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Cai Y, Yan L, Kielt MJ, Cogan JD, Hedges LK, Nunley B, West J, Austin ED, Hamid R. TBX4 Transcription Factor Is a Positive Feedback Regulator of Itself and Phospho-SMAD1/5. Am J Respir Cell Mol Biol 2021; 64:140-143. [PMID: 33385213 DOI: 10.1165/rcmb.2020-0331le] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Ying Cai
- Vanderbilt University Medical Center Nashville, Tennessee and
| | - Ling Yan
- Vanderbilt University Medical Center Nashville, Tennessee and
| | | | - Joy D Cogan
- Vanderbilt University Medical Center Nashville, Tennessee and
| | - Lora K Hedges
- Vanderbilt University Medical Center Nashville, Tennessee and
| | - Bethany Nunley
- Vanderbilt University Medical Center Nashville, Tennessee and
| | - James West
- Vanderbilt University Medical Center Nashville, Tennessee and
| | - Eric D Austin
- Vanderbilt University Medical Center Nashville, Tennessee and
| | - Rizwan Hamid
- Vanderbilt University Medical Center Nashville, Tennessee and
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52
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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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53
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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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54
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Welch CL, Chung WK. Genetics and Genomics of Pediatric Pulmonary Arterial Hypertension. Genes (Basel) 2020; 11:E1213. [PMID: 33081265 PMCID: PMC7603012 DOI: 10.3390/genes11101213] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/02/2020] [Accepted: 10/13/2020] [Indexed: 12/14/2022] Open
Abstract
Pulmonary arterial hypertension (PAH) is a rare disease with high mortality despite recent therapeutic advances. The disease is caused by both genetic and environmental factors and likely gene-environment interactions. While PAH can manifest across the lifespan, pediatric-onset disease is particularly challenging because it is frequently associated with a more severe clinical course and comorbidities including lung/heart developmental anomalies. In light of these differences, it is perhaps not surprising that emerging data from genetic studies of pediatric-onset PAH indicate that the genetic basis is different than that of adults. There is a greater genetic burden in children, with rare genetic factors contributing to ~42% of pediatric-onset PAH compared to ~12.5% of adult-onset PAH. De novo variants are frequently associated with PAH in children and contribute to at least 15% of all pediatric cases. The standard of medical care for pediatric PAH patients is based on extrapolations from adult data. However, increased etiologic heterogeneity, poorer prognosis, and increased genetic burden for pediatric-onset PAH calls for a dedicated pediatric research agenda to improve molecular diagnosis and clinical management. A genomics-first approach will improve the understanding of pediatric PAH and how it is related to other rare pediatric genetic disorders.
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Affiliation(s)
- Carrie L Welch
- Department of Pediatrics, Irving Medical Center, Columbia University, 1150 St. Nicholas Avenue, New York, NY 10032, USA
| | - Wendy K Chung
- Department of Pediatrics, Irving Medical Center, Columbia University, 1150 St. Nicholas Avenue, New York, NY 10032, USA
- Department of Medicine, Irving Medical Center, Columbia University, 622 W 168th St, New York, NY 10032, USA
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55
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van den Heuvel LM, Jansen SMA, Alsters SIM, Post MC, van der Smagt JJ, Handoko-De Man FS, van Tintelen JP, Gille H, Christiaans I, Vonk Noordegraaf A, Bogaard H, Houweling AC. Genetic Evaluation in a Cohort of 126 Dutch Pulmonary Arterial Hypertension Patients. Genes (Basel) 2020; 11:genes11101191. [PMID: 33066286 PMCID: PMC7602048 DOI: 10.3390/genes11101191] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/09/2020] [Accepted: 10/10/2020] [Indexed: 01/28/2023] Open
Abstract
Pulmonary arterial hypertension (PAH) is a severe, life-threatening disease, and in some cases is caused by genetic defects. This study sought to assess the diagnostic yield of genetic testing in a Dutch cohort of 126 PAH patients. Historically, genetic testing in the Netherlands consisted of the analysis of BMPR2 and SMAD9. These genes were analyzed in 70 of the 126 patients. A (likely) pathogenic (LP/P) variant was detected in 22 (31%) of them. After the identification of additional PAH associated genes, a next generation sequencing (NGS) panel consisting of 19 genes was developed in 2018. Additional genetic testing was offered to the 48 BMPR2 and SMAD9 negative patients, out of which 28 opted for NGS analysis. In addition, this gene panel was analyzed in 56 newly identified idiopathic (IPAH) or pulmonary veno occlusive disease (PVOD) patients. In these 84 patients, NGS panel testing revealed LP/P variants in BMPR2 (N = 4), GDF2 (N = 2), EIF2AK4 (N = 1), and TBX4 (N = 3). Furthermore, 134 relatives of 32 probands with a LP/P variant were tested, yielding 41 carriers. NGS panel screening offered to IPAH/PVOD patients led to the identification of LP/P variants in GDF2, EIF2AK4, and TBX4 in six additional patients. The identification of LP/P variants in patients allows for screening of at-risk relatives, enabling the early identification of PAH.
