Genetic and environmental factors in the etiology of esophageal atresia and/or tracheoesophageal fistula: an overview of the current concepts

Oesophageal Atresia: Prevalence in the Valencian Region (Spain) and Associated Anomalies

The objective was to determine the prevalence of oesophageal atresia (OA) and describe the characteristics of OA cases diagnosed before the first year of life, born between 2007 and 2019, and residents in the Valencian Region (VR), Spain. Live births (LB), stillbirths (SB), and termination of pregnancy for fetal anomaly (TOPFA) diagnosed with OA were selected from the Congenital Anomalies population-based Registry of VR (RPAC-CV). The prevalence of OA per 10,000 births with 95% confidence interval was calculated, and socio-demographic and clinical variables were analyzed. A total of 146 OA cases were identified. The overall prevalence was 2.4/10,000 births, and prevalence by type of pregnancy ending was 2.3 in LB and 0.03 in both SB and TOPFA. A mortality rate of 0.03/1000 LB was observed. A relationship was found between case mortality and birth weight (p-value < 0.05). OA was primarily diagnosed at birth (58.2%) and 71.2% of the cases were associated with another congenital anomaly, mainly congenital heart defects. Significant variations in the prevalence of OA in the VR were detected throughout the study period. In conclusion, a lower prevalence in SB and TOPFA was identified compared to EUROCAT data. As several studies have identified, an association between OA cases and birth weight was found.

Esophageal Atresia With or Without Tracheoesophageal Fistula: Comorbidities, Genetic Evaluations, and Neonatal Outcomes

Objective Esophageal atresia with or without tracheoesophageal fistula (EA/TEF) has a reported incidence of 1 in 3500 live births and requires intensive care and surgery. To evaluate the prevalence of a molecularly confirmed genetic etiology of EA/TEF in a level IV neonatal intensive care unit (NICU), focusing on genetic evaluation, diagnostic yield, and clinical outcomes of these neonates. Study design A retrospective cohort study over a period of seven years was performed for all patients admitted with a diagnosis of EA/TEF. Automated data was extracted for demographic information and manual extraction was done to evaluate the frequency of associated anomalies, type of genetic evaluations and diagnoses, and outcomes at NICU discharge. Results Sixty-eight infants met the inclusion criteria. The majority were male (n=42; 62%), born at >37 weeks' gestation (n=36; 53%), and had EA with distal TEF (n=54; 79%). Most (n=53; 78%) had additional associated congenital anomalies, but only 47 (69%) patients had a genetics evaluation performed and genetic testing was sent for 44 (65%) of those patients. The most common genetic testing performed was chromosomal microarray analysis (n=40; 59%), followed by chromosome analysis (n=11; 16%), and whole exome/genome sequencing (n=7; 10%). Five unique genetic diagnoses including CHARGE Syndrome, Fanconi Syndrome, EFTUD2-related mandibulofacial dysostosis, and two different chromosomal deletion syndromes were made for a total of nine (13%) patients in our cohort. The cohort suffered a high rate of morbidity and mortality during their NICU stay with important differences noted in isolated vs non-isolated EA/TEF. Twelve infants (18%) died prior to NICU discharge. Of those surviving, 40 (71%) infants had a primary repair, 37 (66%) infants required G or GJ feedings at NICU discharge, and eight (14%) patients were discharged on some type of respiratory support. Conclusion In this high-risk cohort of EA/TEF patients cared for at a quaternary NICU, a majority were non-isolated and had some form of a genetic evaluation, but a minority underwent exome or genome sequencing. Given the high prevalence of associated anomalies, high mortality, and genetic disease prevalence in this cohort, we recommend standardization of phenotyping and genetic evaluation to allow for precision care and appropriate risk stratification.

Anatomy and embryology of tracheo-esophageal fistula

Anomalies in tracheo-esophageal development result in a spectrum of congenital malformations ranging from, most commonly, esophageal atresia with or without trachea-esophageal fistula (EA+/-TEF) to esophageal web, duplication, stricture, tracheomalacia and tracheal agenesis. Despite the relative frequency of EA, however, the underlying etiology remains unknown and is likely due to a combination of genetic, epigenetic and environmental factors. In recent years, animal models have dramatically increased our understanding of the molecular and morphological processes involved in normal esophageal development during the key stages of anterior-posterior regionalization, dorsal-ventral patterning and morphogenic separation. Moreover, the use of animal models in conjunction with increasingly advanced techniques such as genomic sequencing, sophisticated live imaging studies and organoid models have more recently cast light on potential mechanisms involved in EA pathogenesis. This article aims to unravel some of the mysteries behind the anatomy and embryology of EA whilst providing insights into future directions for research.

Necessity of Prophylactic Extrapleural Chest Tube During Primary Surgical Repair of Esophageal Atresia: A Systematic Review and Meta-Analysis

Background

Esophageal atresia is corrected surgically by anastomosing and recreating esophageal continuity. To allow the removal of excess fluid and air from the anastomosis, a prophylactic and temporary intraoperative chest tube (IOCT) has traditionally been placed in this area during surgery. However, whether the potential benefits of this prophylactic IOCT overweigh the potential harms is unclear.

Objective

To assess the benefits and harms of using a prophylactic IOCT during primary surgical repair of esophageal atresia.

Data Sources

We conducted a systematic review with a meta-analysis. We searched Cochrane Central Register of Controlled Trials (2021, Issue 12), MEDLINE Ovid, Embase Ovid, CINAHL, and Science Citation Index Expanded and Conference Proceedings Citation Index-(Web of Science). Search was performed from inception until December 3rd, 2021.

