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Bzdęga K, Kutkowska-Kaźmierczak A, Deutsch GH, Plaskota I, Smyk M, Niemiec M, Barczyk A, Obersztyn E, Modzelewski J, Lipska I, Stankiewicz P, Gajecka M, Rydzanicz M, Płoski R, Szczapa T, Karolak JA. Prenatal Detection of a FOXF1 Deletion in a Fetus with ACDMPV and Hydronephrosis. Genes (Basel) 2023; 14:genes14030563. [PMID: 36980834 PMCID: PMC10048226 DOI: 10.3390/genes14030563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/08/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a lethal lung developmental disorder caused by the arrest of fetal lung formation, resulting in neonatal death due to acute respiratory failure and pulmonary arterial hypertension. Heterozygous single-nucleotide variants or copy-number variant (CNV) deletions involving the FOXF1 gene and/or its lung-specific enhancer are found in the vast majority of ACDMPV patients. ACDMPV is often accompanied by extrapulmonary malformations, including the gastrointestinal, cardiac, or genitourinary systems. Thus far, most of the described ACDMPV patients have been diagnosed post mortem, based on histologic evaluation of the lung tissue and/or genetic testing. Here, we report a case of a prenatally detected de novo CNV deletion (~0.74 Mb) involving the FOXF1 gene in a fetus with ACDMPV and hydronephrosis. Since ACDMPV is challenging to detect by ultrasound examination, the more widespread implementation of prenatal genetic testing can facilitate early diagnosis, improve appropriate genetic counselling, and further management.
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Affiliation(s)
- Katarzyna Bzdęga
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-806 Poznan, Poland
| | | | - Gail H. Deutsch
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Izabela Plaskota
- Department of Medical Genetics, Institute of Mother and Child, 01-211 Warsaw, Poland
| | - Marta Smyk
- Department of Medical Genetics, Institute of Mother and Child, 01-211 Warsaw, Poland
| | - Magdalena Niemiec
- Department of Medical Genetics, Institute of Mother and Child, 01-211 Warsaw, Poland
| | - Artur Barczyk
- Department of Medical Genetics, Institute of Mother and Child, 01-211 Warsaw, Poland
| | - Ewa Obersztyn
- Department of Medical Genetics, Institute of Mother and Child, 01-211 Warsaw, Poland
| | - Jan Modzelewski
- 1st Clinic of Obstetrics and Gynecology, Centre of Postgraduate Medical Education, 01-004 Warsaw, Poland
| | - Iwona Lipska
- Department of Pathomorphology, Wolski Hospital, 01-211 Warsaw, Poland
| | - Paweł Stankiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Marzena Gajecka
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-806 Poznan, Poland
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland
| | - Małgorzata Rydzanicz
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland
| | - Tomasz Szczapa
- II Department of Neonatology, Neonatal Biophysical Monitoring and Cardiopulmonary Therapies Research Unit, Poznan University of Medical Science, 60-535 Poznan, Poland
| | - Justyna A. Karolak
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-806 Poznan, Poland
- Correspondence:
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2
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Puisney-Dakhli C, Gubana F, Petit F, Bouchghoul H, Gautier V, Martinovic J, Tachdjian G, Receveur A. Early prenatal diagnosis of alveolar capillary dysplasia with misalignment of pulmonary veins due to a 16q24.1 deletion. Am J Med Genet A 2021; 185:1494-1497. [PMID: 33522073 DOI: 10.1002/ajmg.a.62105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/24/2020] [Accepted: 01/15/2021] [Indexed: 11/10/2022]
Abstract
First trimester ultrasound screening is an essential fetal examination performed generally at 11-13 weeks of gestation (WG). However, it does not allow for an accurate description of all fetal organs, partly due to their development in progress. Meanwhile, increased nuchal translucency (INT) is a widely used marker known to be associated with chromosomal deleterious rearrangements. We report on a 14 WG fetus with an association of INT and univentricular congenital heart malformation (CHM) leading to chorionic villous sampling (CVS). Cytogenetic investigations performed using array-Comparative Genomic Hybridization (CGH) and fluorescence in situ hybridization (FISH) demonstrated a 1.17 Mb deletion in 16q24.1 encompassing FOXF1 arisen de novo on maternal inherited chromosome. Fetopathological study confirmed CHM with hypoplastic left heart syndrome (HLHS) associating aortic atresia, mitral stenosis, and left ventricular hypoplasia and revealed in addition specific lung lesions corresponding to alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV). This is so far the first case of first trimester prenatal diagnosis of ACDMPV due to the deletion of FOXF1 gene. An interpretation of the complex genomic data generated by ultrasound markers is facilitated considerably by the genotype-phenotype correlations on fetopathological examination.
