1
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Giunta-Stibb H, Hackett B. Interstitial lung disease in the newborn. J Perinatol 2024:10.1038/s41372-024-02036-9. [PMID: 38956315 DOI: 10.1038/s41372-024-02036-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 05/30/2024] [Accepted: 06/18/2024] [Indexed: 07/04/2024]
Abstract
Although relatively rare, interstitial lung diseases may present with respiratory distress in the newborn period. Most commonly these include developmental and growth disorders, disorders of surfactant synthesis and homeostasis, pulmonary interstitial glycogenosis, and neuroendocrine cell hyperplasia of infancy. Although the diagnosis of these disorders is sometimes made based on clinical presentation and imaging, due to the significant overlap between disorders and phenotypic variability, lung biopsy or, increasingly genetic testing is needed for diagnosis. These diseases may result in significant morbidity and mortality. Effective medical treatment options are in some cases limited and/or invasive. The genetic basis for some of these disorders has been identified, and with increased utilization of exome and whole genome sequencing even before lung biopsy, further insights into their genetic etiologies should become available.
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Affiliation(s)
- Hannah Giunta-Stibb
- Divisions of Neonatology and Pulmonology, Department of Pediatrics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY, 14642, USA.
| | - Brian Hackett
- Mildred Stahlman Division of Neonatology, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
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2
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Szafranski P, Patrizi S, Gambin T, Afzal B, Schlotterbeck E, Karolak JA, Deutsch G, Roberts D, Stankiewicz P. Diminished TMEM100 Expression in a Newborn With Acinar Dysplasia and a Novel TBX4 Variant: A Case Report. Pediatr Dev Pathol 2024; 27:255-259. [PMID: 38044468 PMCID: PMC11087193 DOI: 10.1177/10935266231213464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Acinar dysplasia (AcDys) of the lung is a rare lethal developmental disorder in neonates characterized by severe respiratory failure and pulmonary arterial hypertension refractory to treatment. Recently, abnormalities of TBX4-FGF10-FGFR2-TMEM100 signaling regulating lung development have been reported in patients with AcDys due to heterozygous single-nucleotide variants or copy-number variant deletions involving TBX4, FGF10, or FGFR2. Here, we describe a female neonate who died at 4 hours of life due to severe respiratory distress related to AcDys diagnosed by postmortem histopathologic evaluation. Genomic analyses revealed a novel deleterious heterozygous missense variant c.728A>C (p.Asn243Thr) in TBX4 that arose de novo on paternal chromosome 17. We also identified 6 candidate hypomorphic rare variants in the TBX4 enhancer in trans to TBX4 coding variant. Gene expression analyses of proband's lung tissue showed a significant reduction of TMEM100 expression with near absence of TMEM100 within the endothelium of arteries and capillaries by immunohistochemistry. These results support the pathogenicity of the detected TBX4 variant and provide further evidence that disrupted signaling between TBX4 and TMEM100 may contribute to severe lung phenotypes in humans, including AcDys.
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Affiliation(s)
| | - Silvia Patrizi
- Department of Pediatric Newborn Medicine, Brigham and Women’s Hospital and Newton-Wellesley Hospital, Harvard Medical School, Boston, MA
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Bushra Afzal
- Division of Neonatology, Department of Pediatrics, Harvard University School of Medicine, Boston, MA
| | - Emily Schlotterbeck
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, 55 Fruit St. WRN 219, Boston, MA
| | - Justyna A. Karolak
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-806 Poznan, Poland
| | - Gail Deutsch
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA
| | - Drucilla Roberts
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, 55 Fruit St. WRN 219, Boston, MA
| | - Paweł Stankiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX
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3
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Maddaloni C, Ronci S, De Rose DU, Bersani I, Campi F, Di Nardo M, Stoppa F, Adorisio R, Amodeo A, Toscano A, Digilio MC, Novelli A, Chello G, Braguglia A, Dotta A, Calzolari F. Neonatal persistent pulmonary hypertension related to a novel TBX4 mutation: case report and review of the literature. Ital J Pediatr 2024; 50:41. [PMID: 38443964 PMCID: PMC10916178 DOI: 10.1186/s13052-024-01575-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/03/2024] [Indexed: 03/07/2024] Open
Abstract
TBX4 gene, located on human chromosome 17q23.2, encodes for T-Box Transcription Factor 4, a transcription factor that belongs to the T-box gene family and it is involved in the regulation of some embryonic developmental processes, with a significant impact on respiratory and skeletal illnesses. Herein, we present the case of a female neonate with persistent pulmonary hypertension (PH) who underwent extracorporeal membrane oxygenation (ECMO) on the first day of life and then resulted to have a novel variant of the TBX4 gene identified by Next-Generation Sequencing. We review the available literature about the association between PH with neonatal onset or emerging during the first months of life and mutations of the TBX4 gene, and compare our case to previously reported cases. Of 24 cases described from 2010 to 2023 sixteen (66.7%) presented with PH soon after birth. Skeletal abnormalities have been described in 5 cases (20%). Eleven cases (46%) were due to de novo mutations. Three patients (12%) required ECMO. Identification of this variant in affected individuals has implications for perinatal and postnatal management and genetic counselling. We suggest including TBX4 in genetic studies of neonates with pulmonary hypertension, even in the absence of skeletal abnormalities.
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Affiliation(s)
- Chiara Maddaloni
- Neonatal Intensive Care Unit, "Bambino Gesù" Children's Hospital IRCCS, Rome, Italy
| | - Sara Ronci
- Neonatal Intensive Care Unit, "Bambino Gesù" Children's Hospital IRCCS, Rome, Italy
| | | | - Iliana Bersani
- Neonatal Intensive Care Unit, "Bambino Gesù" Children's Hospital IRCCS, Rome, Italy.
| | - Francesca Campi
- Neonatal Intensive Care Unit, "Bambino Gesù" Children's Hospital IRCCS, Rome, Italy
| | - Matteo Di Nardo
- Paediatric Intensive Care Unit and ECMO Team, "Bambino Gesù" Children's Hospital IRCCS, Rome, Italy
| | - Francesca Stoppa
- Paediatric Intensive Care Unit and ECMO Team, "Bambino Gesù" Children's Hospital IRCCS, Rome, Italy
| | - Rachele Adorisio
- Heart Failure, Transplant and Mechanical Cardiocirculatory Support Unit, Department of Paediatric Cardiology and Cardiac Surgery, Heart Lung Transplantation, ERN GUARD HEART, "Bambino Gesù" Children's Hospital IRCCS, Rome, Italy
| | - Antonio Amodeo
- Heart Failure, Transplant and Mechanical Cardiocirculatory Support Unit, Department of Paediatric Cardiology and Cardiac Surgery, Heart Lung Transplantation, ERN GUARD HEART, "Bambino Gesù" Children's Hospital IRCCS, Rome, Italy
| | - Alessandra Toscano
- Perinatal Cardiology Unit, "Bambino Gesù" Children's Hospital IRCCS, Rome, Italy
| | | | - Antonio Novelli
- Translational Cytogenomics Unit, Multimodal Medicine Research Area, "Bambino Gesù" Children's Hospital IRCCS, Rome, Italy
| | - Giovanni Chello
- Neonatal Intensive Care Unit, Monaldi Hospital, Naples, Italy
| | - Annabella Braguglia
- Neonatal Intensive Care Unit, "Bambino Gesù" Children's Hospital IRCCS, Rome, Italy
| | - Andrea Dotta
- Neonatal Intensive Care Unit, "Bambino Gesù" Children's Hospital IRCCS, Rome, Italy
| | - Flaminia Calzolari
- Neonatal Intensive Care Unit, "Bambino Gesù" Children's Hospital IRCCS, Rome, Italy
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4
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Danhaive O, Galambos C, Lakshminrusimha S, Abman SH. Pulmonary Hypertension in Developmental Lung Diseases. Clin Perinatol 2024; 51:217-235. [PMID: 38325943 DOI: 10.1016/j.clp.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Diverse genetic developmental lung diseases can present in the neonatal period with hypoxemic respiratory failure, often associated with with pulmonary hypertension. Intractable hypoxemia and lack of sustained response to medical management should increase the suspicion of a developmental lung disorder. Genetic diagnosis and lung biopsy are helpful in establishing the diagnosis. Early diagnosis can result in optimizing management and redirecting care if needed. This article reviews normal lung development, various developmental lung disorders that can result from genetic abnormalities at each stage of lung development, their clinical presentation, management, prognosis, and differential diagnoses.
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Affiliation(s)
- Olivier Danhaive
- Division of Neonatology, Saint-Luc University Hospital, UCLouvain, Avenue Hippocrate 10, B-1200 Brussels, Belgium; Department of Pediatrics, University of California San Francisco, 530 Parnassus Avenue, San Francisco, CA 94143, USA.
| | - Csaba Galambos
- Department of Pathology and Laboratory Medicine, University of Colorado Anschutz School of Medicine, 13001 East 17th Place, Aurora, CO 80045, USA
| | - Satyan Lakshminrusimha
- Department of Pediatrics, University of California, UC Davis Children's Hospital, 2516 Stockton Boulevard, Sacramento CA 95817, USA
| | - Steven H Abman
- Department of Pediatrics, The Pediatric Heart Lung Center, University of Colorado Anschutz Medical Campus, Mail Stop B395, 13123 East 16th Avenue, Aurora, CO 80045, USA
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5
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Miao Y, Tan C, Pek NM, Yu Z, Iwasawa K, Kechele DO, Sundaram N, Pastrana-Gomez V, Kishimoto K, Yang MC, Jiang C, Tchieu J, Whitsett JA, McCracken KW, Rottier RJ, Kotton DN, Helmrath MA, Wells JM, Takebe T, Zorn AM, Chen YW, Guo M, Gu M. Deciphering Endothelial and Mesenchymal Organ Specification in Vascularized Lung and Intestinal Organoids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.577460. [PMID: 38370768 PMCID: PMC10871227 DOI: 10.1101/2024.02.06.577460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
To investigate the co-development of vasculature, mesenchyme, and epithelium crucial for organogenesis and the acquisition of organ-specific characteristics, we constructed a human pluripotent stem cell-derived organoid system comprising lung or intestinal epithelium surrounded by organotypic mesenchyme and vasculature. We demonstrated the pivotal role of co-differentiating mesoderm and endoderm via precise BMP regulation in generating multilineage organoids and gut tube patterning. Single-cell RNA-seq analysis revealed organ specificity in endothelium and mesenchyme, and uncovered key ligands driving endothelial specification in the lung (e.g., WNT2B and Semaphorins) or intestine (e.g., GDF15). Upon transplantation under the kidney capsule in mice, these organoids further matured and developed perfusable human-specific sub-epithelial capillaries. Additionally, our model recapitulated the abnormal endothelial-epithelial crosstalk in patients with FOXF1 deletion or mutations. Multilineage organoids provide a unique platform to study developmental cues guiding endothelial and mesenchymal cell fate determination, and investigate intricate cell-cell communications in human organogenesis and disease. Highlights BMP signaling fine-tunes the co-differentiation of mesoderm and endoderm.The cellular composition in multilineage organoids resembles that of human fetal organs.Mesenchyme and endothelium co-developed within the organoids adopt organ-specific characteristics.Multilineage organoids recapitulate abnormal endothelial-epithelial crosstalk in FOXF1-associated disorders.