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Affiliation(s)
- Lieke M. van den Heuvel
- Department of Clinical Genetics, Amsterdam UMC (location VUmc), 1081HV Amsterdam, The Netherlands; (L.M.v.d.H.); (S.I.M.A.); (J.P.v.T.); (H.G.)
- Netherlands Heart Institute, 3511EP Utrecht, The Netherlands
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, 3584CX Utrecht, The Netherlands;
| | - Samara M. A. Jansen
- Department of Lung Disease, Amsterdam UMC (location VUmc), 1081HV Amsterdam, The Netherlands; (S.M.A.J.); (F.S.H.-D.M.); (A.V.N.); (H.B.)
| | - Suzanne I. M. Alsters
- Department of Clinical Genetics, Amsterdam UMC (location VUmc), 1081HV Amsterdam, The Netherlands; (L.M.v.d.H.); (S.I.M.A.); (J.P.v.T.); (H.G.)
| | - Marco C. Post
- Department of Cardiology, St. Antonius hospital, 3435CM Nieuwegein, The Netherlands;
- Department of Cardiology, University Medical Centre Utrecht, Utrecht University, 3584CX Utrecht, The Netherlands
| | - Jasper J. van der Smagt
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, 3584CX Utrecht, The Netherlands;
| | - Frances S. Handoko-De Man
- Department of Lung Disease, Amsterdam UMC (location VUmc), 1081HV Amsterdam, The Netherlands; (S.M.A.J.); (F.S.H.-D.M.); (A.V.N.); (H.B.)
| | - J. Peter van Tintelen
- Department of Clinical Genetics, Amsterdam UMC (location VUmc), 1081HV Amsterdam, The Netherlands; (L.M.v.d.H.); (S.I.M.A.); (J.P.v.T.); (H.G.)
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, 3584CX Utrecht, The Netherlands;
| | - Hans Gille
- Department of Clinical Genetics, Amsterdam UMC (location VUmc), 1081HV Amsterdam, The Netherlands; (L.M.v.d.H.); (S.I.M.A.); (J.P.v.T.); (H.G.)
| | - Imke Christiaans
- Department of Clinical Genetics, University Medical Centre Groningen, 9713GZ Groningen, The Netherlands;
| | - Anton Vonk Noordegraaf
- Department of Lung Disease, Amsterdam UMC (location VUmc), 1081HV Amsterdam, The Netherlands; (S.M.A.J.); (F.S.H.-D.M.); (A.V.N.); (H.B.)
| | - HarmJan Bogaard
- Department of Lung Disease, Amsterdam UMC (location VUmc), 1081HV Amsterdam, The Netherlands; (S.M.A.J.); (F.S.H.-D.M.); (A.V.N.); (H.B.)
| | - Arjan C. Houweling
- Department of Clinical Genetics, Amsterdam UMC (location VUmc), 1081HV Amsterdam, The Netherlands; (L.M.v.d.H.); (S.I.M.A.); (J.P.v.T.); (H.G.)
- Correspondence: ; Tel.: +31-20-444-0150
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56
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Funk E, Lencer E, McCune A. Dorsoventral inversion of the air-filled organ (lungs, gas bladder) in vertebrates: RNAsequencing of laser capture microdissected embryonic tissue. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 334:325-338. [PMID: 32864827 PMCID: PMC8094346 DOI: 10.1002/jez.b.22998] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/04/2020] [Accepted: 08/07/2020] [Indexed: 12/20/2022]
Abstract
How modification of gene expression generates novel traits is key to understanding the evolutionary process. We investigated the genetic basis for the origin of the piscine gas bladder from lungs of ancestral bony vertebrates. Distinguishing these homologous organs is the direction of budding from the foregut during development; lungs bud ventrally and the gas bladder buds dorsally.