Study Selection

Randomized clinical trials (RCT) assessing the effect of a prophylactic IOCT during primary surgical repair of esophageal atresia and observational studies identified during our searches for RCT.

Data Extraction and Synthesis

Two independent reviewers screened studies and performed data extraction. The certainty of the evidence was assessed by GRADE and ROBINS-I.

PROSPERO Registration

A protocol for this review has been registered on PROSPERO (CRD42021257834).

Results

We included three RCTs randomizing 162 neonates, all at overall "some risk of bias." The studies compared the placement of an IOCT vs. none. The meta-analysis did not identify any significant effect of profylacitic IOCT, as confidence intervals were compatible with no effect, but the analyses suggests that the placement of an IOCT might lead to an increase in all-cause mortality (RR 1.66, 95% CI 0.76-3.65; three trials), serious adverse events (RR 1.08, 95% CI 0.58-2.00; three trials), intervention-requiring pneumothorax (RR 1.65, 95% CI 0.28-9.50; two trials), and anastomosis leakage (RR 1.66, 95% CI 0.63-4.40). None of our included studies assessed esophageal stricture or pain. Certainty of evidence was very low for all outcomes.

Conclusions

Evidence from RCTs does not support the routine use of a prophylactic IOCT during primary surgical repair of esophageal atresia.

Maternal mental disorders and risk of pathological abdominal conditions in children

The etiology of pediatric abdominal disorders is poorly understood, and the relationship with maternal mental health is understudied. We sought to determine the association between maternal psychiatric disorders and abdominal conditions in childhood. We performed a retrospective cohort study of 1,080,518 newborns in Quebec, Canada, between 2006 and 2020. We identified maternal mental disorders before or during pregnancy and computed the incidence of abdominal disorders in offspring before 1 year of age. Outcomes included Hirschsprung disease; hypertrophic pyloric stenosis; and esophageal, intestinal, and biliary atresia. We calculated adjusted risk ratios (RR) with 95% confidence intervals (CI) for the association of maternal mental disorders with these pediatric abdominal disorders. Among 51,371 children exposed to maternal mental disorders, 200 children had an abdominal condition, for a rate of 38.9 cases per 10,000 children (95% CI 33.6-44.3) compared with 27.7 per 10,000 for children who were unexposed to maternal mental disorders (95% CI 26.7-28.7). Compared with no mental disorder, maternal mental disorders were associated with hypertrophic pyloric stenosis (RR 1.39, 95% CI 1.16-1.68). Associations were stronger for severe mental disorders and were more marked for depression and stress and anxiety disorders. Maternal mental disorders are associated with the risk of hypertrophic pyloric stenosis in offspring. The origin of hypertrophic pyloric stenosis may relate to maternal mental disorders that were present during pregnancy.

Genetic diagnoses and associated anomalies in fetuses prenatally diagnosed with esophageal atresia

Esophageal atresia (EA) is a congenital anomaly occurring in 2.3 per 10,000 live births. Due to advances in prenatal imaging, EA is more readily diagnosed, but data on the associated genetic diagnoses, other anomalies, and postnatal outcome for fetuses diagnosed prenatally with EA are scarce. We collected data from two academic medical centers (n = 61). Our data included fetuses with suspected EA on prenatal imaging that was confirmed postnatally and had at least one genetic test. In our cohort of 61 cases, 29 (49%) were born prematurely and 19% of those born alive died in the first 9 years of life. The most commonly associated birth defects were cardiac anomalies (67%) and spine anomalies (50%). A diagnosis was made in 61% of the cases; the most common diagnoses were vertebral defects, anal atresia, cardiac anomalies, tracheoesophageal fistula with esophageal atresia, radial or renal dysplasia, and limb anomalies association (43%, although 12% met only 2 of the criteria), trisomy 21 (5%), and CHARGE syndrome (5%). Our findings suggest that most fetuses with prenatally diagnosed EA have one or more additional major anomaly that warrants a more comprehensive clinical genetics evaluation. Fetuses diagnosed prenatally appear to represent a cohort with a worse outcome.

Pregnancy management and outcome in patients with four different tetrahydrobiopterin disorders

INTRODUCTION

Inborn errors of tetrahydrobiopterin (BH4) biosynthesis or recycling are a group of very rare neurometabolic diseases. Following growing awareness and improved availability of drug treatment the number of patients with BH4 disorders reaching adulthood is constantly increasing. Pregnancy care of patients with these disorders is therefore a new challenge for clinicians.

METHODS

This retrospective study summarises for the first time clinical and biochemical monitoring data of 16 pregnancies in seven women with different disorders of BH4 metabolism and evaluates treatment regimens before and during pregnancy in relation to the obstetrical outcome and paediatric follow-up.

RESULTS

Worsening of pre-existing neurological symptoms or occurrence of new symptoms during pregnancy was not observed in most of the cases. Treatment regimens remained mostly unchanged. Pregnancies were not complicated by disease-specific features. Organ abnormalities, miscarriage, prematurity, IUGR and chromosomal changes were occasionally reported, without showing any association with the standard drug treatment for BH4 deficiencies.

CONCLUSION

Although our data on 16 pregnancies in seven patients did not present any association of standard drug treatment with an increased rate of pregnancy complications, abnormal obstetrical or paediatric outcome, an intensive clinical and biochemical supervision by a multidisciplinary team before, during and after the pregnancy in any BH4 deficiency is essential since available data on pregnancies in patients with BH4 deficiencies is limited.

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.

