Genome sequencing of oesophagus atresia families
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ABSTRACT:
PROVIDER: EGAS00001004394 | EGA |
REPOSITORIES: EGA
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Project description:BACKGROUND:Oesophageal atresia (OA) is a life-threatening developmental defect characterized by a lost continuity between the upper and lower oesophagus. The most common form is a distal connection between the trachea and the oesophagus, i.e. a tracheoesophageal fistula (TEF). The condition may be part of a syndrome or occurs as an isolated feature. The recurrence risk in affected families is increased compared to the population-based incidence suggesting contributing genetic factors. METHODS:To gain insight into gene variants and genes associated with isolated OA we conducted whole genome sequencing on samples from three families with recurrent cases affected by congenital and isolated TEF. RESULTS:We identified a combination of single nucleotide variants (SNVs), splice site variants (SSV) and structural variants (SV) annotated to altogether 100 coding genes in the six affected individuals. CONCLUSION:This study highlights rare SVs among candidate gene variants in our individuals with OA and provides a gene framework for further investigations of genetic factors behind this malformation.
| S-EPMC7318369 | BioStudies
Project description:Barrett's esophagus is the assumed precusor to oesophageal adenocarcinoma. We profiled the open chromatin of human Barrett's biopsies to gain insight into its molecular basis.
| E-MTAB-6751 | BioStudies
Project description:Barrett's esophagus is the assumed precusor to oesophageal adenocarcinoma. We profiled the open chromatin of human Barrett's biopsies to gain insight into its molecular basis.
2019-02-04 | E-MTAB-6751 | ArrayExpress
Project description:BACKGROUND:Based on reported familial patterns, inheritance of a predisposition of developing Barrett's oesesophagus (BO) and oesophageal adenocarcinoma (OAC) likely follows an autosomal dominant model of most inherited cancer syndromes. oesophagus (BO) and oesophageal adenocarcinoma (OAC) likely follows an autosomal dominant model of most inherited cancer syndromes. AIMS:We analysed the phenotypic features of 70 familial BO/OAC families accrued for the purpose of initiating a linkage study to search for genes that contribute to susceptibility for BO/OAC. METHODS:Families with young or familial BO/OAC were recruited from participating institutions and self-referral from advertisement. RESULTS:A total of 70 families (173 affected and 784 unaffected individuals) were recruited into this study. Mean ages of diagnosis of BO and OAC among males were 50.6 and 57.4 years, respectively; among females, 52.1 and 63.5 years, respectively. The standardised incidence ratio (SIR) of cancers other than OAC or oesophagogastric junctional adenocarcinoma (OGJAC), among probands was 0.71. Seventy one percent of the pedigrees have "typical" structures with less than three affected individuals. Power calculations under realistic model assumptions suggest that if genetic heterogeneity is absent or limited, then DNA collection from members of these pedigrees could enable the identification of a novel candidate susceptibility gene for BO/OAC in a genome scan. CONCLUSIONS:This is the largest series of families with BO/OAC yet reported, features of which are consistent with inherited germline predisposition. Further, the SIR of cancers other than OAC/OGJAC was 0.71 among 70 probands, indicating these individuals were not more likely to develop non-OAC cancers.
