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1. First genome-wide association study of esophageal atresia identifies three genetic risk loci at CTNNA3, FOXF1/FOXC2/FOXL1, and HNF1B

Author

Jan Gehlen, Ann-Sophie Giel, Ricarda Köllges, Stephan L. Haas, Rong Zhang, Jiri Trcka, Ayse Ö. Sungur, Florian Renziehausen, Dorothea Bornholdt, Daphne Jung, Paul D. Hoyer, Agneta Nordenskjöld, Dick Tibboel, John Vlot, Manon C.W. Spaander, Robert Smigiel, Dariusz Patkowski, Nel Roeleveld, Iris ALM. van Rooij, Ivo de Blaauw, Alice Hölscher, Marcus Pauly, Andreas Leutner, Joerg Fuchs, Joel Niethammer, Maria-Theodora Melissari, Ekkehart Jenetzky, Nadine Zwink, Holger Thiele, Alina Christine Hilger, Timo Hess, Jessica Trautmann, Matthias Marks, Martin Baumgarten, Gaby Bläss, Mikael Landén, Bengt Fundin, Cynthia M. Bulik, Tracie Pennimpede, Michael Ludwig, Kerstin U. Ludwig, Elisabeth Mangold, Stefanie Heilmann-Heimbach, Susanne Moebus, Bernhard G. Herrmann, Kristina Alsabeah, Carmen M. Burgos, Helene E. Lilja, Sahar Azodi, Pernilla Stenström, Einar Arnbjörnsson, Barbora Frybova, Dariusz M. Lebensztejn, Wojciech Debek, Elwira Kolodziejczyk, Katarzyna Kozera, Jaroslaw Kierkus, Piotr Kaliciński, Marek Stefanowicz, Anna Socha-Banasiak, Michal Kolejwa, Anna Piaseczna-Piotrowska, Elzbieta Czkwianianc, Markus M. Nöthen, Phillip Grote, Michal Rygl, Konrad Reinshagen, Nicole Spychalski, Barbara Ludwikowski, Jochen Hubertus, Andreas Heydweiller, Benno Ure, Oliver J. Muensterer, Ophelia Aubert, Jan-Hendrik Gosemann, Martin Lacher, Petra Degenhardt, Thomas M. Boemers, Anna Mokrowiecka, Ewa Małecka-Panas, Markus Wöhr, Michael Knapp, Guido Seitz, Annelies de Klein, Grzegorz Oracz, Erwin Brosens, Heiko Reutter, and Johannes Schumacher

Subjects
genome-wide association study (GWAS), esophageal atresia (EA), multifactorial diseases, CTNNA3, FOXF1/FOXC2/FOXL1, HNF1B, Genetics, QH426-470
Abstract

Summary: Esophageal atresia with or without tracheoesophageal fistula (EA/TEF) is the most common congenital malformation of the upper digestive tract. This study represents the first genome-wide association study (GWAS) to identify risk loci for EA/TEF. We used a European case-control sample comprising 764 EA/TEF patients and 5,778 controls and observed genome-wide significant associations at three loci. On chromosome 10q21 within the gene CTNNA3 (p = 2.11 × 10−8; odds ratio [OR] = 3.94; 95% confidence interval [CI], 3.10–5.00), on chromosome 16q24 next to the FOX gene cluster (p = 2.25 × 10−10; OR = 1.47; 95% CI, 1.38–1.55) and on chromosome 17q12 next to the gene HNF1B (p = 3.35 × 10−16; OR = 1.75; 95% CI, 1.64–1.87). We next carried out an esophageal/tracheal transcriptome profiling in rat embryos at four selected embryonic time points. Based on these data and on already published data, the implicated genes at all three GWAS loci are promising candidates for EA/TEF development. We also analyzed the genetic EA/TEF architecture beyond the single marker level, which revealed an estimated single-nucleotide polymorphism (SNP)-based heritability of around 37% ± 14% standard deviation. In addition, we examined the polygenicity of EA/TEF and found that EA/TEF is less polygenic than other complex genetic diseases. In conclusion, the results of our study contribute to a better understanding on the underlying genetic architecture of ET/TEF with the identification of three risk loci and candidate genes.