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Affiliation(s)
- Chloé Puisney-Dakhli
- Laboratoire de Cytogénétique, Service d'Histologie-Embryologie-Cytogénétique, Hôpital Antoine Béclère, AP-HP Université Paris Saclay, Clamart, France
| | - Francesca Gubana
- UF de Foetopathologie, Hôpital Antoine Béclère, AP-HP Université Paris Saclay, Clamart, France
| | - François Petit
- Laboratoire de Génétique Moléculaire, Hôpital Antoine Béclère, AP-HP Université Paris Saclay, Clamart, France
| | - Hanane Bouchghoul
- Service de Gynecologie Obstétrique, Hopital Bicêtre, AP-HP Université Paris Saclay, Le Kremlin-Bicetre, France
| | - Valérie Gautier
- Laboratoire de Cytogénétique, Service d'Histologie-Embryologie-Cytogénétique, Hôpital Antoine Béclère, AP-HP Université Paris Saclay, Clamart, France
| | - Jelena Martinovic
- UF de Foetopathologie, Hôpital Antoine Béclère, AP-HP Université Paris Saclay, Clamart, France
| | - Gérard Tachdjian
- Laboratoire de Cytogénétique, Service d'Histologie-Embryologie-Cytogénétique, Hôpital Antoine Béclère, AP-HP Université Paris Saclay, Clamart, France
| | - Aline Receveur
- Laboratoire de Cytogénétique, Service d'Histologie-Embryologie-Cytogénétique, Hôpital Antoine Béclère, AP-HP Université Paris Saclay, Clamart, France
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3
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Slot E, Edel G, Cutz E, van Heijst A, Post M, Schnater M, Wijnen R, Tibboel D, Rottier R, de Klein A. Alveolar capillary dysplasia with misalignment of the pulmonary veins: clinical, histological, and genetic aspects. Pulm Circ 2018; 8:2045894018795143. [PMID: 30058937 PMCID: PMC6108021 DOI: 10.1177/2045894018795143] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 07/22/2018] [Indexed: 11/15/2022] Open
Abstract
Alveolar capillary dysplasia with misalignment of the pulmonary veins (ACD/MPV) is a rare and lethal disorder mainly involving the vascular development of the lungs. Since its first description, significant achievements in research have led to a better understanding of the underlying molecular mechanism of ACD/MPV and genetic studies have identified associations with genomic alterations in the locus of the transcription factor FOXF1. This in turn has increased the awareness among clinicians resulting in over 200 cases reported so far, including genotyping of patients in most recent reports. Collectively, this promoted a better stratification of the patient group, leading to new perspectives in research on the pathogenesis. Here, we provide an overview of the clinical aspects of ACD/MPV, including guidance for clinicians, and review the ongoing research into the complex molecular mechanism causing this severe lung disorder.
