ARTICLE Complex Compound Inheritance of Lethal Lung Developmental Disorders Due to Disruption of the TBX-FGF Pathway Justyna A. Karolak, 1,2,61 Marie Vincent, 3,4,61 Gail Deutsch, 5,61 Tomasz Gambin, 6,7,61 Benjamin Cogne ´, 3,4 Olivier Pichon, 3 Francesco Vetrini, 8 Heather C. Mefford, 9 Jennifer N. Dines, 9,10 Katie Golden-Grant, 11 Katrina Dipple, 9,11 Amanda S. Freed, 9,10 Kathleen A. Leppig, 12 Megan Dishop, 13 David Mowat, 14,15 Bruce Bennetts, 16,17,18 Andrew J. Gifford, 15,19 Martin A. Weber, 19,20 Anna F. Lee, 21 Cornelius F. Boerkoel, 22 Tina M. Bartell, 23 Catherine Ward-Melver, 24 Thomas Besnard, 3,4 Florence Petit, 25 Iben Bache, 26,27 Zeynep Tu ¨mer, 28,29 Marie Denis-Musquer, 30 Madeleine Joubert, 30 Jelena Martinovic, 31 Claire Be ´ne ´teau, 3,4 Arnaud Molin, 32 Dominique Carles, 33 Gwenaelle Andre ´, 33 Eric Bieth, 34 Nicolas Chassaing, 34 Louise Devisme, 35 Lara Chalabreysse, 36 Laurent Pasquier, 37 (Author list continued on next page) Primary defects in lung branching morphogenesis, resulting in neonatal lethal pulmonary hypoplasias, are incompletely understood. To elucidate the pathogenetics of human lung development, we studied a unique collection of samples obtained from deceased individuals with clinically and histopathologically diagnosed interstitial neonatal lung disorders: acinar dysplasia (n ¼ 14), congenital alveolar dysplasia (n ¼ 2), and other lethal lung hypoplasias (n ¼ 10). We identified rare heterozygous copy-number variant deletions or single-nucleotide variants (SNVs) involving TBX4 (n ¼ 8 and n ¼ 2, respectively) or FGF10 (n ¼ 2 and n ¼ 2, respectively) in 16/26 (61%) individuals. In addition to TBX4, the overlapping 2 Mb recurrent and nonrecurrent deletions at 17q23.1q23.2 identified in seven individuals with lung hypoplasia also remove a lung-specific enhancer region. Individuals with coding variants involving either TBX4 or FGF10 also harbored at least one non-coding SNV in the predicted lung-specific enhancer region, which was absent in 13 con- trol individuals with the overlapping deletions but without any structural lung anomalies. The occurrence of rare coding variants involving TBX4 or FGF10 with the putative hypomorphic non-coding SNVs implies a complex compound inheritance of these pulmo- nary hypoplasias. Moreover, they support the importance of TBX4-FGF10-FGFR2 epithelial-mesenchymal signaling in human lung organogenesis and help to explain the histopathological continuum observed in these rare lethal developmental disorders of the lung. Introduction Diffuse developmental disorders of the lung comprise a group of rare primary defects in lung branching morpho- genesis and vasculogenesis, including acinar dysplasia (AcDys), congenital alveolar dysplasia (CAD), and alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV [MIM: 265380]) (Figure 1). 1,2 Diagnosis of these disorders has been based largely on their histopathological appearance at lung biopsy or autopsy, which demonstrate 1 Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; 2 Department of Genetics and Pharmaceutical Micro- biology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; 3 Service de Ge ´ne ´tique Me ´dicale, CHU de Nantes, 44000 Nantes, France; 4 Inserm, CNRS, Univ Nantes, l’institut du thorax, 44000 Nantes, France; 5 Department of Pathology, Seattle Children’s Hospital, Seattle, WA 98105, USA; 6 Department of Medical Genetics, Institute of Mother and Child, 01-211 Warsaw, Poland; 7 Institute of Computer Science, Warsaw University of Technol- ogy, 00-665 Warsaw, Poland; 8 Baylor Genetics, Houston, TX 77021, USA; 9 Department of Pediatrics, Division of Genetic Medicine, University of Washing- ton, Seattle, WA 98195, USA; 10 Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA; 11 Division of Genetic Medicine, Seattle Children’s Hospital, Seattle, WA 98105, USA; 12 Genetic Services Kaiser Permanente of Washington, Seattle, WA 98112, USA; 13 Pathology and Laboratory Medicine, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA; 14 Centre for Clinical Genetics, Sydney Children’s Hospital, Randwick Sydney, NSW 2031 Australia; 15 School of Women’s and Children’s Health, The University of New South Wales, Sydney, NSW 2052, Australia; 16 Discipline of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia; 17 Molecular Genetics Department, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia; 18 Discipline of Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia; 19 Department of Anatomical Pathology, Prince of Wales Hospital, Randwick, NSW 2031, Australia; 20 School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia; 21 Department of Pathology and Laboratory Medi- cine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; 22 Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada; 23 Department of Genetics, Kaiser Permanente Sacramento Medical Center, Sacramento, CA 95815, USA; 24 Division of Medical Genetics, Akron Children’s Hospital, Akron, OH 44302, USA; 25 Service de Ge ´ne ´tique Clinique, CHU Lille, 59000 Lille, France; 26 Department of Cellular and Molec- ular Medicine, University of Copenhagen, 2200 N Copenhagen, Denmark; 27 Department of Clinical Genetics, Copenhagen University Hospital, Rigsho- spitalet, 2100 Ø Copenhagen, Denmark; 28 Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2600 Glostrup, Copenhagen, Denmark; 29 Deparment of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 N, Copen- hagen, Denmark; 30 Service d’anatomo-pathologie, CHU Nantes, 44093 Nantes, France; 31 Unit of Fetal Pathology, AP-HP, Antoine Beclere Hospital, 75000 Paris, France; 32 Service de Ge ´ne ´tique Me ´ dicale, CHU Caen, 14000 Caen, France; 33 Service d’anatomo-pathologie, CHU Bordeaux, 33000 Bordeaux, France; 34 Service de ge ´ne ´tique me ´dicale, CHU Toulouse, France and UDEAR, UMR 1056 Inserm - Universite ´ de Toulouse, 31000 Toulouse, France; 35 Institut de Path- ologie, CHU Lille, 59000 Lille, France; 36 Service d’anatomo-pathologie, CHU Lyon, 69000 Lyon, France; 37 Service de ge ´ne ´tique me ´dicale, CHU Rennes, 35000 Rennes, France; 38 Aix Marseille Univ, APHM, Ho ˆpital Nord, Service d’anatomo-pathologie, 13000 Marseille, France; 39 Sant’Antonio General (Affiliations continued on next page) The American Journal of Human Genetics 104, 213–228, February 7, 2019 213 Ó 2018 American Society of Human Genetics.