| S-EPMC1735581 | BioStudies
Project description:Concern exists that patients born with oesophageal atresia (OA) may be at high risk for Barrett's oesophagus (BO), a known malignant precursor to the development of oesophageal adenocarcinoma. Screening endoscopy has a role in early BO identification but is not universal in this population. This study aimed to determine prevalence of BO after OA repair surgery, to quantify the magnitude of this association and inform the need for screening and surveillance. A systematic review, undertaken according to PRISMA guidelines, was preregistered on PROSPERO (CRD42017081001). PubMed and EMBASE were interrogated using a standardized search strategy on 31 July 2020. Included papers, published in English, reported either: one or more patients with either BO (gastric/intestinal metaplasia) or oesophageal cancer in patients born with OA; or long-term (greater than 2 years) follow-up after OA surgery with or without endoscopic screening or surveillance. Some 134 studies were identified, including 19 case reports or series and 115 single- or multi-centre cohort studies. There were 13 cases of oesophageal cancer (9 squamous cell carcinoma, 4 adenocarcinoma) with a mean age at diagnosis of 40.5 (range 20-47) years. From 6282 patients under long-term follow-up, 317 patients with BO were reported. Overall prevalence of BO was 5.0 (95 per cent c.i. 4.5 to 5.6) per cent, with a mean age at detection of 13.8 years (range 8 months to 56 years). Prevalence of BO in series reporting endoscopic screening or surveillance was 12.8 (95 per cent c.i. 11.3 to 14.5) per cent. Despite a limited number of cancers, the prevalence of BO in patients born with OA is relatively high. While limited by the quality of available evidence, this review suggests endoscopic screening and surveillance may be warranted, but uncertainties remain over the design and effectiveness of any putative programme.
| S-EPMC8405903 | BioStudies
Project description:A tissue-engineered oesophageal scaffold could be very useful for the treatment of pediatric and adult patients with benign or malignant diseases such as carcinomas, trauma or congenital malformations. Here we decellularize rat oesophagi inside a perfusion bioreactor to create biocompatible biological rat scaffolds that mimic native architecture, resist mechanical stress and induce angiogenesis. Seeded allogeneic mesenchymal stromal cells spontaneously differentiate (proven by gene-, protein and functional evaluations) into epithelial- and muscle-like cells. The reseeded scaffolds are used to orthotopically replace the entire cervical oesophagus in immunocompetent rats. All animals survive the 14-day study period, with patent and functional grafts, and gain significantly more weight than sham-operated animals. Explanted grafts show regeneration of all the major cell and tissue components of the oesophagus including functional epithelium, muscle fibres, nerves and vasculature. We consider the presented tissue-engineered oesophageal scaffolds a significant step towards the clinical application of bioengineered oesophagi.
| S-EPMC4354271 | BioStudies
Project description:Oesophageal atresia (OA) with or without tracheoesophageal fistula (TOF) are rare anatomical congenital malformations whose cause is unknown in over 90% of patients. A genetic background is suggested, and among the reported genetic defects are copy number variations (CNVs). We hypothesized that CNVs contribute to OA/TOF development. Quantifying their prevalence could aid in genetic diagnosis and clinical care strategies. Therefore, we profiled 375 patients in a combined Dutch, American and German cohort via genomic microarray and compared the CNV profiles with their unaffected parents and published control cohorts. We identified 167 rare CNVs containing genes (frequency<0.0005 in our in-house cohort). Eight rare CNVs - in six patients - were de novo, including one CNV previously associated with oesophageal disease. (hg19 chr7:g.(143820444_143839360)_(159119486_159138663)del) 1.55% of isolated OA/TOF patients and 1.62% of patients with additional congenital anomalies had de novo CNVs. Furthermore, three (15q13.3, 16p13.3 and 22q11.2) susceptibility loci were identified based on their overlap with known OA/TOF-associated CNV syndromes and overlap with loci in published CNV association case-control studies in developmental delay. Our study suggests that CNVs contribute to OA/TOF development. In addition to the identified likely deleterious de novo CNVs, we detected 167 rare CNVs. Although not directly disease-causing, these CNVs might be of interest, as they can act as a modifier in a multiple hit model, or as the second hit in a recessive condition.
