Skip to main content
NIHPA Author Manuscripts logoLink to NIHPA Author Manuscripts
. Author manuscript; available in PMC: 2021 Sep 1.
Published in final edited form as: Dev Biol. 2021 May 21;477:85–97. doi: 10.1016/j.ydbio.2021.05.015

Developmental basis of trachea-esophageal birth defects

Nicole A Edwards 1,2, Vered Shacham-Silverberg 1,2, Leelah Weitz 3,4, Paul S Kingma 6,7, Yufeng Shen 5, James M Wells 1,2,7, Wendy K Chung 3,4, Aaron M Zorn 1,2,7,*
PMCID: PMC8277759  NIHMSID: NIHMS1711530  PMID: 34023332

Abstract

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.

Keywords: trachea, esophagus, development, congenital anomalies, esophageal atresia, tracheoesophageal fistula, EA/TEF, laryngotracheoesophageal cleft, foregut

Graphical Abstract

graphic file with name nihms-1711530-f0006.jpg

Introduction

The esophagus, connecting the mouth to the stomach, is lined by a stratified squamous epithelium and surrounded by smooth muscle that is embedded with enteric neurons that coordinately contract the esophagus to propel ingested food to the stomach. In contrast, the trachea has a mucociliary epithelium with ventral-lateral cartilage rings and dorsal smooth muscle that keep the airway open for breathing. The trachea and esophagus arise from the separation of a common foregut tube during the first trimester of fetal development. Disruptions in tracheoesophageal (TE) development occur in approximately one in every 3000 newborns worldwide, and result in a spectrum of life-threatening congenital trachea-esophageal defects (TEDs) that prevent proper breathing and feeding in newborns (Nassar et al., 2012; van Lennep et al., 2019). The most common TEDs include: esophageal atresia (EA) with varying lengths of absent esophageal continuity, tracheoesophageal fistula (TEF) with an aberrant connection between the trachea and esophagus, and laryngeal-tracheoesophageal clefts (LTEC) with failure of the gut tube to separate into distinct trachea and esophagus, typically near the larynx (Chitkara et al., 2003) (Figure 1AE). Children born with EA/TEF and partial LTEC undergo corrective surgery, and although this is usually effective in repairing TE continuity, there is often long-term and clinically significant dyfunction of the repaired tissue. This long term dysfunction may be due to the specific anatomic defect and surgical repair of the TED, or it may arise from the underlying genetic mutation or syndrome (Mirra et al., 2017). Less common are complete LTECs, congenital high airway obstruction syndrome (CHAOS), with occlusion of the opening from the larynx to the trachea, and tracheoesphageal atresia or tracheal agenesis (TA), with failure of the trachea to develop (Nolan et al., 2019; Smith et al., 2017) (Figure 1F). These less common defects are frequently lethal and in the few patients that survive, long term eshophageal and tracheal morbidities are certain.

Figure 1. Human TEDs.

Figure 1.

A. The trachea is a conduit for air passage from the mouth to the lungs, while the esophagus connects the mouth to the stomach for food passage. Trachea-esophageal birth defects (TEDs) clinically manifest as a spectrum of anatomical anomalies affecting the continuity of the trachea and/or esophagus. B. Esophageal atresia (EA) can present with or without a trachea-esophageal fistula (TEF), with a distal fistula being the most common C. EA results in a blind-ended esophagus with no connection to the stomach. D. TEFs are abnormal connections between the trachea and esophagus. D\E. Incomplete separation of the trachea and esophagus results in laryngotracheal-esophageal clefts. E. Tracheal atresia occurs when the lung buds form directly off of the esophagus with no tracheal tube present. Artwork by Christopher Woods, Department of Pathology, Cincinnati Children’s Hospital Medical Center.

The etiology of TEDs is not well understood. Although there is evidence for a genetic component, causative mutations are only identifiable in about 10–12% of cases worldwide (Brosens et al., 2014b; van Lennep et al., 2019). The majority of TEDs are sporadic with no family history of TEDs and may be caused by de novo mutations. There is an increasing number of registries for TED patients (van Lennep et al., 2019) and although recent genome sequencing efforts have begun to reveal candidate genes in patients, determining which of the many genetic variants is likely to be causative in any single patient remains a challenge. In many cases, TEDs are present with other congenital defects, and emerging evidence from animal models indicates that this is likely due to mutations in genes with pleiotropic effects on developmental pathways. Causative genes have been confirmed in some cases. However, how these mutations result in TEDs is unclear, because until recently the molecular and cellular mechanisms controlling normal TE morphogenesis in the early embryo were poorly understood.

The last five years has seen major advances in our understanding of TE development and the mechanistic basis of TEDs. Functional genomic studies in mouse and Xenopus embryos have begun to elucidate the conserved regulatory network of cell signals, transcription factors, and the downstream genomic programs that pattern the fetal foregut into esophageal and tracheal progenitor domains. High resolution confocal imaging and experimental embryology has defined some of the key biomechanical processes orchestrating TE morphogenesis (Han et al., 2020; Kim et al., 2019; Nasr et al., 2019). Animal model studies have also informed strategies to direct the differentiation of human pluripotent stem cells (hPSCs) into esophageal and respiratory organoids, which are powerful new tools to study human development in vitro and investigate how TE differentiation is disrupted in TED patients (Shacham-Silverberg and Wells, 2020; Trisno et al., 2018; Zhang et al., 2018).

Here we review what is known about the genetic origins of TEDs, and how these new animal models and human organoids provide a platform to systematically evaluate the growing number of genetic variants identified from patients with TEDs identified from genomic sequencing. We summarize the genomic signaling networks and cell behaviors that govern normal TE organogenesis and how these provide a new mechanistic framework for understanding the developmental basis of TEDs. We identify challenges and future directions, exploring how the continued integration of developmental mechanisms with human genetics and clinical data can lead to better understanding of these heterogenous birth defects based upon molecular taxonomy. Finally, we envision how this will facilitate diagnosis, improve treatment, and perhaps in the future lead to the generation of PCS-derived tissue replacement therapy.

Etiology of Human TEDs

Clinical presentation

EA is one of the most common TEDs and is often associated with airway and other organ malformations. In some patients, EA/TEF can be identified in utero by the presence of polyhydramnios, small or absent fluid filled stomach, and a distended esophageal proximal pouch, especially when these findings occur as part of a syndrome in association with other defects (e.g. VACTERL association). However, most cases of EA/TEF and LTEC are not identified until after delivery when infants present with coughing, gagging and respiratory distress, usually during feeding. TA and CHAOS are frequently diagnosed in utero by the presence of enlarged hyperechoic lungs, flattened diaphragms and in CHAOS, a dilated trachea.

Postnatally, infants with TA and CHAOS present with immediate hypoxia, respiratory failure (despite endotracheal intubation) and death unless a surgical airway is immediately established.

Approximately 82–85% of EA cases have a TEF that is distal to the esophageal gap (Type C), 7–8% have no fistula (Type A), 1–4% have a proximal TEF (Type B), 3–4% have both a proximal and distal TEF (Type D), and and 3–4% of TEF occur without EA (Type E) (van Lennep et al., 2019). EA is also found in approximately 20% of LTEC cases (Brunner and van Bokhoven, 2005; Chitkara et al., 2003). EA/TEF can also occur with esophageal or tracheal stenosis as well as tracheomalacia, with collapse of the airway due to defects in formation of the cartilage rings (Poore et al., 2020). Over 55% of EA cases are non-isolated and are associated with other, often syndromic, congenital anomalies affecting the cardiovascular, pulmonary, musculoskeletal, renal, gastrointestinal, and central nervous systems (Bednarczyk et al., 2013; Stoll et al., 2017). Congenital heart malformations, such as ventricular septal defects, patent ductus arteriosus, and aortic arch defects are among the most commonly associated anomalies (Bednarczyk et al., 2013; La Placa et al., 2013; Solomon et al., 2011) as are VACTERL (vertebral, anal, cardiovascular, tracheoesophageal, renal, and limb) defects, which on rare occasion are also present in family members (de Jong et al., 2008; Genevieve et al., 2011; Stoll et al., 2017).

Genetic basis of TEDs

The etiologies of EA/TEF are incompletely understood, but it is increasingly clear that it is a genetically heterogeneous condition associated with aneuploidies, copy number variants, structural chromosomal variants, and monogenic syndromes in at least 11–12% of cases (Brosens et al., 2014b; Stoll et al., 2017). Often, there is no family history of EA, making identification of genetic etiology more challenging. Non-syndromic EA has a low recurrence risk of 1% in siblings and, historically, a recurrence risk of 2–4% in offspring (Brosens et al., 2014b; Scott, 2018). There is a higher concordance rate in monozygotic twins (67%) than in dizygotic twins (42%), indicating a genetic contribution (Brosens et al., 2014b; Schulz et al., 2012). Non-isolated cases usually have a low recurrence risk in siblings, but do rarely segregate as a Mendelian condition with a higher recurrence risk of 25–50% (Scott, 2018).

To date, chromosomal anomalies account for most EA/TEF cases in which a genetic cause has been confirmed (6–10%), in part because copy number variant (CNV) analysis was the most commonly used method to assess genetic etiology in the past (Figure 2) (Marsh et al., 2000; Scott, 2018). The most frequently associated aneuploidies include trisomy 18 and trisomy 21. Twenty five percent of patients with trisomy 18 have EA, while trisomy 21 is associated with EA in 0.5–1% of cases (Brosens et al., 2014a; Felix et al., 2007; Scott, 2018). Trisomy 13 and Trisomy X are also associated with EA, albeit at lower frequency (Brosens et al., 2014a; Felix et al., 2007; Scott, 2018). CNVs have been observed in many individuals with both isolated and non-isolated EA. Most of these are rare de novo CNVs (~1.6% of EA/TEF patients) or arose from parents with a balanced translocation, leading to partial monosomy and partial trisomy (Brosens et al., 2016; Brosens et al., 2014b; Scott, 2018). Examples include: duplications of the homeobox transcription factor gene SHOX on the X chromosome, 10q25.3 duplications containing the cytoskeletal gene ABLIM1 and deletions of 3q28 containing the cell adhesion gene LPP, all of which have been observed recurrently in EA patients (Arrington et al., 2010; Bednarczyk et al., 2013; Brosens et al., 2013). Supplementary Table 1 summarizes 65 potentially pathogenic CNVs identified in patients with EA, with many also being recurrent with VACTERL defects (Felix et al., 2007; Scott, 2018; Walsh et al., 2001).

Figure 2. Locations of TED risk genes and copy number variants on human chromosomes.

Figure 2.

De novo copy number variants are associated with cases of isolated and non-isolated esophageal atresia, arising from parents with balanced translocations leading to partial monosomy and partial trisomy (frequently, trisomy 18, 21, 13, and X) (Supplementary Table 1). De novo mutations in TED patients are heterozygous in constrained genes and have been associated with over 35 single gene disorders (Table 1).

In general, de novo mutations in TED patients are heterozygous, and are in constrained genes that are dosage sensitive. To date there is evidence for EA/TEF causative mutations in approximately 54 different genes and association with over 35 genetic syndromes summarized in Table 1. Interestingly, many risk genes are known to regulate transcription in the embryo, including SOX2, CHD7, and GLI3, which have been implicated in single gene disorders of which EA/TEF is a recurring clinical feature. Mutations in the chromatin modifying DNA helicase CHD7 is frequently mutated in CHARGE syndrome (OMIM #214800) (Brunner and van Bokhoven, 2005; Stoll et al., 2017). Heterozygous loss of function alleles of the transcription factor SOX2 are associated with Microphthalmia and Esophageal Atresia Syndrome (OMIM #206900) (Williamson et al., 2006); and in animal models Sox2 is crucial for esophagus, eye and CNS development (Ferri et al., 2004; Que et al., 2007; Trisno et al., 2018). Truncating variants in the transcription factor GLI3 have been implicated in Pallister-Hall syndrome (OMIM #146510) while de novo polyalanine expansions in ZIC3 have been recurrently found in EA patients with VACTERL defects (Bednarczyk et al., 2013; Brosens et al., 2013; Wessels et al., 2010). Both GLI3 and ZIC3 are involved in Hedgehog signaling (Celli, 2014; Jiang et al., 2013; Zhu et al., 2008), which as detailed later is critical for proper TE development in animals (Brunner and van Bokhoven, 2005; Nasr et al., 2019). Determining the targets of these transcription factors in TE development will provide insight into disease mechanisms and reveal how damaging de novo mutations disrupt morphogenesis.

Table 1.