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6
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Bzdęga K, Biela M, Deutsch GH, Kitzmiller JA, Rydzanicz M, Płoski R, Whitsett JA, Śmigiel R, Karolak JA. A novel non-recurrent CNV deletion involving TBX4 and leaving TBX2 intact causes congenital alveolar dysplasia. Clin Genet 2024; 105:190-195. [PMID: 37821225 PMCID: PMC10842446 DOI: 10.1111/cge.14428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 10/13/2023]
Abstract
Congenital alveolar dysplasia (CAD) belongs to rare lethal lung developmental disorders (LLDDs) in neonates, manifesting with acute respiratory failure and pulmonary arterial hypertension refractory to treatment. The majority of CAD cases have been associated with copy-number variant (CNV) deletions at 17q23.1q23.2 or 5p12. Most CNV deletions at 17q23.1q23.2 were recurrent and encompassed two closely located genes, TBX4 and TBX2. In a few CAD cases, intragenic frameshifting deletions or single-nucleotide variants (SNVs) involved TBX4 but not TBX2. Here, we describe a male neonate who died at 27 days of life from acute respiratory failure caused by lung growth arrest along the spectrum of CAD confirmed by histopathological assessment. Trio-based genome sequencing revealed in the proband a novel non-recurrent ~1.07 Mb heterozygous CNV deletion at 17q23.2, encompassing TBX4 that arose de novo on the paternal chromosome. This is the first report of a larger-sized CNV deletion in a CAD patient involving TBX4 and leaving TBX2 intact. Our results, together with previous reports, indicate that perturbations of TBX4, rather than TBX2, cause severe lung phenotypes in humans.
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Affiliation(s)
- Katarzyna Bzdęga
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Mateusz Biela
- Department of Pediatric Infectious Diseases, Wroclaw Medical University, Wroclaw, Poland
- Department of Pediatrics, Endocrinology, Diabetology and Metabolic Diseases, Wroclaw Medical University, Wroclaw, Poland
| | - Gail H Deutsch
- Department of Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Joseph A Kitzmiller
- Cincinnati Childrens Hospital Medical Center, Neonatology and Pulmonary Biology, Cincinnati, Ohio, USA
| | | | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Jeffrey A Whitsett
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Robert Śmigiel
- Department of Pediatrics, Endocrinology, Diabetology and Metabolic Diseases, Wroclaw Medical University, Wroclaw, Poland
| | - Justyna A Karolak
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
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7
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Ishida H, Maeda J, Uchida K, Yamagishi H. Unique Pulmonary Hypertensive Vascular Diseases Associated with Heart and Lung Developmental Defects. J Cardiovasc Dev Dis 2023; 10:333. [PMID: 37623346 PMCID: PMC10455332 DOI: 10.3390/jcdd10080333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/10/2023] [Accepted: 08/01/2023] [Indexed: 08/26/2023] Open
Abstract
Although pediatric pulmonary hypertension (PH) shares features and mechanisms with adult PH, there are also some significant differences between the two conditions. Segmental PH is a unique pediatric subtype of PH with unclear and/or multifactorial pathophysiological mechanisms, and is often associated with complex congenital heart disease (CHD), pulmonary atresia with ventricular septal defect, and aortopulmonary collateral arteries. Some cases of complex CHD, associated with a single ventricle after Fontan operation, show pathological changes in the small peripheral pulmonary arteries and pulmonary vascular resistance similar to those observed in pulmonary arterial hypertension (PAH). This condition is termed as the pediatric pulmonary hypertensive vascular disease (PPHVD). Recent advances in genetics have identified the genes responsible for PAH associated with developmental defects of the heart and lungs, such as TBX4 and SOX17. Targeted therapies for PAH have been developed; however, their effects on PH associated with developmental heart and lung defects remain to be established. Real-world data analyses on the anatomy, pathophysiology, genetics, and molecular biology of unique PPHVD cases associated with developmental defects of the heart and lungs, using nationwide and/or international registries, should be conducted in order to improve the treatments and prognosis of patients with these types of pediatric PH.
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Affiliation(s)
- Hidekazu Ishida
- Department of Pediatrics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita 565-0871, Osaka, Japan;
| | - Jun Maeda
- Department of Cardiology, Tokyo Metropolitan Children’s Medical Center, 2-8-29 Musashidai, Fuchu 183-8561, Tokyo, Japan;
| | - Keiko Uchida
- Department of Pediatrics, Keio University of Medicine, 35 Shinanomachi, Shinjuku-ku 160-8582, Tokyo, Japan;
- Keio University Health Center, 4-1-1 Hiyoshi, Kohoku-ku, Yokohama 223-8521, Kanagawa, Japan
| | - Hiroyuki Yamagishi
- Department of Pediatrics, Keio University of Medicine, 35 Shinanomachi, Shinjuku-ku 160-8582, Tokyo, Japan;
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8
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Karolak JA, Welch CL, Mosimann C, Bzdęga K, West JD, Montani D, Eyries M, Mullen MP, Abman SH, Prapa M, Gräf S, Morrell NW, Hemnes AR, Perros F, Hamid R, Logan MPO, Whitsett J, Galambos C, Stankiewicz P, Chung WK, Austin ED. Molecular Function and Contribution of TBX4 in Development and Disease. Am J Respir Crit Care Med 2023; 207:855-864. [PMID: 36367783 PMCID: PMC10111992 DOI: 10.1164/rccm.202206-1039tr] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/10/2022] [Indexed: 11/13/2022] Open
Abstract
Over the past decade, recognition of the profound impact of the TBX4 (T-box 4) gene, which encodes a member of the evolutionarily conserved family of T-box-containing transcription factors, on respiratory diseases has emerged. The developmental importance of TBX4 is emphasized by the association of TBX4 variants with congenital disorders involving respiratory and skeletal structures; however, the exact role of TBX4 in human development remains incompletely understood. Here, we discuss the developmental, tissue-specific, and pathological TBX4 functions identified through human and animal studies and review the published TBX4 variants resulting in variable disease phenotypes. We also outline future research directions to fill the gaps in our understanding of TBX4 function and of how TBX4 disruption affects development.
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Affiliation(s)
- Justyna A. Karolak
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | | | | | - Katarzyna Bzdęga
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - James D. West
- Division of Allergy, Pulmonary and Critical Care Medicine, and
| | - David Montani
- Université Paris-Saclay, Assistance Publique–Hôpitaux de Paris, Service de Pneumologie et Soins Intensifs Respiratoires, Hôpital de Bicêtre, DMU 5 Thorinno, Inserm UMR_S999, Le Kremlin-Bicêtre, France
| | - Mélanie Eyries
- Sorbonne Université, AP-HP, Département de Génétique, Hôpital Pitié-Salpêtrière, Paris, France
| | - Mary P. Mullen
- Department of Cardiology, Boston Children’s Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | | | - Matina Prapa
- St. George’s University Hospitals NHS Foundation Trust, London, United Kingdom
| | - Stefan Gräf
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Heart and Lung Research Institute, Cambridge, United Kingdom
| | - Nicholas W. Morrell
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Heart and Lung Research Institute, Cambridge, United Kingdom
| | - Anna R. Hemnes
- Division of Allergy, Pulmonary and Critical Care Medicine, and
| | - Frédéric Perros
- Université Paris-Saclay, Assistance Publique–Hôpitaux de Paris, Service de Pneumologie et Soins Intensifs Respiratoires, Hôpital de Bicêtre, DMU 5 Thorinno, Inserm UMR_S999, Le Kremlin-Bicêtre, France
| | - Rizwan Hamid
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Malcolm P. O. Logan
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, United Kingdom
| | - Jeffrey Whitsett
- Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Perinatal Institute, Cincinnati, Ohio
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio; and
| | - Csaba Galambos
- Department of Pathology, University of Colorado School of Medicine, and Children’s Hospital Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Wendy K. Chung
- Department of Pediatrics and
- Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Eric D. Austin
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
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9
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Johnson B, Dobkin SL, Josephson M. Extracorporeal membrane oxygenation as a bridge to transplant in neonates with fatal pulmonary conditions: A review. Paediatr Respir Rev 2022; 44:31-39. [PMID: 36464576 DOI: 10.1016/j.prrv.2022.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/10/2022] [Indexed: 11/15/2022]
Abstract
Neonates with progressive respiratory failure should be referred early for subspecialty evaluation and lung transplantation consideration. ECMO should be considered for patients with severe cardiopulmonary dysfunction and a high likelihood of death while on maximal medical therapy, either in the setting of reversible medical conditions or while awaiting lung transplantation. While ECMO offers hope to neonates that experience clinical deterioration while awaiting transplant, the risks and benefits of this intervention should be considered on an individual basis. Owing to the small number of infant lung transplants performed yearly, large studies examining the outcomes of various bridging techniques in this age group do not exist. Multiple single-centre experiences of transplanted neonates have been described and currently serve as guidance for transplant teams. Future investigation of outcomes specific to neonatal transplant recipients bridged with advanced devices is needed.