Interkinetic nuclear migration in the tracheal and esophageal epithelia of the mouse embryo: Possible implications for tracheo-esophageal anomalies

Interkinetic nuclear migration (INM) is a cell polarity-based phenomenon in which progenitor cell nuclei migrate along the apico-basal axis of the pseudostratified epithelium in synchrony with the cell cycle. INM is suggested to be at least partially cytoskeleton-dependent and to regulate not only the proliferation/differentiation of stem/progenitor cells but also the localized/overall size and shape of organs/tissues. INM occurs in all three of the germ-layer derived epithelia, including the endoderm-derived gut. However, INM has not been documented in the esophagus and respiratory tube arising from the anterior foregut. Esophageal atresia with or without trachea-esophageal fistula (EA/TEF) is a relatively common developmental defect. Transcription factors and signaling molecules have been implicated in EA/TEF, but the etiology of EA/TEF-which has been suggested to involve cell polarity-related mechanisms-remains highly controversial. In the present study, we first examined whether INM exists in the trachea and esophagus of mouse embryos at embryonic day 11.5 (E11.5), just after separation of the two tubes from the anterior foregut. By labeling the DNA-synthesizing stem cell nuclei with 5-ethynyl-2'-deoxyuridine, a nucleotide analogue, and statistically analyzing chronological changes in the distribution pattern of the labeled nuclei by using multidimensional scaling, we showed the existence of INM in both the esophagus and trachea, with differences in the INM magnitude and cycle pattern. We further showed morphological changes from the INM-based pseudostratified single layer to the stratified multilayer in the esophageal epithelium in association with a temporal loss/perturbation of AB polarity, suggesting a possible relation with the pathogenesis of EA/TEF.

Long-term functional outcomes after replacement of the esophagus in pediatric patients: A systematic literature review

BACKGROUND

The indications of esophageal replacement (ER) in pediatric patients include long gap esophageal atresia (LGEA), intractable post-corrosive esophageal strictures (PCES), and some rare esophageal diseases. Various conduits and procedures are currently used worldwide with a lack of consensus regarding the ideal substitute to replace the esophagus replacement. The short-term outcomes of these advanced procedures are well known; there are few data available describing long-term functional outcomes of these patients with long life expectancy.

OBJECTIVES

The objective of this study is to investigate the long-term functional outcomes of the most widely used techniques for ER in pediatric patients based on a comprehensive literature search covering the last 10years.

METHODS

Eligible were all clinical studies reporting outcomes after esophagectomy in pediatric patients, which contained information on at least 3years of follow-up after the operation. The review was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. A systematic web-based search using MEDLINE, the Cochrane Library and EMBASE databases was performed, reviewing all medical literature published between January 2006 and December 2015.

RESULTS

The scientific quality of the data was generally poor, converging toward only 14 full-text articles for the final analysis. The stomach was the preferred organ for esophageal replacement, where the tubulization of the stomach resulted in significant gastroesophageal reflux. Dysphagia symptoms were more seldom reported, but several authors presented growing figures with the length of follow-up. Dumping syndrome and delayed gastric emptying were only scarcely reported upon. Following colonic graft, chronic gastrocolic reflux affects these patients, in the range of 35-70.8%, while 4 studies reported any dysphagia from 2.7% to 50% of the children. Only one study reported the outcome of the use of a long jejunal segment, where presence of symptoms of functional obstruction was mentioned in 46% of cases. Very few if any data were available on a structured assessment of postprandial dumping and disturbed bowel functions.

CONCLUSIONS

Available data in pediatric patients, on the long-term functional outcomes after esophageal replacement with a gastric tube, colonic graft or a long jejunal segment, are of poor scientific quality. Although symptoms are frequently reported currently no conclusions can be drawn regarding potential advantages of one graft over another.

TYPE OF STUDY

Treatment study, systematic review.

LEVEL OF EVIDENCE

IV.

Long-Gap Esophageal Atresia Is a Unique Entity within the Esophageal Atresia Defect Spectrum

BACKGROUND

Long-gap esophageal atresia (LGEA) may have clinical and syndromic presentations different from those of esophageal atresia (EA) that affects shorter segments of the esophagus (non-LGEA). This may suggest unique underlying developmental mechanisms.

OBJECTIVES

We sought to characterize clinical differences between LGEA and non-LGEA by carefully phenotyping a cohort of EA patients, and furthermore to assess molecular genetic findings in a subset of them.

METHODS

This is a retrospective cohort study to systematically evaluate clinical and genetic findings in EA infants who presented at our institution over a period of 10 years (2005-2015).

RESULTS

Two hundred twenty-nine EA patients were identified, 69 (30%) of whom had LGEA. Tracheoesophageal fistula was present in most non-LGEA patients (158 of 160) but in only 30% of LGEA patients. The VACTERL association was more commonly seen with non-LGEA compared to LGEA (70 vs. 25%; p < 0.001). Further, trisomy 21 was more common in LGEA than in non-LGEA. 25% of LGEA patients had an isolated EA diagnosis without other anomalies, compared to <1% for non-LGEA. Chromosomal microarray analysis showed copy number variations (CNV) in 4 of 39 non-LGEA patients and 0 of 3 LGEA patients. A review of the ClinGen database showed that none of those CNV have been previously described with EA.

CONCLUSIONS

LGEA represents a unique type of EA. Compared to non-LGEA, it is more likely to be an isolated defect and associated with trisomy 21. Further, it is less commonly seen with VACTERL anomalies. Our findings suggest the involvement of unique pathways that may be distinct from those causing non-LGEA.