Risk genes associated with human and animal TEDs

Gene Associated human syndrome (OMIM#) Associated clinical features Type of TE defect Animal model TE defect
CHD7 CHARGE syndrome (214800) Choanal atresia, cardiac, inner ear, retinal defects EA (10–15%) (Vissers et al., 2004) Mouse; embryonic lethal (Hurd et al., 2007; Jiang et al., 2012)
EFTUD2 Mandibulofacial dysostosis with microcephaly (610536) Developmental delay, craniofacial abnormalities EA (40%) (Need et al., 2012) Mouse; embryonic lethal (Beauchamp et al., 2019)
ERCC4 Fanconi anemia (615272) VACTERL defects, cancer - Mouse; postnatal lethal (IMPC)
FANCA/B/C/D1/G Fanconi anemia (227650, 300514, 227645, 605724, 614082) VACTERL defects, cancer EA/TEF (1–14%) (Brosens et al., 2014b) Mouse (Fancd1); embryonic lethal (Ludwig et al., 1997)
FBN2 Congenital contractural arachnodactyly (121050) Scoliosis TEF (occasional) Mouse; normal phenotype (IMPC)
FGFR2 Apert syndrome (101200) Craniosynostosis, syndactyly EA (rare) (Wilkie et al., 1995) Mouse; respiratory distress (Mai et al., 2010)
FLNA Ehlers-Danlos syndrome Articular hypermobility, tissue fragility EA (rare) (Kroes et al., 2003) Mouse; embryonic lethal (Feng et al., 2006, Hart et al., 2006)
FOXF1 Alveolar capillary dysplasia with misalignment of pulmonary veins (265380) Heterotaxia, VACTERL defects EA/TEF (<1%) (Stankiewicz et al., 2009) Mouse; LTEC (Mahlapuu et al., 2001)
FREM2 Fraser syndrome (617666) Syndactyly, respiratory, urogenital tract defects CHAOS; TA (Ikeda et al., 2020) Mouse; defects in lung septation (Timmer et al., 2005)
GDF3 Klippel-Feil syndrome (613702) Fused cervical vertebrae EA (rare) (Clarke et al., 1998) Mouse; embryonic lethal (Chen et al., 2006)
GDF6 Kilppel-Feil syndrome (118100) Fused cervical vertebrae EA (rare) (Clarke et al., 1998) Mouse; normal phenotype (Settle et al., 2003)
GLI3 Pallister-Hall syndrome (146510) Polydactyly, VACTERL Laryngeal cleft (58%) (Ondrey et al., 2000) EA (rare) (Kause et al., 2018; Yang et al., 2014) Mouse, Xenopus; LTEC (Bose et al., 2002; Nasr et al., 2019)
MDM2 Lessel-Kubisch syndrome (618681) Short stature, renal failure Mouse; LTEC (Sui et al., 2019)
MEOX2 Klippel-Feil syndrome (214300) Fused cervical vertebrae EA (rare) (Clarke et al., 1994) Unknown
MID1 Optiz GBBB (300000) Cleft lip/palate, developmental delay Laryngeal cleft, EA (rare) (Quaderi et al., 1997) Mouse; normal phenotype (Prakash et al., 2002)
MKKS McKusick-Kaufman syndrome (236700) Genitourinary defects, polydactyly - Mouse; partial embryonic lethality (Fath et al., 2005)
MYCN Feingold syndrome (164280) Microcephaly, limb malformations EA (50%) (Cognet et al., 2011) Mouse; respiratory failure (Moens et al., 1992; Stanton et al., 1992)
NKX2-1 Choreoathetosis, hypothyroidism, and neonatal respiratory distress (610978) Ataxia, developmental delay - Mouse; LTEC, TA (Kuwahara et al., 2020; Minoo et al., 1999)
NOG Brachydactyly (611377) - EA/TEF (<1%) (Murphy et al., 2012) Mouse; EA/TEF (Li et al., 2007)
PLEC1 Junctional epidermolysis bullosa with pyloric atresia (226670) GI defects - Mouse; neonatal lethal (Andrä et al., 1997)
PTEN VACTERL, hydrocephalus - - Mouse; embryonic lethal (Wang et al., 2020)
RARA; RARB Microphthalmia (615524) Pulmonary hypoplasia - Mouse; LTEC (Mendelsohn et al., 1994)
RBM8A Thrombocytopenia-absent radius (274000) Skeletal anomalies EA (rare) (Klopocki et al., 2007) Mouse; normal phenotype (Mao et al., 2015)
RIPK4 Bartsocas-Papas syndrome (263650) Syndactyly - Mouse; esophageal atresia (Holland et al., 2002)
RMRP Cartilage-hair hypoplasia (250250) - EA (rare) (Bonafé et al., 2002) Mouse; embryonic lethal (Rosenbluh et al., 2011)
ROBO2 CAKUT - Rare (Brosens et al., 2014b) Mouse; normal phenotype (Lu et al., 2007)
SALL1 Townes Brocks syndrome (107480) VACTERL defects - Mouse; normal phenotype (Kiefer et al., 2003)
SEMA3E CHARGE syndrome (214800) Choanal atresia, cardiac, inner ear, retinal defects - Mouse; normal phenotype (Pecho-Vrieseling et al., 2009)
SMARCD1 Coffin-Siris syndrome (618779) Developmental delay EA (20%) (Nixon et al., 2019) -
SOX2 Anophthalmia/microphthalmia-esophageal atresia syndrome (206900) - EA (100%) (Williamson et al., 2006) Mouse; LTEC, EA/TEF (Que et al., 2007; Trisno et al., 2018)
SOX4 Coffin-Siris syndrome (618506) Developmental delay - Mouse; LTEC (Ya et al., 1998)
SPECC1L Opitz syndrome (145410) Cleft lip/palate, developmental delay Rare (Saisawat et al., 2014) Mouse; embryonic lethality (Wilson et al., 2016)
TBX1 DiGeorge syndrome (188400) Parathyroid/thyroid hypoplasia, cardiac defects EA/TEF (33%) (Lee et al., 2008) Mouse; respiratory failure, LTEC (Jerome and Papaioannou, 2001)
TCOF1 Treacher-Collins syndrome (154500) Craniofacial defects, coloboma EA (5%) (Sutphen et al., 1995) Mouse; respiratory failure (Dixon et al., 2006)
WBP11 - - EA/TEF (45%) (Martin et al., 2020) Mouse; small lungs (Martin et al., 2020)
YY1 Gabriele-de Vries syndrome (617557) Developmental delay Rare (Gabriele et al., 2017) Mouse; respiratory failure (Boucherat et al., 2015)
ZIC3 Heterotaxia (306955) X-linked VACTERL (314390) - - Mouse; partial embryonic lethality (Purandare et al., 2002)
In animal models
BARX1 - - - Mouse; LTEC (Woo et al., 2011)
BMP4 Microphthalmia (607932) - - Mouse; LTEC (Li et al., 2008)
BMPR1a;BMPR1b Juvenile polyposis (174900) - - Mouse; LTEC (Domyan et al., 2011)
CTNNB1 - - - Mouse; LTEC (Goss et al., 2009; Harris-Johnson et al., 2009)
DYNC2H1 Short rib polydactyly syndrome (613091) Skeletal abnormalities - Mouse; TEF (Lo, Bench to Bassinet direct data submission 2011)
EFNB2 - - - Mouse; LTEC (Dravis and Henkemeyer, 2011)
FOXP4 - - - Mouse; LTEC (Li et al., 2004)
IFT172 Retinitis pigmentosa (616394) Short-rib thoracic dysplasia (615630) Skeletal defects - Mouse; hypoplastic esophagus (Friedland-Little et al., 2011)
ITGA6 Junctional epidermolysis bullosa with pyloric atresia (226730) GI defects - Mouse; perinatal lethal (Georges-Labouesse et al., 1996)
ITGB4 Junctional epidermolysis bullosa with pyloric atresia (226730) GI defects - Mouse; abnormal esophageal epithelium and respiratory failure (Dowling et al., 1996)
ISL1 - - - Mouse, Xenopus; LTEC (Kim et al., 2019)
PCSK5 VACTERL - - Mouse; LTEC (Szumska et al., 2008)
RAB11A - - - Mouse; embryonic lethal (IMPC) Xenopus; LTEC (Nasr et al., 2019)
RAB25 - - - Mouse; esophageal atresia (Nam et al., 2010)
SHH Holoprosencephaly - Mouse; LTEC (Litingtung et al., 1998)
WDPCP Bardet-Biedl syndrome (615992) Renal defects, polydactyly - Mouse; LTEC (Cui et al., 2013)
WDR35 Cranioectodermal dysplasia (613610) VACTERL defects - Mouse; LTEC (Mill et al., 2011)
New variants identified from recent studies
ADD1, AMER3, AP1G2, APC2, CELSR2, GLS, GTF3C1, ITSN1, KLHL17, PCDH1, PIK3C2G, POLR2B, PTPN14, RAB3GAP2, SMAD6, TECPR1 (Wang et al., 2021)
ZFHX3, TRPS1, APOL2, EEF1D, GGT6, KIAA0556, NFX1, NPR2, PIGC, SLC5A2, TANC2, UBA3, CELSR1, CLP1, GPR133, HPS3, MTA3, PLEC, STAB1, PPIP5K2 (Zhang et al., 2020)

Data obtained from Online Mendelian Inheritance in Man (OMIM; www.omim.org), Mouse Genome Informatics (Jackson Labs, www.informatics.jax.org) and the Monarch Initiative (www.monarchinitiative.org). IMPC = International Mouse Phenotyping Consortium (www.mousephenotype.org).

Genome sequencing of TED patients

Two recent whole exome sequencing studies of patient-parent trios have significantly expanded the number of potential genes associated with EA. One study sequenced 30 trios and prioritized 23 de novo deleterious variants (Table 1) including the known risk genes FANCB, CHD7 and the novel transcription factor ZFHX3 which is also expressed in the mouse fetal foregut (Zhang et al., 2020). Wang et al., (2021) sequenced 45 trios identifying 19 de novo deleterious variants (Table 1), including a frameshift variant in EFTUD2, which encodes a ubiquitously expressed RNA-binding protein involved in splicing that has been reported to be mutated in 35 other EA/TEF patients (Gordon et al., 2012; Huang et al., 2016). Bioinformatic analysis revealed that 15 of 19 de novo deleterious missense mutations were putative targets of EFTUD2 and/or SOX2 including: SMAD6, PDCH1, ITSN1 and RAB3GAP2, suggesting a larger molecular network underlying EA/TEF (Wang et al., 2021).

While genome sequencing identified an increasing number of potentially pathogenic variants, unless mutations recur in the same gene in different patients, it is difficult to conclusively assign causality based upon human genetic data alone. For many reccurring TED mutations such those in transcription factors, epigenetic regulators, or cytoskeleton modulators, the developmental mechanism is plausible. However, the basis of tissue-specific functions for ubiquitously expressed factors like FANC DNA-repair enzymes or the EFTUD2 RNA-biogenesis machinery are unclear. Complementary studies in animal models and human organoids are increasingly important to validate candidate genes and for mechanistic experiments to place each gene’s function into a comprehensive network of genes controlling TE development.

Development of the trachea and esophagus: lessons from animal models

In humans, the fetal foregut separates into distinct tracheal and esophageal tubes between day 25–35 of gestation, and functional studies in mice and Xenopus indicate that this TE morphogenesis is controlled by conserved genetic and cellular mechanisms. Moreover, animal models are being used to test the functional significance of de novo genetic variants identified in patients. If mutation of the orthologous gene in Xenopus or mouse also results in a TED phenotype, this strongly supports the etiologic role of the genetic variant in humans. Characterizing the molecular and cellular basis of the phenotype in animals will provide insight into how the patient’s congenital anomaly arose.

Dorsal-ventral patterning of the foregut

TE development occurs between embryonic day (E) 8.5 and E11.5 in mice, and 2–3 days post fertilization in Xenopus (stage NF35-45). The process begins with an evolutionarily conserved signaling interaction between the endoderm and the surrounding splanchnic mesoderm that patterns the foregut endoderm epithelium along the dorsal ventral (D-V) axis into a presumptive dorsal esophageal domain that expresses the transcription factor Sox2 and a ventral respiratory domain expressing the transcription factor Nkx2-1 (Figure 3A). Between E8.5 to E9 in mice and NF14 to NF25 in Xenopus, retinoic acid (RA) from the foregut splanchnic mesoderm stimulates expression of Hedgehog (HH) ligands Shh and Ihh in the foregut endoderm epithelium (Edwards and Zorn, 2021; Rankin et al., 2016). Endodermal HH ligands then signal back to the mesoderm activating Gli transcription factors, which are required to induce expression of Wnt2, Wnt2b and Bmp4 in ventral splanchnic mesoderm next to the heart (Rankin et al., 2016). BMP/Smad1 signaling downregulates Sox2 in the ventral foregut epithelium, while Wnt2/2b are essential to induce Nkx2-1+ respiratory progenitors (Domyan et al., 2011; Goss et al., 2009; Harris-Johnson et al., 2009). In contrast, the notochord and dorsal foregut secrete BMP and Wnt antagonists including Noggin and Sfrp2 that restrict BMP/Smad1 and Wnt/βcatenin activity in the dorsal foregut to maintain Sox2 expression (Bachiller et al., 2000; Bachiller et al., 2003; Li et al., 2007; Trisno et al., 2018). Thus, differential Wnt/BMP activity along the D-V axis patterns the foregut epithelium into respiratory and esophageal domains. Less is known about the mechanisms that pattern the TE mesoderm, but recent single cell transcriptomics and genetic analysis indicate that the mesoderm also exhibits considerable heterogenetity along the D-V axis prior to differentiating into esophageal smooth muscle and tracheal cartilage, with HH and Wnt being involved (Han et al., 2020; Kishimoto et al., 2020; Nasr et al., 2020).