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Affiliation(s)
- Brandy Johnson
- Division of Pediatric Pulmonary Medicine, UF Health Shands Children's Hospital, Gainesville, FL, USA; Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL, USA.
| | - Shoshana Leftin Dobkin
- Division of Pulmonary and Sleep Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Maureen Josephson
- Division of Pulmonary and Sleep Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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10
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Temple SEL, Ho G, Bennetts B, Boggs K, Vidic N, Mowat D, Christodoulou J, Schultz A, Gayagay T, Roscioli T, Zhu Y, Lunke S, Armstrong D, Harrison J, Kapur N, McDonald T, Selvadurai H, Tai A, Stark Z, Jaffe A. The role of exome sequencing in childhood interstitial or diffuse lung disease. Orphanet J Rare Dis 2022; 17:350. [PMID: 36085161 PMCID: PMC9463757 DOI: 10.1186/s13023-022-02508-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 09/04/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Children's interstitial and diffuse lung disease (chILD) is a complex heterogeneous group of lung disorders. Gene panel approaches have a reported diagnostic yield of ~ 12%. No data currently exist using trio exome sequencing as the standard diagnostic modality. We assessed the diagnostic utility of using trio exome sequencing in chILD. We prospectively enrolled children meeting specified clinical criteria between 2016 and 2020 from 16 Australian hospitals. Exome sequencing was performed with analysis of an initial gene panel followed by trio exome analysis. A subset of critically ill infants underwent ultra-rapid trio exome sequencing as first-line test. RESULTS 36 patients [median (range) age 0.34 years (0.02-11.46); 11F] were recruited from multiple States and Territories. Five patients had clinically significant likely pathogenic/pathogenic variants (RARB, RPL15, CTCF, RFXANK, TBX4) and one patient had a variant of uncertain significance (VIP) suspected to contribute to their clinical phenotype, with VIP being a novel gene candidate. CONCLUSIONS Trio exomes (6/36; 16.7%) had a better diagnostic rate than gene panel (1/36; 2.8%), due to the ability to consider a broader range of underlying conditions. However, the aetiology of chILD in most cases remained undetermined, likely reflecting the interplay between low penetrant genetic and environmental factors.
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Affiliation(s)
- Suzanna E L Temple
- Department of Clinical Genetics, Liverpool Hospital, Sydney, NSW, Australia. .,School of Women's and Children's Health, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia.
| | - Gladys Ho
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, NSW, Australia.,Disciplines of Child and Adolescent Health and Genomic Medicine, University of Sydney, Sydney, NSW, Australia
| | - Bruce Bennetts
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, NSW, Australia.,Disciplines of Child and Adolescent Health and Genomic Medicine, University of Sydney, Sydney, NSW, Australia
| | - Kirsten Boggs
- Australian Genomics Health Alliance, Melbourne, VIC, Australia.,Department of Clinical Genetics, Children's Hospital Westmead, Sydney, NSW, Australia.,Centre for Clinical Genetics, Sydney Children's Hospital Randwick, Sydney, NSW, Australia
| | - Nada Vidic
- School of Women's and Children's Health, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia.,Australian Genomics Health Alliance, Melbourne, VIC, Australia
| | - David Mowat
- School of Women's and Children's Health, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia.,Centre for Clinical Genetics, Sydney Children's Hospital Randwick, Sydney, NSW, Australia
| | - John Christodoulou
- Disciplines of Child and Adolescent Health and Genomic Medicine, University of Sydney, Sydney, NSW, Australia.,Australian Genomics Health Alliance, Melbourne, VIC, Australia.,University of Melbourne, Melbourne, VIC, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - André Schultz
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Perth, Australia.,Department of Respiratory Medicine, Perth Children's Hospital, Nedlands, WA, Australia.,Division of Paediatrics, Faculty of Medicine, University of Western Australia, Perth, Australia
| | - Thet Gayagay
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Tony Roscioli
- Centre for Clinical Genetics, Sydney Children's Hospital Randwick, Sydney, NSW, Australia.,Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia.,Neuroscience Research Australia (NeuRA), Sydney, NSW, Australia
| | - Ying Zhu
- Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Sebastian Lunke
- Australian Genomics Health Alliance, Melbourne, VIC, Australia.,University of Melbourne, Melbourne, VIC, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - David Armstrong
- Department of Paediatrics, Monash University, Clayton Rd, Clayton, VIC, Australia.,Department of Respiratory and Sleep Medicine, Monash Children's Hospital, Clayton Rd, Clayton, VIC, Australia
| | - Joanne Harrison
- University of Melbourne, Melbourne, VIC, Australia.,Department of Respiratory and Sleep Medicine, The Royal Children's Hospital, Melbourne, VIC, Australia
| | - Nitin Kapur
- Department of Respiratory and Sleep Medicine, Queensland Children's Hospital, Brisbane, QLD, Australia.,School of Medicine, University of Queensland, Brisbane, QLD, Australia
| | | | - Hiran Selvadurai
- Disciplines of Child and Adolescent Health and Genomic Medicine, University of Sydney, Sydney, NSW, Australia.,Children's Hospital Westmead, Sydney, NSW, Australia
| | - Andrew Tai
- Paediatric Respiratory and Sleep Department, Women's and Children's Hospital, Adelaide, SA, Australia.,Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Zornitza Stark
- Australian Genomics Health Alliance, Melbourne, VIC, Australia.,University of Melbourne, Melbourne, VIC, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Adam Jaffe
- School of Women's and Children's Health, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia.,Department Respiratory and Sleep Medicine, Sydney Children's Hospital, Randwick, NSW, Australia
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11
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Sankaran D, Lakshminrusimha S. Pulmonary hypertension in the newborn- etiology and pathogenesis. Semin Fetal Neonatal Med 2022; 27:101381. [PMID: 35963740 DOI: 10.1016/j.siny.2022.101381] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A disruption in the well-orchestrated fetal-to-neonatal cardiopulmonary transition at birth results in the clinical conundrum of severe hypoxemic respiratory failure associated with elevated pulmonary vascular resistance (PVR), referred to as persistent pulmonary hypertension of the newborn (PPHN). In the past three decades, the advent of surfactant, newer modalities of ventilation, inhaled nitric oxide, other pulmonary vasodilators, and finally extracorporeal membrane oxygenation (ECMO) have made giant strides in improving the outcomes of infants with PPHN. However, death or the need for ECMO occurs in 10-20% of term infants with PPHN. Better understanding of the etiopathogenesis of PPHN can lead to physiology-driven management strategies. This manuscript reviews the fetal circulation, cardiopulmonary transition at birth, etiology, and pathophysiology of PPHN.
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Affiliation(s)
- Deepika Sankaran
- Division of Neonatology, Department of Pediatrics, University of California, Davis, California, USA; Department of Pediatrics, Adventist Health Rideout Hospital, Marysville, CA, USA.
| | - Satyan Lakshminrusimha
- Division of Neonatology, Department of Pediatrics, University of California, Davis, California, USA.
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12
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Genetic and functional analyses of TBX4 reveal novel mechanisms underlying pulmonary arterial hypertension. J Mol Cell Cardiol 2022; 171:105-116. [PMID: 35914404 DOI: 10.1016/j.yjmcc.2022.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 06/29/2022] [Accepted: 07/07/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Pulmonary arterial hypertension (PAH) is a fatal disease, with approximately 10% of cases associated with genetic variants. Recent genetic studies have reported pathogenic variants in the TBX4 gene in patients with PAH, especially in patients with childhood-onset of the disease, but the pathogenesis of PAH caused by TBX4 variant has not been fully uncovered. METHODS We analysed the TBX4 gene in 75 Japanese patients with sporadic or familial PAH using a PCR-based bidirectional sequencing method. Detected variants were evaluated using in silico analyses as well as in vitro analyses including luciferase assay, immunocytochemistry and chromatin immunoprecipitation (ChIP) whether they have altered function. We also analysed the function of TBX4 using mouse embryonic lung explants with inhibition of Tbx4 expression. RESULTS Putative pathogenic variants were detected in three cases (4.0%). Our in vitro functional analyses revealed that TBX4 directly regulates the transcriptional activity of fibroblast growth factor 10 (FGF10), whereas the identified TBX4 variant proteins failed to activate the FGF10 gene because of disruption of nuclear localisation signal or poor DNA-binding affinity. Furthermore, ex vivo inhibition of Tbx4 resulted in insufficiency of lung morphogenesis along with specific downregulation of Tie2 and Kruppel-like factor 4 expression. CONCLUSION Our results implicate variants in TBX4 as a genetic cause of PAH in a subset of the Japanese population. Variants in TBX4 may lead to PAH through insufficient lung morphogenesis by disrupting the TBX4-mediated direct regulation of FGF10 signalling and pulmonary vascular endothelial dysfunction involving PAH-related molecules.
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13
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Tsoi SM, Jones K, Colglazier E, Parker C, Nawaytou H, Teitel D, Fineman JR, Keller RL. Persistence of persistent pulmonary hypertension of the newborn: A case of de novo TBX4 variant. Pulm Circ 2022; 12:e12108. [PMID: 35874850 PMCID: PMC9297023 DOI: 10.1002/pul2.12108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/07/2022] [Accepted: 06/20/2022] [Indexed: 11/17/2022] Open
Abstract
We present a case of a late preterm infant placed on extracorporeal life support in the first day of life for persistent pulmonary hypertension of the newborn. Developmental arrest, pulmonary vascular hypertensive changes, and pulmonary interstitial glycogenosis were present on lung biopsy at 7 weeks of age. Pulmonary hypertension has persisted through childhood. Genetic testing at 8 years identified a novel mutation in TBX4.
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Affiliation(s)
- Stephanie M. Tsoi
- Division of Pediatric Critical Care, Department of PediatricsUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Kirk Jones
- Department of PathologyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Elizabeth Colglazier
- Department of NursingUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Claire Parker
- Department of NursingUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Hythem Nawaytou
- Division of Cardiology, Department of PediatricsUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - David Teitel
- Division of Cardiology, Department of PediatricsUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Jeffrey R. Fineman
- Division of Pediatric Critical Care, Department of PediatricsUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Roberta L. Keller
- Division of Neonatology, Department of PediatricsUniversity of California San FranciscoSan FranciscoCaliforniaUSA
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14
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Wade EM, Parthasarathy P, Mi J, Morgan T, Wollnik B, Robertson SP, Cundy T. Deletion of the last two exons of FGF10 in a family with LADD syndrome and pulmonary acinar hypoplasia. Eur J Hum Genet 2022; 30:480-484. [PMID: 33967277 PMCID: PMC8106901 DOI: 10.1038/s41431-021-00902-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/18/2021] [Accepted: 04/21/2021] [Indexed: 12/11/2022] Open
Abstract
Pulmonary acinar hypoplasia (PAH) and lacrimo-auriculo-dento-digital (LADD) syndrome have both been associated with loss-of-function variants in, or deletions of FGF10. Here we report a multi-generational family with seven members manifesting varying features of LADD syndrome, with one individual dying in early infancy of PAH. Whole genome sequencing in one family member identified a 12,158 bp deletion on chromosome 5p12 that removes two of the three exons of FGF10. Allele-specific PCR demonstrated that all affected family members, including the individual with PAH, carried the 12 kb deletion. We conclude the deletion is pathogenic and expands the mutational spectrum of FGF10 variants in LADD syndrome. The common mechanism underlying the variable clinical features of LADD syndrome is defective terminal branching of salivary and lacrimal glands and pulmonary acini, regulated by the TBX4-FGF10-FGFR2 pathway. The variable phenotypic expressivity of FGF10 haploinsufficiency from relatively benign to lethal is likely due to variation at other genetic loci.