Esophageal atresia with tracheoesophageal fistula in a patient with 7q35-36.3 deletion including SHH gene

Terminal 7q deletion is rarely reported in the literature. Holoprosencephaly and sacral dysgenesis are found in association with this deletion, due to haploinsufficiency of SHH and HLBX9 genes respectively. We report on a 2-year-old boy with 7q35-36.3 deletion encompassing SHH identified by oligonucleotide array comparative genomic hybridization. In addition to other frequent features, the patient presented with esophageal atresia and tracheoeosophageal fistula diagnosed at birth. This case, together with two others previously described, one presenting with esophageal atresia, the other with congenital esophageal stenosis, confirms the possible association between congenital esophageal malformations and 7q terminal deletion including SHH.

Prevalence and descriptive epidemiology of esophageal atresia in the Russian Federation

BACKGROUND

This study examined the prevalence of esophageal atresia (EA) and the relationship between EA and demographic factors in the Russian Federation.

METHODS

Data were obtained from a population-based congenital malformations registry across 14 years (2000-2013) in 24 regions of the Russian Federation and included cases of EA among live births and stillbirths.

RESULTS

The total number of births was 6,478,706. There were 1317 cases of isolated EA, resulting in a rate of 2.03 (95% confidence interval [CI], 1.92-2.15) per 10,000 births or 1 case per 4926 births. There were differences in the prevalence of EA among regional registries of the Russian Federation. The prevalence of EA during the study period was stable. 57.3% of all cases were cases of EA with tracheo-esophageal fistula (compared with 42.7% of cases without fistula). The male/female sex ratio was 1.3. The relative risk of EA was higher for live births with birth weight less than 3000 g (relative risk [RR] = 2.58 (95% CI, 2.36-2.82), for older maternal age (RR = 1.47 (95% CI, 1.24-1.75), for males (RR = 1.09; 95% CI, 1.03-1.17), and for the first gravidity (RR = 1.17; 95% CI, 1.09-1.25).

CONCLUSION

In this study, the prevalence of EA across different regions of the Russian Federation was analyzed. The prevalence of EA in the period under study remained stable, and the relative risk of EA was associated with maternal age, birth weight and gravidity. Birth Defects Research (Part A) 106:854-859, 2016. © 2016 Wiley Periodicals, Inc.

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.

Oesophageal atresia and tracheo-oesophageal fistula in Western Australia: Prevalence and trends

AIM

A recent international study reported a higher prevalence of oesophageal atresia with or without tracheo-oesophageal fistula (OA±TOF) in Western Australia (WA). The aim of this study was to examine the prevalence and trends of OA and/or TOF in WA, determine the proportion of cases with associated anomalies and explore the impact of time of diagnosis.

METHODS

The study population comprised all infants born in WA, 1980-2009, and registered with OA and/or TOF on the WA Register of Developmental Anomalies (WARDA).

RESULTS

OA±TOF and TOF alone affect, on average, one in every 2927 births in WA, with a total prevalence of 3.00 and 0.42 per 10 000 births, respectively. The prevalence of OA±TOF increased by 2.0% per annum, with only cases with associated anomalies (64% of cases) demonstrating an increase. TOF rates were stable. Among OA±TOF infants, the proportion of live births, stillbirths and elective terminations of pregnancy for fetal anomaly (TOPFA) was 79%, 6% and 15%, respectively, whereas the majority (94%) of TOF only cases were live births. In 2000-2009, there was 30% fall in OA±TOF live births with 61 (58%) cases diagnosed in first week of life, 10 (9%) prenatally and 34 (32%) at post-mortem only.

CONCLUSIONS

A higher prevalence of OA±TOF in WA was observed with increase over time attributable to increase with associated anomalies. Consistent reporting, availability of prenatal diagnosis and ascertainment of cases following TOPFA or post-mortem examinations can significantly affect prevalence of OA and/or TOF.

A cross-sectional nationwide survey on esophageal atresia and tracheoesophageal fistula

BACKGROUND

Our study aims at disclosing epidemiology and most relevant clinical features of esophageal atresia (EA) pointing to a model of multicentre collaboration.

METHODS

A detailed questionnaire was sent to all Italian Units of pediatric surgery in order to collect data of patients born with EA between January and December 2012. The results were crosschecked by matching date and place of birth of the patients with those of diagnosis-related group provided by the Italian Ministry of Health (MOH).

RESULTS

A total of 146 questionnaires were returned plus a further 32 patients reported in the MOH database. Basing on a total of 178 patients with EA born in Italy in 2012, the incidence of EA was calculated in 3.33 per 10,000 live births. Antenatal diagnosis was suspected in 29.5% patients. 55.5% showed associated anomalies. The most common type of EA was Gross type C (89%). Postoperative complications occurred in 37% of type C EA and 100% of type A EA. A 9.5% mortality rate was reported.

CONCLUSIONS

This is the first Italian cross-sectional nationwide survey on EA. We can now develop shared guidelines and provide more reliable prognostic expectations for our patients.

Abnormal Sonic hedgehog signaling in the lung of rats with esophageal atresia induced by adriamycin

BACKGROUND

Abnormal lung development was recently described in the rat model of esophageal atresia and tracheoesophageal fistula (EA-TEF). Since in this condition the ventral-to-dorsal switch of Shh expression in the foregut is disturbed, the present study tested the hypothesis that this abnormal expression at the emergence of the tracheobronchial bud might be translated into the developing lung.