Figure 3. Patterning and morphogenesis of the animal embryonic foregut.

Figure 3.

A. The embryonic anterior foregut is first patterned into Sox2+ dorsal (green) and Nkx2-1+ ventral (purple) endoderm domains by reciprocal RA, HH, WNT, and BMP signaling between the foregut endoderm and mesoderm. Nkx2-1 expression is promoted by high levels of WNT and BMP ligands, while the BMP antagonist Noggin and the WNT antagonist Sfrp1/2 maintain Sox2 expression by inhibiting WNT and BMP signaling. B. Morphogenesis initiates with the constriction of the embryonic foregut at the midline Nkx2-1+/Sox2+ epithelial cells. Cells of the opposing epithelial walls contact and adhere to form a transient septum. The septum is then resolved by endosome-mediated epithelial remodeling and extracellular matrix breakdown to separate the epithelium into two tubes and allow the mesenchyme to invade the intervening space. The trachea and esophagus then elongate and differentiate as development proceeds. C. Mouse TED mutant models. Disruptions in the major signaling pathways (RA, WNT, BMP, HH) regulating dorsal-ventral patterning in the embryonic foregut results in the loss of Nkx2-1 patterning and the foregut remaining as a single tube or complete LTEC, often accompanied by tracheal atresia. Hypomorphic loss of Sox2, or Noggin mutations, result in the loss of Sox2 patterning and EA/TEF. Loss of Barx1, a mesenchymal transcription factor regulating WNT signaling, mispatterns the embryonic foregut resulting in a complete LTEC. Loss of Gli2 with one allele of Gli3 (Gli2−/−;Gli3+/−) correctly patterns the embryonic foregut but results in a LTEC, suggesting that subsequent cellular mechanisms regulating TE separation are disrupted. Mice harboring Gli3 dominant repressor alleles or mesenchyme-specific Foxf1 knockout have partial LTECs and tracheomalacia.

Mice harboring mutations in the signaling pathways and transcription factors that govern foregut patterning exhibit TEDs, with the severity of the phenotype correlating with the extent to which the activity is completely or only partially lost (Table 1 and Figure 3C). Complete loss of RA, HH, Wnt2/2b or BMP signaling results in failure to specify Nkx2-1+ respiratory progenitors, pulmonary agenesis, and a single undivided foregut that has ectopic Sox2+ esophageal character (Goss et al., 2009, Harris-Johnson et al., 2009; Rankin et al., 2016). Interestingly, null mutations in these pleitropic patterning pathways are frequently embryonic lethal due to co-occurring heart defects, as the reciprocal signaling between the foregut endoderm and surrounding mesoderm coordinates cardiopulmonary development (Steimle et al., 2018). Indeed, similar defects have been reported in stillborn human fetuses with lethal cardiac defects and tracheal agenesis (Hirt-Armon et al., 1996; Perri et al., 2020). Nkx2-1−/− mouse mutants lack a trachea and have hypoplastic lungs emerging from a single undivided Sox2+ foregut tube (Minoo et al., 1999; Que et al., 2007). On the other hand, conditional deletion of Sox2 from the foregut epithelium results in esophageal agenesis with a single undivided tube that is Nkx2-1+ tracheal in nature (Que et al., 2007; Trisno et al., 2018). However, conditional deletion of Sox2 from the Nkx2-5+ ventral foregut epithelium, does not impair TE separation, suggesting that Sox2 regulation of TE separation is specific to its function in the dorsal endoderm (Que et al., 2009).

The observation that Sox2 expression is upregulated in Nkx2-1−/− mutants and vice-versa suggests mutually repressive regulatory modules. Recent single cell genomics have identified the fetal trachea and esophageal transcriptomes, including Sox2 and Nkx2-1 targets genes, and has demonstrated that Nkx2-1 binds silencer sequences near the Sox2 gene to represses its transcription (Han et al., 2020; Kim et al., 2019; Kuwahara et al., 2020; Trisno et al., 2018). However, contrary to Nkx2-1 being a master regulator, more than 90% of tracheal-specific transcripts appear to be Nkx2-1 independent, indicating that other critical genes are yet to be discovered (Kuwahara et al., 2020). Indeed, over 20 transcription factors were recently found to be enriched in the developing foregut, such as Isl, a critical upstream regulator of Nkx2-1 and conditional deletion of which results in EA/TEF (Kim et al., 2019).

In contrast to the tracheal agenesis or esophageal agenesis caused by a complete disruption of foregut patterning, a partial loss of signaling activity often results in relatively normal Sox2/Nkx2-1 patterning but variably penetrant EA/TEF or LTEC, often with VACTERL defects similar to those found in patients (Figure 3C). For example, Noggin−/− mice have a smaller domain of Sox2+ dorsal endoderm and have EA (Fausett et al., 2014; Li et al., 2007). Knockout of Barx1, a transcription factor expressed in the medial foregut mesenchyme, reduces Sfrp2 expression, leading to elevated Wnt activity and resulting in a complete LTEC with ectopic Nkx2-1 and a smaller Sox2 domain (Woo et al., 2011). In humans, SOX2+/− heterozygous haploinsufficient mutations are frequently associated with EA (Williamson et al., 2006). Heterozygous Sox2+/− inbred mice do not have TEDs; however if the single copy of Sox2 is hypomorphic (Sox2EGFP/cond), then the embryos exhibit EA/TEF and the esophageal epithelium fails to differentiate properly (Que et al., 2007). Gli2−/−;Gli3−/− double null mouse embryos that lack all HH-response exhibit pulmonary agenesis and have a single foregut tube. Gli2−/−;Gli3+/− embryos with one allele of Gli3 pattern Nkx2-1 and Sox2 normally, but the foregut fails to separate resulting in a complete LTEC and tracheomalacia (Nasr et al., 2020; Nasr et al., 2019; Rankin et al., 2016). Similarly, in both mouse and Xenopus, truncating mutations in Gli3, which result in a dominant repressor form of the transcription factor mimicking human GLI3 mutations in Pallister-Hall syndrome, also result anterior LTECs and tracheomalacia, as does conditional deletion of the HH-target gene Foxf1 (Bose et al., 2002; Nasr et al., 2020; Nasr et al., 2019). These data indicate that HH has multiple roles in TE patterning, morphogenesis and differentiation.

Trachea-esophageal morphogenesis

Separation of the foregut into distinct TE tubes occurs between E10 and E11.5 in mice, and NF37 and NF44 in Xenopus. A number of models have previously been proposed to explain TE morphogenesis, although they were largely based on histology and for the most part lacked experimental data. An outgrowth model proposed that the like the lung buds, the trachea evaginated from the foregut and elongated due to growth. However, cell proliferation studies do not support this model (Ioannides et al., 2010). A septation model suggested that the common foregut tube separates along its entire length. Time lapse movies suggest an alternative “splitting and extension” model in which a “saddle” tissue forms just anterior to the lung buds. The saddle moves anteriorly as the esophagus and trachea grow posteriorly around it to split the tubes (Zhang et al., 2017). Recent studies using the complementary advantages of Xenopus and mouse have uncovered conserved cellular processes that underlie TE morphogenesis (Figure 3B).

Following D-V patterning, the foregut tube constricts at the midline (Figure 3B). Embryological experiments in Xenopus suggest that this is driven in part by a local condensation of Foxf1+ mesenchyme. Confocal imaging and single cell transcriptomics have revealed that from E9.5 to E10.5, the midline epithelial cells where the constriction occurs co-express Sox2, Nkx2-1, and Isl1 (Han et al., 2020; Kim et al., 2019; Nasr et al., 2019). This suggests that this combination of transcription factors might influence the local cells’ behaviors, although this remains to be experimentally tested. As the foregut constricts, the Sox2+/Nkx2-1+ midline epithelia on either side of the gut tube touch and adhere to one another, forming a transient bilayered epithelial septum. This process involves the GTPase Rab11 and endosome-mediated epithelial remodeling that downregulates the apical character of the luminal epithelium at the contact point and translocates basal-lateral cadherins to the luminal surface, presumably to promote adhesion. The transient septum then resolves by downregulation of adhesion and junctional complexes as midline epithelial cells interdigitate into either the esophagus or trachea; there appears to be minimal cell death involved. Simultaneously, matrix metalloproteases degrade the basement membrane surrounding the septum, allowing the Foxf1+ mesenchyme to invade between the separating trachea and esophagus (Nasr et al., 2019).

Analysis of Gli3 mutants in mouse and Xenopus reveal that this epithelial remodeling is controlled by HH signaling (Nasr et al., 2019), although the molecular mechanisms are unclear. Several other pathways have been implicated in TE morphogenesis, but how they fit into this new mechanistic model remains to be determined. EphrinB2 mouse mutants have EA/TEF (Dravis and Henkemeyer, 2011) and given the known role of Ephrin signaling in tissue fusion and tissue separation (Niethamer and Bush, 2019), it is tempting to speculate that Ephrins are involved in endosome-mediated epithelial remodeling. Mutations in genes that modulate interkinetic nuclear migration (Kaneda et al., 2018), and ubiquitin-dependent regulation of p53 also cause TEDs in mice (Sui et al., 2019), suggesting that apical-basal epithelial polarity and survival of progenitor cells, respectively, are also critical for TE morphogenesis. More mechanistic studies are needed to determine how ubiquitously expressed factors such as p53, Eftud2 and Fanc exhibit tissue specific functions in TE development.

These animal studies provide a framework for understanding the developmental basis of TEDs in humans. We now appreciate that LTEC, EA, TA, and TEF can all result from disruptions in the same morphogenetic process. A major defect in patterning or epithelial remodeling can result in a long gap EA or a LTEC with an undivided foregut of mixed trachea and esophageal identity, whereas a brief pause in the resolution of the septum or mesenchymal invasion could result in less severe TEF. Consistent with this hypothesis, recent histological and gene expression analyses of tissue surgically removed from EA/TEF patients have revealed a mix airway-esophageal character similar to what is frequently observed in animal models (Brosens et al., 2020; Pinzon-Guzman et al., 2020). One limitation of animal studies is that they typically involve null loss of function alleles on inbred strains and may not necessarily model the genetically diversity in humans. To overcome this, studies with patient derived stem cells and organoids offer a promising complementary strategy to investigate genetically complex human biology.

Using human stem cell-derived models to study tracheoesophageal congenital anomalies

Human stem cell-derived organoid cultures

In recent years, hPSC-derived cultures have gained importance as a model system to study human developmental disorders. hPSC-derived cultures can be either derived from embryonic stem cells (ESC) or induced pluripotent stem cells (iPSC) (Dutta et al., 2017; Kim et al., 2020). These cells can then be differentiated into specific cell and tissue types by recapitulating the developmental pathways identified in animal models (Dutta et al., 2017; Kechele and Wells, 2019; Kim et al., 2020; McCauley and Wells, 2017). Importantly, differentiated hPSCs can undergo self-organization into three-dimensional organoids that resemble fetal tissue (H. A. McCauley & Wells, 2017; Spence et al., 2011). To date, many organoid systems have been generated, including lung and esophageal organoids (McCauley et al., 2017; Miller et al., 2019; Shacham-Silverberg and Wells, 2020; Trisno et al., 2018; Wang et al., 2020; Zhang et al., 2018) (Figure 4). By temporally manipulating the signaling pathways that control embryonic development, hPCS are induced in a step-wise manner to first become definitive endoderm and then foregut progenitors. By activation of BMP, WNT and RA pathways, foregut progenitors are directed to form respiratory organoids whereas inhibition of BMP signaling with Noggin promotes development of esophageal organoids (McCauley et al., 2017; Trisno et al., 2018; Zhang et al., 2018). Alternatively, HEOs can be generated by purifying EPCAM+/ITGβ4+ cells that emerge after inhibiting BMP, TGFβ and WNT signaling during esophageal progenitor cell (EPC) specification. Once cultured in Matrigel, the purified cells form HEOs with differentiated squamous epithelium (Zhang et al., 2018). Both BMP and Notch signaling promotes differentiation and maturation of the esophageal epithelium while Hippo/YAP signaling regulates basal cell proliferation and organoid size (Bailey et al., 2019; Zhang et al., 2018).

Figure 4. Studying EA/TEF causing mutations using hPSCs.

