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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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2
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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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3
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Bai K, Yang L, Xue J, Zhao L, Hao F. Pathogenicity classification of missense mutations based on deep generative model. Comput Biol Med 2024; 170:107980. [PMID: 38242017 DOI: 10.1016/j.compbiomed.2024.107980] [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] [Received: 10/02/2023] [Revised: 01/12/2024] [Accepted: 01/12/2024] [Indexed: 01/21/2024]
Abstract
Missense mutations affect the function of human proteins and are closely associated with multiple acute and chronic diseases. The identification of disease-associated missense mutations and their classification for pathogenicity can provide insights into the genetic basis of disease and protein function. This paper proposes MLAE (Method based on LSTM-Ladder AutoEncoder), a deep learning classification model for identifying disease-associated missense mutations and classifying their pathogenicity based on the Variational AutoEncoder (VAE) framework. MLAE overcomes the limitations of the VAE framework by introducing the Ladder structure, combined with LSTM networks. This reduces the loss of original information during the transmission process, thereby making the model more effective in learning. In the experiment, MLAE classified all 27572 possible missense variants of the three input proteins with an average classification AUC of 0.941. This result provides evidence that MLAE is effective in predicting pathogenicity. Additionally, MLAE provides results for multi-label classification, with an average Hamming loss of 0.196, supporting the classification of complex variants. The proposed MLAE method provides an insightful approach to effectively capture amino acid sequence information and accurately predict the pathogenicity of mutations, thereby providing an analytical basis for the study and prevention of related diseases.
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Affiliation(s)
- Ke Bai
- Shandong Jianzhu University, Jinan, 250101, PR China
| | - Lu Yang
- Shandong Jianzhu University, Jinan, 250101, PR China
| | - Jian Xue
- Shandong Jianzhu University, Jinan, 250101, PR China
| | - Lin Zhao
- Shandong Jianzhu University, Jinan, 250101, PR China
| | - Fanchang Hao
- Shandong Jianzhu University, Jinan, 250101, PR China.
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4
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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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Faridi R, Yousaf R, Gu S, Inagaki S, Turriff AE, Pelstring K, Guan B, Naik A, Griffith AJ, Adadey SM, Aboagye ET, Awandare GA, Morell RJ, Tsilou E, Noyes AG, Sulmonte LAG, Wonkam A, Schrauwen I, Leal SM, Azaiez H, Brewer CC, Riazuddin S, Hufnagel RB, Hoa M, Zein WM, de Dios JK, Friedman TB. Variants of LRP2, encoding a multifunctional cell-surface endocytic receptor, associated with hearing loss and retinal dystrophy. Clin Genet 2023; 103:699-703. [PMID: 36807241 DOI: 10.1111/cge.14312] [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: 10/04/2022] [Revised: 02/06/2023] [Accepted: 02/12/2023] [Indexed: 02/22/2023]
Abstract
Hereditary deafness and retinal dystrophy are each genetically heterogenous and clinically variable. Three small unrelated families segregating the combination of deafness and retinal dystrophy were studied by exome sequencing (ES). The proband of Family 1 was found to be compound heterozygous for NM_004525.3: LRP2: c.5005A > G, p.(Asn1669Asp) and c.149C > G, p.(Thr50Ser). In Family 2, two sisters were found to be compound heterozygous for LRP2 variants, p.(Tyr3933Cys) and an experimentally confirmed c.7715 + 3A > T consensus splice-altering variant. In Family 3, the proband is compound heterozygous for a consensus donor splice site variant LRP2: c.8452_8452 + 1del and p.(Cys3150Tyr). In mouse cochlea, Lrp2 is expressed abundantly in the stria vascularis marginal cells demonstrated by smFISH, single-cell and single-nucleus RNAseq, suggesting that a deficiency of LRP2 may compromise the endocochlear potential, which is required for hearing. LRP2 variants have been associated with Donnai-Barrow syndrome and other multisystem pleiotropic phenotypes different from the phenotypes of the four cases reported herein. Our data expand the phenotypic spectrum associated with pathogenic variants in LRP2 warranting their consideration in individuals with a combination of hereditary hearing loss and retinal dystrophy.