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Affiliation(s)
- Emma M Wade
- Department of Women's and Children's Health, Otago Medical School, University of Otago, Dunedin, Aotearoa, New Zealand.
| | - Padmini Parthasarathy
- Department of Women's and Children's Health, Otago Medical School, University of Otago, Dunedin, Aotearoa, New Zealand
| | - Jingyi Mi
- Department of Women's and Children's Health, Otago Medical School, University of Otago, Dunedin, Aotearoa, New Zealand
| | - Tim Morgan
- Department of Women's and Children's Health, Otago Medical School, University of Otago, Dunedin, Aotearoa, New Zealand
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center, University of Göttingen, Göttingen, Germany
| | - Stephen P Robertson
- Department of Women's and Children's Health, Otago Medical School, University of Otago, Dunedin, Aotearoa, New Zealand
| | - Tim Cundy
- Department of Medicine, University of Auckland, Auckland, Aotearoa, New Zealand
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15
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Li P, Lan W, Li J, Zhang Y, Xiong Q, Ye J, Wu C, Xiao H. Identification and Functional Evaluation of a Novel TBX4 Mutation Underlies Small Patella Syndrome. Int J Mol Sci 2022; 23:ijms23042075. [PMID: 35216193 PMCID: PMC8875086 DOI: 10.3390/ijms23042075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/30/2022] [Accepted: 02/02/2022] [Indexed: 02/04/2023] Open
Abstract
Small patella syndrome (SPS) is a rare autosomal dominant disorder caused by mutations in TBX4 gene which encodes a transcription factor of FGF10. However, how TBX4 mutations result in SPS is poorly understood. Here, a novel TBX4 mutation c.1241C>T (p.P414L) was identified in a SPS family and series of studies were performed to evaluate the influences of TBX4 mutations (including c.1241C>T and two known mutations c.256G>C and c.743G>T). Results showed that mesenchymal stem cells (MSCs) with stable overexpression of either TBX4 wild-type (TBX4wt) or mutants (TBX4mt) were successfully generated. Immunofluorescence study revealed that both the overexpressed TBX4 wild-type and mutants were evenly expressed in the nucleus suggesting that these mutations do not alter the translocation of TBX4 into the nucleus. Interestingly, MSCs overexpression of TBX4mt exhibited reduced differentiation activities and decreased FGF10 expression. Chromatin immunoprecipitation (ChIP) study demonstrated that TBX4 mutants still could bind to the promoter of FGF10. However, dual luciferase reporter assay clarified that the binding efficiencies of TBX4 mutants to FGF10 promoter were reduced. Taken together, MSCs were firstly used to study the function of TBX4 mutations in this study and the results indicate that the reduced binding efficiencies of TBX4 mutants (TBX4mt) to the promoter of FGF10 result in the abnormal biological processes which provide important information for the pathogenesis of SPS.
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Affiliation(s)
- Ping Li
- Correspondence: (P.L.); (H.X.)
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16
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Yıldız Bölükbaşı E, Karolak JA, Szafranski P, Gambin T, Murik O, Zeevi DA, Altarescu G, Stankiewicz P. Exacerbation of mild lung disorders to lethal pulmonary hypoplasia by a noncoding hypomorphic SNV in a lung-specific enhancer in trans to the frameshifting TBX4 variant. Am J Med Genet A 2022; 188:1420-1425. [PMID: 35075769 PMCID: PMC8995354 DOI: 10.1002/ajmg.a.62656] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/20/2021] [Accepted: 12/30/2021] [Indexed: 12/26/2022]
Abstract
Variants involving TBX4 are associated with a wide variety of disorders, including pulmonary arterial hypertension, ischiocoxopodopatellar syndrome (ICPPS)/small patella syndrome (SPS), lethal lung developmental disorders (LLDDs) in neonates, heart defects, and prenatally lethal posterior amelia with pelvic and pulmonary hypoplasia syndrome. The objective of our study was to elucidate the wide variable phenotypic expressivity and incomplete penetrance in a three-generation family with a truncating variant in TBX4. In addition to exome and genome sequencing analyses, a candidate noncoding regulatory single nucleotide variant (SNV) within the lung-specific TBX4 enhancer was functionally tested using an in vitro luciferase reporter assay. A heterozygous frameshift variant c.1112dup (p.Pro372Serfs*14) in TBX4 was identified in patients with mild interstitial lung disease (1), bronchiolitis obliterans (1), recurrent pneumothorax (1), ICPPS/SPS (1), LLDD (2), and in unaffected individuals (4). In two deceased neonates with LLDD, we identified a noncoding SNV rs62069651-C located in trans to the mutated TBX4 allele that reduced the TBX4 promoter activity by 63% in the reporter assay. Our findings provide a functional evidence for the recently reported model of complex compound inheritance in which both TBX4 coding and in trans noncoding hypomorphic variants in the lung-specific enhancer of TBX4 contribute to LLDD.
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Affiliation(s)
- Esra Yıldız Bölükbaşı
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Justyna A Karolak
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Omer Murik
- Translational Genomics Lab, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - David A Zeevi
- Translational Genomics Lab, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Gheona Altarescu
- Preimplantation Genetic Unit, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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17
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Karolak JA, Gambin T, Szafranski P, Maywald RL, Popek E, Heaney JD, Stankiewicz P. Perturbation of semaphorin and VEGF signaling in ACDMPV lungs due to FOXF1 deficiency. Respir Res 2021; 22:212. [PMID: 34315444 PMCID: PMC8314029 DOI: 10.1186/s12931-021-01797-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 07/01/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a rare lethal congenital lung disorder in neonates characterized by severe progressive respiratory failure and refractory pulmonary hypertension, resulting from underdevelopment of the peripheral pulmonary tree. Causative heterozygous single nucleotide variants (SNVs) or copy-number variant (CNV) deletions involving FOXF1 or its distant lung-specific enhancer on chromosome 16q24.1 have been identified in 80-90% of ACDMPV patients. FOXF1 maps closely to and regulates the oppositely oriented FENDRR, with which it also shares regulatory elements. METHODS To better understand the transcriptional networks downstream of FOXF1 that are relevant for lung organogenesis, using RNA-seq, we have examined lung transcriptomes in 12 histopathologically verified ACDMPV patients with or without pathogenic variants in the FOXF1 locus and analyzed gene expression profile in FENDRR-depleted fetal lung fibroblasts, IMR-90. RESULTS RNA-seq analyses in ACDMPV neonates revealed changes in the expression of several genes, including semaphorins (SEMAs), neuropilin 1 (NRP1), and plexins (PLXNs), essential for both epithelial branching and vascular patterning. In addition, we have found deregulation of the vascular endothelial growth factor (VEGF) signaling that also controls pulmonary vasculogenesis and a lung-specific endothelial gene TMEM100 known to be essential in vascular morphogenesis. Interestingly, we have observed a substantial difference in gene expression profiles between the ACDMPV samples with different types of FOXF1 defect. Moreover, partial overlap between transcriptome profiles of ACDMPV lungs with FOXF1 SNVs and FENDRR-depleted IMR-90 cells suggests contribution of FENDRR to ACDMPV etiology. CONCLUSIONS Our transcriptomic data imply potential crosstalk between several lung developmental pathways, including interactions between FOXF1-SHH and SEMA-NRP or VEGF/VEGFR2 signaling, and provide further insight into complexity of lung organogenesis in humans.
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Affiliation(s)
- Justyna A Karolak
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Rm ABBR-R809, Houston, TX, 77030, USA.,Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-781, Poznań, Poland
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Rm ABBR-R809, Houston, TX, 77030, USA.,Institute of Computer Science, Warsaw University of Technology, 00-665, Warsaw, Poland
| | - Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Rm ABBR-R809, Houston, TX, 77030, USA
| | - Rebecca L Maywald
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Rm ABBR-R809, Houston, TX, 77030, USA
| | - Edwina Popek
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jason D Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Rm ABBR-R809, Houston, TX, 77030, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Rm ABBR-R809, Houston, TX, 77030, USA.
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18
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Genetic Testing for Neonatal Respiratory Disease. CHILDREN-BASEL 2021; 8:children8030216. [PMID: 33799761 PMCID: PMC8001923 DOI: 10.3390/children8030216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 02/27/2021] [Accepted: 03/08/2021] [Indexed: 11/16/2022]
Abstract
Genetic mechanisms are now recognized as rare causes of neonatal lung disease. Genes potentially responsible for neonatal lung disease include those encoding proteins important in surfactant function and metabolism, transcription factors important in lung development, proteins involved in ciliary assembly and function, and various other structural and immune regulation genes. The phenotypes of infants with genetic causes of neonatal lung disease may have some features that are difficult to distinguish clinically from more common, reversible causes of lung disease, and from each other. Multigene panels are now available that can allow for a specific diagnosis, providing important information for treatment and prognosis. This review discusses genes in which abnormalities are known to cause neonatal lung disease and their associated phenotypes, and advantages and limitations of genetic testing.
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19
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Abstract
PURPOSE OF REVIEW In 2013, the association between T-Box factor 4 (TBX4) variants and pulmonary arterial hypertension (PAH) has first been described. Now - in 2020 - growing evidence is emerging indicating that TBX4 variants associate with a wide spectrum of lung disorders. RECENT FINDINGS TBX4 variants are enriched in both children and adults with PAH. The clinical phenotype associated with a TBX4 variant seems to be milder than that in other PAH-associated gene mutations. Further, TBX4 variants have increasingly been associated with a variety of clinical and histopathological phenotypes, including lethal developmental parenchymal lung diseases such as not only acinar dysplasia in neonates, but also less outspoken parenchymal lung diseases in children and adults. SUMMARY The clinical phenotype of a TBX4 variant has recently been recognised to expand from bone disorders to different types of lung diseases. Recent data suggest that variants of TBX4, a transcription factor known to be an important regulator in embryonic development, are not rare in both children and adults with PAH and/or developmental parenchymal lung diseases.