Figure 4.

hPSCs can be directly differatiated to definitive endoderm fate, which than can be further differentiated into dorsal anterior foregut (A) or ventral anterior foregut (B) by the manipulation of FGF, Noggin, Wnt and RA. Dorsal anterior foregut organoids will comtinue to grow and differentiate to give rise to human esophageal organoids (HEO), while ventral anterior foregut organoids will differentiate into human airway organoids (HAO).

hPSC-derived HEOs contain squamous epithelium transcriptionally comparable to the human esophagus, with proliferating basal layers expressing SOX2, P63, and KRT5 that will give rise to the entire esophageal epithleium, and differentiated suprabasal layers expressing KRT13 and IVL (Shacham-Silverberg & Wells, 2020; Trisno et al., 2018; Y. Zhang et al., 2018). An important feature of HEOs is that they provide a “human” tissue architecture which lacks the keratinized layers present in the mouse. Differentiated HEOs or purified esophageal progenitor cells can also be used to generate organotypic raft cultures. Dissociated HEOs or EPCs cultured on cell inserts in air-liquid interface give rise to differentiated esophagus epithelium containing basal and suprabasal layers. Raft cultures permit lumen manipulations like viral infections or acid exposure to model esophagus-related disease like esophagus squamous cell carcinoma and Barrett’s esophagus.

The respiratory system is comprised of the proximal airways, the trachea and main stem brochi, and distal airways including bronchioles and alveoli. Using knowledge obtained from studying the development of the proximal-distal respiratory axis in animal models, protocols have been designed to generate both HAOs and well as more distal human lung organoids (HLOs) (Dye et al., 2016; Dye et al., 2015; Hawkins et al., 2021; Miller et al., 2019). Proximal airway organoids modeling the epithelial character of the trachea and primary bronchi can be generated by treating foregut hPSC cultures with high levels of WNT, giving rise to NKX2-1+ lung progenitors. These can then be purified and transitioned to low WNT conditions to create airway organoids containing P63+ basal cells and SCGB3A2+ secretory cells. NOTCH inhibition promotes the differentiation of FOXJ1+ ciliated cells, modeling the mucocillary epithelia of the trachea and bronchi (Hawkins et al., 2021; McCauley et al., 2017; Wang et al., 2020).

Using human pluripotent stem cells to study congenital defects of the digestive and respiratory systems

Although hPSC-derived organoids are not yet capable of modeling the complex tissue morphogenesis of the fetal foregut, they have proven a good system to study how patient mutations effect TE development, differentiation and physiology (Que, 2015; Raad et al., 2020). Using patient-specific iPSCs and organoids, it is possible to examine both monogenic diseases and genetically complex diseases. For example, in the digestive system, PSC-derived GI organoids have been used to study diseases ranging from Hirschsprung’s disease to malabsorption (McCauley et al., 2020; Workman et al., 2017; Zhang et al., 2019). Now that HAOs, HEOs, and esophageal raft tissue can be efficiently derived, disease-related studies using these models will become increasingly common.

HAOs have been used to model disease mechanisms of cystic fibrosis by generating patient-derived airway organoids and assaying the swelling response to forskolin. This approach allows the study of patient-specific phenotypes as well as acting as a possible platform for drug screening for disease treatment (McCauley et al., 2017). Studies using hPSC-derived HEOs have also revealed important insight into EA. For example, CRISPR-mediated downregulation of SOX2 in HEOs mimics SOX2+/− heterozygous mutations in EA patients, reinforcing the conserved role of SOX2 in human esophageal development (Trisno et al., 2018). Moreover, transcriptomic studies using this organoid based-model helped define the transcriptional targets of SOX2 in humans, including the WNT-antagonist SFRP2 (Trisno et al., 2018). With the advent of effective CRISPR-mediated gene editing hPSC-derive organoids are also ideal for validating patient variants for causation. Making an analogous mutation in a healthy iPSC line or correcting the variant in the patient line and determining if this is sufficient to cause or correct the defective organoid phenotype (Dutta et al., 2017). Correcting the variant in the patient iPSCs is particularly valuable as it provides an isogenic line with the same complex genetic background. In principle, it should be possible to modify more than one gene at a time to examine multigenic contributions.

Despite the advantages of human organoids, there are some limitations that still need to be addressed before these reach their full potential for disease modeling. For example, while HEOs closely resemble human esophagus epithelium and have confirmed the involvement of various signaling pathways in esophagus development, they lack both mesenchyme and the enteric nervous system, two cell types which may frequently be defective in EA/TEF patients. Development of new HEO models that consist of all three components of the adult esophagus will enable better modeling of esophagus related congenital anomalies and disease. Similar approaches used with intestinal organoids to incorporate the enteric nervous sytem could be applied to esophageal and airway organoids (Workman et al., 2017). With new single-cell data from mouse embryos, hPSCs can now be differentiated into splanchnic mesoderm that gives rise to tracheal and esophageal mesenchyme in vivo (Han et al., 2020). Modifying current esophageal and airway organoids protocols to incoporate both epithelium and mesenchyme, either by the co-differentiation in the same culture or by combining separately differentiated progenitors can be beneficial for the study of TED-related genes. Because of the self-organizing behaviors of organoids, we predict that it might be possible in the near future to model some aspects of foregut morphogenesis in culture. A recent proof of principle for in vitro morphogenesis showed that multi-organ hepato-biliary-pancreatic structures can be generated in culture by aggregating foregut and midgut spheroids to replicate the foregut-midgut boundary (Koike et al., 2019).

Future prospectives

In the last five years, animal model studies have begun to reveal the developmental basis of TEDs. These studies have largely focused on null mutants in critical developmental regulators which are frequently embryonic lethal and would not be present in liveborn patients. Going forward, it will be important to use CRISPR gene editing to introduce patient specific variants to improve the understanding of the human conditions and co-occurring anomalies. Additionally, most animal model studies to date have focused on transcription factors and cell signaling pathways, but much less is known about the downstream cellular effectors that control morphogenesis. We expect that these effector genes are frequently mutated in patients. Integrating single cell genomic studies from animals to identify downstream target genes will help rigorously prioritize the growing number of genetic variants identified from patient genome sequencing. Prioritized variants can then be assessed in animals to provide functional evidence for validation and to better assess molecular mechanism. Another important advance that is needed with animal models is the development of live imaging approaches to observe in real time how mutations disrupt cell behaviours and tissue morphogenesis.

We expect that the use of patient derived organoids will help define defects in patient’s tissue function and physiology, and may provide platforms for screening drugs to improve organ functionality. For example, the long-term co-morbidities of dysmotility, gastroesophageal reflux disease, or reoccurring strictures might be due to defects in smooth muscle differentiation, metaplasia of the epithelium and/or defective enteric neurons, all of which could be characterized in organoid models. Finally, while there have been many, mostly failed, attempts at bioengineering artificial esophagus or trachea structures, mainly by seeding mesenchyumal stem cells onto scaffolds, it may be possible to make genetically correct patient cells for repair in the future. Creating bonafide esophageal or tracheal tissue with all the appropriate cell types should be possible in the next decade.

Traditional care of patients with TEDs has relied on clinical history and chest radiography to identify the presence of a TED while the precise anatomy of the defect was not delineated until surgery and direct visualization of the defect. This approach has limited the clinical care of these patients and also our understanding of the undisturbed anatomy of these anomalies. New imaging modalities, particularly novel non-invasive ultrashort echo time MRI of newborn TED patients prior to surgical repair, provides impressive views of undisrupted anatomy at a resolution rivaling confocal microscopy in animals (Figure 5). Combining this type of detailed patient phenotyping along with comprehensive longitudinal medical follow up with whole genome sequencing will provide a better genotype-phenotype understanding of these heterogenous conditions. Ultimately, in utero genetic diagnosis might be able to predict the severity of the defects and the likelihood of other comorbidities that would benefit from early detection and management. With advances in treatment over the last few decades improved diagnosis will be also be important for pateints having families as their de novo risk mutation might now be passed on to their children. It might also be possible to begin to incorporate non-genetic factors into our understanding of TED etiology, since developmental pathways such as Hedeghog and vitamin A dependent-RA signaling can be impacted by environmental chemicals and teratogens.

Figure 5. Ultrashort echotime MRI of EA/TEF.

Figure 5.

An infant with an unrepaired type C (distal TEF) EA/TEF was imaged on the first day of life with ultrashort echotime MRI. This technique removes motion artifact and is able to gather detailed anatomy of the chest to a 0.7 mm resolution in a free breathing, non-sedated infant. The specific anatomy of the trachea, dilated proximal esophageal pouch and distal tracheal esophageal fistula are presented as a three dimensional reconstruction from anterior (A) and posterior (B) perspective.

Looking forward, we envisage that a systems level approach, integrating data from animal models and organoids with genome sequencing and deep patient phenotyping, will continue to inform our understanding of the developmental basis of TEDs. This will impact the diagnosis and management of these life-threatening birth defects. This will require collaborative team science such as the CLEAR Consortium (www.CLEARconsortium.org), which brings together developmental and stem cell biologists, human geneticists, data scientists, clinicians, and surgeons all focused on elucidating the origins of TEDs. In addition, efforts to aggregate phenotypic data from different model organism knowledge bases such as Mouse Genome Informatics (MGI; http://www.informatics.jax.org; RRID SCR_006460) (Bult et al., 2019) and Xenbase (www.Xenbase.org; RRID SCR_003280) (Karimi et al., 2018) will be critical. An excellent example is the Monarch Initiative (www.Monarchinitiative.org; RRID SCR_000824) (Shefchek et al., 2020) which is establishing ontologies and computational approaches to integrate animal models phenotypes from the scientific literature with human diseases and patient genomic data. Since these birth defects are rare, it would also be helpful to share deidentified clinical and genetic data from the many independent international patient registries to increase the power for robust statistical analysis. The NIH funded Gabriela Miller Kids First Data Resource Portal (http://kidsfirstdrc.org; RRID SCR_016493) that aggregates and disseminates genome data from patients with congenital anomalies, including TEDs, is an example of such a resource. There is growing momentum in the biomedical community for such collaborative multiscale approaches that should accelerate our understanding to the developmental basis of TEDs and many other congenital anomalies.

Supplementary Material

1

Supplementary Table 1 – Copy number variants (CNVs) associated with human TEDs.

Highlights.

  • The trachea and esophagus arise from the separation of a common fetal foregut tube.

  • The developmental genetic basis of tracheoesophageal birth defects are poorly understood.

  • Patient genome sequencing is increasingly identifying candidate risk alleles

  • Animal models and human organoids reveal the molecular basis of normal and disrupted tracheoesophageal development

  • Integration of clinical, genetic and single cell omic data from animals and organoids promise a systems-level understanding

Acknowledgements

TED research in the labs of WKC, PSK, YS, JMW and AMZ is supported by NICHD P01HD093363. We thank Christopher Woods in the Department of Pathology, Cincinnati Children’s Hospital Medical Center for the artwork in Figure 1.