| S-EPMC5117935 | BioStudies
Project description:<h4>Objectives</h4>Bile reflux contributes to oesophageal injury and neoplasia. COX-2 is involved in both inflammation and carcinogenesis; however, the precise mechanisms by which bile acids promote COX-2 expression in the oesophagus are largely unknown. We analysed the molecular mechanisms that govern bile acid-mediated expression of COX-2 in Barrett's oesophagus and oesophageal adenocarcinoma (OA).<h4>Design</h4>The effects of bile acids on COX-2 expression were analysed in immortalised Barrett's oesophagus and OA cells using immunoblotting and transient transfections. Pharmacological inhibitors, phospho-specific antibodies, dominant-negative mutants and siRNA techniques were used to identify relevant signalling pathways. Flow cytometry and reactive oxygen species (ROS) scavengers were used to examine ROS involvement. Immunohistochemistry was performed on oesophageal mucosa obtained from an established rat model of bile reflux.<h4>Results</h4>Unconjugated bile acids potently stimulated COX-2 expression and induced AKT and ERK1/2 phosphorylation in concert with COX-2 induction. These findings were mimicked in the in vivo rat model. Dominant-negative (DN) AKT and LY294002 (PI3K inhibitor) or U0126 (MEK-1/2 inhibitor) blocked chenodeoxycholic acid (CD) and deoxycholic acid (DC) mediated COX-2 induction. CD and DC also induced CREB phosphorylation and AP-1 activity. CREB-specific siRNA and DN AP-1 blocked CD and DC-induced COX-2 induction. Finally, CD and DC increased intracellular ROS, while ROS scavengers blocked COX-2 induction and the signalling pathways involved.<h4>Conclusions</h4>Unconjugated bile acids induce CREB and AP-1-dependent COX-2 expression in Barrett's oesophagus and OA through ROS-mediated activation of PI3K/AKT and ERK1/2. This study enhances our understanding of the molecular mechanisms by which bile acids promote the development of oesophageal adenocarcinoma.
| S-EPMC2095641 | BioStudies
Project description:OBJECTIVE:Oesophageal adenocarcinoma (OA) incidence has risen sharply in Western countries over recent decades. Local and systemic inflammation is considered an important contributor to OA pathogenesis. Established risk factors for OA and its precursor, Barrett's oesophagus (BE), include symptomatic reflux, obesity and smoking. The role of inherited genetic susceptibility remains an area of active investigation. Here, we explore whether germline variation related to inflammatory processes influences susceptibility to BE/OA. DESIGN:We used data from a genomewide association study of 2515 OA cases, 3295 BE cases and 3207 controls. Our analysis included 7863 single-nucleotide polymorphisms (SNPs) in 449 genes assigned to five pathways: cyclooxygenase (COX), cytokine signalling, oxidative stress, human leucocyte antigen and nuclear factor-?B. A principal components-based analytic framework was employed to evaluate pathway-level and gene-level associations with disease risk. RESULTS:We identified a significant signal for the COX pathway in relation to BE risk (p=0.0059, false discovery rate q=0.03), and in gene-level analyses found an association with microsomal glutathione-S-transferase 1 (MGST1); (p=0.0005, q=0.005). Assessment of 36 MGST1 SNPs identified 14 variants associated with elevated BE risk (q<0.05). Four of these were subsequently confirmed (p<5.5×10-5) in a meta-analysis encompassing an independent set of 1851 BE cases and 3496 controls, and are known strong expression quantitative trait loci for MGST1. Three such variants were associated with similar elevations in OA risk. CONCLUSIONS:This study provides the most comprehensive evaluation of inflammation-related germline variation in relation to risk of BE/OA and suggests that variants in MGST1 influence disease susceptibility.
| S-EPMC5296402 | BioStudies
Project description:A 72-year-old woman presented with long-standing gastro-oesophageal reflux, regurgitation of swallowed food and worsening cervical dysphagia. Fluoroscopic barium oesophagography revealed a posterolateral pharyngeal pouch (Zenker's diverticulum (ZD)) complicating a 'cup and spill' oesophageal deformity with a smoothly tapered segment at the gastro-oesophageal junction. CT and high-resolution manometry confirmed that the underlying abnormality was a massively dilated oesophagus with aperistalsis and pan-oesophageal pressurisation, consistent with a diagnosis of oesophageal achalasia (type II). She underwent endoscopic stapled diverticulotomy, with good symptomatic relief. We discuss the aetiology of ZD, its management and the association here with oesophageal achalasia.
2013-01-01 | S-EPMC3863039 | BioStudies