Human Exome and Mouse Embryonic Expression Data Implicate ZFHX3, TRPS1, and CHD7 in Human Esophageal Atresia

Introduction: Esophageal atresia with or without tracheoesophageal fistula (EA/TEF) occurs approximately 1 in 3.500 live births representing the most common malformation of the upper digestive tract. Only half a century ago, EA/TEF was fatal among affected newborns suggesting that the steady birth prevalence might in parts be due to mutational de novo events in genes involved in foregut development.

Methods: To identify mutational de novo events in EA/TEF patients, we surveyed the exome of 30 case-parent trios. Identified and confirmed de novo variants were prioritized using in silico prediction tools. To investigate the embryonic role of genes harboring prioritized de novo variants we performed targeted analysis of mouse transcriptome data of esophageal tissue obtained at the embryonic day (E) E8.5, E12.5, and postnatal.

Results: In total we prioritized 14 novel de novo variants in 14 different genes (APOL2, EEF1D, CHD7, FANCB, GGT6, KIAA0556, NFX1, NPR2, PIGC, SLC5A2, TANC2, TRPS1, UBA3, and ZFHX3) and eight rare de novo variants in eight additional genes (CELSR1, CLP1, GPR133, HPS3, MTA3, PLEC, STAB1, and PPIP5K2). Through personal communication during the project, we identified an additional EA/TEF case-parent trio with a rare de novo variant in ZFHX3. In silico prediction analysis of the identified variants and comparative analysis of mouse transcriptome data of esophageal tissue obtained at E8.5, E12.5, and postnatal prioritized CHD7, TRPS1, and ZFHX3 as EA/TEF candidate genes. Re-sequencing of ZFHX3 in additional 192 EA/TEF patients did not identify further putative EA/TEF-associated variants.

Conclusion: Our study suggests that rare mutational de novo events in genes involved in foregut development contribute to the development of EA/TEF.

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References

Yeo G, Burge C . Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol. 2004; 11(2-3):377-94. DOI: 10.1089/1066527041410418. View

Torfs C, Curry C, Bateson T . Population-based study of tracheoesophageal fistula and esophageal atresia. Teratology. 1995; 52(4):220-32. DOI: 10.1002/tera.1420520408. View

McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A . The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010; 20(9):1297-303. PMC: 2928508. DOI: 10.1101/gr.107524.110. View

Kawalia A, Motameny S, Wonczak S, Thiele H, Nieroda L, Jabbari K . Leveraging the power of high performance computing for next generation sequencing data analysis: tricks and twists from a high throughput exome workflow. PLoS One. 2015; 10(5):e0126321. PMC: 4420499. DOI: 10.1371/journal.pone.0126321. View

MOTOYAMA J, Liu J, Mo R, Ding Q, Post M, Hui C . Essential function of Gli2 and Gli3 in the formation of lung, trachea and oesophagus. Nat Genet. 1998; 20(1):54-7. DOI: 10.1038/1711. View

Dobin A, Davis C, Schlesinger F, Drenkow J, Zaleski C, Jha S . STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2012; 29(1):15-21. PMC: 3530905. DOI: 10.1093/bioinformatics/bts635. View

David T, OCallaghan S . Oesophageal atresia in the South West of England. J Med Genet. 1975; 12(1):1-11. PMC: 1013225. DOI: 10.1136/jmg.12.1.1. View

Maas S, Shaw A, Bikker H, Ludecke H, van der Tuin K, Badura-Stronka M . Phenotype and genotype in 103 patients with tricho-rhino-phalangeal syndrome. Eur J Med Genet. 2015; 58(5):279-92. DOI: 10.1016/j.ejmg.2015.03.002. View

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

10.

Durinck S, Spellman P, Birney E, Huber W . Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat Protoc. 2009; 4(8):1184-91. PMC: 3159387. DOI: 10.1038/nprot.2009.97. View

11.

Love M, Anders S, Kim V, Huber W . RNA-Seq workflow: gene-level exploratory analysis and differential expression. F1000Res. 2015; 4:1070. PMC: 4670015. DOI: 10.12688/f1000research.7035.1. View

12.

Love M, Huber W, Anders S . Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014; 15(12):550. PMC: 4302049. DOI: 10.1186/s13059-014-0550-8. View

13.

Ramu A, Noordam M, Schwartz R, Wuster A, Hurles M, Cartwright R . DeNovoGear: de novo indel and point mutation discovery and phasing. Nat Methods. 2013; 10(10):985-7. PMC: 4003501. DOI: 10.1038/nmeth.2611. View

14.

Liu X, Jian X, Boerwinkle E . dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions. Hum Mutat. 2011; 32(8):894-9. PMC: 3145015. DOI: 10.1002/humu.21517. View

15.

Quan L, Smith D . The VATER association. Vertebral defects, Anal atresia, T-E fistula with esophageal atresia, Radial and Renal dysplasia: a spectrum of associated defects. J Pediatr. 1973; 82(1):104-7. DOI: 10.1016/s0022-3476(73)80024-1. View

16.

Jongmans M, Admiraal R, van der Donk K, Vissers L, Baas A, Kapusta L . CHARGE syndrome: the phenotypic spectrum of mutations in the CHD7 gene. J Med Genet. 2005; 43(4):306-14. PMC: 2563221. DOI: 10.1136/jmg.2005.036061. View

17.

DePaepe A, Dolk H, Lechat M . The epidemiology of tracheo-oesophageal fistula and oesophageal atresia in Europe. EUROCAT Working Group. Arch Dis Child. 1993; 68(6):743-8. PMC: 1029365. DOI: 10.1136/adc.68.6.743. View

18.

Ewels P, Magnusson M, Lundin S, Kaller M . MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016; 32(19):3047-8. PMC: 5039924. DOI: 10.1093/bioinformatics/btw354. View

19.

Williamson K, Hever A, Rainger J, Rogers R, Magee A, Fiedler Z . Mutations in SOX2 cause anophthalmia-esophageal-genital (AEG) syndrome. Hum Mol Genet. 2006; 15(9):1413-22. DOI: 10.1093/hmg/ddl064. View

20.

Brosens E, Marsch F, de Jong E, Zaveri H, Hilger A, Choinitzki V . Copy number variations in 375 patients with oesophageal atresia and/or tracheoesophageal fistula. Eur J Hum Genet. 2016; 24(12):1715-1723. PMC: 5117935. DOI: 10.1038/ejhg.2016.86. View