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Affiliation(s)
- Emily Funk
- Cornell University, Department of Ecology and Evolutionary Biology, 215 Tower Rd, Ithaca, NY 14853
- University of California Davis, Genomic Variation Lab, Animal Science Department, 2235 Meyer Hall, Davis, CA 95616
| | - Ezra Lencer
- University of Colorado Denver - Anschutz Medical Campus, Department of Craniofacial Biology, 12081 East 17 Ave, RC 1 South, Campus Box 8120, Aurora, CO 80045
| | - Amy McCune
- Cornell University, Department of Ecology and Evolutionary Biology, 215 Tower Rd, Ithaca, NY 14853
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57
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Riccetti M, Gokey JJ, Aronow B, Perl AKT. The elephant in the lung: Integrating lineage-tracing, molecular markers, and single cell sequencing data to identify distinct fibroblast populations during lung development and regeneration. Matrix Biol 2020; 91-92:51-74. [PMID: 32442602 PMCID: PMC7434667 DOI: 10.1016/j.matbio.2020.05.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 05/08/2020] [Accepted: 05/08/2020] [Indexed: 12/26/2022]
Abstract
During lung development, the mesenchyme and epithelium are dependent on each other for instructive morphogenic cues that direct proliferation, cellular differentiation and organogenesis. Specification of epithelial and mesenchymal cell lineages occurs in parallel, forming cellular subtypes that guide the formation of both transitional developmental structures and the permanent architecture of the adult lung. While epithelial cell types and lineages have been relatively well-defined in recent years, the definition of mesenchymal cell types and lineage relationships has been more challenging. Transgenic mouse lines with permanent and inducible lineage tracers have been instrumental in identifying lineage relationships among epithelial progenitor cells and their differentiation into distinct airway and alveolar epithelial cells. Lineage tracing experiments with reporter mice used to identify fibroblast progenitors and their lineage trajectories have been limited by the number of cell specific genes and the developmental timepoint when the lineage trace was activated. In this review, we discuss major developmental mesenchymal lineages, focusing on time of origin, major cell type, and other lineage derivatives, as well as the transgenic tools used to find and define them. We describe lung fibroblasts using function, location, and molecular markers in order to compare and contrast cells with similar functions. The temporal and cell-type specific expression of fourteen "fibroblast lineage" genes were identified in single-cell RNA-sequencing data from LungMAP in the LGEA database. Using these lineage signature genes as guides, we clustered murine lung fibroblast populations from embryonic day 16.5 to postnatal day 28 (E16.5-PN28) and generated heatmaps to illustrate expression of transcription factors, signaling receptors and ligands in a temporal and population specific manner.
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Affiliation(s)
- Matthew Riccetti
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States; Molecular and Developmental Biology Graduate Program, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Jason J Gokey
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Bruce Aronow
- Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States; Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, United States
| | - Anne-Karina T Perl
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States; Molecular and Developmental Biology Graduate Program, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States; Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, United States.
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58
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Han L, Chaturvedi P, Kishimoto K, Koike H, Nasr T, Iwasawa K, Giesbrecht K, Witcher PC, Eicher A, Haines L, Lee Y, Shannon JM, Morimoto M, Wells JM, Takebe T, Zorn AM. Single cell transcriptomics identifies a signaling network coordinating endoderm and mesoderm diversification during foregut organogenesis. Nat Commun 2020; 11:4158. [PMID: 32855417 PMCID: PMC7453027 DOI: 10.1038/s41467-020-17968-x] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 07/24/2020] [Indexed: 12/12/2022] Open
Abstract
Visceral organs, such as the lungs, stomach and liver, are derived from the fetal foregut through a series of inductive interactions between the definitive endoderm (DE) and the surrounding splanchnic mesoderm (SM). While DE patterning is fairly well studied, the paracrine signaling controlling SM regionalization and how this is coordinated with epithelial identity is obscure. Here, we use single cell transcriptomics to generate a high-resolution cell state map of the embryonic mouse foregut. This identifies a diversity of SM cell types that develop in close register with the organ-specific epithelium. We infer a spatiotemporal signaling network of endoderm-mesoderm interactions that orchestrate foregut organogenesis. We validate key predictions with mouse genetics, showing the importance of endoderm-derived signals in mesoderm patterning. Finally, leveraging these signaling interactions, we generate different SM subtypes from human pluripotent stem cells (hPSCs), which previously have been elusive. The single cell data can be explored at: https://research.cchmc.org/ZornLab-singlecell. The fetal murine foregut develops into visceral organs via interactions between the mesoderm and endoderm, but how is unclear. Here, the authors use single cell RNAseq to show a diversity in organ specific splanchnic mesoderm cell-types, infer a signalling network governing organogenesis and use this to differentiate human pluripotent stem cells.