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Affiliation(s)
- Evelien Slot
- Department of Pediatric Surgery, Sophia
Children's Hospital, Erasmus University Medical Center, Rotterdam, The
Netherlands
- Department of Clinical Genetics, Erasmus
University Medical Center, Rotterdam, The Netherlands
| | - Gabriëla Edel
- Department of Pediatric Surgery, Sophia
Children's Hospital, Erasmus University Medical Center, Rotterdam, The
Netherlands
| | - Ernest Cutz
- Division of Pathology, Department of
Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, ON,
Canada
| | - Arno van Heijst
- Department of Neonatology, Radboud
University Medical Center –Amalia Children’s Hospital, Nijmegen, The
Netherlands
| | - Martin Post
- Department of Translational Medicine,
Hospital for Sick Children, Toronto, ON, Canada
| | - Marco Schnater
- Department of Pediatric Surgery, Sophia
Children's Hospital, Erasmus University Medical Center, Rotterdam, The
Netherlands
| | - René Wijnen
- Department of Pediatric Surgery, Sophia
Children's Hospital, Erasmus University Medical Center, Rotterdam, The
Netherlands
| | - Dick Tibboel
- Department of Pediatric Surgery, Sophia
Children's Hospital, Erasmus University Medical Center, Rotterdam, The
Netherlands
| | - Robbert Rottier
- Department of Pediatric Surgery, Sophia
Children's Hospital, Erasmus University Medical Center, Rotterdam, The
Netherlands
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus
University Medical Center, Rotterdam, The Netherlands
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4
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Zirpoli S, Munari AM, Rustico M, Bulfamante G, Lista G, Spaccini L, Cesaretti C. Fetal-MRI prenatal diagnosis of severe bilateral lung hypoplasia: alveolar capillary dysplasia case report. J Prenat Med 2017; 10:15-19. [PMID: 28725341 DOI: 10.11138/jpm/2016.10.3.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Alveolar capillary dysplasia with misalignment of pulmonary veins (ACD/MPV) is a rare and lethal developmental disorder of the lung that affect both acinar structure and the intrinsic pulmonary vasculature. We report prenatal and postnatal imaging with histopathological findings of this rare condition. We, first, describe MR imaging features and discuss its role in prenatal imaging.
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Affiliation(s)
- Salvatore Zirpoli
- Pediatric Radiology and Neuroradiology, Children's Hospital V. Buzzi, Milan, Italy
| | | | - Mariangela Rustico
- Unit of Prenatal Diagnosis and Fetal Surgery, Children's Hospital V. Buzzi, Milan, Italy
| | - Gaetano Bulfamante
- Department of Health Sciences, San Paolo Hospital, University of Milan, Milan, Italy
| | - Gianluca Lista
- Division of Neonatology, Children's Hospital V. Buzzi, Milan, Italy
| | - Luigina Spaccini
- Clinical Genetics Service, Children's Hospital V. Buzzi, Milan, Italy
| | - Claudia Cesaretti
- Medical Genetics Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
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5
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Goel D, Oei JL, Lui K, Ward M, Shand AW, Mowat D, Gifford AJ, Loo C. Antenatal gastrointestinal anomalies in neonates subsequently found to have alveolar capillary dysplasia. Clin Case Rep 2017; 5:559-566. [PMID: 28469849 PMCID: PMC5412771 DOI: 10.1002/ccr3.888] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/18/2016] [Accepted: 11/06/2016] [Indexed: 11/06/2022] Open
Abstract
Alveolar capillary dysplasia (ACD) is a rare condition with variable presentation and clinical course. Clinicians should consider this diagnosis in neonates presenting with nonlethal congenital gastrointestinal malformation, a period of well-being after birth then unremitting hypoxemia and refractory pulmonary hypertension. Lung biopsy and FOXF1 gene testing may help in diagnosis.