METHODS

Pregnant rats received either 1.75 mg/kg i.p. adriamycin or vehicle from E7 to E9. Three groups were studied: control and adriamycin-exposed with and without EA-TEF. Embryos were recovered and the lungs were harvested and processed for reverse transcription polymerase chain reaction and immunofluorescence analysis of the Shh signaling cascade.

RESULTS

Shh signaling was downregulated at the late embryonic stage of lung development (E13) in embryos with EA-TEF. Throughout the subsequent stages of development, the expression of both Shh and its downstream components increased significantly and remained upregulated throughout gestation. Immunofluorescent localization was consistent with these findings.

CONCLUSION

Defective Shh signaling environment in the foregut is present beyond the emergence of lung buds and probably impairs lung development. Later in gestation, lungs exhibited a remarkable ability to upregulate the Shh cascade, suggesting a compensatory response. These findings may be relevant to understand pulmonary disease suffered by children with EA-TEF.

Inspissated bile syndrome in an infant with citrin deficiency and congenital anomalies of the biliary tract and esophagus: identification and pathogenicity analysis of a novel SLC25A13 mutation with incomplete penetrance

Biallelic mutations of the SLC25A13 gene result in citrin deficiency (CD) in humans. Neonatal intrahepatic cholestasis caused by citrin deficiency (NICCD) is the major CD phenotype in pediatrics; however, knowledge on its genotypic and phenotypic characteristics remains limited. The present study aimed to explore novel molecular and clinical characteristics of CD. An infant suspected to have NICCD as well as her parents were enrolled as the research subjects. SLC25A13 mutations were investigated using various methods, including cDNA cloning and sequencing. The pathogenicity of a novel mutation was analyzed bioinformatically and functionally with a yeast model. Both the infant and her father were heterozygous for c.2T>C and c.790G>A, while the mother was only a c.2T>C carrier. The novel c.790G>A mutation proved bioinformatically and functionally pathogenic. The infant had esophageal atresia and an accessory hepatic duct, along with bile plug formation confirmed by laparoscopic surgery. However, the father seemed to be healthy thus far. The findings of the present study enrich the genotypic and phenotypic characteristics of CD patients, and provided clinical and molecular evidence suggesting the possible non-penetrance of SLC25A13 mutations and the likely involvement of this gene in primitive foregut development during early embryonic life.

Altered Tbx1 gene expression is associated with abnormal oesophageal development in the adriamycin mouse model of oesophageal atresia/tracheo-oesophageal fistula

INTRODUCTION

Oesophageal atresia/tracheo-oesophageal atresia (OA/TOF) frequently arises with associated anomalies and has been clinically linked with 22q11 deletion syndromes, a group of conditions due to Tbx1 gene mutation which include Di George syndrome. Tbx1 and Tbx2 genes modulate pharyngeal and cardiac development, but are also expressed in the developing foregut and are known to interact with key signalling pathways described in oesophageal formation including bone morphogenic proteins. The adriamycin mouse model (AMM) reliably displays OA/TOF-like foregut malformations providing a powerful system for investigating the disturbances in gene regulation and morphology involved in tracheo-oesophageal malformations. We hypothesised that foregut abnormalities observed in the AMM are associated with altered Tbx1 and Tbx2 gene expression.

METHODS

Time-mated CBA/Ca mice received intra-peritoneal injection of adriamycin (for treated) or saline (for controls) on embryonic days (E)7 and 8. Untreated Cd1 embryos were used to establish normal expression patterns. Embryos harvested on E9-E11 underwent whole-mount in situ hybridization with labelled RNA probes for Tbx1 and Tbx2. Optical projection tomography was used to visualise expression in whole embryos by 3D imaging.

RESULTS

Tbx1 expression was visualised in a highly specific pattern in the proximal oesophageal endoderm in normal and control embryos. In the AMM, extensive ectopic expression of Tbx1 was detected in the dorsal foregut and adjacent to the TOF. The focally restricted oesophageal expression pattern persisted in the AMM, but was posteriorly displaced in relation to the tracheal bifurcation. Tbx2 was widely expressed in the ventral foregut mesoderm of controls, lacking specific endoderm localisation. In the AMM, altered Tbx2 expression in the foregut was only seen in severely affected embryos.

CONCLUSION

Highly specific Tbx1 expression in the proximal oesophageal endoderm suggests that Tbx1 may be an important regulator of normal oesophageal development. Altered Tbx1 expression in dorsal foregut and adjacent to the TOF in the AMM suggests that Tbx1 gene disruption may contribute to the pathogenesis of tracheo-oesophageal malformations.

[Esophageal atresia: prevalence, prenatal diagnosis and prognosis]

Esophageal atresia (EA) is a rare congenital malformation (1 in 2,500 to 3,500 births). Prenatal diagnosis (PN) is particularly interesting allowing search for associated malformations related to worse prognosis forms (reference ultrasound, MRI and amniocentesis) and planning the birth in an adapted medico-surgical center. Diagnosis of EA is usually suspected because of indirect and non-specific signs: association of polyhydramnios and absent or small stomach bubble. The visualization in ultrasound or MRI of cervical or thoracic fluid image corresponding to the expansion of the bottom of upper esophageal ("pouch sign") increases the specificity of diagnosis. However, prenatal diagnosis remains difficult and less than 50 % of EA are diagnosed prenatally. Biochemical analysis could improve these results. If EA is confirmed at birth, surgical management consists in a primary end-to-end anastomosis in first days of life, or in two-steps surgery if the defect is too large. Although current prognosis of EA is good, frequency of surgical complications and esophageal lesions secondary to gastroesophageal reflux justify a systematic and multidisciplinary extended follow-up.

