Genetic factors in isolated and syndromic esophageal atresia

Developmental basis of trachea-esophageal birth defects

Trachea-esophageal defects (TEDs), including esophageal atresia (EA), tracheoesophageal fistula (TEF), and laryngeal-tracheoesophageal clefts (LTEC), are a spectrum of life-threatening congenital anomalies in which the trachea and esophagus do not form properly. Up until recently, the developmental basis of these conditions and how the trachea and esophagus arise from a common fetal foregut was poorly understood. However, with significant advances in human genetics, organoids, and animal models, and integrating single cell genomics with high resolution imaging, we are revealing the molecular and cellular mechanisms that orchestrate tracheoesophageal morphogenesis and how disruption in these processes leads to birth defects. Here we review the current understanding of the genetic and developmental basis of TEDs. We suggest future opportunities for integrating developmental mechanisms elucidated from animals and organoids with human genetics and clinical data to gain insight into the genotype-phenotype basis of these heterogeneous birth defects. Finally, we envision how this will enhance diagnosis, improve treatment, and perhaps one day, lead to new tissue replacement therapy.

Novel candidate genes in esophageal atresia/tracheoesophageal fistula identified by exome sequencing

The various malformations of the aerodigestive tract collectively known as esophageal atresia/tracheoesophageal fistula (EA/TEF) constitute a rare group of birth defects of largely unknown etiology. Previous studies have identified a small number of rare genetic variants causing syndromes associated with EA/TEF. We performed a pilot exome sequencing study of 45 unrelated simplex trios (probands and parents) with EA/TEF. Thirteen had isolated and 32 had nonisolated EA/TEF; none had a family history of EA/TEF. We identified de novo variants in protein-coding regions, including 19 missense variants predicted to be deleterious (D-mis) and 3 likely gene-disrupting (LGD) variants. Consistent with previous studies of structural birth defects, there is a trend of increased burden of de novo D-mis in cases (1.57-fold increase over the background mutation rate), and the burden is greater in constrained genes (2.55-fold, p = 0.003). There is a frameshift de novo variant in EFTUD2, a known EA/TEF risk gene involved in mRNA splicing. Strikingly, 15 out of 19 de novo D-mis variants are located in genes that are putative target genes of EFTUD2 or SOX2 (another known EA/TEF gene), much greater than expected by chance (3.34-fold, p value = 7.20e-5). We estimated that 33% of patients can be attributed to de novo deleterious variants in known and novel genes. We identified APC2, AMER3, PCDH1, GTF3C1, POLR2B, RAB3GAP2, and ITSN1 as plausible candidate genes in the etiology of EA/TEF. We conclude that further genomic analysis to identify de novo variants will likely identify previously undescribed genetic causes of EA/TEF.

Characterization of mesenchymal stem cells in patients with esophageal atresia

BACKGROUND

Preclinical studies demonstrate that tissue engineering and patient-derived stem cells can regenerate tissue. The goal of this study was to determine whether stem cells from esophageal atresia patients (EA) could be utilized for this purpose.

METHODS

Adipose tissue was obtained from control, esophageal atresia (EA) and long gap esophageal atresia (LGEA) patients. Mesenchymal stem cells (MSCs) were isolated, expanded, characterized and seeded onto tubular scaffolds for 6 days. Scaffolds were characterized for viability, gene expression and cytokine production.

RESULTS

The average weight of tissue from the EA and LGEA patients was 145.8mg compared to 2981 mg in controls. Despite the small amount of tissue obtained from neonatal patients, cells were expanded to cover a scaffold. After incubating 6 days on the scaffold, cells were viable and proliferating with differences in gene expression between groups. VEGFA production in the supernatant was increased in EA and LGEA patients; while IL6 production was significantly increased in the control patients.

CONCLUSIONS

This study demonstrates the ability to utilize small amounts of adipose tissue from esophageal atresia patients as a cell source for regenerative medicine. Future studies will focus on use of these cells for tissue regeneration in vivo.

Surgical treatment and major complications Within the first year of life in newborns with long-gap esophageal atresia gross type A and B - a systematic review

BACKGROUND

The surgical repair of long-gap esophageal atresia (LGEA) is still a challenge and there is no consensus on the preferred method of reconstruction. We performed a systematic review of the surgical treatment of LGEA Gross type A and B with the primary aim to compare the postoperative complications related to the different methods within the first postoperative year.

METHODS

Systematic literature review on the surgical repair of LGEA Gross type A and B within the first year of life published from January 01, 1996 to November 01, 2016.