Published
2022
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2. First genome-wide association study of esophageal atresia identifies three genetic risk loci at

Author

Jan, Gehlen, Ann-Sophie, Giel, Ricarda, Köllges, Stephan L, Haas, Rong, Zhang, Jiri, Trcka, Ayse Ö, Sungur, Florian, Renziehausen, Dorothea, Bornholdt, Daphne, Jung, Paul D, Hoyer, Agneta, Nordenskjöld, Dick, Tibboel, John, Vlot, Manon C W, Spaander, Robert, Smigiel, Dariusz, Patkowski, Nel, Roeleveld, Iris Alm, van Rooij, Ivo, de Blaauw, Alice, Hölscher, Marcus, Pauly, Andreas, Leutner, Joerg, Fuchs, Joel, Niethammer, Maria-Theodora, Melissari, Ekkehart, Jenetzky, Nadine, Zwink, Holger, Thiele, Alina Christine, Hilger, Timo, Hess, Jessica, Trautmann, Matthias, Marks, Martin, Baumgarten, Gaby, Bläss, Mikael, Landén, Bengt, Fundin, Cynthia M, Bulik, Tracie, Pennimpede, Michael, Ludwig, Kerstin U, Ludwig, Elisabeth, Mangold, Stefanie, Heilmann-Heimbach, Susanne, Moebus, Bernhard G, Herrmann, Kristina, Alsabeah, Carmen M, Burgos, Helene E, Lilja, Sahar, Azodi, Pernilla, Stenström, Einar, Arnbjörnsson, Barbora, Frybova, Dariusz M, Lebensztejn, Wojciech, Debek, Elwira, Kolodziejczyk, Katarzyna, Kozera, Jaroslaw, Kierkus, Piotr, Kaliciński, Marek, Stefanowicz, Anna, Socha-Banasiak, Michal, Kolejwa, Anna, Piaseczna-Piotrowska, Elzbieta, Czkwianianc, Markus M, Nöthen, Phillip, Grote, Michal, Rygl, Konrad, Reinshagen, Nicole, Spychalski, Barbara, Ludwikowski, Jochen, Hubertus, Andreas, Heydweiller, Benno, Ure, Oliver J, Muensterer, Ophelia, Aubert, Jan-Hendrik, Gosemann, Martin, Lacher, Petra, Degenhardt, Thomas M, Boemers, Anna, Mokrowiecka, Ewa, Małecka-Panas, Markus, Wöhr, Michael, Knapp, Guido, Seitz, Annelies, de Klein, Grzegorz, Oracz, Erwin, Brosens, Heiko, Reutter, and Johannes, Schumacher

Abstract

Esophageal atresia with or without tracheoesophageal fistula (EA/TEF) is the most common congenital malformation of the upper digestive tract. This study represents the first genome-wide association study (GWAS) to identify risk loci for EA/TEF. We used a European case-control sample comprising 764 EA/TEF patients and 5,778 controls and observed genome-wide significant associations at three loci. On chromosome 10q21 within the gene

Published
2021

3. The Tissue-Specific lncRNA Fendrr Is an Essential Regulator of Heart and Body Wall Development in the Mouse

Author

Gaby Bläss, Bernhard G. Herrmann, Karol Macura, David A. Hendrix, Arica Beisaw, Phillip Grote, Sandra Währisch, Manolis Kellis, Lars Wittler, Martin Werber, and Frederic Koch

Subjects
Mesoderm, animal structures, Cellular differentiation, Molecular Sequence Data, Regulator, Mammalian embryology, Embryonic Development, macromolecular substances, General Biochemistry, Genetics and Molecular Biology, Article, Histones, Mice, medicine, Animals, Promoter Regions, Genetic, Molecular Biology, Transcription factor, Homeodomain Proteins, biology, Lateral plate mesoderm, fungi, Polycomb Repressive Complex 2, Cell Differentiation, Forkhead Transcription Factors, Heart, Cell Biology, Histone-Lysine N-Methyltransferase, DNA Methylation, Embryo, Mammalian, Molecular biology, Chromatin, Cell biology, medicine.anatomical_structure, biology.protein, RNA, Long Noncoding, PRC2, Myeloid-Lymphoid Leukemia Protein, Transcription Factors, Developmental Biology
Abstract

The histone modifying complexes PRC2 and TrxG/MLL play pivotal roles in determining the activation state of genes controlling pluripotency, lineage commitment, and cell differentiation. Long non-coding RNAs (lncRNAs) can bind to either complex, and some have been shown to act as modulators of PRC2 or TrxG/MLL activity. Here we show that the lateral mesoderm-specific lncRNA Fendrr is essential for proper heart and body wall development in the mouse. Embryos lacking Fendrr displayed upregulation of several transcription factors controlling lateral plate or cardiac mesoderm differentiation, accompanied by a drastic reduction in PRC2 occupancy along with decreased H3K27 trimethylation and/or an increase in H3K4 trimethylation at their promoters. Fendrr binds to both the PRC2 and TrxG/MLL complexes, suggesting that it acts as modulator of chromatin signatures that define gene activity. Thus, our work identifies a lncRNA that plays an essential role in fine-tuning the regulatory networks which control the fate of lateral mesoderm derivatives.

Published
2013
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