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20
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Karolak JA, Gambin T, Szafranski P, Stankiewicz P. Potential interactions between the TBX4-FGF10 and SHH-FOXF1 signaling during human lung development revealed using ChIP-seq. Respir Res 2021; 22:26. [PMID: 33478486 PMCID: PMC7818749 DOI: 10.1186/s12931-021-01617-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/06/2021] [Indexed: 12/17/2022] Open
Abstract
Background The epithelial-mesenchymal signaling involving SHH-FOXF1, TBX4-FGF10, and TBX2 pathways is an essential transcriptional network operating during early lung organogenesis. However, precise regulatory interactions between different genes and proteins in this pathway are incompletely understood. Methods To identify TBX2 and TBX4 genome-wide binding sites, we performed chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) in human fetal lung fibroblasts IMR-90. Results We identified 14,322 and 1,862 sites strongly-enriched for binding of TBX2 and TBX4, respectively, 43.95% and 18.79% of which are located in the gene promoter regions. Gene Ontology, pathway enrichment, and DNA binding motif analyses revealed a number of overrepresented cues and transcription factor binding motifs relevant for lung branching that can be transcriptionally regulated by TBX2 and/or TBX4. In addition, TBX2 and TBX4 binding sites were found enriched around and within FOXF1 and its antisense long noncoding RNA FENDRR, indicating that the TBX4-FGF10 cascade may directly interact with the SHH-FOXF1 signaling. Conclusions We highlight the complexity of transcriptional network driven by TBX2 and TBX4 and show that disruption of this crosstalk during morphogenesis can play a substantial role in etiology of lung developmental disorders.
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Affiliation(s)
- Justyna A Karolak
- Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Rm ABBR-R809, Houston, TX, 77030, USA.,Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-781, Poznan, Poland
| | - Tomasz Gambin
- Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Rm ABBR-R809, Houston, TX, 77030, USA.,Institute of Computer Science, Warsaw University of Technology, 00-665, Warsaw, Poland
| | - Przemyslaw Szafranski
- Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Rm ABBR-R809, Houston, TX, 77030, USA
| | - Paweł Stankiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Rm ABBR-R809, Houston, TX, 77030, USA.
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21
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Swietlik EM, Prapa M, Martin JM, Pandya D, Auckland K, Morrell NW, Gräf S. 'There and Back Again'-Forward Genetics and Reverse Phenotyping in Pulmonary Arterial Hypertension. Genes (Basel) 2020; 11:E1408. [PMID: 33256119 PMCID: PMC7760524 DOI: 10.3390/genes11121408] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/17/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023] Open
Abstract
Although the invention of right heart catheterisation in the 1950s enabled accurate clinical diagnosis of pulmonary arterial hypertension (PAH), it was not until 2000 when the landmark discovery of the causative role of bone morphogenetic protein receptor type II (BMPR2) mutations shed new light on the pathogenesis of PAH. Since then several genes have been discovered, which now account for around 25% of cases with the clinical diagnosis of idiopathic PAH. Despite the ongoing efforts, in the majority of patients the cause of the disease remains elusive, a phenomenon often referred to as "missing heritability". In this review, we discuss research approaches to uncover the genetic architecture of PAH starting with forward phenotyping, which in a research setting should focus on stable intermediate phenotypes, forward and reverse genetics, and finally reverse phenotyping. We then discuss potential sources of "missing heritability" and how functional genomics and multi-omics methods are employed to tackle this problem.
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Affiliation(s)
- Emilia M. Swietlik
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
- Royal Papworth Hospital NHS Foundation Trust, Cambridge CB2 0AY, UK
- Addenbrooke’s Hospital NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Matina Prapa
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
- Addenbrooke’s Hospital NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Jennifer M. Martin
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
| | - Divya Pandya
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
| | - Kathryn Auckland
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
| | - Nicholas W. Morrell
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
- Royal Papworth Hospital NHS Foundation Trust, Cambridge CB2 0AY, UK
- Addenbrooke’s Hospital NHS Foundation Trust, Cambridge CB2 0QQ, UK
- NIHR BioResource for Translational Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Stefan Gräf
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
- NIHR BioResource for Translational Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
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22
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An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues. Sci Rep 2020; 10:20457. [PMID: 33235280 PMCID: PMC7686352 DOI: 10.1038/s41598-020-77586-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 11/11/2020] [Indexed: 12/11/2022] Open
Abstract
Long non-coding RNAs (LNC) regulate numerous biological processes. In contrast to human, the identification of LNC in farm species, like chicken, is still lacunar. We propose a catalogue of 52,075 chicken genes enriched in LNC (http://www.fragencode.org/), built from the Ensembl reference extended using novel LNC modelled here from 364 RNA-seq and LNC from four public databases. The Ensembl reference grew from 4,643 to 30,084 LNC, of which 59% and 41% with expression ≥ 0.5 and ≥ 1 TPM respectively. Characterization of these LNC relatively to the closest protein coding genes (PCG) revealed that 79% of LNC are in intergenic regions, as in other species. Expression analysis across 25 tissues revealed an enrichment of co-expressed LNC:PCG pairs, suggesting co-regulation and/or co-function. As expected LNC were more tissue-specific than PCG (25% vs. 10%). Similarly to human, 16% of chicken LNC hosted one or more miRNA. We highlighted a new chicken LNC, hosting miR155, conserved in human, highly expressed in immune tissues like miR155, and correlated with immunity-related PCG in both species. Among LNC:PCG pairs tissue-specific in the same tissue, we revealed an enrichment of divergent pairs with the PCG coding transcription factors, as for example LHX5, HXD3 and TBX4, in both human and chicken.
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23
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Abstract
There is a wide differential diagnosis of early onset respiratory distress especially in term babies, and interstitial lung disease (chILD) is a rare but important consideration in this context. chILD manifesting immediately after birth is usually related to mutations in surfactant protein genes, or conditions related to the Congenital Acinar Dysplasia -Alveolar capillary dysplasia - Congenital Alveolar Dysplasia (CAD-ACD) spectrum. There is currently no specific treatment for these conditions, and management is supportive. Prognosis is very poor in most of these babies if onset is early, with relentless respiratory deterioration unless transplanted. Ideally, the diagnosis is made on genetic analysis, but this may be time-consuming and complex in CAD-ACD spectrum, so lung biopsy may be needed to avoid prolonged and futile treatment being instituted. Milder forms with prolonged survival have been reported. Early onset, less severe chILD is usually related to neuroendocrine cell hyperplasia of infancy (NEHI), pulmonary interstitial glycogenosis (PIG) and less severe disorders of surfactant proteins. PIG and NEHI are not specific entities, but are pulmonary dysmaturity syndromes, and there may be a number of underlying genetic and other cause. If the child is stable and thriving, many will not be subject to lung biopsy, and slow improvement and weaning of supplemental oxygen can be anticipated. Where possible, a precise genetic diagnosis should be made in early onset cHILD allow for genetic counselling. chILD survivors and their families have complex respiratory and other needs, and co-ordinated, multi-disciplinary support in the community is essential.
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Affiliation(s)
- Andrew Bush
- Imperial College, UK; Royal Brompton and Harefield NHS Foundation Trust, UK.
| | | | - Jo Gregory
- Royal Brompton and Harefield NHS Foundation Trust, UK
| | - Andrew Gordon Nicholson
- Royal Brompton and Harefield NHS Foundation Trust, UK; National Heart and Lung Institute, Imperial College, UK
| | - Thomas Semple
- Imperial College, UK; Royal Brompton and Harefield NHS Foundation Trust, UK
| | - Rishi Pabary
- Imperial College, UK; Royal Brompton and Harefield NHS Foundation Trust, UK
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24
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Haarman MG, Kerstjens-Frederikse WS, Vissia-Kazemier TR, Breeman KTN, Timens W, Vos YJ, Roofthooft MTR, Hillege HL, Berger RMF. The Genetic Epidemiology of Pediatric Pulmonary Arterial Hypertension. J Pediatr 2020; 225:65-73.e5. [PMID: 32502478 DOI: 10.1016/j.jpeds.2020.05.051] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/27/2020] [Accepted: 05/26/2020] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To describe the prevalence of pulmonary arterial hypertension (PAH)-associated gene mutations, and other genetic characteristics in a national cohort of children with PAH from the Dutch National registry and to explore genotype-phenotype associations and outcomes. STUDY DESIGN Children (n = 70) diagnosed with idiopathic PAH, heritable PAH, PAH associated with congenital heart disease with coincidental shunt (PAH-congenital heart disease group 3), PAH after closure of a cardiac shunt (PAH-congenital heart disease group 4), or PAH associated with other noncardiac conditions were enrolled. Targeted next-generation sequencing was performed on PAH-associated genes (BMPR2, ACVRL1, EIF2AK4, CAV1, ENG, KCNK3, SMAD9, and TBX4). Also, children were tested for specific genetic disorders in case of clinical suspicion. Additionally, children were tested for copy number variations. RESULTS Nineteen children (27%) had a PAH-associated gene mutation/variant: BMPR2 n = 7, TBX4 n = 8, ACVRL1 n = 1, KCNK3 n = 1, and EIF2AK4 n = 2. Twelve children (17%) had a genetic disorder with an established association with PAH (including trisomy 21 and cobalamin C deficiency). In another 16 children (23%), genetic disorders without an established association with PAH were identified (including Noonan syndrome, Beals syndrome, and various copy number variations). Survival rates differed between groups and was most favorable in TBX4 variant carriers. CONCLUSIONS Children with PAH show a high prevalence of genetic disorders, not restricted to established PAH-associated genes. Genetic architecture could play a role in risk-stratified care management in pediatric PAH.