Footnotes

Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

References

  1. Andrä K, Lassmann H, Bittner R, Shorny S, Fässler R, Propst F, Wiche G, 1997. Targeted inactivation of plectin reveals essential function in maintaining the integrity of skin, muscle, and heart cytoarchitecture. Genes Dev 11, 3143–3156. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Arrington CB, Patel A, Bacino CA, Bowles NE, 2010. Haploinsufficiency of the LIM domain containing preferred translocation partner in lipoma (LPP) gene in patients with tetralogy of Fallot and VACTERL association. Am J Med Genet A 152A, 2919–2923. [DOI] [PubMed] [Google Scholar]
  3. Bachiller D, Klingensmith J, Kemp C, Belo JA, Anderson RM, May SR, McMahon JA, McMahon AP, Harland RM, Rossant J, De Robertis EM, 2000. The organizer factors Chordin and Noggin are required for mouse forebrain development. Nature 403, 658–661. [DOI] [PubMed] [Google Scholar]
  4. Bachiller D, Klingensmith J, Shneyder N, Tran U, Anderson R, Rossant J, De Robertis EM, 2003. The role of chordin/Bmp signals in mammalian pharyngeal development and DiGeorge syndrome. Development 130, 3567–3578. [DOI] [PubMed] [Google Scholar]
  5. Bailey DD, Zhang Y, van Soldt BJ, Jiang M, Suresh S, Nakagawa H, Rustgi AK, Aceves SS, Cardoso WV, Que J, 2019. Use of hPSC-derived 3D organoids and mouse genetics to define the roles of YAP in the development of the esophagus. Development (Cambridge) 146. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Beauchamp MC, Djedid A, Daupin K, Clokie K, Kumar S, Majewski J, Jerome-Majewska LA, 2019. Loss of function mutation of Eftud2, the gene responsible for mandibulofacial dysostosis with microcephaly (MFDM), leads to pre-implantation arrest in mouse. PLoS One 14, e0219280. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Bednarczyk D, Sasiadek MM, Smigiel R, 2013. Chromosome aberrations and gene mutations in patients with esophageal atresia. J Pediatr Gastroenterol Nutr 57, 688–693. [DOI] [PubMed] [Google Scholar]
  8. Bonafé L, Schmitt K, Eich G, Giedion A, Superti-Furga A, 2002. RMRP gene sequence analysis confirms a cartilage-hair hypoplasia variant with only skeletal manifestations and reveals a high density of single-nucleotide polymorphisms. Clin Genet 61, 146–151. [DOI] [PubMed] [Google Scholar]
  9. Bose J, Grotewold L, Ruther U, 2002. Pallister-Hall syndrome phenotype in mice mutant for Gli3. Hum Mol Genet 11, 1129–1135. [DOI] [PubMed] [Google Scholar]
  10. Boucherat O, Landry-Truchon K, Bérubé-Simard FA, Houde N, Beuret L, Lezmi G, Foulkes WD, Delacourt C, Charron J, Jeannotte L, 2015. Epithelial inactivation of Yy1 abrogates lung branching morphogenesis. Development 142, 2981–2995. [DOI] [PubMed] [Google Scholar]
  11. Brosens E, de Jong EM, Barakat TS, Eussen BH, D’Haene B, De Baere E, Verdin H, Poddighe PJ, Galjaard RJ, Gribnau J, Brooks AS, Tibboel D, de Klein A, 2014a. Structural and numerical changes of chromosome X in patients with esophageal atresia. Eur J Hum Genet 22, 1077–1084. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Brosens E, Eussen H, van Bever Y, van der Helm RM, Ijsselstijn H, Zaveri HP, Wijnen R, Scott DA, Tibboel D, de Klein A, 2013. VACTERL Association Etiology: The Impact of de novo and Rare Copy Number Variations. Mol Syndromol 4, 20–26. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Brosens E, Felix JF, Boerema-de Munck A, de Jong EM, Lodder EM, Swagemakers S, Buscop-van Kempen M, de Krijger RR, Wijnen RMH, van IWFJ, van der Spek P, de Klein A, Tibboel D, Rottier RJ, 2020. Histological, immunohistochemical and transcriptomic characterization of human tracheoesophageal fistulas. PLoS One 15, e0242167. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Brosens E, Marsch F, de Jong EM, Zaveri HP, Hilger AC, Choinitzki VG, Holscher A, Hoffmann P, Herms S, Boemers TM, Ure BM, Lacher M, Ludwig M, Eussen BH, van der Helm RM, Douben H, Van Opstal D, Wijnen RM, Beverloo HB, van Bever Y, Brooks AS, H IJ, Scott DA, Schumacher J, Tibboel D, Reutter H, de Klein A, 2016. Copy number variations in 375 patients with oesophageal atresia and/or tracheoesophageal fistula. Eur J Hum Genet 24, 1715–1723. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Brosens E, Ploeg M, van Bever Y, Koopmans AE, H IJ, Rottier RJ, Wijnen R, Tibboel D, de Klein A, 2014b. Clinical and etiological heterogeneity in patients with tracheo-esophageal malformations and associated anomalies. Eur J Med Genet 57, 440–452. [DOI] [PubMed] [Google Scholar]
  16. Brunner HG, van Bokhoven H, 2005. Genetic players in esophageal atresia and tracheoesophageal fistula. Curr Opin Genet Dev 15, 341–347. [DOI] [PubMed] [Google Scholar]
  17. Bult CJ, Blake JA, Smith CL, Kadin JA, Richardson JE, 2019. Mouse Genome Database (MGD) 2019. Nucleic Acids Res 47, D801–d806. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Celli J, 2014. Genetics of gastrointestinal atresias. Eur J Med Genet 57, 424–439. [DOI] [PubMed] [Google Scholar]
  19. Chen C, Ware SM, Sato A, Houston-Hawkins DE, Habas R, Matzuk MM, Shen MM, Brown CW, 2006. The Vg1-related protein Gdf3 acts in a Nodal signaling pathway in the pre-gastrulation mouse embryo. Development 133, 319–329. [DOI] [PubMed] [Google Scholar]
  20. Chitkara AE, Tadros M, Kim HJ, Harley EH, 2003. Complete laryngotracheoesophageal cleft: complicated management issues. Laryngoscope 113, 1314–1320. [DOI] [PubMed] [Google Scholar]
  21. Clarke RA, Catalan G, Diwan AD, Kearsley JH, 1998. Heterogeneity in Klippel-Feil syndrome: a new classification. Pediatr Radiol 28, 967–974. [DOI] [PubMed] [Google Scholar]
  22. Clarke RA, Davis PJ, Tonkin J, 1994. Klippel-Feil syndrome associated with malformed larynx. Case report. Ann Otol Rhinol Laryngol 103, 201–207. [DOI] [PubMed] [Google Scholar]
  23. Cognet M, Nougayrede A, Malan V, Callier P, Cretolle C, Faivre L, Genevieve D, Goldenberg A, Heron D, Mercier S, Philip N, Sigaudy S, Verloes A, Sarnacki S, Munnich A, Vekemans M, Lyonnet S, Etchevers H, Amiel J, de Pontual L, 2011. Dissection of the MYCN locus in Feingold syndrome and isolated oesophageal atresia. Eur J Hum Genet 19, 602–606. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Cui C, Chatterjee B, Lozito TP, Zhang Z, Francis RJ, Yagi H, Swanhart LM, Sanker S, Francis D, Yu Q, San Agustin JT, Puligilla C, Chatterjee T, Tansey T, Liu X, Kelley MW, Spiliotis ET, Kwiatkowski AV, Tuan R, Pazour GJ, Hukriede NA, Lo CW, 2013. Wdpcp, a PCP protein required for ciliogenesis, regulates directional cell migration and cell polarity by direct modulation of the actin cytoskeleton. PLoS Biol 11, e1001720. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. de Jong EM, Felix JF, Deurloo JA, van Dooren MF, Aronson DC, Torfs CP, Heij HA, Tibboel D, 2008. Non-VACTERL-type anomalies are frequent in patients with esophageal atresia/tracheo-esophageal fistula and full or partial VACTERL association. Birth Defects Res A Clin Mol Teratol 82, 92–97. [DOI] [PubMed] [Google Scholar]
  26. Dixon J, Jones NC, Sandell LL, Jayasinghe SM, Crane J, Rey JP, Dixon MJ, Trainor PA, 2006. Tcof1/Treacle is required for neural crest cell formation and proliferation deficiencies that cause craniofacial abnormalities. Proc Natl Acad Sci U S A 103, 13403–13408. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Domyan ET, Ferretti E, Throckmorton K, Mishina Y, Nicolis SK, Sun X, 2011. Signaling through BMP receptors promotes respiratory identity in the foregut via repression of Sox2. Development 138, 971–981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Dowling J, Yu QC, Fuchs E, 1996. Beta4 integrin is required for hemidesmosome formation, cell adhesion and cell survival. J Cell Biol 134, 559–572. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Dravis C, Henkemeyer M, 2011. Ephrin-B reverse signaling controls septation events at the embryonic midline through separate tyrosine phosphorylation-independent signaling avenues. Dev Biol 355, 138–151. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Dutta D, Heo I, Clevers H, 2017. Disease Modeling in Stem Cell-Derived 3D Organoid Systems. Trends in Molecular Medicine 23, 393––410. [DOI] [PubMed] [Google Scholar]
  31. Dye BR, Dedhia PH, Miller AJ, Nagy MS, White ES, Shea LD, Spence JR, 2016. A bioengineered niche promotes in vivo engraftment and maturation of pluripotent stem cell derived human lung organoids. Elife 5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Dye BR, Hill DR, Ferguson MA, Tsai YH, Nagy MS, Dyal R, Wells JM, Mayhew CN, Nattiv R, Klein OD, White ES, Deutsch GH, Spence JR, 2015. In vitro generation of human pluripotent stem cell derived lung organoids. Elife 4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Edwards NA, Zorn AM, 2021. Modeling endoderm development and disease in Xenopus. [DOI] [PubMed]
  34. Fath MA, Mullins RF, Searby C, Nishimura DY, Wei J, Rahmouni K, Davis RE, Tayeh MK, Andrews M, Yang B, Sigmund CD, Stone EM, Sheffield VC, 2005. Mkks-null mice have a phenotype resembling Bardet-Biedl syndrome. Hum Mol Genet 14, 1109–1118. [DOI] [PubMed] [Google Scholar]
  35. Fausett SR, Brunet LJ, Klingensmith J, 2014. BMP antagonism by Noggin is required in presumptive notochord cells for mammalian foregut morphogenesis. Dev Biol 391, 111–124. [DOI] [PubMed] [Google Scholar]
  36. Felix JF, Tibboel D, de Klein A, 2007. Chromosomal anomalies in the aetiology of oesophageal atresia and tracheo-oesophageal fistula. Eur J Med Genet 50, 163–175. [DOI] [PubMed] [Google Scholar]
  37. Ferri AL, Cavallaro M, Braida D, Di Cristofano A, Canta A, Vezzani A, Ottolenghi S, Pandolfi PP, Sala M, DeBiasi S, Nicolis SK, 2004. Sox2 deficiency causes neurodegeneration and impaired neurogenesis in the adult mouse brain. Development 131, 3805–3819. [DOI] [PubMed] [Google Scholar]
  38. Friedland-Little JM, Hoffmann AD, Ocbina PJ, Peterson MA, Bosman JD, Chen Y, Cheng SY, Anderson KV, Moskowitz IP, 2011. A novel murine allele of Intraflagellar Transport Protein 172 causes a syndrome including VACTERL-like features with hydrocephalus. Hum Mol Genet 20, 3725–3737. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Gabriele M, Vulto-van Silfhout AT, Germain PL, Vitriolo A, Kumar R, Douglas E, Haan E, Kosaki K, Takenouchi T, Rauch A, Steindl K, Frengen E, Misceo D, Pedurupillay CRJ, Stromme P, Rosenfeld JA, Shao Y, Craigen WJ, Schaaf CP, Rodriguez-Buritica D, Farach L, Friedman J, Thulin P, McLean SD, Nugent KM, Morton J, Nicholl J, Andrieux J, Stray-Pedersen A, Chambon P, Patrier S, Lynch SA, Kjaergaard S, Tørring PM, Brasch-Andersen C, Ronan A, van Haeringen A, Anderson PJ, Powis Z, Brunner HG, Pfundt R, Schuurs-Hoeijmakers JHM, van Bon BWM, Lelieveld S, Gilissen C, Nillesen WM, Vissers L, Gecz J, Koolen DA, Testa G, de Vries BBA, 2017. YY1 Haploinsufficiency Causes an Intellectual Disability Syndrome Featuring Transcriptional and Chromatin Dysfunction. Am J Hum Genet 100, 907–925. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Genevieve D, de Pontual L, Amiel J, Lyonnet S, 2011. Genetic factors in isolated and syndromic esophageal atresia. J Pediatr Gastroenterol Nutr 52 Suppl 1, S6–8. [DOI] [PubMed] [Google Scholar]
