marked by extensive heterozygous alteration of genes implicated in tumor suppression, epithelial planarity, and epigenetic regulation. Transplantation of transformed Barrett’s stem cells yields tumors with hallmarks of esophageal adenocarcinoma, whereas transformed esophageal stem cells yield squamous cell carcinomas. Thus Barrett’s develops from cells distinct from local eponymous epithelia, emerges without obvious driver mutations, and likely progresses through and from the generation of dominant clones. These findings define a stem cell target for preemptive therapies of a precancerous lesion.

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HOXA13 in etiology and oncogenic potential of Barrett’s esophagus [BAR-T]

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HOXA13 in etiology and oncogenic potential of Barrett’s esophagus [KH2 mESC diff]

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HOXA13 in etiology and oncogenic potential of Barrett’s esophagus [KH2 mESC non diff]

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Profiling of circulating microRNAs in patients with Barrett’s esophagus and esophageal adenocarcinoma

Project description:miRNAs were extracted from plasma samples of healthy volunteers, patients with Barrett’s esophagus and patients with esophageal adenocarcinoma. We used the Serum / Plasma Focus miRNA PCR panel (Exiqon, Denmark) to quantitate miRNA presence in the different patient groups.

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Esophageal tissue and serum microRNAs changed in the progression of Barrett’s esophagus in mice

Project description:Circulating microRNAs (miRNAs) are promising biomarkers for the early detection of cancers. This assay aimed to address potential circulating miRNAs to monitor the progression from Barrett’s esophagus to esophageal adenocarcinoma (EAC).

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Increased PXR and suppressed T-cell signaling are associated with malignant degeneration of Barrett’s esophagus

Project description:Barrett’s esophagus (BE) is the precursor lesion for esophageal adenocarcinoma (EAC). To detect EAC in early stage, patients with BE undergo endoscopic surveillance. Surveillance cohorts largely consist of non-dysplastic Barrett’s esophagus (NDBE) patients with a low annual progression risk (<0.5%). Predictive biomarkers for malignant progression of NDBE could improve efficacy of surveillance. Biomarker research has mostly focused on aberrant protein expression on BE epithelial cells. Moreover, insight in cell signaling driving malignant transformation is unknown. This study uses a data-driven approach to analyze tumor-stroma interaction in NDBE which progressed to high grade dysplasia (HGD) or EAC.

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