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Affiliation(s)
- Dimple Goel
- Department of Newborn Care Royal Hospital for Women Sydney New South Wales Australia.,School of Women's and Children's Health University of New South Wales Randwick New South Wales Australia
| | - Ju Lee Oei
- Department of Newborn Care Royal Hospital for Women Sydney New South Wales Australia.,School of Women's and Children's Health University of New South Wales Randwick New South Wales Australia
| | - Kei Lui
- Department of Newborn Care Royal Hospital for Women Sydney New South Wales Australia.,School of Women's and Children's Health University of New South Wales Randwick New South Wales Australia
| | - Meredith Ward
- Department of Newborn Care Royal Hospital for Women Sydney New South Wales Australia.,School of Women's and Children's Health University of New South Wales Randwick New South Wales Australia
| | - Antonia W Shand
- School of Women's and Children's Health University of New South Wales Randwick New South Wales Australia.,Department of Maternal Fetal Medicine Royal Hospital for Women Sydney New South Wales Australia
| | - David Mowat
- School of Women's and Children's Health University of New South Wales Randwick New South Wales Australia.,Department of Medical Genetics Sydney Children's Hospital Sydney New South Wales Australia
| | - Andrew J Gifford
- School of Women's and Children's Health University of New South Wales Randwick New South Wales Australia.,Department of Anatomical Pathology (Seals) Prince of Wales Hospital Sydney New South Wales Australia
| | - Christine Loo
- Department of Anatomical Pathology (Seals) Prince of Wales Hospital Sydney New South Wales Australia.,University of Western Sydney Sydney New South Wales Australia
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6
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Reiter J, Szafranski P, Breuer O, Perles Z, Dagan T, Stankiewicz P, Kerem E. Variable phenotypic presentation of a novel FOXF1 missense mutation in a single family. Pediatr Pulmonol 2016; 51:921-7. [PMID: 27145217 DOI: 10.1002/ppul.23425] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 02/05/2016] [Accepted: 03/05/2016] [Indexed: 11/11/2022]
Abstract
BACKGROUND Heterozygous mutations in the FOXF1 transcription factor gene are implicated in alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV), a developmental disorder of the lungs classically presenting with pulmonary hypertension and early demise. Evidence has suggested haploinsufficiency and partial paternal imprinting. We present a family with several affected members with an extremely variable phenotype. PATIENTS The index patient presented several hours after birth with severe pulmonary hypertension. She is now 3-years old, thriving on maximal pulmonary hypertension therapy, chronic steroids, and oxygen. One of the patient's siblings died at 16 days with pulmonary hypertension and an annular pancreas, consistent with classical ACDMPV. METHODS Whole exome sequencing was performed in the index case. The identified variant was confirmed by Sanger sequencing, and tested in the remaining family members. Parental origin was determined by PCR amplification and cloning, sequencing, and identification of adjacent single nucleotide polymorphisms. Echocardiography was performed in the asymptomatic carriers. RESULTS Whole exome analysis revealed a novel, predictably pathogenic heterozygous missense mutation, g.chr16:86544406 C>A NM_001451, c.C231A, p.F77L, in the FOXF1 gene. The mutation arose in the father, de novo, early postzygotically, with 70% somatic mosaicism in the blood, on the grandpaternal chromosome. It was also present in the proband's asymptomatic sister, found to have partial anomalous pulmonary venous return. CONCLUSION FOXF1 mutations may have an extremely variable phenotype, possibly as a result of somatic mosaicism and complex gene regulation including unorthodox imprinting of the gene locus. The prolonged survival of the proband suggests the need for aggressive treatment. Pediatr Pulmonol. 2016; 51:921-927. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Joel Reiter
- Pediatric Pulmonary Unit, Division of Pediatrics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Oded Breuer
- Pediatric Pulmonary Unit, Division of Pediatrics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Zeev Perles
- Pediatric Cardiology Department, Division of Pediatrics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Tamir Dagan
- Pediatric Cardiology Institute, Department of Pediatrics, Schneider Childrens' Medical Center, Petach Tikvah, Israel
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Eitan Kerem
- Pediatric Pulmonary Unit, Division of Pediatrics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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7
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Pathogenetics of alveolar capillary dysplasia with misalignment of pulmonary veins. Hum Genet 2016; 135:569-586. [PMID: 27071622 DOI: 10.1007/s00439-016-1655-9] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
Abstract
Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a lethal lung developmental disorder caused by heterozygous point mutations or genomic deletion copy-number variants (CNVs) of FOXF1 or its upstream enhancer involving fetal lung-expressed long noncoding RNA genes LINC01081 and LINC01082. Using custom-designed array comparative genomic hybridization, Sanger sequencing, whole exome sequencing (WES), and bioinformatic analyses, we studied 22 new unrelated families (20 postnatal and two prenatal) with clinically diagnosed ACDMPV. We describe novel deletion CNVs at the FOXF1 locus in 13 unrelated ACDMPV patients. Together with the previously reported cases, all 31 genomic deletions in 16q24.1, pathogenic for ACDMPV, for which parental origin was determined, arose de novo with 30 of them occurring on the maternally inherited chromosome 16, strongly implicating genomic imprinting of the FOXF1 locus in human lungs. Surprisingly, we have also identified four ACDMPV families with the pathogenic variants in the FOXF1 locus that arose on paternal chromosome 16. Interestingly, a combination of the severe cardiac defects, including hypoplastic left heart, and single umbilical artery were observed only in children with deletion CNVs involving FOXF1 and its upstream enhancer. Our data demonstrate that genomic imprinting at 16q24.1 plays an important role in variable ACDMPV manifestation likely through long-range regulation of FOXF1 expression, and may be also responsible for key phenotypic features of maternal uniparental disomy 16. Moreover, in one family, WES revealed a de novo missense variant in ESRP1, potentially implicating FGF signaling in the etiology of ACDMPV.