Specific biochemical amniotic fluid pattern of fetal isolated esophageal atresia

BACKGROUND

Perinatal care of esophageal atresia (EA) may be improved by prenatal diagnosis. Ultrasound findings (polyhydramnios and/or nonvisualization of fetal stomach) lead to a detection rate of ~50%. An amniotic fluid (AF) biochemical pattern characterized by high total protein, γ-glutamyl transpeptidase (GGTP), and normal l-leucine-aminopeptidase (AMP) leads to a 100% detection rate. The aim of this study was to explain this specific pattern.

METHODS

On the basis of enzyme activities assay, the following four objectives were sought: (i) comparing AF markers between EA and other digestive tract atresias, (ii) determining local GGTP synthesis in the esophagus (immunohistobiochemistry), (iii) determining the presence of a specific AF-AMP activity inhibitor, and (iv) comparing AF-AMP and AF-GGTP half-lives.

RESULTS

The AF-EA pattern was similar to that observed in upper duodenal atresia (above the Oddi sphincter). No local synthesis of GGTP was observed in the esophagus. No AF-AMP activity inhibitor was found. AF-GGTP had a longer half-life than AF-AMP.

CONCLUSION

Due to the swallowing anomaly observed in EA, GGTP and AMP values physiologically observed at 18 wk will decrease on the basis of the half-lives of markers, with a flat slope for GGTP and a sharp slope for AMP, therefore explaining the differences observed in the AF-EA pattern.

Esophageal atresia: data from a national cohort

PURPOSE

A prospective national register was established in 2008 to record all new cases of live-birth newborns with esophageal atresia (EA). This epidemiological survey was recommended as part of a national rare diseases plan.

METHODS

All 38 national centers treating EA participated by completing for each patient at first discharge a questionnaire validated by a national committee of experts. Data were centralized by the national reference center for esophageal anomalies. Quantitative and qualitative analyses were performed, with P-values of less than 0.05 considered statistically significant. Results of the 2008-2009 data collection are presented in this report.

RESULTS

Three hundred seven new living cases of EA were recorded between January 1, 2008, and December 31, 2009. The male/female sex ratio was 1.3, and the live-birth prevalence of EA was 1.8 per 10,000 births. Major characteristics were comparable to those reported in the literature. Survival was 95%, and no correlation with caseload was noted.

CONCLUSIONS

Epidemiologic surveys of congenital anomalies such as EA, which is a rare disease, provide valuable data for public health authorities and fulfill one important mission of reference centers. When compared with previous epidemiological data, this national population-based registry suggests that the incidence of EA remains stable.

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.

Expanding the BP1-BP2 15q11.2 Microdeletion Phenotype: Tracheoesophageal Fistula and Congenital Cataracts

The proximal q arm of chromosome 15 contains breakpoint regions BP1–BP5 with the classic deletion of BP1–BP3 best known to be associated with Prader-Willi and Angelman syndromes. The region is approximately 500 kb and microdeletions within the BP1-BP2 region have been reported in patients with developmental delay, behavioral abnormalities, and motor apraxia as well as dysmorphic features including hypertelorism, cleft or narrow palate, ear abnormalities, and recurrent upper airway infections. We report two patients with unique, never-before-reported 15q11.2 BP1-2 microdeletion syndrome findings, one with proximal esophageal atresia and distal tracheoesophageal fistula (type C) and one with congenital cataracts. Cataracts have been described in Prader-Willi syndrome but we could not find any description of cataracts in Angelman syndrome. Esophageal atresia and tracheoesophageal fistula have not been reported to our knowledge in either syndrome. A chance exists that both cases are sporadic birth defects; however, the findings of the concomitant microdeletion cannot be overlooked as a possible cause. Based on our review of the literature and the presentation of our patients, we recommend that esophageal atresia and distal tracheoesophageal fistula as well as congenital cataracts be included in the phenotypic spectrum of 15q11.2 BP1-2 microdeletion syndrome.

Adriamycin-Induced Models of VACTERL Association

Animal models are of great importance for medical research. They have enabled analysis of the aetiology and pathogenesis of complex congenital malformations and have also led to major advances in the surgical and therapeutic management of these conditions. Animal models allow us to comprehend the morphological and molecular basis of disease and consequently to discover novel approaches for both surgical and medical therapy. The anthracycline antibiotic adriamycin was incidentally found to have teratogenic effects on rats, producing a range of defects remarkably similar to the VACTERL association of congenital anomalies in humans, providing a reproducible animal model of this condition. VACTERL association is a spectrum of birth defects which includes vertebral, anal, cardiovascular, tracheo-oesophageal, renal and limb anomalies. In recent years, adriamycin rodent models of VACTERL have provided valuable insights into the pathogenesis of this complex association, particularly in relation to tracheo-oesophageal malformations. The adriamycin rat model and adriamycin mouse model are now well established in the investigation of the morphology of faulty organogenesis and the regulation of gene expression in tracheo-oesophageal anomalies.

Epidemiology of esophageal atresia

Esophageal atresia (EA) is a rare congenital malformation consisting of a lack of continuity between the upper and lower esophageal pouches, frequently associated with tracheoesophageal fistula. The prevalence of such rare abnormalities is established by global birth surveillance programs over the world. EUROCAT is a European program covering 1.7 million births since its creation. The prevalence of EA in Europe seems stable over decades. The National Birth Defects Prevention Network in the USA also shows a stable prevalence with a wide range between states or regions. In France, with the implementation of the national rare diseases plan, a reference center for congenital abnormalities of the esophagus was created in 2006 and a national registry for EA began patient inclusion in 2008. This has resulted in the establishment of the national live birth prevalence for EA, prenatal diagnosis rates, and clinical characteristics of EA patients, early survival, and early morbidity. Prevalence rates seem stable all over the world since many decades. Continuous surveillance of congenital abnormalities and specific registries are useful for epidemiologic data but also for public health authorities for helping families of rare diseases patients.