  41. Georges-Labouesse E, Messaddeq N, Yehia G, Cadalbert L, Dierich A, Le Meur M, 1996. Absence of integrin alpha 6 leads to epidermolysis bullosa and neonatal death in mice. Nat Genet 13, 370–373. [DOI] [PubMed] [Google Scholar]
  42. Gordon CT, Petit F, Oufadem M, Decaestecker C, Jourdain AS, Andrieux J, Malan V, Alessandri JL, Baujat G, Baumann C, Boute-Benejean O, Caumes R, Delobel B, Dieterich K, Gaillard D, Gonzales M, Lacombe D, Escande F, Manouvrier-Hanu S, Marlin S, Mathieu-Dramard M, Mehta SG, Simonic I, Munnich A, Vekemans M, Porchet N, de Pontual L, Sarnacki S, Attie-Bitach T, Lyonnet S, Holder-Espinasse M, Amiel J, 2012. EFTUD2 haploinsufficiency leads to syndromic oesophageal atresia. J Med Genet 49, 737–746. [DOI] [PubMed] [Google Scholar]
  43. Goss AM, Tian Y, Tsukiyama T, Cohen ED, Zhou D, Lu MM, Yamaguchi TP, Morrisey EE, 2009. Wnt2/2b and beta-catenin signaling are necessary and sufficient to specify lung progenitors in the foregut. Dev Cell 17, 290–298. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Han L, Chaturvedi P, Kishimoto K, Koike H, Nasr T, Iwasawa K, Giesbrecht K, Witcher PC, Eicher A, Haines L, Lee Y, Shannon JM, Morimoto M, Wells JM, Takebe T, Zorn AM, 2020. Single cell transcriptomics identifies a signaling network coordinating endoderm and mesoderm diversification during foregut organogenesis. Nat Commun 11, 4158. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Harris-Johnson KS, Domyan ET, Vezina CM, Sun X, 2009. beta-Catenin promotes respiratory progenitor identity in mouse foregut. Proc Natl Acad Sci U S A 106, 16287–16292. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Hawkins FJ, Suzuki S, Beermann ML, Barillà C, Wang R, Villacorta-Martin C, Berical A, Jean JC, Le Suer J, Matte T, Simone-Roach C, Tang Y, Schlaeger TM, Crane AM, Matthias N, Huang SXL, Randell SH, Wu J, Spence JR, Carraro G, Stripp BR, Rab A, Sorsher EJ, Horani A, Brody SL, Davis BR, Kotton DN, 2021. Derivation of Airway Basal Stem Cells from Human Pluripotent Stem Cells. Cell Stem Cell 28, 79–95.e78. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Hirt-Armon K, Pober BR, Holmes LB, 1996. Type III tracheal agenesis with familial tetralogy of Fallot and absent pulmonary valve syndrome. Am J Med Genet 65, 266–268. [DOI] [PubMed] [Google Scholar]
  48. Holland P, Willis C, Kanaly S, Glaccum M, Warren A, Charrier K, Murison J, Derry J, Virca G, Bird T, Peschon J, 2002. RIP4 is an ankyrin repeat-containing kinase essential for keratinocyte differentiation. Curr Biol 12, 1424–1428. [DOI] [PubMed] [Google Scholar]
  49. Huang L, Vanstone MR, Hartley T, Osmond M, Barrowman N, Allanson J, Baker L, Dabir TA, Dipple KM, Dobyns WB, Estrella J, Faghfoury H, Favaro FP, Goel H, Gregersen PA, Gripp KW, Grix A, Guion-Almeida ML, Harr MH, Hudson C, Hunter AG, Johnson J, Joss SK, Kimball A, Kini U, Kline AD, Lauzon J, Lildballe DL, Lopez-Gonzalez V, Martinezmoles J, Meldrum C, Mirzaa GM, Morel CF, Morton JE, Pyle LC, Quintero-Rivera F, Richer J, Scheuerle AE, Schonewolf-Greulich B, Shears DJ, Silver J, Smith AC, Temple IK, Center UCG, van de Kamp JM, van Dijk FS, Vandersteen AM, White SM, Zackai EH, Zou R, Care4Rare Canada, C., Bulman DE, Boycott KM, Lines MA, 2016. Mandibulofacial Dysostosis with Microcephaly: Mutation and Database Update. Hum Mutat 37, 148–154. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Hurd EA, Capers PL, Blauwkamp MN, Adams ME, Raphael Y, Poucher HK, Martin DM, 2007. Loss of Chd7 function in gene-trapped reporter mice is embryonic lethal and associated with severe defects in multiple developing tissues. Mamm Genome 18, 94–104. [DOI] [PubMed] [Google Scholar]
  51. Ikeda S, Akamatsu C, Ijuin A, Nagashima A, Sasaki M, Mochizuki A, Nagase H, Enomoto Y, Kuroda Y, Kurosawa K, Ishikawa H, 2020. Prenatal diagnosis of Fraser syndrome caused by novel variants of FREM2. Human Genome Variation 7, 32. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Ioannides AS, Massa V, Ferraro E, Cecconi F, Spitz L, Henderson DJ, Copp AJ, 2010. Foregut separation and tracheo-oesophageal malformations: the role of tracheal outgrowth, dorso-ventral patterning and programmed cell death. Dev Biol 337, 351–362. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Jerome LA, Papaioannou VE, 2001. DiGeorge syndrome phenotype in mice mutant for the T-box gene, Tbx1. Nat Genet 27, 286–291. [DOI] [PubMed] [Google Scholar]
  54. Jiang X, Zhou Y, Xian L, Chen W, Wu H, Gao X, 2012. The mutation in Chd7 causes misexpression of Bmp4 and developmental defects in telencephalic midline. Am J Pathol 181, 626–641. [DOI] [PubMed] [Google Scholar]
  55. Jiang Z, Zhu L, Hu L, Slesnick TC, Pautler RG, Justice MJ, Belmont JW, 2013. Zic3 is required in the extra-cardiac perinodal region of the lateral plate mesoderm for left-right patterning and heart development. Hum Mol Genet 22, 879–889. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Kaneda R, Saeki Y, Getachew D, Matsumoto A, Furuya M, Ogawa N, Motoya T, Rafiq AM, Jahan E, Udagawa J, Hashimoto R, Otani H, 2018. Interkinetic nuclear migration in the tracheal and esophageal epithelia of the mouse embryo: Possible implications for tracheo-esophageal anomalies. Congenit Anom (Kyoto) 58, 62–70. [DOI] [PubMed] [Google Scholar]
  57. Karimi K, Fortriede JD, Lotay VS, Burns KA, Wang DZ, Fisher ME, Pells TJ, James-Zorn C, Wang Y, Ponferrada VG, Chu S, Chaturvedi P, Zorn AM, Vize PD, 2018. Xenbase: a genomic, epigenomic and transcriptomic model organism database. Nucleic Acids Res 46, D861–d868. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Kause F, Reutter H, Marsch F, Thiele H, Altmüller J, Ludwig M, Zhang R, 2018. Whole exome sequencing identifies a mutation in EYA1 and GLI3 in a patient with branchio-otic syndrome and esophageal atresia: Coincidence or a digenic mode of inheritance? Mol Med Rep 17, 3200–3205. [DOI] [PubMed] [Google Scholar]
  59. Kechele DO, Wells JM, 2019. Recent advances in deriving human endodermal tissues from pluripotent stem cells. Current Opinion in Cell Biology 61, 92––100. [DOI] [PubMed] [Google Scholar]
  60. Kiefer SM, Ohlemiller KK, Yang J, McDill BW, Kohlhase J, Rauchman M, 2003. Expression of a truncated Sall1 transcriptional repressor is responsible for Townes-Brocks syndrome birth defects. Hum Mol Genet 12, 2221–2227. [DOI] [PubMed] [Google Scholar]
  61. Kim E, Jiang M, Huang H, Zhang Y, Tjota N, Gao X, Robert J, Gilmore N, Gan L, Que J, 2019. Isl1 Regulation of Nkx2.1 in the Early Foregut Epithelium Is Required for Trachea-Esophageal Separation and Lung Lobation. Dev Cell 51, 675–683 e674. [DOI] [PMC free article] [PubMed] [Google Scholar]
  62. Kim J, Koo BK, Knoblich JA, 2020. Human organoids: model systems for human biology and medicine. Nature Reviews Molecular Cell Biology 21, 571––584. [DOI] [PMC free article] [PubMed] [Google Scholar]
  63. Kishimoto K, Furukawa KT, Luz-Madrigal A, Yamaoka A, Matsuoka C, Habu M, Alev C, Zorn AM, Morimoto M, 2020. Bidirectional Wnt signaling between endoderm and mesoderm confers tracheal identity in mouse and human cells. Nat Commun 11, 4159. [DOI] [PMC free article] [PubMed] [Google Scholar]
  64. Klopocki E, Schulze H, Strauss G, Ott CE, Hall J, Trotier F, Fleischhauer S, Greenhalgh L, Newbury-Ecob RA, Neumann LM, Habenicht R, König R, Seemanova E, Megarbane A, Ropers HH, Ullmann R, Horn D, Mundlos S, 2007. Complex inheritance pattern resembling autosomal recessive inheritance involving a microdeletion in thrombocytopenia-absent radius syndrome. Am J Hum Genet 80, 232–240. [DOI] [PMC free article] [PubMed] [Google Scholar]
  65. Koike H, Iwasawa K, Ouchi R, Maezawa M, Giesbrecht K, Saiki N, Ferguson A, Kimura M, Thompson WL, Wells JM, Zorn AM, Takebe T, 2019. Modelling human hepato-biliary-pancreatic organogenesis from the foregut–midgut boundary. Nature 574, 112––116. [DOI] [PMC free article] [PubMed] [Google Scholar]
  66. Kroes HY, Pals G, van Essen AJ, 2003. Ehlers-Danlos syndrome type IV: unusual congenital anomalies in a mother and son with a COL3A1 mutation and a normal collagen III protein profile. Clin Genet 63, 224–227. [DOI] [PubMed] [Google Scholar]
  67. Kuwahara A, Lewis AE, Coombes C, Leung FS, Percharde M, Bush JO, 2020. Delineating the early transcriptional specification of the mammalian trachea and esophagus. Elife 9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  68. La Placa S, Giuffre M, Gangemi A, Di Noto S, Matina F, Nociforo F, Antona V, Di Pace MR, Piccione M, Corsello G, 2013. Esophageal atresia in newborns: a wide spectrum from the isolated forms to a full VACTERL phenotype? Ital J Pediatr 39, 45. [DOI] [PMC free article] [PubMed] [Google Scholar]
  69. Lee KD, Okazaki T, Kato Y, Lane GJ, Yamataka A, 2008. Esophageal atresia and tracheo-esophageal fistula associated with coarctation of the aorta, CHARGE association, and DiGeorge syndrome: a case report and literature review. Pediatr Surg Int 24, 1153–1156. [DOI] [PubMed] [Google Scholar]
  70. Li S, Zhou D, Lu MM, Morrisey EE, 2004. Advanced cardiac morphogenesis does not require heart tube fusion. Science 305, 1619–1622. [DOI] [PubMed] [Google Scholar]
  71. Li Y, Litingtung Y, Ten Dijke P, Chiang C, 2007. Aberrant Bmp signaling and notochord delamination in the pathogenesis of esophageal atresia. Dev Dyn 236, 746–754. [DOI] [PubMed] [Google Scholar]
  72. Litingtung Y, Lei L, Westphal H, Chiang C, 1998. Sonic hedgehog is essential to foregut development. Nature Genetics 20, 58–61. [DOI] [PubMed] [Google Scholar]
  73. Lu W, van Eerde AM, Fan X, Quintero-Rivera F, Kulkarni S, Ferguson H, Kim HG, Fan Y, Xi Q, Li QG, Sanlaville D, Andrews W, Sundaresan V, Bi W, Yan J, Giltay JC, Wijmenga C, de Jong TP, Feather SA, Woolf AS, Rao Y, Lupski JR, Eccles MR, Quade BJ, Gusella JF, Morton CC, Maas RL, 2007. Disruption of ROBO2 is associated with urinary tract anomalies and confers risk of vesicoureteral reflux. Am J Hum Genet 80, 616–632. [DOI] [PMC free article] [PubMed] [Google Scholar]
  74. Mahlapuu M, Enerback S, Carlsson P, 2001. Haploinsufficiency of the forkhead gene Foxf1, a target for sonic hedgehog signaling, causes lung and foregut malformations. Development 128, 2397–2406. [DOI] [PubMed] [Google Scholar]
  75. Mai S, Wei K, Flenniken A, Adamson SL, Rossant J, Aubin JE, Gong SG, 2010. The missense mutation W290R in Fgfr2 causes developmental defects from aberrant IIIb and IIIc signaling. Dev Dyn 239, 1888–1900. [DOI] [PubMed] [Google Scholar]
  76. Mao H, Pilaz LJ, McMahon JJ, Golzio C, Wu D, Shi L, Katsanis N, Silver DL, 2015. Rbm8a haploinsufficiency disrupts embryonic cortical development resulting in microcephaly. J Neurosci 35, 7003–7018. [DOI] [PMC free article] [PubMed] [Google Scholar]