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8
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Prothro SL, Plosa E, Markham M, Szafranski P, Stankiewicz P, Killen SAS. Prenatal Diagnosis of Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins. J Pediatr 2016; 170:317-8. [PMID: 26703872 PMCID: PMC5476418 DOI: 10.1016/j.jpeds.2015.11.041] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 10/16/2015] [Accepted: 11/12/2015] [Indexed: 11/18/2022]
Abstract
Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a rare, lethal cause of neonatal respiratory failure and persistent pulmonary hypertension. We present a presumptive prenatal diagnosis of ACDMPV based on chorionic villus sampling of a FOXF1 mutation in a fetus with extra-pulmonary anomalies often associated with ACDMPV.
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Affiliation(s)
- Stephanie L Prothro
- Division of Pediatric Cardiology, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN
| | - Erin Plosa
- Division of Neonatology, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN
| | - Melinda Markham
- Division of Neonatology, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN
| | | | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Stacy A S Killen
- Division of Pediatric Cardiology, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN.
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9
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Dharmadhikari AV, Szafranski P, Kalinichenko VV, Stankiewicz P. Genomic and Epigenetic Complexity of the FOXF1 Locus in 16q24.1: Implications for Development and Disease. Curr Genomics 2015; 16:107-16. [PMID: 26085809 PMCID: PMC4467301 DOI: 10.2174/1389202916666150122223252] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/09/2015] [Accepted: 01/21/2015] [Indexed: 01/01/2023] Open
Abstract
The FOXF1 (Forkhead box F1) gene, located on chromosome 16q24.1 encodes a member of the FOX family of transcription factors characterized by a distinct forkhead DNA binding domain. FOXF1 plays an important role in epithelium-mesenchyme signaling, as a downstream target of Sonic hedgehog pathway. Heterozygous point mutations and genomic deletions involving FOXF1 have been reported in newborns with a lethal lung developmental disorder, Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins (ACDMPV). In addition, genomic deletions upstream to FOXF1 identified in ACDMPV patients have revealed that FOXF1 expression is tightly regulated by distal tissue-specific enhancers. Interestingly, FOXF1 has been found to be incompletely paternally imprinted in human lungs; characterized genomic deletions arose de novo exclusively on maternal chromosome 16, with most of them being Alu-Alu mediated. Regulation of FOXF1 expression likely utilizes a combination of chromosomal looping, differential methylation of an upstream CpG island overlapping GLI transcription factor binding sites, and the function of lung-specific long non-coding RNAs (lncRNAs). FOXF1 knock-out mouse models demonstrated its critical role in mesoderm differentiation and in the development of pulmonary vasculature. Additionally, epigenetic inactivation of FOXF1 has been reported in breast and colorectal cancers, whereas overexpression of FOXF1 has been associated with a number of other human cancers, e.g. medulloblastoma and rhabdomyosarcoma. Constitutional duplications of FOXF1 have recently been reported in congenital intestinal malformations. Thus, understanding the genomic and epigenetic complexity at the FOXF1 locus will improve diagnosis, prognosis, and treatment of ACDMPV and other human disorders associated with FOXF1 alterations.
