Molecular signatures of esophageal atresia: towards the identification of the molecular causes of the different forms of esophageal atresia and prenatal diagnosis – OESOMICS

Esophageal Atresia (EA) is a rare developmental defect of the foregut that presents with or without a Tracheo-Esophageal Fistula (TEF). The prevalence of EA/TEF over time and around the world has been relatively stable (> 165 new EA/year on average in France). EA/TEF is manifested in a broad spectrum of anomalies: in some patients it manifests as an isolated atresia, but in more than 60% of the cases it affects several organ systems. While the associated malformations are often those of the VACTERL spectrum (Vertebral, Anorectal, Cardiac, Tracheo-Esophageal, Renal and Limb), many patients are affected by other malformations, such as anomalies of the genitourinary, respiratory and gastrointestinal systems. Though EA/TEF is a genetically heterogeneous condition, recurrent genes and loci are sometimes affected. Trachea-Esophageal (TE) defects are in fact a variable feature in several known single gene disorders and in patients with specific recurrent Copy Number Variations and structural chromosomal aberrations. At present, a causal genetic aberration can be identified in less than 10% of patients. In most, EA/TEF is a sporadic finding; the familial recurrence rate is low (1%). As this suggests that epigenetic and environmental factors also contribute to the disease, non-syndromic EA/TEF is generally believed to be a multifactorial condition. Several population-based studies and case reports describe a wide range of associated risks, including age, diabetes, drug use, herbicides, smoking and fetal alcohol exposure. The phenotypical and genetic heterogeneity seen in EA/TEF patients indicates not one underlying cause, but several. In this project we will combine the French register of EA and multiomic studies in order to elucidate new causes or mechanisms in the etiology within specific sub-populations. Improved knowledge of predictive factors and molecular mechanisms may improve prediction and parental counseling and prevent co-morbidity. In this context, state of the art multi-omics will be performed from esophageal biopsies. Systemic/integrative biology will be then undertaken to establish predictive networks. Validation of EA pathways will be investigated using cross link coupled to mass spectrometry (XL-MS) and with BioID in order to evaluate the protein-protein partner involved in networks to better understand physiopathological mechanisms occurring in EA etiology. Integration of all the data using robust bioinformatics and biostatistics will give hypotheses for EA etiology. Based on these fundamental knowledges acquired on the EA pathology, a translational research step will be launched. Multi-omics analyses will be then performed on extracellular vesicles (EVs) issued from amniotic liquid. EVs have raised interest as a potential source of biomarker discovery because of the resemblance of their molecular content to that of the releasing cells. EVs in amniotic liquid will be the mirror of the EA pathology occurring in course of fetus development. Thus, multi-omic analyses of these EVs will be the first steps to improve the prenatal EA/TEF diagnostic.