RESULTS

We included 57 articles involving a total of 326 patients of whom 289 had a Gross type A LGEA. Delayed primary anastomosis (DPA) was the most applied surgical method (68.4%) in both types, followed by gastric pull-up (GPU) (8.3%). Anastomotic stricture (53.7%), gastro-esophageal reflux (GER) (32.2%) and anastomotic leakage (22.7%) were the most common postoperative complications, with stricture and GER occurring more often after DPA (61.9% and 40.8% respectively) compared to other methods (p < 0.001).

CONCLUSION

The majority of patients in this review were managed by DPA and postoperative complications were common despite the surgical method, with anastomotic stricture and GER being most common after DPA.

LEVEL OF EVIDENCE

Systematic review of case series and case reports with no comparison group (level IV).

Surgical repair of long-gap esophageal atresia: A retrospective study comparing the management of long-gap esophageal atresia in the Nordic countries

BACKGROUND

Several surgical procedures have been described in the reconstruction of long-gap esophageal atresia (LGEA). We reviewed the surgical methods used in children with LGEA in the Nordic countries over a 15-year period and the postoperative complications within the first postoperative year.

METHODS

Retrospective multicenter medical record review of all children born with Gross type A or B esophageal atresia between 01/01/2000 and 12/31/2014 reconstructed within their first year of life.

RESULTS

We included 71 children; 56 had Gross type A and 15 type B LGEA. Delayed primary anastomosis (DPA) was performed in 52.1% and an esophageal replacement procedure in 47.9%. Gastric pull-up (GPU) was the most frequent procedure (25.4%). The frequency of chromosomal abnormalities, congenital heart defects and other anomalies was significantly higher in patients who had a replacement procedure. The frequency of gastroesophageal reflux (GER) was significantly higher after DPA compared to esophageal replacement (p = 0.013). At 1-year follow-up the mean body weight was higher after DPA than after organ interposition (p = 0.043).

CONCLUSION

DPA and esophageal replacement procedures were equally applied. Postoperative complications and follow-up were similar except for the development of GER and the body weight at 1-year follow-up. Long-term results should be investigated.

TYPE OF STUDY

Treatment study.

LEVEL OF EVIDENCE

Level III.

Identification of rare heterozygous missense mutations in FANCA in esophageal atresia patients using next-generation sequencing

Esophageal atresia and tracheoesophageal fistula (EA/TEF) are relatively common malformations in newborns, but the etiology of EA/TEF remains unknown. Fanconi anemia (FA) complementation group A (FANCA) is a key component of the FA core complex and is essential for the activation of the DNA repair pathway. The middle region (amino acids 674-1208) of FANCA is required for its interaction with FAAP20. We performed targeted sequencing of this binding region of FANCA (exons 23-36) in 40 EA/TEF patients. We also investigated the effect of the p.A958V mutation on the protein-protein interaction between FANCA and FAAP20 using an in vitro binding assay and co-immunoprecipitation. Immunolocalization analysis was performed to investigate the subcellular localization of FANCA, and tissue sections and immunohistochemistry were used to explore the expression of FANCA. We identified four rare missense variants in the FANCA binding region. FANCA mutations were significantly overrepresented in EA/TEF patients compared with 4300 control subjects from the NHLBI-ESP project (Fisher's exact p = 2.17 × 10^-5, odds ratio = 31.75). p.A958V, a novel de novo mutation in the FANCA gene, was identified in one patient with EA/TEF. We provide further evidence that the p.A958V mutation reduces the binding affinity of FANCA for FAAP20. Interestingly, the p.A958V mutation impaired the nuclear localization of the FANCA protein expressed in HeLa cells. We found that FANCA was more highly expressed in stratified squamous epithelium than in smooth muscle. In conclusion, mutations in the FANCA gene are associated with EA/TEF in humans.

Multicentre survey on the current surgical management of oesophageal atresia in Belgium and Luxembourg

INTRODUCTION

The surgical management of oesophageal atresia (OA) differs between pediatric surgical teams without consensus. We aimed to describe the current practice of OA treatment in Belgium and Luxembourg and compare this to the literature.

MATERIALS AND METHODS

A questionnaire was created and sent to all 18 hospitals (14 pediatric surgical units) performing OA surgery in Belgium and Luxembourg. The results were compared to the literature.