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Affiliation(s)
- Meindina G Haarman
- Center for Congenital Heart Diseases, Department of Pediatric Cardiology, Beatrix Children's Hospital, University Medical Center Groningen, Groningen, the Netherlands.
| | | | - Theresia R Vissia-Kazemier
- Center for Congenital Heart Diseases, Department of Pediatric Cardiology, Beatrix Children's Hospital, University Medical Center Groningen, Groningen, the Netherlands
| | - Karel T N Breeman
- Center for Congenital Heart Diseases, Department of Pediatric Cardiology, Beatrix Children's Hospital, University Medical Center Groningen, Groningen, the Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, the Netherlands
| | - Yvonne J Vos
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marc T R Roofthooft
- Center for Congenital Heart Diseases, Department of Pediatric Cardiology, Beatrix Children's Hospital, University Medical Center Groningen, Groningen, the Netherlands
| | - Hans L Hillege
- Department of Epidemiology, University Medical Center Groningen, Groningen, the Netherlands; Department of Cardiology, University Medical Center Groningen, Groningen, the Netherlands
| | - Rolf M F Berger
- Center for Congenital Heart Diseases, Department of Pediatric Cardiology, Beatrix Children's Hospital, University Medical Center Groningen, Groningen, the Netherlands
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25
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Jansen SMA, van den Heuvel L, Meijboom LJ, Alsters SIM, Vonk Noordegraaf A, Houweling A, Bogaard HJ. Correspondence regarding "T-box protein 4 mutation causing pulmonary arterial hypertension and lung disease": a single-centre case series. Eur Respir J 2020; 55:55/5/1902272. [PMID: 32409423 DOI: 10.1183/13993003.02272-2019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 01/27/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Samara M A Jansen
- Dept of Pulmonary Diseases, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Lieke van den Heuvel
- Dept of Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Lilian J Meijboom
- Dept Of Radiology and Nuclear Medicine, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Suzanne I M Alsters
- Dept of Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Anton Vonk Noordegraaf
- Dept of Pulmonary Diseases, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Arjan Houweling
- Dept of Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Harm Jan Bogaard
- Dept of Pulmonary Diseases, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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26
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Austin ED, Elliott CG. TBX4 syndrome: a systemic disease highlighted by pulmonary arterial hypertension in its most severe form. Eur Respir J 2020; 55:55/5/2000585. [PMID: 32409426 DOI: 10.1183/13993003.00585-2020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 03/16/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Eric D Austin
- Dept of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - C Gregory Elliott
- Dept of Medicine, Intermountain Medical Center and the University of Utah, Murray, UT, USA
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27
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Vincent M, Karolak JA, Deutsch G, Gambin T, Popek E, Isidor B, Szafranski P, Le Caignec C, Stankiewicz P. Clinical, Histopathological, and Molecular Diagnostics in Lethal Lung Developmental Disorders. Am J Respir Crit Care Med 2020; 200:1093-1101. [PMID: 31189067 DOI: 10.1164/rccm.201903-0495tr] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Lethal lung developmental disorders are a rare but important group of pediatric diffuse lung diseases presenting with neonatal respiratory failure. On the basis of histopathological appearance at lung biopsy or autopsy, they have been termed: alveolar capillary dysplasia with misalignment of the pulmonary veins, acinar dysplasia, congenital alveolar dysplasia, and other unspecified primary pulmonary hypoplasias. However, the histopathological continuum in these lethal developmental disorders has made accurate diagnosis challenging, which has implications for recurrence risk. Over the past decade, genetic studies in infants with alveolar capillary dysplasia with misalignment of the pulmonary veins have revealed the causative role of the dosage-sensitive FOXF1 gene and its noncoding regulatory variants in the distant lung-specific enhancer at chromosome 16q24.1. In contrast, the molecular bases of acinar dysplasia and congenital alveolar dysplasia have remained poorly understood. Most recently, disruption of the TBX4-FGF10-FGFR2 epithelial-mesenchymal signaling pathway has been reported in patients with these lethal pulmonary dysplasias. Application of next-generation sequencing techniques, including exome sequencing and whole-genome sequencing, has demonstrated their complex compound inheritance. These data indicate that noncoding regulatory elements play a critical role in lung development in humans. We propose that for more precise lethal lung developmental disorder diagnosis, a diagnostic pathway including whole-genome sequencing should be implemented.
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Affiliation(s)
- Marie Vincent
- Service de Genetique Medicale, Centre Hospitalier Universitaire de Nantes, Nantes, France.,Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Université de Nantes, L'institut du Thorax, Nantes, France
| | - Justyna A Karolak
- Department of Molecular and Human Genetics and.,Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Gail Deutsch
- Department of Pathology, Seattle Children's Hospital, Seattle, Washington
| | - Tomasz Gambin
- Department of Molecular and Human Genetics and.,Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland; and.,Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Edwina Popek
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Bertrand Isidor
- Service de Genetique Medicale, Centre Hospitalier Universitaire de Nantes, Nantes, France.,Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Université de Nantes, L'institut du Thorax, Nantes, France
| | | | - Cedric Le Caignec
- Service de Genetique Medicale, Centre Hospitalier Universitaire de Nantes, Nantes, France
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28
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Karolak JA, Gambin T, Honey EM, Slavik T, Popek E, Stankiewicz P. A de novo 2.2 Mb recurrent 17q23.1q23.2 deletion unmasks novel putative regulatory non-coding SNVs associated with lethal lung hypoplasia and pulmonary hypertension: a case report. BMC Med Genomics 2020; 13:34. [PMID: 32143628 PMCID: PMC7060516 DOI: 10.1186/s12920-020-0701-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 02/27/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Application of whole genome sequencing (WGS) enables identification of non-coding variants that play a phenotype-modifying role and are undetectable by exome sequencing. Recently, non-coding regulatory single nucleotide variants (SNVs) have been reported in patients with lethal lung developmental disorders (LLDDs) or congenital scoliosis with recurrent copy-number variant (CNV) deletions at 17q23.1q23.2 or 16p11.2, respectively. CASE PRESENTATION Here, we report a deceased newborn with pulmonary hypertension and pulmonary interstitial emphysema with features suggestive of pulmonary hypoplasia, resulting in respiratory failure and neonatal death soon after birth. Using the array comparative genomic hybridization and WGS, two heterozygous recurrent CNV deletions: ~ 2.2 Mb on 17q23.1q23.2, involving TBX4, and ~ 600 kb on 16p11.2, involving TBX6, that both arose de novo on maternal chromosomes were identified. In the predicted lung-specific enhancer upstream to TBX4, we have detected seven novel putative regulatory non-coding SNVs that were absent in 13 control individuals with the overlapping deletions but without any structural lung anomalies. CONCLUSIONS Our findings further support a recently reported model of complex compound inheritance of LLDD in which both non-coding and coding heterozygous TBX4 variants contribute to the lung phenotype. In addition, this is the first report of a patient with combined de novo heterozygous recurrent 17q23.1q23.2 and 16p11.2 CNV deletions.
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Affiliation(s)
- Justyna A Karolak
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-781, Poznan, Poland
| | - Tomasz Gambin
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Institute of Computer Science, Warsaw University of Technology, 00-665, Warsaw, Poland
| | - Engela M Honey
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Science, University of Pretoria, Pretoria, South Africa
| | - Tomas Slavik
- Ampath Pathology Laboratories, and Department of Anatomical Pathology, University of Pretoria, Pretoria, South Africa
| | - Edwina Popek
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Paweł Stankiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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29
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Wei M, Fu H, Han A, Ma L. A Term Neonatal Case With Lethal Respiratory Failure Associated With a Novel Homozygous Mutation in ABCA3 Gene. Front Pediatr 2020; 8:138. [PMID: 32363169 PMCID: PMC7181334 DOI: 10.3389/fped.2020.00138] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 03/11/2020] [Indexed: 11/13/2022] Open
Abstract
The mutations in the ABCA3 (ATP-binding cassette transporter subfamily A member 3) gene could result in lethal respiratory distress syndrome (RDS) in neonates and interstitial lung disease (ILD) in infants and children. Here, we describe a full-term newborn who manifested respiratory distress 20 min after birth and then gradually developed hypoxemic respiratory failure and died on 53 days of life. A homozygous missense mutation (c.746C >T) was identified in exon 8 of ABCA3 gene in the neonate by next-generation sequencing, and the mutations were inherited from parents, respectively. This homozygous mutation is the first reported to date.
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Affiliation(s)
- Meili Wei
- Department of Pediatrics, Zibo Central Hospital, Shandong, China
| | - Haibo Fu
- Department of Pediatrics, Zibo Central Hospital, Shandong, China
| | - Aiqin Han
- Department of Pediatrics, Zibo Central Hospital, Shandong, China
| | - Liji Ma
- Department of Pediatrics, Zibo Central Hospital, Shandong, China
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30
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Kariminejad A, Szenker-Ravi E, Lekszas C, Tajsharghi H, Moslemi AR, Naert T, Tran HT, Ahangari F, Rajaei M, Nasseri M, Haaf T, Azad A, Superti-Furga A, Maroofian R, Ghaderi-Sohi S, Najmabadi H, Abbaszadegan MR, Vleminckx K, Nikuei P, Reversade B. Homozygous Null TBX4 Mutations Lead to Posterior Amelia with Pelvic and Pulmonary Hypoplasia. Am J Hum Genet 2019; 105:1294-1301. [PMID: 31761294 DOI: 10.1016/j.ajhg.2019.10.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 10/25/2019] [Indexed: 12/16/2022] Open
Abstract
The development of hindlimbs in tetrapod species relies specifically on the transcription factor TBX4. In humans, heterozygous loss-of-function TBX4 mutations cause dominant small patella syndrome (SPS) due to haploinsufficiency. Here, we characterize a striking clinical entity in four fetuses with complete posterior amelia with pelvis and pulmonary hypoplasia (PAPPA). Through exome sequencing, we find that PAPPA syndrome is caused by homozygous TBX4 inactivating mutations during embryogenesis in humans. In two consanguineous couples, we uncover distinct germline TBX4 coding mutations, p.Tyr113∗ and p.Tyr127Asn, that segregated with SPS in heterozygous parents and with posterior amelia with pelvis and pulmonary hypoplasia syndrome (PAPPAS) in one available homozygous fetus. A complete absence of TBX4 transcripts in this proband with biallelic p.Tyr113∗ stop-gain mutations revealed nonsense-mediated decay of the endogenous mRNA. CRISPR/Cas9-mediated TBX4 deletion in Xenopus embryos confirmed its restricted role during leg development. We conclude that SPS and PAPPAS are allelic diseases of TBX4 deficiency and that TBX4 is an essential transcription factor for organogenesis of the lungs, pelvis, and hindlimbs in humans.
