Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

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

European Journal of Human Genetics volume 29, pages 122–130 (2021)Cite this article

Subjects

Abstract

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

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to the full article PDF.

USD 39.95

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Genes with LGD or D-mis de novo variants and their relationship with EFTUD2 and SOX2.

Similar content being viewed by others

Data availability

All likely pathogenic variants are in ClinVar submission number SUB7053346. Accession numbers of submitted variants can be found in Supplemental Table 1.

References

  1. Pinheiro PFM, e Silva ACS, Pereira RM. Current knowledge on esophageal atresia. World J Gastroenterol. 2012;18:3662.

    Article  PubMed  PubMed Central  Google Scholar 

  2. Krishnan U, Mousa H, Dall’Oglio L, Homaira N, Rosen R, Faure C, et al. ESPGHAN-NASPGHAN guidelines for the evaluation and treatment of gastrointestinal and nutritional complications in children with esophageal atresia-tracheoesophageal fistula. J Pediatr Gastroenterol Nutr. 2016;63:550–70.

    Article  PubMed  Google Scholar 

  3. Stoll C, Alembik Y, Dott B, Roth M-P. Associated malformations in patients with esophageal atresia. Eur J Med Genet. 2009;52:287–90.

    Article  PubMed  Google Scholar 

  4. Shaw-Smith C. Genetic factors in esophageal atresia, tracheo-esophageal fistula and the VACTERL association: roles for FOXF1 and the 16q24. 1 FOX transcription factor gene cluster, and review of the literature. Eur J Med Genet. 2010;53:6–13.

    Article  PubMed  PubMed Central  Google Scholar 

  5. Geneviève D, de Pontual L, Amiel J, Lyonnet S. Genetic factors in isolated and syndromic esophageal atresia. J Pediatr Gastroenterol Nutr. 2011;52:S6–8.

    Article  PubMed  Google Scholar 

  6. Felix JF, Tibboel D, de Klein A. Chromosomal anomalies in the aetiology of oesophageal atresia and tracheo-oesophageal fistula. Eur J Med Genet. 2007;50:163–75.

    Article  PubMed  Google Scholar 

  7. Murphy AJ, Li Y, Pietsch JB, Chiang C, Lovvorn HN. Mutational analysis of NOG in esophageal atresia and tracheoesophageal fistula patients. Pediatr Surg Int. 2012;28:335–40.

    Article  PubMed  Google Scholar 

  8. Que J, Okubo T, Goldenring JR, Nam K-T, Kurotani R, Morrisey EE, et al. Multiple dose-dependent roles for Sox2 in the patterning and differentiation of anterior foregut endoderm. Development. 2007;134:2521–31.

    Article  CAS  PubMed  Google Scholar 

  9. Kormish JD, Sinner D, Zorn AM. Interactions between SOX factors and Wnt/β-catenin signaling in development and disease. Dev Dyn. 2010;239:56–68.

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Morrisey EE, Hogan BL. Preparing for the first breath: genetic and cellular mechanisms in lung development. Dev Cell. 2010;18:8–23.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Gordon CT, Petit F, Oufadem M, Decaestecker C, Jourdain AS, Andrieux J, et al. EFTUD2 haploinsufficiency leads to syndromic oesophageal atresia. J Med Genet. 2012;49:737–46.

    Article  CAS  PubMed  Google Scholar 

  12. Voigt C, Mégarbané A, Neveling K, Czeschik JC, Albrecht B, Callewaert B, et al. Oto-facial syndrome and esophageal atresia, intellectual disability and zygomatic anomalies-expanding the phenotypes associated with EFTUD2 mutations. Orphanet J Rare Dis. 2013;8:110.