RESULTS

Most units treat an average of 2-5 OA+TOF (71%) and ≤1 pure OA (pOA) per year (86%). The preferred surgical approach for OA+TOF is thoracotomy (86%), mostly extra-pleural (75%). Thoracoscopic OA repair is performed in 21%. All centers perform an end-to-end anastomosis (interrupted sutures), and all leave a transanastomotic tube. A chest drain is routinely used in 8units (57%). In pOA the preferred surgical approach is gastrostomy formation with delayed primary anastomosis (77%). The timing for delayed anastomosis is 2 to 24months. Intra-operative lengthening is mostly attempted with Foker technique (46%). If oesophageal replacement is needed, gastric interposition is mostly used (75%). A postoperative contrast study is routinely performed in 86% for OA+TOF and in 100% for pOA. Anti-reflux medication is routinely prescribed by all units but one.

CONCLUSION

There are still many differences and controversies in the perioperative management of OA. Part of this is based on habits and is difficult to change without scientific evidence. There is a need for prospective (inter)national registries to further identify the existing differences, leading to a more widely accepted consensus.

LEVEL OF EVIDENCE

Level III.

Environmental factors in the etiology of isolated and nonisolated esophageal atresia in a Chinese population: A case-control study

BACKGROUND

Esophageal atresia (EA) is a common birth defect that occurs with tracheoesophageal fistula (TEF), although etiological studies on EA/TEF have produced inconsistent results.

METHODS

The aim of this study was to examine the association between environmental factors during pregnancy and the risk of EA/TEF in a Chinese population. Cases of isolated EA and nonisolated EA and unaffected controls were identified between July 2005 and November 2015, and face-to-face questionnaires concerning exposure to environmental factors were administered to the birth mothers of 130 cases and 400 controls. The adjusted odds ratio (OR) and 95% confidence interval (CI) were calculated to assess the association between environmental factors and the risk of EA/TEF.

RESULTS

The results of this case-control study suggest that lower maternal education (p < 0.0001), maternal binge drinking (OR = 2.63; 95% CI, 1.05-6.6) and pickled food consumption (OR = 2.04; 95% CI, 1.31-3.71) during pregnancy increase the risk of EA in offspring, while maternal folic acid supplementation (OR = 0.45; 95% CI, 0.29-0.71) is significantly associated with a decreased risk of EA.

CONCLUSION

These results suggest a role for environmental exposures in the etiology of EA/TEF; however, further studies are needed to replicate the observed associations. Birth Defects Research (Part A) 106:840-846, 2016. © 2016 Wiley Periodicals, Inc.

Copy number variations in 375 patients with oesophageal atresia and/or tracheoesophageal fistula

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.

Eosinophilic esophagitis in patients with esophageal atresia and chronic dysphagia

Esophageal atresia (EA) is defined as a discontinuity of the lumen of the esophagus repaired soon after birth. Dysphagia is a common symptom in these patients, usually related to stricture, dysmotility or peptic esophagitis. We present 4 cases of patients with EA who complained of dysphagia and the diagnosis of Eosinophilic esophagitis (EoE) was made, ages ranging from 9 to 16 years. Although our patients were on acid suppression years after their EA repair, they presented with acute worsening of dysphagia. Esophogastroduodenoscopy and/or barium swallow did not show stricture and biopsies revealed elevated eosinophil counts consistent with EoE. Two of 4 patients improved symptomatically with the topical steroids. It is important to note that all our patients have asthma and 3 out of 4 have tested positive for food allergies. One of our patients developed recurrent anastomotic strictures that improved with the treatment of the EoE. A previous case report linked the recurrence of esophageal strictures in patients with EA repair with EoE. Once the EoE was treated the strictures resolved. On the other hand, based on our observation, EoE could be present in patients without recurrent anastomotic strictures. There appears to be a spectrum in the disease process. We are suggesting that EoE is a frequent concomitant problem in patients with history of congenital esophageal deformities, and for this reason any of these patients with refractory reflux symptoms or dysphagia (with or without anastomotic stricture) may benefit from an endoscopic evaluation with biopsies to rule out EoE.