  77. Marsh AJ, Wellesley D, Burge D, Ashton M, Browne C, Dennis NR, Temple K, 2000. Interstitial deletion of chromosome 17 (del(17)(q22q23.3)) confirms a link with oesophageal atresia. J Med Genet 37, 701–704. [DOI] [PMC free article] [PubMed] [Google Scholar]
  78. Martin E, Enriquez A, Sparrow DB, Humphreys DT, McInerney-Leo AM, Leo PJ, Duncan EL, Iyer KR, Greasby JA, Ip E, Giannoulatou E, Sheng D, Wohler E, Dimartino C, Amiel J, Capri Y, Lehalle D, Mory A, Wilnai Y, Lebenthal Y, Gharavi AG, Krzemień GG, Miklaszewska M, Steiner RD, Raggio C, Blank R, Baris Feldman H, Milo Rasouly H, Sobreira NLM, Jobling R, Gordon CT, Giampietro PF, Dunwoodie SL, Chapman G, 2020. Heterozygous loss of WBP11 function causes multiple congenital defects in humans and mice. Hum Mol Genet 29, 3662–3678. [DOI] [PMC free article] [PubMed] [Google Scholar]
  79. McCauley H, Matthis A, Enriquez J, Nichol J, Sanchez JG, Stone W, Sundaram N, Helmrath M, Montrose M, Aihara E, Wells J, 2020. Enteroendocrine cells couple nutrient sensing to nutrient absorption by regulating ion transport. Nature Communications, 1––10. [DOI] [PMC free article] [PubMed] [Google Scholar]
  80. McCauley HA, Wells JM, 2017. Pluripotent stem cell-derived organoids: Using principles of developmental biology to grow human tissues in a dish. Development (Cambridge) 144, 958––962. [DOI] [PMC free article] [PubMed] [Google Scholar]
  81. McCauley KB, Hawkins F, Serra M, Thomas DC, Jacob A, Kotton DN, 2017. Efficient Derivation of Functional Human Airway Epithelium from Pluripotent Stem Cells via Temporal Regulation of Wnt Signaling. Cell Stem Cell 20, 844––857.e846. [DOI] [PMC free article] [PubMed] [Google Scholar]
  82. Mendelsohn C, Lohnes D, Décimo D, Lufkin T, LeMeur M, Chambon P, Mark M, 1994. Function of the retinoic acid receptors (RARs) during development (II). Multiple abnormalities at various stages of organogenesis in RAR double mutants. Development 120, 2749–2771. [DOI] [PubMed] [Google Scholar]
  83. Mill P, Lockhart PJ, Fitzpatrick E, Mountford HS, Hall EA, Reijns MA, Keighren M, Bahlo M, Bromhead CJ, Budd P, Aftimos S, Delatycki MB, Savarirayan R, Jackson IJ, Amor DJ, 2011. Human and mouse mutations in WDR35 cause short-rib polydactyly syndromes due to abnormal ciliogenesis. Am J Hum Genet 88, 508–515. [DOI] [PMC free article] [PubMed] [Google Scholar]
  84. Miller AJ, Dye BR, Ferrer-Torres D, Hill DR, Overeem AW, Shea LD, Spence JR, 2019. Generation of lung organoids from human pluripotent stem cells in vitro. Nat Protoc 14, 518–540. [DOI] [PMC free article] [PubMed] [Google Scholar]
  85. Minoo P, Su G, Drum H, Bringas P, Kimura S, 1999. Defects in tracheoesophageal and lung morphogenesis in Nkx2.1(−/−) mouse embryos. Dev Biol 209, 60–71. [DOI] [PubMed] [Google Scholar]
  86. Mirra V, Maglione M, Di Micco LL, Montella S, Santamaria F, 2017. Longitudinal Follow-up of Chronic Pulmonary Manifestations in Esophageal Atresia: A Clinical Algorithm and Review of the Literature. Pediatr Neonatol 58, 8–15. [DOI] [PubMed] [Google Scholar]
  87. Moens CB, Auerbach AB, Conlon RA, Joyner AL, Rossant J, 1992. A targeted mutation reveals a role for N-myc in branching morphogenesis in the embryonic mouse lung. Genes Dev 6, 691–704. [DOI] [PubMed] [Google Scholar]
  88. Murphy AJ, Li Y, Pietsch JB, Chiang C, Lovvorn HN 3rd, 2012. Mutational analysis of NOG in esophageal atresia and tracheoesophageal fistula patients. Pediatr Surg Int 28, 335–340. [DOI] [PMC free article] [PubMed] [Google Scholar]
  89. Nam KT, Lee HJ, Smith JJ, Lapierre LA, Kamath VP, Chen X, Aronow BJ, Yeatman TJ, Bhartur SG, Calhoun BC, Condie B, Manley NR, Beauchamp RD, Coffey RJ, Goldenring JR, 2010. Loss of Rab25 promotes the development of intestinal neoplasia in mice and is associated with human colorectal adenocarcinomas. J Clin Invest 120, 840–849. [DOI] [PMC free article] [PubMed] [Google Scholar]
  90. Nasr T, Holderbaum AM, Chaturvedi P, Agarwal K, Kinney JL, Daniels K, Trisno SL, Ustiyan V, Shannon JM, Wells JM, Sinner D, Kalinichenko VV, Zorn AM, 2020. Disruption of a hedgehog-foxf1-rspo2 signaling axis leads to tracheomalacia and a loss of sox9+ tracheal chondrocytes. Dis Model Mech. [DOI] [PMC free article] [PubMed] [Google Scholar]
  91. Nasr T, Mancini P, Rankin SA, Edwards NA, Agricola ZN, Kenny AP, Kinney JL, Daniels K, Vardanyan J, Han L, Trisno SL, Cha SW, Wells JM, Kofron MJ, Zorn AM, 2019. Endosome-Mediated Epithelial Remodeling Downstream of Hedgehog-Gli Is Required for Tracheoesophageal Separation. Dev Cell 51, 665–674 e666. [DOI] [PMC free article] [PubMed] [Google Scholar]
  92. Nassar N, Leoncini E, Amar E, Arteaga-Vazquez J, Bakker MK, Bower C, Canfield MA, Castilla EE, Cocchi G, Correa A, Csaky-Szunyogh M, Feldkamp ML, Khoshnood B, Landau D, Lelong N, Lopez-Camelo JS, Lowry RB, McDonnell R, Merlob P, Metneki J, Morgan M, Mutchinick OM, Palmer MN, Rissmann A, Siffel C, Sipek A, Szabova E, Tucker D, Mastroiacovo P, 2012. Prevalence of esophageal atresia among 18 international birth defects surveillance programs. Birth Defects Res A Clin Mol Teratol 94, 893–899. [DOI] [PMC free article] [PubMed] [Google Scholar]
  93. Need AC, Shashi V, Hitomi Y, Schoch K, Shianna KV, McDonald MT, Meisler MH, Goldstein DB, 2012. Clinical application of exome sequencing in undiagnosed genetic conditions. J Med Genet 49, 353–361. [DOI] [PMC free article] [PubMed] [Google Scholar]
  94. Niethamer TK, Bush JO, 2019. Getting direction(s): The Eph/ephrin signaling system in cell positioning. Dev Biol 447, 42–57. [DOI] [PMC free article] [PubMed] [Google Scholar]
  95. Nixon KCJ, Rousseau J, Stone MH, Sarikahya M, Ehresmann S, Mizuno S, Matsumoto N, Miyake N, Baralle D, McKee S, Izumi K, Ritter AL, Heide S, Héron D, Depienne C, Titheradge H, Kramer JM, Campeau PM, 2019. A Syndromic Neurodevelopmental Disorder Caused by Mutations in SMARCD1, a Core SWI/SNF Subunit Needed for Context-Dependent Neuronal Gene Regulation in Flies. Am J Hum Genet 104, 596–610. [DOI] [PMC free article] [PubMed] [Google Scholar]
  96. Nolan HR, Gurria J, Peiro JL, Tabbah S, Diaz-Primera R, Polzin W, Habli M, Lim F-Y, 2019. Congenital high airway obstruction syndrome (CHAOS): Natural history, prenatal management strategies, and outcomes at a single comprehensive fetal center. Journal of Pediatric Surgery 54, 1153–1158. [DOI] [PubMed] [Google Scholar]
  97. Ondrey F, Griffith A, Van Waes C, Rudy S, Peters K, McCullagh L, Biesecker LG, 2000. Asymptomatic laryngeal malformations are common in patients with Pallister-Hall syndrome. Am J Med Genet 94, 64–67. [DOI] [PubMed] [Google Scholar]
  98. Pecho-Vrieseling E, Sigrist M, Yoshida Y, Jessell TM, Arber S, 2009. Specificity of sensory-motor connections encoded by Sema3e-Plxnd1 recognition. Nature 459, 842–846. [DOI] [PMC free article] [PubMed] [Google Scholar]
  99. Perri A, Patti ML, Sbordone A, Vento G, Luciano R, 2020. Unexpected tracheal agenesis with prenatal diagnosis of aortic coarctation, lung hyperecogenicity and polyhydramnios: a case report. Ital J Pediatr 46, 96. [DOI] [PMC free article] [PubMed] [Google Scholar]
  100. Pinzon-Guzman C, Sangadala S, Riera KM, Popova EY, Manning E, Huh WJ, Alexander MS, Shelton JS, Boden SD, Goldenring JR, 2020. Noggin regulates foregut progenitor cell programming, and misexpression leads to esophageal atresia. J Clin Invest 130, 4396–4410. [DOI] [PMC free article] [PubMed] [Google Scholar]
  101. Poore TS, Weinman JP, Handley E, Wine T, Helland S, Corbett B, Antoniolli N, Somme S, Friedlander J, Prager JD, DeBoer EM, 2020. Vascular and pulmonary comorbidities in children with congenital EA/TEF. Pediatr Pulmonol. [DOI] [PubMed] [Google Scholar]
  102. Prakash SK, Cormier TA, McCall AE, Garcia JJ, Sierra R, Haupt B, Zoghbi HY, Van Den Veyver IB, 2002. Loss of holocytochrome c-type synthetase causes the male lethality of X-linked dominant microphthalmia with linear skin defects (MLS) syndrome. Hum Mol Genet 11, 3237–3248. [DOI] [PubMed] [Google Scholar]
  103. Purandare SM, Ware SM, Kwan KM, Gebbia M, Bassi MT, Deng JM, Vogel H, Behringer RR, Belmont JW, Casey B, 2002. A complex syndrome of left-right axis, central nervous system and axial skeleton defects in Zic3 mutant mice. Development 129, 2293–2302. [DOI] [PubMed] [Google Scholar]
  104. Quaderi NA, Schweiger S, Gaudenz K, Franco B, Rugarli EI, Berger W, Feldman GJ, Volta M, Andolfi G, Gilgenkrantz S, Marion RW, Hennekam RC, Opitz JM, Muenke M, Ropers HH, Ballabio A, 1997. Opitz G/BBB syndrome, a defect of midline development, is due to mutations in a new RING finger gene on Xp22. Nat Genet 17, 285–291. [DOI] [PubMed] [Google Scholar]
  105. Que J, 2015. The initial establishment and epithelial morphogenesis of the esophagus: a new model of tracheal-esophageal separation and transition of simple columnar into stratified squamous epithelium in the developing esophagus. Wiley Interdisciplinary Reviews: Developmental Biology 4, 419––430. [DOI] [PMC free article] [PubMed] [Google Scholar]
  106. Que J, Luo X, Schwartz RJ, Hogan BL, 2009. Multiple roles for Sox2 in the developing and adult mouse trachea. Development 136, 1899–1907. [DOI] [PMC free article] [PubMed] [Google Scholar]
  107. Que J, Okubo T, Goldenring JR, Nam KT, Kurotani R, Morrisey EE, Taranova O, Pevny LH, Hogan BL, 2007. Multiple dose-dependent roles for Sox2 in the patterning and differentiation of anterior foregut endoderm. Development 134, 2521–2531. [DOI] [PMC free article] [PubMed] [Google Scholar]
  108. Raad S, David A, Que J, Faure C, 2020. Genetic Mouse Models and Induced Pluripotent Stem Cells for Studying Tracheal-Esophageal Separation and Esophageal Development. Stem Cells and Development 29, 953–966. [DOI] [PMC free article] [PubMed] [Google Scholar]
  109. Rankin SA, Han L, McCracken KW, Kenny AP, Anglin CT, Grigg EA, Crawford CM, Wells JM, Shannon JM, Zorn AM, 2016. A Retinoic Acid-Hedgehog Cascade Coordinates Mesoderm-Inducing Signals and Endoderm Competence during Lung Specification. Cell Rep 16, 66–78. [DOI] [PMC free article] [PubMed] [Google Scholar]
  110. Rosenbluh J, Nijhawan D, Chen Z, Wong KK, Masutomi K, Hahn WC, 2011. RMRP is a non-coding RNA essential for early murine development. PLoS One 6, e26270. [DOI] [PMC free article] [PubMed] [Google Scholar]
  111. Saisawat P, Kohl S, Hilger AC, Hwang DY, Yung Gee H, Dworschak GC, Tasic V, Pennimpede T, Natarajan S, Sperry E, Matassa DS, Stajić N, Bogdanovic R, de Blaauw I, Marcelis CL, Wijers CH, Bartels E, Schmiedeke E, Schmidt D, Märzheuser S, Grasshoff-Derr S, Holland-Cunz S, Ludwig M, Nöthen MM, Draaken M, Brosens E, Heij H, Tibboel D, Herrmann BG, Solomon BD, de Klein A, van Rooij IA, Esposito F, Reutter HM, Hildebrandt F, 2014. Whole-exome resequencing reveals recessive mutations in TRAP1 in individuals with CAKUT and VACTERL association. Kidney Int 85, 1310–1317. [DOI] [PMC free article] [PubMed] [Google Scholar]
