Researching the cause and treatment of trachea-esophageal birth defects


Contact us at
info@clearconsortium.org

Research Projects

The CLEAR Consortium is a collaborative program (P01 HD093363) funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development investigating the genetic and developmental basis of trachea-esophageal birth defects.

The causes of trachea-esophageal birth defects (TEDs) and related complex upper airway malformations, which occur in approximately 1 in 3000 births, are poorly understood. Although there is compelling evidence for a major genetic component, causative mutations are only known in 12% of cases worldwide. Even for the few cases where the genes involved have been identified, such as the Hedgehog (HH) and BMP signaling pathway genes, how these regulate fetal trachea-esophageal morphogenesis, and hence the structural basis of trachea-esophageal birth defects, is unclear.  The basic developmental and cellular processed controlling morphogenesis of the esophagus and trachea from the fetal foregut in humans or in animal models are largely unknown. Our poor understanding of the genetic and developmental etiology of trachea-esophageal defects is a major impediment in our ability to accurately and effectively diagnose and manage these congenital conditions.

We aim to discover additional causative mutations (genotype) resulting in trachea-esophageal defects (phenotype), and to understand the underlying mechanisms of trachea and esophageal development. To achieve this our research program uses 1) anatomical and genetic observations from human patients, 2) animal models to study normal trachea-esophageal development and model disease, and 3) stem cell-derived organoids to model how genetic mutations cause trachea-esophageal defects.

This is a multi-leadership program centered at Cincinnati Children’s Hospital Medical Center (CCHMC) and Columbia University Medical Center. The co-leaders are: Aaron M. Zorn (CCHMC), Paul Kingma (CCHMC), Wendy Chung (Columbia), and James M. Wells (CCHMC).

 

Project 1: Anatomical and genetic assessment of tracheoesophageal defects in patients

Lead investigators: Paul Kingma (CCHMC) and Wendy Chung (Columbia)
Co-investigators: Jason Woods, Jean Tkach, Peter White, Foong-Yen Lim, Robert Fleck (CCHMC)

Photo by Iaremenko/iStock / Getty Images

This collaborative project combines novel MRI techniques and genetic sequencing to provide a comprehensive phenotype-genotype assessment of TED patients. 

  • Perform genomic sequencing of trios using whole exome sequencing to identify candidate causative mutations. Genes with a high probability of causing TEDs will be compared to anatomic findings to determine genotype-phenotype associations.

  • Characterize the trachea-esophageal anatomy in trachea-esophageal defect patients before and after surgical repair. This will help determine if pre-repair anatomy can predict and improve surgical outcomes.

  • Create the first North American multi-center registry of phenotype-genotype clinical data from TED patients. The registry will integrate clinical and anatomical phenotype, genotype, surgical repair strategy, and long-term clinical outcome in TED patients.

 

Project 2: Modeling trachea-esophageal birth defects in animals

Lead investigator: Aaron Zorn (CCHMC)
Co-investigators: James Wells, Debora Sinner (CCHMC), Sang-Wook Cha (University of Central Missouri)

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This project uses an innovative combination of frog (Xenopus) and mouse models to define the genetic and cellular mechanisms of TE development.

  • Characterize the molecular and cellular mechanisms of trachea-esophageal development in Xenopus and mouse. Though several models have been proposed, the cellular processes controlling trachea-esophageal morphogenesis are unknown.

  • To determine the cellular processes regulated by developmental cell signaling pathways. Disruption of key pathway genes can cause TEDs in humans, mouse, and Xenopus, but the cellular basis of these phenotypes are not known.

  • To model trachea-esophageal defect-causing mutations from TED patients in Xenopus and mouse. Genes with unknown function in trachea-esophageal development and genetic variants from TED patients can be tested using animal models.