    Article  PubMed  PubMed Central  Google Scholar 

  13. Lines MA, Huang L, Schwartzentruber J, Douglas SL, Lynch DC, Beaulieu C, et al. Haploinsufficiency of a spliceosomal GTPase encoded by EFTUD2 causes mandibulofacial dysostosis with microcephaly. Am J Hum Genet. 2012;90:369–77.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Zhang X, Yan C, Hang J, Finci LI, Lei J, Shi Y. An atomic structure of the human spliceosome. Cell. 2017;169:918–29e.14.

    Article  CAS  PubMed  Google Scholar 

  15. Bertram K, Agafonov DE, Dybkov O, Haselbach D, Leelaram MN, Will CL, et al. Cryo-EM structure of a pre-catalytic human spliceosome primed for activation. Cell. 2017;170:701–13.e11.

    Article  CAS  PubMed  Google Scholar 

  16. Schulz AC, Bartels E, Stressig R, Ritgen J, Schmiedeke E, Mattheisen M, et al. Nine new twin pairs with esophageal atresia: a review of the literature and performance of a twin study of the disorder. Birth Defects Res Part A: Clin Mol Teratol. 2012;94:182–6.

    Article  CAS  Google Scholar 

  17. Maroszyńska I, Fortecka-Piestrzeniewicz K, Niedźwiecka M, Żarkowska-Szaniawska A. Isolated esophageal atresia in both premature twins. Pediatr Pol. 2015;90:91–3.

    Article  Google Scholar 

  18. Shaw-Smith C. Oesophageal atresia, tracheo-oesophageal fistula, and the VACTERL association: review of genetics and epidemiology. J Med Genet. 2006;43:545–54.

    Article  CAS  PubMed  Google Scholar 

  19. Zhang Y, Jiang M, Kim E, Lin S, Liu K, Que J, et al. Development and stem cells of the esophagus. Semin Cell Dev Biol. 2017;66:25–35.

    Article  CAS  PubMed  Google Scholar 

  20. Al-Salem AH, Kothari M, Oquaish M, Khogeer S, Desouky MS. Morbidity and mortality in esophageal atresia and tracheoesophageal fistula: a 20-year review. Ann Pediatr Surg. 2013;9:93–8.

    Article  Google Scholar 

  21. Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:13033997. 2013. https://arxiv.org/abs/1303.3997.

  22. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43:491.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Homsy J, Zaidi S, Shen Y, Ware JS, Samocha KE, Karczewski KJ, et al. De novo mutations in congenital heart disease with neurodevelopmental and other congenital anomalies. Science. 2015;350:1262–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Qi H, Yu L, Zhou X, Wynn J, Zhao H, Guo Y, et al. De novo variants in congenital diaphragmatic hernia identify MYRF as a new syndrome and reveal genetic overlaps with other developmental disorders. PLoS Genet. 2018;14:e1007822.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  25. Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14:178–92.

    Article  CAS  PubMed  Google Scholar 

  26. Fromer M, Moran JL, Chambert K, Banks E, Bergen SE, Ruderfer DM, et al. Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth. Am J Hum Genet. 2012;91:597–607.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38:e164.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  28. Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016;536:285.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Kircher M, Witten DM, Jain P, O’roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014;46:310.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Ioannidis NM, Rothstein JH, Pejaver V, Middha S, McDonnell SK, Baheti S, et al. REVEL: an ensemble method for predicting the pathogenicity of rare missense variants. Am J Hum Genet. 2016;99:877–85.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Van Nostrand EL, Freese P, Pratt GA, Wang X, Wei X, Blue SM, et al. A large-scale binding and functional map of human RNA binding proteins. bioRxiv. 2018. https://doi.org/10.1101/179648.

  32. Feng H, Bao S, Rahman MA, Weyn-Vanhentenryck SM, Khan A, Wong J, et al. Modeling RNA-binding protein specificity in vivo by precisely registering protein-RNA crosslink sites. Mol Cell. 2019;74:1189–1204.e6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Sarkar A, Huebner AJ, Sulahian R, Anselmo A, Xu X, Flattery K, et al. Sox2 suppresses gastric tumorigenesis in mice. Cell Rep. 2016;16:1929–41.