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Affiliation(s)
- Avinash V Dharmadhikari
- Department of Molecular and Human Genetics; ; Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, USA
| | | | - Vladimir V Kalinichenko
- Divisions of Pulmonary Biology and Developmental Biology, Perinatal Institute, Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics; ; Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, USA
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10
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Herriges MJ, Swarr DT, Morley MP, Rathi KS, Peng T, Stewart KM, Morrisey EE. Long noncoding RNAs are spatially correlated with transcription factors and regulate lung development. Genes Dev 2014; 28:1363-79. [PMID: 24939938 PMCID: PMC4066405 DOI: 10.1101/gad.238782.114] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Long noncoding RNAs (lncRNAs) are thought to play important roles in regulating gene transcription, yet few have known biological functions. Using a conservative pipeline, Herriges et al. identify lncRNAs with key functions during mammalian development. Loss-of-function analyses show that two lncRNAs play distinct roles in endoderm development by controlling the expression of critical transcription factors and pathways, including retinoic acid signaling. The data demonstrate that lncRNAs regulate multiple aspects of gene transcription during foregut and lung endoderm development. Long noncoding RNAs (lncRNAs) are thought to play important roles in regulating gene transcription, but few have well-defined expression patterns or known biological functions during mammalian development. Using a conservative pipeline to identify lncRNAs that have important biological functions, we identified 363 lncRNAs in the lung and foregut endoderm. Importantly, we show that these lncRNAs are spatially correlated with transcription factors across the genome. In-depth expression analyses of lncRNAs with genomic loci adjacent to the critical transcription factors Nkx2.1, Gata6, Foxa2 (forkhead box a2), and Foxf1 mimic the expression patterns of their protein-coding neighbor. Loss-of-function analysis demonstrates that two lncRNAs, LL18/NANCI (Nkx2.1-associated noncoding intergenic RNA) and LL34, play distinct roles in endoderm development by controlling expression of critical developmental transcription factors and pathways, including retinoic acid signaling. In particular, we show that LL18/NANCI acts upstream of Nkx2.1 and downstream from Wnt signaling to regulate lung endoderm gene expression. These studies reveal that lncRNAs play an important role in foregut and lung endoderm development by regulating multiple aspects of gene transcription, often through regulation of transcription factor expression.
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Affiliation(s)
- Michael J Herriges
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Daniel T Swarr
- Division of Neonatology, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | | | | | | | | | - Edward E Morrisey
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; Department of Medicine, Institute for Regenerative Medicine, Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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11
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Szafranski P, Dharmadhikari AV, Wambach JA, Towe CT, White FV, Grady RM, Eghtesady P, Cole FS, Deutsch G, Sen P, Stankiewicz P. Two deletions overlapping a distant FOXF1 enhancer unravel the role of lncRNA LINC01081 in etiology of alveolar capillary dysplasia with misalignment of pulmonary veins. Am J Med Genet A 2014; 164A:2013-9. [PMID: 24842713 PMCID: PMC4107046 DOI: 10.1002/ajmg.a.36606] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 04/14/2014] [Indexed: 01/18/2023]
Abstract
Position effects due to disruption of distant cis-regulatory regions have been reported for over 40 human gene loci; however, the underlying mechanisms of long-range gene regulation remain largely unknown. We report on two patients with alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) caused by overlapping genomic deletions that included a distant FOXF1 transcriptional enhancer mapping 0.3 Mb upstream to FOXF1 on 16q24.1. In one patient with atypical late-onset ACDMPV, a ∼1.5 Mb deletion removed the proximal 43% of this enhancer, leaving the lung-specific long non-coding RNA (lncRNA) gene LINC01081 intact. In the second patient with severe neonatal-onset ACDMPV, an overlapping ∼194 kb deletion disrupted LINC01081. Both deletions arose de novo on maternal copy of the chromosome 16, supporting the notion that FOXF1 is paternally imprinted in the human lungs. RNAi-mediated knock-down of LINC01081 in normal fetal lung fibroblasts showed that this lncRNA positively regulates FOXF1 transcript level, further indicating that decrease in LINC01081 expression can contribute to development of ACDMPV.
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Affiliation(s)
- Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Avinash V. Dharmadhikari
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, USA
| | | | | | | | | | - Pirooz Eghtesady
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Gail Deutsch
- Department of Pathology, Seattle Children’s Hospital, Seattle, WA
| | - Partha Sen
- Department of Pediatrics – Newborn, Baylor College of Medicine, Houston, TX, USA
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, USA
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