 

Project 3: Modeling tracheoesophageal defects in human pluripotent stem cell-derived embryonic tissues

Lead investigator: James Wells (CCHMC)
Co-investigators: Michael Helmrath, Aaron Zorn, Christopher Mayhew (CCHMC)

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This project uses a novel pluripotent stem cell-derived human organoid system to investigate the molecular basis of human esophageal and respiratory development. The project will further examine how mutations in an important transcriptional regulator of early esophageal specification, SOX2, cause TED.

  • Identify SOX2 gene regulatory networks mediating the development of human esophageal and respiratory lineages in collaboration with animal models of TEDs.

  • Using CRISPR-Cas-9 mediated gene editing of human pluripotent stem cells, investigate how SOX2 mutations cause human esophageal atresia (EA). This will inform anatomical and genetic assessments of TED patients.

  • Using patient-derived esophageal organdies to model esophageal atresia defects in vitro.

CLEAR Consortium Publications

Identification and validation of candidate risk genes in endocytic vesicular trafficking associated with esophageal atresia and tracheoesophageal fistulas.
Zhong G, Ahimaz P, Edwards NA, Hagen JJ, Faure C, Lu Q, Kingma P, Middlesworth W, Khlevner J, El Fiky M, Schindel D, Fialkowski E, Kashyap A, Forlenza S, Kenny AP, Zorn AM, Shen Y, Chung WK. HGG Adv. 2022 Apr 16;3(3):100107. doi: 10.1016/j.xhgg.2022.100107. eCollection 2022 Jul 14. PMID: 35519826

Functional human gastrointestinal organoids can be engineered from three primary germ layers derived separately from pluripotent stem cells.
Eicher AK, Kechele DO, Sundaram N, Berns HM, Poling HM, Haines LE, Sanchez JG, Kishimoto K, Krishnamurthy M, Han L, Zorn AM, Helmrath MA, Wells JM. Cell Stem Cell. 2022 Jan 6;29(1):36-51.e6. doi: 10.1016/j.stem.2021.10.010. Epub 2021 Dec 1. PMID:34856121

Novel candidate genes in esophageal atresia/tracheoesophageal fistula identified by exome sequencing.
Wang J, Ahimaz PR, Hashemifar S, Khlevner J, Picoraro JA, Middlesworth W, Elfiky MM, Que J, Shen Y, Chung WK. Eur J Hum Genet. 2021 Jan;29(1):122-130. doi: 10.1038/s41431-020-0680-2. Epub 2020 Jul 8.PMID: 32641753

Disruption of a hedgehog-foxf1-rspo2 signaling axis leads to tracheomalacia and a loss of sox9+ tracheal chondrocytes. 
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. Dis Model Mech. 2020 Dec 16;. doi: 10.1242/dmm.046573. [Epub ahead of print] PubMed PMID: 33328171

Maximizing CRISPR/Cas9 phenotype penetrance applying predictive modeling of editing outcomes in Xenopus and zebrafish embryos.
Naert T, Tulkens D, Edwards NA, Carron M, Shaidani NI, Wlizla M, Boel A, Demuynck S, Horb ME, Coucke P, Willaert A, Zorn AM, Vleminckx K. Sci Rep. 2020 Sep 4;10(1):14662. doi: 10.1038/s41598-020-71412-0.PMID: 32887910

Single cell transcriptomics identifies a signaling network coordinating endoderm and mesoderm diversification during foregut organogenesis.
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. Nat Commun. 2020 Aug 27;11(1):4158. doi: 10.1038/s41467-020-17968-x.PMID: 32855417 

Bidirectional Wnt signaling between endoderm and mesoderm confers tracheal identity in mouse and human cells.
Kishimoto K, Furukawa KT, Luz-Madrigal A, Yamaoka A, Matsuoka C, Habu M, Alev C, Zorn AM, Morimoto M.Nat Commun. 2020 Aug 27;11(1):4159. doi: 10.1038/s41467-020-17969-w. PMID: 32855415 

Ultrashort Echo-Time MRI for the Assessment of Tracheomalacia in Neonates.
Hysinger EB, Bates AJ, Higano NS, Benscoter D, Fleck RJ, Hart CK, Burg G, De Alarcon A, Kingma PS, Woods JC. Chest. 2020 Mar;157(3):595-602. doi: 10.1016/j.chest.2019.11.034. Epub 2019 Dec 17. PMID: 31862439