    Article  CAS  PubMed  Google Scholar 

  34. Lachmann A, Xu H, Krishnan J, Berger SI, Mazloom AR, Ma’ayan A. ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinformatics. 2010;26:2438–44.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Han X, Chen S, Flynn E, Wu S, Wintner D, Shen Y. Distinct epigenomic patterns are associated with haploinsufficiency and predict risk genes of developmental disorders. Nat Commun. 2018;9:2138.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  36. Samocha KE, Robinson EB, Sanders SJ, Stevens C, Sabo A, McGrath LM, et al. A framework for the interpretation of de novo mutation in human disease. Nat Genet. 2014;46:944.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Walsh R, Mazzarotto F, Whiffin N, Buchan R, Midwinter W, Wilk A, et al. Quantitative approaches to variant classification increase the yield and precision of genetic testing in Mendelian diseases: the case of hypertrophic cardiomyopathy. Genome Med. 2019;11:5.

    Article  PubMed  PubMed Central  Google Scholar 

  38. Jin SC, Homsy J, Zaidi S, Lu Q, Morton S, DePalma SR, et al. Contribution of rare inherited and de novo variants in 2871 congenital heart disease probands. Nat Genet. 2017;49:1593–601.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Deciphering Developmental Disorders S. Prevalence and architecture of de novo mutations in developmental disorders. Nature. 2017;542:433–8.

    Article  CAS  Google Scholar 

  40. Feliciano P, Zhou X, Astrovskaya I, Turner T, Wang T, Brueggeman L, et al. Exome sequencing of 457 autism families recruited online provides evidence for novel ASD genes. bioRxiv. 2019: 516625. https://www.biorxiv.org/content/10.1101/516625v1.

  41. He X, Sanders SJ, Liu L, De Rubeis S, Lim ET, Sutcliffe JS, et al. Integrated model of de novo and inherited genetic variants yields greater power to identify risk genes. PLoS Genet. 2013;9:e1003671.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Hussain NK, Jenna S, Glogauer M, Quinn CC, Wasiak S, Guipponi M, et al. Endocytic protein intersectin-l regulates actin assembly via Cdc42 and N-WASP. Nat Cell Biol. 2001;3:927–32.

    Article  CAS  PubMed  Google Scholar 

  43. Takatsu H, Sakurai M, Shin HW, Murakami K, Nakayama K. Identification and characterization of novel clathrin adaptor-related proteins. J Biol Chem. 1998;273:24693–700.

    Article  CAS  PubMed  Google Scholar 

  44. Ogawa M, Yoshikawa Y, Kobayashi T, Mimuro H, Fukumatsu M, Kiga K, et al. A Tecpr1-dependent selective autophagy pathway targets bacterial pathogens. Cell Host Microbe. 2011;9:376–89.

    Article  CAS  PubMed  Google Scholar 

  45. Spang N, Feldmann A, Huesmann H, Bekbulat F, Schmitt V, Hiebel C, et al. RAB3GAP1 and RAB3GAP2 modulate basal and rapamycin-induced autophagy. Autophagy. 2014;10:2297–309.

    Article  CAS  PubMed  Google Scholar 

  46. Gaudet P, Livstone MS, Lewis SE, Thomas PD. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Brief Bioinform. 2011;12:449–62.

    Article  PubMed  PubMed Central  Google Scholar 

  47. Mische SM, Mooseker MS, Morrow JS. Erythrocyte adducin: a calmodulin-regulated actin-bundling protein that stimulates spectrin-actin binding. J Cell Biol. 1987;105:2837–45.

    Article  CAS  PubMed  Google Scholar 

  48. Brauburger K, Akyildiz S, Ruppert JG, Graeb M, Bernkopf DB, Hadjihannas MV, et al. Adenomatous polyposis coli (APC) membrane recruitment 3, a member of the APC membrane recruitment family of APC-binding proteins, is a positive regulator of Wnt-beta-catenin signalling. FEBS J. 2014;281:787–801.