Clinical geneticists' views of VACTERL/VATER association

VACTERL association (sometimes termed "VATER association" depending on which component features are included) is typically defined by the presence of at least three of the following congenital malformations, which tend to statistically co-occur in affected individuals: Vertebral anomalies, Anal atresia, Cardiac malformations, Tracheo-Esophageal fistula, Renal anomalies, and Limb abnormalities. Although the clinical criteria for VACTERL association may appear to be straightforward, there is wide variability in the way clinical geneticists define the disorder and the genetic testing strategy they use when confronted with an affected patient. In order to describe this variability and determine the most commonly used definitions and testing modalities, we present the results of survey responses by 121 clinical geneticists. We discuss the results of the survey responses, provide a literature review and commentary from a group of physicians who are currently involved in clinical and laboratory-based research on VACTERL association, and offer an algorithm for genetic testing in patients with this association.

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.

Current knowledge on esophageal atresia

Esophageal atresia (EA) with or without tracheoesophageal fistula (TEF) is the most common congenital anomaly of the esophagus. The improvement of survival observed over the previous two decades is multifactorial and largely attributable to advances in neonatal intensive care, neonatal anesthesia, ventilatory and nutritional support, antibiotics, early surgical intervention, surgical materials and techniques. Indeed, mortality is currently limited to those cases with coexisting severe life-threatening anomalies. The diagnosis of EA is most commonly made during the first 24 h of life but may occur either antenatally or may be delayed. The primary surgical correction for EA and TEF is the best option in the absence of severe malformations. There is no ideal replacement for the esophagus and the optimal surgical treatment for patients with long-gap EA is still controversial. The primary complications during the postoperative period are leak and stenosis of the anastomosis, gastro-esophageal reflux, esophageal dysmotility, fistula recurrence, respiratory disorders and deformities of the thoracic wall. Data regarding long-term outcomes and follow-ups are limited for patients following EA/TEF repair. The determination of the risk factors for the complicated evolution following EA/TEF repair may positively impact long-term prognoses. Much remains to be studied regarding this condition. This manuscript provides a literature review of the current knowledge regarding EA.

Mutational analysis of NOG in esophageal atresia and tracheoesophageal fistula patients

PURPOSE

The NOG protein is a secretory antagonist of bone morphogenetic proteins (BMPs). Nog-/- mouse embryos demonstrate proximal esophageal atresia (EA) and distal tracheoesophageal fistula (TEF) compatible with the most common configuration of EA/TEF observed in humans. Four microdeletions that span the NOG locus at 17q22 have been described in human patients having EA/TEF. We investigated the incidence of point mutations in the coding region of the NOG gene in human EA/TEF.

METHODS

DNA was collected from 50 patients previously treated for EA/TEF. PCR was used to amplify the coding region of NOG. To detect single nucleotide polymorphisms (SNPs), amplicons were subjected to temperature gradient capillary electrophoresis (TGCE). Candidate SNPs were directly sequenced.

RESULTS

TGCE analysis revealed a SNP in the coding region of NOG in 1 of 50 patients (2%). DNA sequencing revealed a synonymous SNP at position 468 (C-T) of the NOG coding region.

CONCLUSION

SNPs in the coding region of the NOG gene are identified infrequently in human cases of EA/TEF. Further investigation of SNPs in the promoter region of NOG is warranted, as is the effect of synonymous SNPs on NOG mRNA stability.

Nine new twin pairs with esophageal atresia: a review of the literature and performance of a twin study of the disorder

BACKGROUND

Isolated esophageal atresia (EA) is a rare congenital malformation whose etiology remains largely unknown. Nine twin pairs with EA were identified from our clinical service, prompting the performance of a systematic review of the literature and the first reported twin study of isolated EA.

METHODS

A total of 330 twin pairs with EA were identified from the literature. The zygosity, concordance, and malformation (isolated vs. nonisolated) status of all 339 twin pairs were evaluated. A total of 72 twin pairs (4 of 9 / 68 of 330) fulfilled the criteria for inclusion in a classic twin study of isolated EA.

RESULTS

The pairwise concordance rates were 50% (95% confidence interval [CI], 34-66%) for monozygous (MZ) twin pairs and 26% (95% CI, 15-42%) for dizygous (DZ) twin pairs (p = 0.033). The probandwise concordance rates were 67% (95% CI, 53-78%) for MZ twin pairs and 42% (95% CI, 29-56%) for DZ twin pairs (p = 0.011). The MZ/DZ ratios were 1.9 for pairwise analysis and 1.6 for probandwise analysis. The familial risk ratios for MZ and DZ twin pairs were 1700 and 900, respectively.

CONCLUSION

The observation of higher concordance rates for MZ compared to DZ twin pairs indicates that genetic factors contribute to isolated EA.