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Affiliation(s)
| | - Emmanuelle Szenker-Ravi
- Institute of Medical Biology, Agency for Science, Technology, and Research, 8A Biomedical Grove, Singapore 138648, Republic of Singapore
| | - Caroline Lekszas
- Institute of Human Genetics, Julius-Maximilians-Universität, 97074 Würzburg, Germany
| | - Homa Tajsharghi
- School of Health Sciences, Division Biomedicine, University of Skövde, 54128 Skövde, Sweden
| | - Ali-Reza Moslemi
- Institute of Biomedicine, Sahlgrenska University Hospital, Gothenburg University, 41390 Gothenburg, Sweden
| | - Thomas Naert
- Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium
| | - Hong Thi Tran
- Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium
| | - Fatemeh Ahangari
- Kariminejad-Najmabadi Pathology and Genetics Center, Tehran 14665, Iran
| | - Minoo Rajaei
- Fertility and Infertility Research Center, Hormozgan University of Medical Sciences, Bandar Abbas 7919915519, Iran
| | - Mojila Nasseri
- Pardis Clinical and Genetics Laboratory, Mashhad 9177948974, Iran
| | - Thomas Haaf
- Institute of Human Genetics, Julius-Maximilians-Universität, 97074 Würzburg, Germany
| | - Afrooz Azad
- Fertility and Infertility Research Center, Hormozgan University of Medical Sciences, Bandar Abbas 7919915519, Iran
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital (CHUV), University of Lausanne, 1011 Lausanne, Switzerland
| | - Reza Maroofian
- Molecular and Clinical Sciences Institute, St. George's University of London, Cranmer Terrace, London SW17 0RE, UK
| | | | - Hossein Najmabadi
- Kariminejad-Najmabadi Pathology and Genetics Center, Tehran 14665, Iran; Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran 1985713834, Iran
| | - Mohammad Reza Abbaszadegan
- Pardis Clinical and Genetics Laboratory, Mashhad 9177948974, Iran; Division of Human Genetics, Immunology Research Center, Avicenna Research Institute, Mashhad University of Medical Sciences, Mashhad 15731, Iran
| | - Kris Vleminckx
- Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium
| | - Pooneh Nikuei
- Fertility and Infertility Research Center, Hormozgan University of Medical Sciences, Bandar Abbas 7919915519, Iran.
| | - Bruno Reversade
- Institute of Medical Biology, Agency for Science, Technology, and Research, 8A Biomedical Grove, Singapore 138648, Republic of Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research, 61 Biopolis Drive, Singapore 138673, Republic of Singapore; Department of Medical Genetics, Koç University, School of Medicine, 34010 Topkapı, Istanbul, Turkey.
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31
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Lignelli E, Palumbo F, Myti D, Morty RE. Recent advances in our understanding of the mechanisms of lung alveolarization and bronchopulmonary dysplasia. Am J Physiol Lung Cell Mol Physiol 2019; 317:L832-L887. [PMID: 31596603 DOI: 10.1152/ajplung.00369.2019] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Bronchopulmonary dysplasia (BPD) is the most common cause of morbidity and mortality in preterm infants. A key histopathological feature of BPD is stunted late lung development, where the process of alveolarization-the generation of alveolar gas exchange units-is impeded, through mechanisms that remain largely unclear. As such, there is interest in the clarification both of the pathomechanisms at play in affected lungs, and the mechanisms of de novo alveoli generation in healthy, developing lungs. A better understanding of normal and pathological alveolarization might reveal opportunities for improved medical management of affected infants. Furthermore, disturbances to the alveolar architecture are a key histopathological feature of several adult chronic lung diseases, including emphysema and fibrosis, and it is envisaged that knowledge about the mechanisms of alveologenesis might facilitate regeneration of healthy lung parenchyma in affected patients. To this end, recent efforts have interrogated clinical data, developed new-and refined existing-in vivo and in vitro models of BPD, have applied new microscopic and radiographic approaches, and have developed advanced cell-culture approaches, including organoid generation. Advances have also been made in the development of other methodologies, including single-cell analysis, metabolomics, lipidomics, and proteomics, as well as the generation and use of complex mouse genetics tools. The objective of this review is to present advances made in our understanding of the mechanisms of lung alveolarization and BPD over the period 1 January 2017-30 June 2019, a period that spans the 50th anniversary of the original clinical description of BPD in preterm infants.
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Affiliation(s)
- Ettore Lignelli
- Department of Lung Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center, member of the German Center for Lung Research, Giessen, Germany
| | - Francesco Palumbo
- Department of Lung Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center, member of the German Center for Lung Research, Giessen, Germany
| | - Despoina Myti
- Department of Lung Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center, member of the German Center for Lung Research, Giessen, Germany
| | - Rory E Morty
- Department of Lung Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center, member of the German Center for Lung Research, Giessen, Germany
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32
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Galambos C, Mullen MP, Shieh JT, Schwerk N, Kielt MJ, Ullmann N, Boldrini R, Stucin-Gantar I, Haass C, Bansal M, Agrawal PB, Johnson J, Peca D, Surace C, Cutrera R, Pauciulo MW, Nichols WC, Griese M, Ivy D, Abman SH, Austin ED, Danhaive O. Phenotype characterisation of TBX4 mutation and deletion carriers with neonatal and paediatric pulmonary hypertension. Eur Respir J 2019; 54:13993003.01965-2018. [PMID: 31151956 DOI: 10.1183/13993003.01965-2018] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 04/19/2019] [Indexed: 11/05/2022]
Abstract
Rare variants in the T-box transcription factor 4 gene (TBX4) have recently been recognised as an emerging cause of paediatric pulmonary hypertension (PH). Their pathophysiology and contribution to persistent pulmonary hypertension in neonates (PPHN) are unknown. We sought to define the spectrum of clinical manifestations and histopathology associated with TBX4 variants in neonates and children with PH.We assessed clinical data and lung tissue in 19 children with PH, including PPHN, carrying TBX4 rare variants identified by next-generation sequencing and copy number variation arrays.Variants included six 17q23 deletions encompassing the entire TBX4 locus and neighbouring genes, and 12 likely damaging mutations. 10 infants presented with neonatal hypoxic respiratory failure and PPHN, and were subsequently discharged home. PH was diagnosed later in infancy or childhood. Three children died and two required lung transplantation. Associated anomalies included patent ductus arteriosus, septal defects, foot anomalies and developmental disability, the latter with a higher prevalence in deletion carriers. Histology in seven infants showed abnormal distal lung development and pulmonary hypertensive remodelling.TBX4 mutations and 17q23 deletions underlie a new form of developmental lung disease manifesting with severe, often biphasic PH at birth and/or later in infancy and childhood, often associated with skeletal anomalies, cardiac defects, neurodevelopmental disability and other anomalies.
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Affiliation(s)
- Csaba Galambos
- Dept of Pathology and Laboratory Services, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA.,Contributed equally to this work as joint first authors
| | - Mary P Mullen
- Dept of Cardiology, Boston Children's Hospital and Pediatrics Harvard Medical School, Boston, MA, USA.,Contributed equally to this work as joint first authors
| | - Joseph T Shieh
- Institute for Human Genetics, Medical Genetics, University of California San Francisco, UCSF Benioff Children's Hospital, San Francisco, CA, USA
| | - Nicolaus Schwerk
- Clinic for Pediatric Pulmonology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Matthew J Kielt
- Division of Pediatric Pulmonology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nicola Ullmann
- Division of Pediatric Pulmonology, Bambino Gesù Children's Hospital, Rome, Italy
| | - Renata Boldrini
- Dept of Laboratory Medicine, Bambino Gesù Children's Hospital, Rome, Italy
| | | | - Cristina Haass
- Division of Neonatology, San Pietro-Fatebenefratelli Hospital, Rome, Italy
| | - Manish Bansal
- Division of Pediatric Cardiology, University of Iowa Children's Hospital, Iowa City, IA, USA
| | - Pankaj B Agrawal
- Division of Newborn Medicine and Genetics and Genomics, Harvard School of Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Joyce Johnson
- Dept of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Donatella Peca
- Dept of Laboratory Medicine, Bambino Gesù Children's Hospital, Rome, Italy
| | - Cecilia Surace
- Dept of Laboratory Medicine, Bambino Gesù Children's Hospital, Rome, Italy
| | - Renato Cutrera
- Division of Pediatric Pulmonology, Bambino Gesù Children's Hospital, Rome, Italy
| | - Michael W Pauciulo
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Dept of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - William C Nichols
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Dept of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Matthias Griese
- Division of Pediatric Pulmonology, Ludwig-Maximilians-University, Munich, Germany
| | - Dunbar Ivy
- Division of Pediatric Cardiology, Dept of Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Steven H Abman
- Division of Pulmonary Medicine, Dept of Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Eric D Austin
- Division of Pediatric Pulmonology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Olivier Danhaive
- Division of Neonatology, University of California San Francisco Benioff Children's Hospital, San Francisco, CA, USA .,Division of Neonatology, Catholic University of Louvain, Brussels, Belgium
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33
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Haarman MG, Kerstjens-Frederikse WS, Berger RM. The ever-expanding phenotypical spectrum of human TBX4 mutations: from toe to lung. Eur Respir J 2019; 54:54/2/1901504. [DOI: 10.1183/13993003.01504-2019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 07/29/2019] [Indexed: 11/05/2022]
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34
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Karolak JA, Szafranski P, Kilner D, Patel C, Scurry B, Kinning E, Chandler K, Jhangiani SN, Coban Akdemir ZH, Lupski JR, Popek E, Stankiewicz P. Heterozygous CTNNB1 and TBX4 variants in a patient with abnormal lung growth, pulmonary hypertension, microcephaly, and spasticity. Clin Genet 2019; 96:366-370. [PMID: 31309540 DOI: 10.1111/cge.13605] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 02/06/2023]
Abstract
The canonical wingless (Wnt) and fibroblast growth factor (FGF) signaling pathways involving CTNNB1 and TBX4, respectively, are crucial for the regulation of human development. Perturbations of these pathways and disruptions from biological homeostasis have been associated with abnormal morphogenesis of multiple organs, including the lung. The aim of this study was to identify the underlying genetic cause of abnormal lung growth, pulmonary hypertension (PAH), severe microcephaly, and muscle spasticity in a full-term newborn, who died at 4 months of age due to progressively worsening PAH and respiratory failure. Family trio exome sequencing showed a de novo heterozygous nonsense c.1603C>T (p.Arg535*) variant in CTNNB1 and a paternally inherited heterozygous missense c.1198G>A (p.Glu400Lys) variant in TBX4, both predicted to be likely deleterious. We expand the phenotypic spectrum associated with CTNNB1 and TBX4 variants and indicate that they could act synergistically to produce a distinct more severe phenotype. Our findings further support a recently proposed complex compound inheritance model in lethal lung developmental diseases and the contention that dual molecular diagnoses can parsimoniously explain blended phenotypes.