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Affiliation(s)
- Lu Han
- Center for Stem Cell and Organoid Medicine (CuSTOM), Perinatal Institute, Division of Developmental Biology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - Praneet Chaturvedi
- Center for Stem Cell and Organoid Medicine (CuSTOM), Perinatal Institute, Division of Developmental Biology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - Keishi Kishimoto
- Center for Stem Cell and Organoid Medicine (CuSTOM), Perinatal Institute, Division of Developmental Biology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA.,Laboratory for Lung Development, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, 650-0047, Japan.,CuSTOM-RIKEN BDR Collaborative Laboratory, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - Hiroyuki Koike
- CuSTOM, Division of Gastroenterology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - Talia Nasr
- Center for Stem Cell and Organoid Medicine (CuSTOM), Perinatal Institute, Division of Developmental Biology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - Kentaro Iwasawa
- CuSTOM, Division of Gastroenterology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - Kirsten Giesbrecht
- CuSTOM, Division of Gastroenterology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - Phillip C Witcher
- Center for Stem Cell and Organoid Medicine (CuSTOM), Perinatal Institute, Division of Developmental Biology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - Alexandra Eicher
- Center for Stem Cell and Organoid Medicine (CuSTOM), Perinatal Institute, Division of Developmental Biology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - Lauren Haines
- Center for Stem Cell and Organoid Medicine (CuSTOM), Perinatal Institute, Division of Developmental Biology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - Yarim Lee
- Center for Stem Cell and Organoid Medicine (CuSTOM), Perinatal Institute, Division of Developmental Biology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - John M Shannon
- Division of Pulmonary Biology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - Mitsuru Morimoto
- Laboratory for Lung Development, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, 650-0047, Japan.,CuSTOM-RIKEN BDR Collaborative Laboratory, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - James M Wells
- Center for Stem Cell and Organoid Medicine (CuSTOM), Perinatal Institute, Division of Developmental Biology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - Takanori Takebe
- CuSTOM, Division of Gastroenterology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - Aaron M Zorn
- Center for Stem Cell and Organoid Medicine (CuSTOM), Perinatal Institute, Division of Developmental Biology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA. .,CuSTOM-RIKEN BDR Collaborative Laboratory, Cincinnati Children's Hospital, Cincinnati, OH, USA.
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59
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Kishimoto K, Furukawa KT, Luz-Madrigal A, Yamaoka A, Matsuoka C, Habu M, Alev C, Zorn AM, Morimoto M. Bidirectional Wnt signaling between endoderm and mesoderm confers tracheal identity in mouse and human cells. Nat Commun 2020; 11:4159. [PMID: 32855415 PMCID: PMC7453000 DOI: 10.1038/s41467-020-17969-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 07/24/2020] [Indexed: 12/20/2022] Open
Abstract
The periodic cartilage and smooth muscle structures in mammalian trachea are derived from tracheal mesoderm, and tracheal malformations result in serious respiratory defects in neonates. Here we show that canonical Wnt signaling in mesoderm is critical to confer trachea mesenchymal identity in human and mouse. At the initiation of tracheal development, endoderm begins to express Nkx2.1, and then mesoderm expresses the Tbx4 gene. Loss of β-catenin in fetal mouse mesoderm causes loss of Tbx4+ tracheal mesoderm and tracheal cartilage agenesis. The mesenchymal Tbx4 expression relies on endodermal Wnt activation and Wnt ligand secretion but is independent of known Nkx2.1-mediated respiratory development, suggesting that bidirectional Wnt signaling between endoderm and mesoderm promotes trachea development. Activating Wnt, Bmp signaling in mouse embryonic stem cell (ESC)-derived lateral plate mesoderm (LPM) generates tracheal mesoderm containing chondrocytes and smooth muscle cells. For human ESC-derived LPM, SHH activation is required along with WNT to generate proper tracheal mesoderm. Together, these findings may contribute to developing applications for human tracheal tissue repair.
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Affiliation(s)
- Keishi Kishimoto
- Laboratory for Lung Development and Regeneration, Riken Center for Biosystems Dynamics Research (BDR), Kobe, 650-0047, Japan
- RIKEN BDR-CuSTOM Joint Laboratory, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Kana T Furukawa
- Laboratory for Lung Development and Regeneration, Riken Center for Biosystems Dynamics Research (BDR), Kobe, 650-0047, Japan
| | - Agustin Luz-Madrigal
- Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Akira Yamaoka
- Laboratory for Lung Development and Regeneration, Riken Center for Biosystems Dynamics Research (BDR), Kobe, 650-0047, Japan
| | - Chisa Matsuoka
- Laboratory for Lung Development and Regeneration, Riken Center for Biosystems Dynamics Research (BDR), Kobe, 650-0047, Japan
| | - Masanobu Habu
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
| | - Cantas Alev
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, 606-8501, Japan
| | - Aaron M Zorn
- RIKEN BDR-CuSTOM Joint Laboratory, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Mitsuru Morimoto
- Laboratory for Lung Development and Regeneration, Riken Center for Biosystems Dynamics Research (BDR), Kobe, 650-0047, Japan.