Biochemical amniotic fluid pattern for prenatal diagnosis of esophageal atresia

Prenatal diagnosis of esophageal atresia (EA) may improve the outcome of affected neonates by allowing optimization of both prenatal and postnatal care. Prenatal sonographic detection is based on polyhydramnios and/or nonvisualization of the fetal stomach bubble, two signs with a large number of etiologies. We evaluated a biochemical approach to improving diagnostic efficiency. We compared amniotic fluid biochemical markers in 44 EA cases with 88 polyhydramnios and 88 nonpolyhydramnios controls. Both matched for GA with cases. Total proteins, alpha-fetoprotein (AFP), and digestive enzyme activities were assayed, including gamma-glutamyl transpeptidase (GGTP). We defined an EA index (AFP multiplied by GGTP). A significant difference (p < 0.0001) was observed for total protein, AFP, GGTP, and EA index between the EA group and each of the two control groups. No statistical difference was observed for any marker between the two most frequent EA subgroups (type I and type III) or between the two control groups. Using a cutoff of 3 for the EA index, 98% sensitivity and 100% specificity were observed for amniotic fluid prenatal diagnosis of EA, whatever the anatomical type. A large prospective series is required to confirm these results.

Chronic hypertension with related drug treatment of pregnant women and congenital abnormalities in their offspring: a population-based study

Chronic hypertension (CH) is a common chronic disease and occurs frequently in pregnant women. The teratogenic/fetotoxic effect of certain antihypertensive drugs has been shown. The objective of this study was to investigate the association between pregnant women with CH and the possible risk of congenital abnormalities (CAs) among their offspring. The prevalence of medically recorded CH in the prenatal maternity logbook was compared between 1030 pregnant women who later had offspring with CA (case group) and 1579 pregnant women with CH who later delivered newborn infants without CA (control group). Control newborn infants were matched to cases in the population-based data set of the Hungarian Case-Control Surveillance System of Congenital Abnormalities during 1980-1996. Of 23 different CA groups with informative offspring, esophageal atresia/stenosis was a greater risk in pregnant women with CH (adjusted odds ratios with 95% confidence intervals: 3.1, 1.4-6.8). In conclusion, a higher risk of esophageal atresia/stenosis was found in the offspring of pregnant women with severe CH, which could not be explained by related drug treatments. This finding requires confirmation or lack thereof by future studies.

Pre- and postnatal diagnosis and outcome of fetuses and neonates with esophageal atresia and tracheoesophageal fistula

OBJECTIVES

Clinical symptoms and ultrasound signs during pregnancy could suggest the presence of esophageal atresia (EA). However, most often EA is diagnosed postnatally. The aim of our study is to evaluate the course and outcome for prenatally and postnatally diagnosed EA. In addition, we studied the outcome of isolated versus nonisolated EA.

METHODS

In a retrospective data analysis, ultrasound characteristics, maternal and neonatal variables as well as clinical outcome were compared for fetuses/neonates with prenatal (n = 30) or postnatal (n = 49) diagnosis of EA. Clinical outcome in terms of morbidity and mortality of isolated EA was compared with that of EA complicated by chromosomal or structural anomalies.

RESULTS

Prenatally diagnosed children were born 2 weeks earlier than postnatally diagnosed children (36.4 weeks vs 38.2 weeks; P = 0.02). The former had higher mortality rates (30 vs 12%; P = 0.05) and more associated anomalies (80 vs 59%; P = 0.04). In both subsets, there was a high morbidity rate in the survivors (not significant). Nonisolated EA was associated with greater occurrence of polyhydramnios (53 vs 27%; P = 0.04) and higher mortality rate (28 vs 0%; P = 0.002).

CONCLUSIONS

Mortality was significantly higher in prenatally diagnosed infants and in infants with additional congenital anomalies. Isolated EA is associated with good outcome.

Environmental exposures and development

PURPOSE OF REVIEW

Summarize recent studies exploring the relationship between paternal and maternal environmental exposures to chemicals before, at the time of and after conception to adverse developmental outcomes including preterm birth, death, structural and functional abnormalities and growth restriction.

RECENT FINDINGS

Recent studies have demonstrated that human pregnancy and development are vulnerable to environmental exposures of the father and mother to chemical, biological and physical agents. Exposures associated with adverse developmental outcomes include air and water pollution, chemicals in foods, occupational exposures, agricultural chemicals, metals, persistent and volatile organics. Developmental endpoints which are linked with these exposures include growth restriction, functional abnormalities, structural abnormalities, preterm delivery and death. Despite this general understanding we still have incomplete knowledge concerning most exposures and the biological interactions responsible for impaired development and preterm delivery.

SUMMARY

Whereas single genes and individual chemical exposures are responsible for some instances of adverse pregnancy outcome or developmental disease, gene-environment interactions are responsible for the majority. These gene-environment interactions may occur in the father, mother, placenta or fetus, suggesting that critical attention be given to maternal and paternal exposures and gene expression as they relate to the mode of action of the putative developmental toxicant both prior to and during pregnancy.

Lung organogenesis

Developmental lung biology is a field that has the potential for significant human impact: lung disease at the extremes of age continues to cause major morbidity and mortality worldwide. Understanding how the lung develops holds the promise that investigators can use this knowledge to aid lung repair and regeneration. In the decade since the "molecular embryology" of the lung was first comprehensively reviewed, new challenges have emerged-and it is on these that we focus the current review. Firstly, there is a critical need to understand the progenitor cell biology of the lung in order to exploit the potential of stem cells for the treatment of lung disease. Secondly, the current familiar descriptions of lung morphogenesis governed by growth and transcription factors need to be elaborated upon with the reinclusion and reconsideration of other factors, such as mechanics, in lung growth. Thirdly, efforts to parse the finer detail of lung bud signaling may need to be combined with broader consideration of overarching mechanisms that may be therapeutically easier to target: in this arena, we advance the proposal that looking at the lung in general (and branching in particular) in terms of clocks may yield unexpected benefits.