    Article  CAS  PubMed  Google Scholar 

  49. Zhang X, Zhang J, Bauer A, Zhang L, Selinger DW, Lu CX, et al. Fine-tuning BMP7 signalling in adipogenesis by UBE2O/E2-230K-mediated monoubiquitination of SMAD6. EMBO J. 2013;32:996–1007.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  50. Au AC, Hernandez PA, Lieber E, Nadroo AM, Shen YM, Kelley KA, et al. Protein tyrosine phosphatase PTPN14 is a regulator of lymphatic function and choanal development in humans. Am J Hum Genet. 2010;87:436–44.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We would like to acknowledge the patients and their families who participated in the study and are grateful for their tremendous contribution. We thank Steve Wyles and Sue Paul from EA for adults, as well as the TOFS UK, OARA, Bridging the Gap of EA/TEF and the Canadian EA network organizations for publicizing the study and assisting with recruitment. We are also appreciative for the technical assistance provided by Patricia Lanzano, Jiangyuan Hu, Liyong Deng, Nikita Chintalapudi, and Charles LeDuc from Columbia University and the study team at Cairo University General Hospital. We thank Na Zhu for help with the calculation of background mutation rate. Funding support provided by P01HD093363 (JW, YS, and WKC) and R01GM120609 (YS).

Author information

Author notes

  1. These authors contributed equally: Jiayao Wang, Priyanka R. Ahimaz, Somaye Hashemifar

Authors and Affiliations

  1. Department of Pediatrics, Columbia University Medical Center, New York, NY, USA

    Jiayao Wang, Priyanka R. Ahimaz, Somaye Hashemifar & Wendy K. Chung

  2. Departments of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York, NY, USA

    Jiayao Wang, Somaye Hashemifar & Yufeng Shen

  3. Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA

    Julie Khlevner & Joseph A. Picoraro

  4. Division of Pediatric Surgery, Department of Surgery, Columbia University Medical Center, New York, NY, USA

    William Middlesworth

  5. Pediatric Surgery, Faculty of Medicine, Cairo University, Cairo, Egypt

    Mahmoud M. Elfiky

  6. Department of Medicine, Columbia University Medical Center, New York, NY, USA

    Jianwen Que & Wendy K. Chung

Authors
  1. Jiayao Wang
    View author publications

    Search author on:PubMed Google Scholar

  2. Priyanka R. Ahimaz
    View author publications

    Search author on:PubMed Google Scholar

  3. Somaye Hashemifar
    View author publications

    Search author on:PubMed Google Scholar

  4. Julie Khlevner
    View author publications

    Search author on:PubMed Google Scholar

  5. Joseph A. Picoraro
    View author publications

    Search author on:PubMed Google Scholar

  6. William Middlesworth
    View author publications

    Search author on:PubMed Google Scholar

  7. Mahmoud M. Elfiky
    View author publications

    Search author on:PubMed Google Scholar

  8. Jianwen Que
    View author publications

    Search author on:PubMed Google Scholar

  9. Yufeng Shen
    View author publications

    Search author on:PubMed Google Scholar

  10. Wendy K. Chung
    View author publications

    Search author on:PubMed Google Scholar

Corresponding authors

Correspondence to Yufeng Shen or Wendy K. Chung.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wang, J., Ahimaz, P.R., Hashemifar, S. et al. Novel candidate genes in esophageal atresia/tracheoesophageal fistula identified by exome sequencing. Eur J Hum Genet 29, 122–130 (2021). https://doi.org/10.1038/s41431-020-0680-2

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Version of record:

  • Issue date:

  • DOI: https://doi.org/10.1038/s41431-020-0680-2

This article is cited by

Search

Advanced search

Quick links