De novo GLI3 mutation in esophageal atresia: reproducing the phenotypic spectrum of Gli3 defects in murine models

Esophageal atresia is a common and life-threatening birth defect with a poorly understood etiology. In this study, we analyzed the sequence variants of coding regions for a set of esophageal atresia-related genes including MYCN, SOX2, CHD7, GLI3, FGFR2 and PTEN for mutations using PCR-based target enrichment and next-generation sequencing in 27 patients with esophageal atresia. Genomic copy number variation analysis was performed using Affymetrix SNP 6.0. We found a de novo heterozygous mutation in the N-terminal region of the GLI3 gene (c.332T>C, p.M111T) in a patient with esophageal atresia and hemivertebrae. The N-terminal region (amino acids 1-397) of GLI3 contains the repressor domain, which interacts with SKI family proteins. Using the co-immunoprecipitation assay, we found that interaction of GLI3 with the SKI family protein SKIL was significantly compromised by the p.M111T mutation of GLI3. Thus far, all the identified mutations mapped within the repressor domain of GLI3 were nonsense and frame-shift mutations. In this study, a missense mutation was initially detected in this region. Our finding is the first to link this GLI3 gene mutation with esophageal atresia in humans, which was previously suggested in an animal model.

The multifactorial origin of respiratory morbidity in patients surviving neonatal repair of esophageal atresia

Esophageal atresia with or without tracheoesophageal fistula (EA ± TEF) occurs in 1 out of every 3000 births. Current survival approaches 95%, and research is therefore focused on morbidity and health-related quality of life issues. Up to 50% of neonates with EA ± TEF have one or more additional malformations including those of the respiratory tract that occur in a relatively high proportion of them and particularly of those with vertebral, anal, cardiac, tracheoesophageal, renal, and limb association. Additionally, a significant proportion of survivors suffer abnormal pulmonary function and chronic respiratory tract disease. The present review summarizes the current knowledge about the nature of these symptoms in patients treated for EA ± TEF, and explores the hypothesis that disturbed development and maturation of the respiratory tract could contribute to their pathogenesis.

Esophageal atresia: gastroesophageal functional follow-up in 5-15 year old children

PURPOSE

Esophageal atresia (EA) is one of the most frequent congenital alimentary tract anomalies with a considerable morbidity throughout childhood. This study evaluates the gastroesophageal problems in 5-15 year old children with EA and aims to identify factors predisposing to esophagitis in EA.

MATERIAL AND METHODS

Fifty-nine patients primarily operated at Odense University Hospital, Denmark, during 1993-2005 were included in this follow-up study. The patients underwent the following examinations: Interview, upper endoscopy, endoscopic ultrasonography, high-resolution esophageal manometry (HREM), and pH- and multichannel intraluminal impedance (MII) measurements. Twenty-five patients with suspected gastro-esophageal reflux disease (GERD) underwent the same investigations and served as controls.

RESULTS

Median age was 10.2 years (7.1-13.3). Thirty-three (55.9%) presented with GERD symptoms, 41 (69.5%) with dysphagia, and 33 (55.9%) with respiratory symptoms. Twenty-nine (49.2%) had endoscopic esophagitis, and 26 (44.1%) histological esophagitis. Median reflux index (RI) was 8.3 (4.8-14.9). In 32 (55.2%) RI was above 7. Ten percent had eosinophilic inflammation. HREM showed dysmotility in the esophagus in all EA patients, 83.3% had no propagating swallows. No predictive factors predisposing the development of endoscopic esophagitis were identified.

CONCLUSIONS

Gastroesophageal problems in children born with EA are common. Routine follow-up with endoscopy and pH-metry in EA patients is warranted.

Microdeletion 11q13.1.q13.2 in a patient presenting with developmental delay, facial dysmorphism, and esophageal atresia: possible role of the GSTP1 gene in esophagus malformation

BACKGROUND

Esophageal atresia is a major congenital malformation characterized by a complete interruption of the esophageal continuity. It is frequently observed in associations and syndromes. As an isolated finding, it has a multifactorial etiology whose genetic factors are poorly known. Recently, the GST family, especially the GSTM1 null genotype (but not the GSTP1 polymorphism I105V), has been associated with esophageal atresia. These enzymes play a role in phase II detoxification of xenobiotics. Here we present the clinical and molecular findings observed in a patient suggesting that the loss of the GSTP1 allele might predispose to this malformation.

CASE

We describe a patient presenting with esophageal atresia associated with developmental delay and facial dysmorphism, whose mother used tobacco and alcohol during the first 2 months of her pregnancy. Microdeletion/microduplication analysis was performed using comparative genomic hybridization and a 180K Agilent array. It detected a de novo 2 Mb chromosome 11q13.1.q13.2 deletion.

CONCLUSION

The deleted chromosomal segment includes the GSTP1 gene. We hypothesize that the deletion of one GSTP1 allele (an isoform highly expressed in embryonic tissues), associated with specific environmental factors, such as tobacco and alcohol, could cause the esophageal atresia observed in our patient.