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Affiliation(s)
- Justyna A Karolak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - David Kilner
- Department of Respiratory and Sleep Medicine, Queensland Children's Hospital, South Brisbane, Queensland, Australia.,The University of Queensland, Brisbane, Queensland, Australia
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Bonnie Scurry
- Pathology Queensland, Royal Brisbane and Women's Hospital and Lady Cilento Children's Hospital, Brisbane, Queensland, Australia
| | - Esther Kinning
- West of Scotland Regional Genetics Service, Queen Elizabeth Hospital, Glasgow, UK
| | - Kate Chandler
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | | | | | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Edwina Popek
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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Maurac A, Lardenois É, Eyries M, Ghigna MR, Petit I, Montani D, Guillaumot A, Caput B, Chabot F, Chaouat A. T-box protein 4 mutation causing pulmonary arterial hypertension and lung disease. Eur Respir J 2019; 54:13993003.00388-2019. [DOI: 10.1183/13993003.00388-2019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/05/2019] [Indexed: 12/26/2022]
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Karolak JA, Vincent M, Deutsch G, Gambin T, Cogné B, Pichon O, Vetrini F, Mefford HC, Dines JN, Golden-Grant K, Dipple K, Freed AS, Leppig KA, Dishop M, Mowat D, Bennetts B, Gifford AJ, Weber MA, Lee AF, Boerkoel CF, Bartell TM, Ward-Melver C, Besnard T, Petit F, Bache I, Tümer Z, Denis-Musquer M, Joubert M, Martinovic J, Bénéteau C, Molin A, Carles D, André G, Bieth E, Chassaing N, Devisme L, Chalabreysse L, Pasquier L, Secq V, Don M, Orsaria M, Missirian C, Mortreux J, Sanlaville D, Pons L, Küry S, Bézieau S, Liet JM, Joram N, Bihouée T, Scott DA, Brown CW, Scaglia F, Tsai ACH, Grange DK, Phillips JA, Pfotenhauer JP, Jhangiani SN, Gonzaga-Jauregui CG, Chung WK, Schauer GM, Lipson MH, Mercer CL, van Haeringen A, Liu Q, Popek E, Coban Akdemir ZH, Lupski JR, Szafranski P, Isidor B, Le Caignec C, Stankiewicz P. Complex Compound Inheritance of Lethal Lung Developmental Disorders Due to Disruption of the TBX-FGF Pathway. Am J Hum Genet 2019; 104:213-228. [PMID: 30639323 DOI: 10.1016/j.ajhg.2018.12.010] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 12/13/2018] [Indexed: 12/24/2022] Open
Abstract
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 = 14), congenital alveolar dysplasia (n = 2), and other lethal lung hypoplasias (n = 10). We identified rare heterozygous copy-number variant deletions or single-nucleotide variants (SNVs) involving TBX4 (n = 8 and n = 2, respectively) or FGF10 (n = 2 and n = 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 control 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 pulmonary 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.
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MESH Headings
- DNA Copy Number Variations/genetics
- Female
- Fibroblast Growth Factor 10/genetics
- Fibroblast Growth Factor 10/metabolism
- Gene Expression Regulation
- Gestational Age
- Humans
- Infant, Newborn
- Infant, Newborn, Diseases/genetics
- Infant, Newborn, Diseases/metabolism
- Infant, Newborn, Diseases/mortality
- Infant, Newborn, Diseases/pathology
- Lung/embryology
- Lung/growth & development
- Lung Diseases/genetics
- Lung Diseases/metabolism
- Lung Diseases/mortality
- Lung Diseases/pathology
- Male
- Maternal Inheritance
- Organogenesis
- Paternal Inheritance
- Pedigree
- Polymorphism, Single Nucleotide/genetics
- Receptor, Fibroblast Growth Factor, Type 2/metabolism
- Signal Transduction/genetics
- T-Box Domain Proteins/genetics
- T-Box Domain Proteins/metabolism
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Affiliation(s)
- Justyna A Karolak
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-781 Poznan, Poland
| | - Marie Vincent
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Gail Deutsch
- Department of Pathology, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Tomasz Gambin
- Department of Medical Genetics, Institute of Mother and Child, 01-211 Warsaw, Poland; Institute of Computer Science, Warsaw University of Technology, 00-665 Warsaw, Poland
| | - Benjamin Cogné
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Olivier Pichon
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France
| | | | - Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jennifer N Dines
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA; Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | - Katie Golden-Grant
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Katrina Dipple
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA; Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Amanda S Freed
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA; Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | - Kathleen A Leppig
- Genetic Services Kaiser Permanente of Washington, Seattle, WA 98112, USA
| | - Megan Dishop
- Pathology and Laboratory Medicine, Phoenix Children's Hospital, Phoenix, AZ 85016, USA
| | - David Mowat
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick Sydney, NSW 2031 Australia; School of Women's and Children's Health, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Bruce Bennetts
- Discipline of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia; Molecular Genetics Department, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia; Discipline of Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - Andrew J Gifford
- School of Women's and Children's Health, The University of New South Wales, Sydney, NSW 2052, Australia; Department of Anatomical Pathology, Prince of Wales Hospital, Randwick, NSW 2031, Australia
| | - Martin A Weber
- Department of Anatomical Pathology, Prince of Wales Hospital, Randwick, NSW 2031, Australia; School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Anna F Lee
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Cornelius F Boerkoel
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Tina M Bartell
- Department of Genetics, Kaiser Permanente Sacramento Medical Center, Sacramento, CA 95815, USA
| | | | - Thomas Besnard
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Florence Petit
- Service de Génétique Clinique, CHU Lille, 59000 Lille, France
| | - Iben Bache
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 N Copenhagen, Denmark; Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2100 Ø Copenhagen, Denmark
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2600 Glostrup, Copenhagen, Denmark; Deparment of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 N, Copenhagen, Denmark
| | | | | | - Jelena Martinovic
- Unit of Fetal Pathology, AP-HP, Antoine Beclere Hospital, 75000 Paris, France
| | - Claire Bénéteau
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Arnaud Molin
- Service de Génétique Médicale, CHU Caen, 14000 Caen, France
| | - Dominique Carles
- Service d'anatomo-pathologie, CHU Bordeaux, 33000 Bordeaux, France
| | - Gwenaelle André
- Service d'anatomo-pathologie, CHU Bordeaux, 33000 Bordeaux, France
| | - Eric Bieth
- Service de génétique médicale, CHU Toulouse, France and UDEAR, UMR 1056 Inserm - Université de Toulouse, 31000 Toulouse, France
| | - Nicolas Chassaing
- Service de génétique médicale, CHU Toulouse, France and UDEAR, UMR 1056 Inserm - Université de Toulouse, 31000 Toulouse, France
| | | | | | | | - Véronique Secq
- Aix Marseille Univ, APHM, Hôpital Nord, Service d'anatomo-pathologie, 13000 Marseille, France
| | - Massimiliano Don
- Sant'Antonio General Hospital, Pediatric Care Unit, San Daniele del Friuli, 33100 Udine, Italy
| | - Maria Orsaria
- Department of Medical and Biological Sciences, Pathology Unit, University of Udine, Udine, Italy
| | - Chantal Missirian
- Aix Marseille Univ, APHM, INSERM, MMG, Marseille, Timone Hospital, 13000 Marseille, France
| | - Jérémie Mortreux
- Aix Marseille Univ, APHM, INSERM, MMG, Marseille, Timone Hospital, 13000 Marseille, France
| | - Damien Sanlaville
- Hospices Civils de Lyon, GHE, Genetics department, and Lyon University, 69000 Lyon, France
| | - Linda Pons
- Hospices Civils de Lyon, GHE, Genetics department, and Lyon University, 69000 Lyon, France
| | - Sébastien Küry
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Stéphane Bézieau
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Jean-Michel Liet
- Service de réanimation pédiatrique, CHU Nantes, 44000 Nantes, France
| | - Nicolas Joram
- Service de réanimation pédiatrique, CHU Nantes, 44000 Nantes, France
| | | | - Daryl A Scott
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chester W Brown
- Department of Pediatrics, Genetics Division, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Fernando Scaglia
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Joint BCM-CUHK Center of Medical Genetics, Prince of Wales Hospital, ShaTin, New Territories, Hong Kong SAR
| | - Anne Chun-Hui Tsai
- Department of Pediatrics, The Children's Hospital, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Dorothy K Grange
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis Children's Hospital, St. Louis, MO 63110, USA
| | - John A Phillips
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jean P Pfotenhauer
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY 10032, USA
| | - Galen M Schauer
- Department of Pathology, Kaiser Permanente Oakland Medical Center, Oakland, CA 94611, USA
| | - Mark H Lipson
- Department of Genetics, Kaiser Permanente Sacramento Medical Center, Sacramento, CA 95815, USA
| | - Catherine L Mercer
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Princess Anne Hospital, Southampton SO16 5YA, UK
| | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Qian Liu
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Edwina Popek
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep H Coban Akdemir
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Przemyslaw Szafranski
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | | | - Paweł Stankiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA; Institute of Mother and Child, 01-211 Warsaw, Poland.
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37
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Single cell RNA analysis identifies cellular heterogeneity and adaptive responses of the lung at birth. Nat Commun 2019; 10:37. [PMID: 30604742 PMCID: PMC6318311 DOI: 10.1038/s41467-018-07770-1] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 11/19/2018] [Indexed: 12/12/2022] Open
Abstract
The respiratory system undergoes a diversity of structural, biochemical, and functional changes necessary for adaptation to air breathing at birth. To identify the heterogeneity of pulmonary cell types and dynamic changes in gene expression mediating adaptation to respiration, here we perform single cell RNA analyses of mouse lung on postnatal day 1. Using an iterative cell type identification strategy we unbiasedly identify the heterogeneity of murine pulmonary cell types. We identify distinct populations of epithelial, endothelial, mesenchymal, and immune cells, each containing distinct subpopulations. Furthermore we compare temporal changes in RNA expression patterns before and after birth to identify signaling pathways selectively activated in specific pulmonary cell types, including activation of cell stress and the unfolded protein response during perinatal adaptation of the lung. The present data provide a single cell view of the adaptation to air breathing after birth. The respiratory system is transformed in terms of functional change at birth to adapt to breathing air. Here, the authors examine the molecular changes behind the first breath in the mouse by Drop-seq based RNA sequencing, identifying activation of the unfolded protein response as a perinatal adaptation of the lung.
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