Recent advances in deriving human endodermal tissues from pluripotent stem cells.
Kechele DO, Wells JM. Curr Opin Cell Biol. 2019 Dec;61:92-100. doi: 10.1016/j.ceb.2019.07.009. Epub 2019 Aug 16. PMID: 31425933 Review

Organoids by design.
Takebe T, Wells JM. Science. 2019 Jun 7;364(6444):956-959. doi: 10.1126/science.aaw7567. PMID: 31171692

Quantitative Assessment of Regional Dynamic Airway Collapse in Neonates via Retrospectively Respiratory-Gated Ultrashort Echo Time MRI.
Bates AJ, Higano NS, Hysinger EB, Fleck RJ, Hahn AD, Fain SB, Kingma PS, Woods JC. 
Journal of Magnetic Resonance Imaging: JMRI. 2019 March;49(3):659-667. PubMed PMID: 30252988; PubMed Central PMCID: PMC6375762.

Evolutionarily conserved Tbx5-Wnt2/2b pathway orchestrates cardiopulmonary development.
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.Proc Natl Acad Sci U S A. 2018 Nov 6;115(45):E10615-E10624. doi: 10.1073/pnas.1811624115. Epub 2018 Oct 23. PMID: 30352852

FOXF1 transcription factor promotes lung morphogenesis by inducing cellular proliferation in fetal lung mesenchyme. Developmental biology.
Ustiyan V, Bolte C, Zhang Y, Han L, Xu Y, Yutzey KE, Zorn AM, Kalin TV, Shannon JM, Kalinichenko VV.
Developmental Biology. 2018 November 1;443(1):50-63. PubMed PMID: 30153454; PubMed Central PMCID: PMC6191344.

Esophageal Organoids from Human Pluripotent Stem Cells Delineate Sox2 Functions during Esophageal Specification.
Trisno SL, Philo KED, McCracken KW, Catá EM, Ruiz-Torres S, Rankin SA, Han L, Nasr T, Chaturvedi P, Rothenberg ME, Mandegar MA, Wells SI, Zorn AM, Wells JM. Cell Stem Cell. 2018 Oct 4;23(4):501-515

Timing is everything: Reiterative Wnt, BMP and RA signaling regulate developmental competence during endoderm organogenesis.
Rankin SA, McCracken KW, Luedeke DM, Han L, Wells JM, Shannon JM, Zorn AM. Dev Biol. 2018 Feb 1;434(1):121-132. doi: 10.1016/j.ydbio.2017.11.018. Epub 2017 Dec 5. PMID: 29217200

Pre- and post-operative visualization of neonatal esophageal atresia/tracheoesophageal fistula via magnetic resonance imaging.
Higano NS, Bates AJ, Tkach JA, Fleck RJ, Lim FY, Woods JC, Kingma PS.
J Pediatr Surg Case Rep. 2018 Feb;29:5-8. doi: 10.1016/j.epsc.2017.10.001. Epub 2017 Oct 3. PMID: 29399473.

A Retinoic Acid-Hedgehog Cascade Coordinates Mesoderm-Inducing Signals and Endoderm Competence during Lung Specification.
Rankin SA, Han L, McCracken KW, Kenny AP, Anglin CT, Grigg EA, Crawford CM, Wells JM, Shannon JM, Zorn AM. Cell Rep. 2016 Jun 28;16(1):66-78.

Collaborate

We are actively seeking clinical or basic research collaborators who treat EA/TEF or investigate the cause of these conditions. Please contact us at info@clearconsortium.org for more information or if you are interested in collaborating with us.

Clear TED Registry (coming soon)

A national registry integrating clinical, genotype, and phenotype data collected from tracheoesophageal defects in patients will be collated into a database of clinical records, accessible by login. Check back for updates on this project.