Psychological impact of esophageal atresia: review of the research and clinical evidence

Esophageal atresia (EA) occurs in one out of 2500 to 4500 live births. As the vast majority of infants are now surviving neonatal corrective surgery, the focus has shifted from mortality to morbidity associated with EA. However, little is known about its psychological morbidity. This paper synthesizes research and clinical evidence to highlight the psychological sequelae of EA, including its impact on parents' psychological functioning and its effects on child development from infancy to adulthood. Whether it is discovered at birth or prenatally, EA is a psychologically traumatic event, and parents are at risk for developing traumatic stress reactions following diagnosis. Neonatal surgery and intensive care, risk of complications, associated anomalies, and genetic etiologies multiply risk for parents' acute and post-traumatic stress disorders (PTSD). Parental PTSD has a negative impact on infant and child development through its effects on parenting skills and parent-child interactions. EA children are also at risk for PTSD because of invasive and stressful procedures they undergo during the neonatal period. Consequences of EA can have an important long-term impact on children's psychological and social development. The scant studies pertaining to cognitive functioning suggest that EA does not affect mental development during infancy, but may be associated with deficits as children reach school age. Long-term sequelae are unclear because psychological functioning in adults has not yet been adequately examined. Research and clinical evidence of psychological morbidity associated with EA has implications for clinical practice. Psychological support for parents must begin during the neonatal period and should continue as an integral component of long-term follow up for both children and parents. Support is best provided within the context of a multidisciplinary treatment team that follows patients from birth through childhood and adolescence. Psychological follow up should continue into adulthood, as patients grow up and transition from pediatric to adult health-care settings.

Prevalence of esophageal atresia among 18 international birth defects surveillance programs

BACKGROUND

The prevalence of esophageal atresia (EA) has been shown to vary across different geographical settings. Investigation of geographical differences may provide an insight into the underlying etiology of EA.

METHODS

The study population comprised infants diagnosed with EA during 1998 to 2007 from 18 of the 46 birth defects surveillance programs, members of the International Clearinghouse for Birth Defects Surveillance and Research. Total prevalence per 10,000 births for EA was defined as the total number of cases in live births, stillbirths, and elective termination of pregnancy for fetal anomaly (ETOPFA) divided by the total number of all births in the population.

RESULTS

Among the participating programs, a total of 2943 cases of EA were diagnosed with an average prevalence of 2.44 (95% confidence interval [CI], 2.35-2.53) per 10,000 births, ranging between 1.77 and 3.68 per 10,000 births. Of all infants diagnosed with EA, 2761 (93.8%) were live births, 82 (2.8%) stillbirths, 89 (3.0%) ETOPFA, and 11 (0.4%) had unknown outcomes. The majority of cases (2020, 68.6%), had a reported EA with fistula, 749 (25.5%) were without fistula, and 174 (5.9%) were registered with an unspecified code.

CONCLUSIONS

On average, EA affected 1 in 4099 births (95% CI, 1 in 3954-4251 births) with prevalence varying across different geographical settings, but relatively consistent over time and comparable between surveillance programs. Findings suggest that differences in the prevalence observed among programs are likely to be attributable to variability in population ethnic compositions or issues in reporting or registration procedures of EA, rather than a real risk occurrence difference. Birth Defects Research (Part A), 2012.

Future treatment strategies for celiac disease

INTRODUCTION

Ingestion of dietary gluten in wheat, rye and barley by celiac patients leads to small-bowel mucosal villous atrophy, crypt hyperplasia and massive inflammation, often coupled with clinical symptoms and signs. Currently, the only effective treatment is a strict life-long gluten-free diet excluding all gluten-containing food products. In view of the extremely restricted nature of the diet, new treatment options would clearly be desirable.

AREAS COVERED

The improved understanding of celiac disease pathogenesis has enabled researchers to suggest alternative strategies to treat the disorder. This review covers current approaches toward developing an appropriate drug and discusses the possible problems associated with these approaches.

EXPERT OPINION

Phase II clinical trials are already ongoing to test the efficacy of novel alternative treatments for celiac disease. Before any of the candidates can enter Phase III trials, however, researchers must develop novel reliable non-invasive surrogate markers for intestinal injury and disease activity which also accurately reflect patient-related outcomes. Any novel medication for celiac disease should be as effective and safe as the gluten-free diet, and this constitutes a challenge for drug development. It is thus likely that the first medication entering the market will be supplementary to rather than substitute the gluten-free diet.