  112. Schulz AC, Bartels E, Stressig R, Ritgen J, Schmiedeke E, Mattheisen M, Draaken M, Ludwig M, Bagci S, Muller A, Gembruch U, Geipel A, Berg C, Heydweiller A, Bachour H, Schumacher J, Bartmann P, Nothen MM, Reutter H, 2012. Nine new twin pairs with esophageal atresia: a review of the literature and performance of a twin study of the disorder. Birth Defects Res A Clin Mol Teratol 94, 182–186. [DOI] [PubMed] [Google Scholar]
  113. Scott DA, 2018. Esophageal Atresia / Tracheoesophageal Fistula Overview. BTI - GeneReviews(®). [PubMed]
  114. Settle SH Jr., Rountree RB, Sinha A, Thacker A, Higgins K, Kingsley DM, 2003. Multiple joint and skeletal patterning defects caused by single and double mutations in the mouse Gdf6 and Gdf5 genes. Dev Biol 254, 116–130. [DOI] [PubMed] [Google Scholar]
  115. Shacham-Silverberg V, Wells JM, 2020. Generation of esophageal organoids and organotypic raft cultures from human pluripotent stem cells. Methods Cell Biol 159, 1–22. [DOI] [PMC free article] [PubMed] [Google Scholar]
  116. Shefchek KA, Harris NL, Gargano M, Matentzoglu N, Unni D, Brush M, Keith D, Conlin T, Vasilevsky N, Zhang XA, Balhoff JP, Babb L, Bello SM, Blau H, Bradford Y, Carbon S, Carmody L, Chan LE, Cipriani V, Cuzick A, Della Rocca M, Dunn N, Essaid S, Fey P, Grove C, Gourdine JP, Hamosh A, Harris M, Helbig I, Hoatlin M, Joachimiak M, Jupp S, Lett KB, Lewis SE, McNamara C, Pendlington ZM, Pilgrim C, Putman T, Ravanmehr V, Reese J, Riggs E, Robb S, Roncaglia P, Seager J, Segerdell E, Similuk M, Storm AL, Thaxon C, Thessen A, Jacobsen JOB, McMurry JA, Groza T, Köhler S, Smedley D, Robinson PN, Mungall CJ, Haendel MA, Munoz-Torres MC, Osumi-Sutherland D, 2020. The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res 48, D704–d715. [DOI] [PMC free article] [PubMed] [Google Scholar]
  117. Smith MM, Huang A, Labbé M, Lubov J, Nguyen LHP, 2017. Clinical presentation and airway management of tracheal atresia: A systematic review. International Journal of Pediatric Otorhinolaryngology 101, 57–64. [DOI] [PubMed] [Google Scholar]
  118. Solomon BD, Pineda-Alvarez DE, Hadley DW, Keaton AA, Agochukwu NB, Raam MS, Carlson-Donohoe HE, Kamat A, Chandrasekharappa SC, 2011. De novo deletion of chromosome 20q13.33 in a patient with tracheo-esophageal fistula, cardiac defects and genitourinary anomalies implicates GTPBP5 as a candidate gene. Birth Defects Res A Clin Mol Teratol 91, 862–865. [DOI] [PMC free article] [PubMed] [Google Scholar]
  119. Stankiewicz P, Sen P, Bhatt SS, Storer M, Xia Z, Bejjani BA, Ou Z, Wiszniewska J, Driscoll DJ, Maisenbacher MK, Bolivar J, Bauer M, Zackai EH, McDonald-McGinn D, Nowaczyk MM, Murray M, Hustead V, Mascotti K, Schultz R, Hallam L, McRae D, Nicholson AG, Newbury R, Durham-O’Donnell J, Knight G, Kini U, Shaikh TH, Martin V, Tyreman M, Simonic I, Willatt L, Paterson J, Mehta S, Rajan D, Fitzgerald T, Gribble S, Prigmore E, Patel A, Shaffer LG, Carter NP, Cheung SW, Langston C, Shaw-Smith C, 2009. Genomic and genic deletions of the FOX gene cluster on 16q24.1 and inactivating mutations of FOXF1 cause alveolar capillary dysplasia and other malformations. Am J Hum Genet 84, 780–791. [DOI] [PMC free article] [PubMed] [Google Scholar]
  120. Stanton BR, Perkins AS, Tessarollo L, Sassoon DA, Parada LF, 1992. Loss of N-myc function results in embryonic lethality and failure of the epithelial component of the embryo to develop. Genes Dev 6, 2235–2247. [DOI] [PubMed] [Google Scholar]
  121. Steimle JD, Rankin SA, Slagle CE, Bekeny J, Rydeen AB, Chan SS, Kweon J, Yang XH, Ikegami K, Nadadur RD, Rowton M, Hoffmann AD, Lazarevic S, Thomas W, Boyle Anderson EAT, Horb ME, Luna-Zurita L, Ho RK, Kyba M, Jensen B, Zorn AM, Conlon FL, Moskowitz IP, 2018. Evolutionarily conserved Tbx5-Wnt2/2b pathway orchestrates cardiopulmonary development. Proc Natl Acad Sci U S A 115, E10615–E10624. [DOI] [PMC free article] [PubMed] [Google Scholar]
  122. Stoll C, Alembik Y, Dott B, Roth MP, 2017. Associated anomalies in cases with esophageal atresia. Am J Med Genet A 173, 2139–2157. [DOI] [PubMed] [Google Scholar]
  123. Sui P, Li R, Zhang Y, Tan C, Garg A, Verheyden JM, Sun X, 2019. E3 ubiquitin ligase MDM2 acts through p53 to control respiratory progenitor cell number and lung size. Development 146. [DOI] [PMC free article] [PubMed] [Google Scholar]
  124. Sutphen R, Galan-Gomez E, Cortada X, Newkirk PN, Kousseff BG, 1995. Tracheoesophageal anomalies in oculoauriculovertebral (Goldenhar) spectrum. Clin Genet 48, 66–71. [DOI] [PubMed] [Google Scholar]
  125. Szumska D, Pieles G, Essalmani R, Bilski M, Mesnard D, Kaur K, Franklyn A, El Omari K, Jefferis J, Bentham J, Taylor JM, Schneider JE, Arnold SJ, Johnson P, Tymowska-Lalanne Z, Stammers D, Clarke K, Neubauer S, Morris A, Brown SD, Shaw-Smith C, Cama A, Capra V, Ragoussis J, Constam D, Seidah NG, Prat A, Bhattacharya S, 2008. VACTERL/caudal regression/Currarino syndrome-like malformations in mice with mutation in the proprotein convertase Pcsk5. Genes Dev 22, 1465–1477. [DOI] [PMC free article] [PubMed] [Google Scholar]
  126. Trisno SL, Philo KED, McCracken KW, Cata EM, Ruiz-Torres S, Rankin SA, Han L, Nasr T, Chaturvedi P, Rothenberg ME, Mandegar MA, Wells SI, Zorn AM, Wells JM, 2018. Esophageal Organoids from Human Pluripotent Stem Cells Delineate Sox2 Functions during Esophageal Specification. Cell Stem Cell 23, 501–515 e507. [DOI] [PMC free article] [PubMed] [Google Scholar]
  127. van Lennep M, Singendonk MMJ, Dall’Oglio L, Gottrand F, Krishnan U, Terheggen-Lagro SWJ, Omari TI, Benninga MA, van Wijk MP, 2019. Oesophageal atresia. Nat Rev Dis Primers 5, 26. [DOI] [PubMed] [Google Scholar]
  128. Vissers LE, van Ravenswaaij CM, Admiraal R, Hurst JA, de Vries BB, Janssen IM, van der Vliet WA, Huys EH, de Jong PJ, Hamel BC, Schoenmakers EF, Brunner HG, Veltman JA, van Kessel AG, 2004. Mutations in a new member of the chromodomain gene family cause CHARGE syndrome. Nat Genet 36, 955–957. [DOI] [PubMed] [Google Scholar]
  129. Walsh LE, Vance GH, Weaver DD, 2001. Distal 13q Deletion Syndrome and the VACTERL association: case report, literature review, and possible implications. Am J Med Genet 98, 137–144. [DOI] [PubMed] [Google Scholar]
  130. Wang J, Ahimaz PR, Hashemifar S, Khlevner J, Picoraro JA, Middlesworth W, Elfiky MM, Que J, Shen Y, Chung WK, 2021. Novel candidate genes in esophageal atresia/tracheoesophageal fistula identified by exome sequencing. Eur J Hum Genet 29, 122–130. [DOI] [PMC free article] [PubMed] [Google Scholar]
  131. Wang R, McCauley KB, Kotton DN, Hawkins F, 2020. Differentiation of human airway-organoids from induced pluripotent stem cells (iPSCs), 1 ed. Elsevier Inc. [DOI] [PubMed] [Google Scholar]
  132. Wessels MW, Kuchinka B, Heydanus R, Smit BJ, Dooijes D, de Krijger RR, Lequin MH, de Jong EM, Husen M, Willems PJ, Casey B, 2010. Polyalanine expansion in the ZIC3 gene leading to X-linked heterotaxy with VACTERL association: a new polyalanine disorder? J Med Genet 47, 351–355. [DOI] [PubMed] [Google Scholar]
  133. Wilkie AO, Slaney SF, Oldridge M, Poole MD, Ashworth GJ, Hockley AD, Hayward RD, David DJ, Pulleyn LJ, Rutland P, et al. , 1995. Apert syndrome results from localized mutations of FGFR2 and is allelic with Crouzon syndrome. Nat Genet 9, 165–172. [DOI] [PubMed] [Google Scholar]
  134. Williamson KA, Hever AM, Rainger J, Rogers RC, Magee A, Fiedler Z, Keng WT, Sharkey FH, McGill N, Hill CJ, Schneider A, Messina M, Turnpenny PD, Fantes JA, van Heyningen V, FitzPatrick DR, 2006. Mutations in SOX2 cause anophthalmia-esophageal-genital (AEG) syndrome. Hum Mol Genet 15, 1413–1422. [DOI] [PubMed] [Google Scholar]
  135. Wilson NR, Olm-Shipman AJ, Acevedo DS, Palaniyandi K, Hall EG, Kosa E, Stumpff KM, Smith GJ, Pitstick L, Liao EC, Bjork BC, Czirok A, Saadi I, 2016. SPECC1L deficiency results in increased adherens junction stability and reduced cranial neural crest cell delamination. Sci Rep 6, 17735. [DOI] [PMC free article] [PubMed] [Google Scholar]
  136. Woo J, Miletich I, Kim BM, Sharpe PT, Shivdasani RA, 2011. Barx1-mediated inhibition of Wnt signaling in the mouse thoracic foregut controls tracheo-esophageal septation and epithelial differentiation. PLoS One 6, e22493. [DOI] [PMC free article] [PubMed] [Google Scholar]
  137. Workman MJ, Mahe MM, Trisno S, Poling HM, Watson CL, Sundaram N, Chang CF, Schiesser J, Aubert P, Stanley EG, Elefanty AG, Miyaoka Y, Mandegar MA, Conklin BR, Neunlist M, Brugmann SA, Helmrath MA, Wells JM, 2017. Engineered human pluripotent-stem-cell-derived intestinal tissues with a functional enteric nervous system. Nature Medicine 23, 49––59. [DOI] [PMC free article] [PubMed] [Google Scholar]
  138. Ya J, Schilham MW, de Boer PA, Moorman AF, Clevers H, Lamers WH, 1998. Sox4-deficiency syndrome in mice is an animal model for common trunk. Circ Res 83, 986–994. [DOI] [PubMed] [Google Scholar]
  139. Yang L, Shen C, Mei M, Zhan G, Zhao Y, Wang H, Huang G, Qiu Z, Lu W, Zhou W, 2014. De novo GLI3 mutation in esophageal atresia: reproducing the phenotypic spectrum of Gli3 defects in murine models. Biochim Biophys Acta 1842, 1755–1761. [DOI] [PubMed] [Google Scholar]
  140. Zhang R, Gehlen J, Kawalia A, Melissari MT, Dakal TC, Menon AM, Hofele J, Riedhammer K, Waffenschmidt L, Fabian J, Breuer K, Kalanithy J, Hilger AC, Sharma A, Holscher A, Boemers TM, Pauly M, Leutner A, Fuchs J, Seitz G, Ludwikowski BM, Gomez B, Hubertus J, Heydweiller A, Kurz R, Leonhardt J, Kosch F, Holland-Cunz S, Munsterer O, Ure B, Schmiedeke E, Neser J, Degenhardt P, Marzheuser S, Kleine K, Schafer M, Spychalski N, Deffaa OJ, Gosemann JH, Lacher M, Heilmann-Heimbach S, Zwink N, Jenetzky E, Ludwig M, Grote P, Schumacher J, Thiele H, Reutter H, 2020. Human exome and mouse embryonic expression data implicate ZFHX3, TRPS1, and CHD7 in human esophageal atresia. PLoS One 15, e0234246. [DOI] [PMC free article] [PubMed] [Google Scholar]
  141. Zhang X, McGrath PS, Salomone J, Rahal M, McCauley HA, Schweitzer J, Kovall R, Gebelein B, Wells JM, 2019. A Comprehensive Structure-Function Study of Neurogenin3 Disease-Causing Alleles during Human Pancreas and Intestinal Organoid Development. Developmental Cell 50, 367––380.e367. [DOI] [PMC free article] [PubMed] [Google Scholar]
  142. Zhang Y, Jiang M, Kim E, Lin S, Liu K, Lan X, Que J, 2017. Development and stem cells of the esophagus. Semin Cell Dev Biol 66, 25–35. [DOI] [PMC free article] [PubMed] [Google Scholar]
  143. Zhang Y, Yang Y, Jiang M, Huang SX, Zhang W, Al Alam D, Danopoulos S, Mori M, Chen YW, Balasubramanian R, Chuva de Sousa Lopes SM, Serra C, Bialecka M, Kim E, Lin S, Toste de Carvalho ALR, Riccio PN, Cardoso WV, Zhang X, Snoeck HW, Que J, 2018. 3D Modeling of Esophageal Development using Human PSC-Derived Basal Progenitors Reveals a Critical Role for Notch Signaling. Cell Stem Cell 23, 516–529 e515. [DOI] [PMC free article] [PubMed] [Google Scholar]
  144. Zhu L, Zhou G, Poole S, Belmont JW, 2008. Characterization of the interactions of human ZIC3 mutants with GLI3. Hum Mutat 29, 99–105. [DOI] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

1

Supplementary Table 1 – Copy number variants (CNVs) associated with human TEDs.

RESOURCES