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Affiliation(s)
- Rabia Faridi
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Rizwan Yousaf
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Shoujun Gu
- Auditory Development and Restoration Program, NIDCD, NIH, Bethesda, Maryland, USA
| | - Sayaka Inagaki
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Amy E Turriff
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, NIH, Bethesda, Maryland, USA
| | - Keith Pelstring
- Division of Medical Genetics, Dayton Children's Hospital, Dayton, Ohio, USA
| | - Bin Guan
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, NIH, Bethesda, Maryland, USA
| | - Amelia Naik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, NIH, Bethesda, Maryland, USA
| | | | - Samuel Mawuli Adadey
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
- Division of Human Genetics, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Elvis Twumasi Aboagye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
- Division of Human Genetics, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Robert J Morell
- Genomics and Computational Biology Core, NIDCD, NIH, Bethesda, Maryland, USA
| | - Ekaterini Tsilou
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, NIH, Bethesda, Maryland, USA
| | | | | | - Ambroise Wonkam
- Division of Human Genetics, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- McKusick-Nathans Institute and Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, New York, USA
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, New York, USA
- Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, New York, USA
| | - Hela Azaiez
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | | | - Sheikh Riazuddin
- Allama Iqbal Medical Research Centre, Jinnah Hospital Complex, Lahore, Pakistan
| | - Robert B Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, NIH, Bethesda, Maryland, USA
| | - Michael Hoa
- Auditory Development and Restoration Program, NIDCD, NIH, Bethesda, Maryland, USA
| | - Wadih M Zein
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, NIH, Bethesda, Maryland, USA
| | - J Karl de Dios
- Division of Medical Genetics, Dayton Children's Hospital, Dayton, Ohio, USA
| | - Thomas B Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, Maryland, USA
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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: 4] [Impact Index Per Article: 4.0] [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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7
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Yıldız Bölükbaşı E, Karolak JA, Szafranski P, Gambin T, Matsika A, McManus S, Scott HS, Arts P, Ha T, Barnett CP, Rodgers J, Stankiewicz P. Variable expressivity in a four-generation ACDMPV family with a non-coding hypermorphic SNV in trans to the frameshifting FOXF1 variant. Eur J Hum Genet 2022; 30:1182-1186. [PMID: 35902696 PMCID: PMC9554184 DOI: 10.1038/s41431-022-01159-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 06/22/2022] [Accepted: 07/11/2022] [Indexed: 12/15/2022] Open
Abstract
Heterozygous single nucleotide variants (SNVs) or copy-number variant deletions involving FOXF1 or its distant lung-specific enhancer on chromosome 16q24.1 have been identified in 80-90% of patients with Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV), a lethal neonatal lung developmental disorder. We describe a four-generation family with a deceased ACDMPV neonate, her sibling from the electively terminated pregnancy, healthy mother with a history of pulmonary arterial hypertension (PAH), an unaffected aunt, an aunt deceased due to findings consistent with ACDMPV, and a reportedly unaffected grandmother, all with the frameshifting variant c.881_902dup (p.Gly302Profs*46) in FOXF1, and a deceased great-grandmother with a history of PAH. Genome sequencing analyses in the proband's unaffected mother revealed a non-coding putative regulatory SNV rs560517434-A within the lung-specific distant FOXF1 enhancer in trans to the FOXF1 frameshift mutation. Functional testing of this variant using an in vitro luciferase reporter assay showed that it increased FOXF1 promoter activity 10-fold. Our studies further demonstrate that non-coding SNVs in the FOXF1 enhancer region can rescue the lethal ACDMPV phenotype and support the compound inheritance gene dosage model.
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Affiliation(s)
- Esra Yıldız Bölükbaşı
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Justyna A Karolak
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Przemyslaw Szafranski
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Admire Matsika
- Mater Pathology, Mater Hospital Brisbane, South Brisbane, QLD, Australia
| | - Sam McManus
- Mater Pathology, Mater Hospital Brisbane, South Brisbane, QLD, Australia
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, SA, Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
- ACRF Genomics Facility, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, , SA Pathology, Adelaide, SA, Australia
- Australian Genomics, Melbourne, VIC, Australia
| | - Peer Arts
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, SA, Australia
| | - Thuong Ha
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, SA, Australia
- ACRF Genomics Facility, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, SA, Australia
| | - Christopher P Barnett
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
- Paediatric and Reproductive Genetics Unit, South Australian Clinical Genetics Service, Women's and Children's Hospital, North Adelaide, SA, Australia
| | - Jonathan Rodgers
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
- School of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Paweł Stankiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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