- RIKEN BDR-CuSTOM Joint Laboratory, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
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Palacios-Martinez J, Caballero-Perez J, Espinal-Centeno A, Marquez-Chavoya G, Lomeli H, Salas-Vidal E, Schnabel D, Chimal-Monroy J, Cruz-Ramirez A. Multi-organ transcriptomic landscape of Ambystoma velasci metamorphosis. Dev Biol 2020; 466:22-35. [PMID: 32828730 DOI: 10.1016/j.ydbio.2020.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/11/2020] [Accepted: 08/04/2020] [Indexed: 12/21/2022]
Abstract
Metamorphosis is a postembryonic developmental process that involves morphophysiological and behavioral changes, allowing organisms to adapt into a novel environment. In some amphibians, aquatic organisms undergo metamorphosis to adapt in a terrestrial environment. In this process, these organisms experience major changes in their circulatory, respiratory, digestive, excretory and reproductive systems. We performed a transcriptional global analysis of heart, lung and gills during diverse stages of Ambystoma velasci to investigate its metamorphosis. In our analyses, we identified eight gene clusters for each organ, according to the expression patterns of differentially expressed genes. We found 4064 differentially expressed genes in the heart, 4107 in the lung and 8265 in the gills. Among the differentially expressed genes in the heart, we observed genes involved in the differentiation of cardiomyocytes in the interatrial zone, vasculogenesis and in the maturation of coronary vessels. In the lung, we found genes differentially expressed related to angiogenesis, alveolarization and synthesis of the surfactant protein. In the case of the gills, the most prominent biological processes identified are degradation of extracellular matrix, apoptosis and keratin production. Our study sheds light on the transcriptional responses and the pathways modulation involved in the transformation of the facultative metamorphic salamander A. velasci in an organ-specific manner.
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Affiliation(s)
- Janet Palacios-Martinez
- Molecular & Developmental Complexity Group, Unit of Advanced Genomics, UGA-CINVESTAV, Irapuato, Mexico
| | - Juan Caballero-Perez
- Molecular & Developmental Complexity Group, Unit of Advanced Genomics, UGA-CINVESTAV, Irapuato, Mexico; Department of Biochemistry, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México City, Mexico
| | - Annie Espinal-Centeno
- Molecular & Developmental Complexity Group, Unit of Advanced Genomics, UGA-CINVESTAV, Irapuato, Mexico
| | - Gilberto Marquez-Chavoya
- Molecular & Developmental Complexity Group, Unit of Advanced Genomics, UGA-CINVESTAV, Irapuato, Mexico
| | - Hilda Lomeli
- Departamento de Genética del Desarrollo y FisioloMéxico Citygía Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, AP 510-3, Cuernavaca, Mor, 62250, Mexico
| | - Enrique Salas-Vidal
- Departamento de Genética del Desarrollo y FisioloMéxico Citygía Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, AP 510-3, Cuernavaca, Mor, 62250, Mexico
| | - Denhi Schnabel
- Departamento de Genética del Desarrollo y FisioloMéxico Citygía Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, AP 510-3, Cuernavaca, Mor, 62250, Mexico
| | - Jesus Chimal-Monroy
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, México, DF, 04510, Mexico
| | - Alfredo Cruz-Ramirez
- Molecular & Developmental Complexity Group, Unit of Advanced Genomics, UGA-CINVESTAV, Irapuato, Mexico.
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61
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Huang W, Li P, Qiu X. [A Literature Review on the Role of TBX5 in Expression and Progression of Lung Cancer: Current Perspectives]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2020; 23:883-888. [PMID: 32810974 PMCID: PMC7583881 DOI: 10.3779/j.issn.1009-3419.2020.102.27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
T-box转录因子(T-box transcription factor gene, TBX)基因涉及器官的发生,TBX5在人的正常心脏和肺组织中表达水平最高。TBX5的缺乏可能导致胸廓发育畸形和膈肌发育异常,其异位表达和过表达会诱导细胞凋亡和抑制细胞生长。既往研究发现了TBX5在食管腺癌、胃癌、结肠癌和乳腺癌的发生和发展中的潜在作用。我们对TBX2亚家族的基因表达和预后之间的关系进行了综述,同时探究TBX5在调控肺癌发生发展机制中的研究进展。虽然TBX5和肺癌发生之间的关系尚不明确,不过TBX5可以显著抑制人体内肿瘤生长,其表达水平和肺癌的进展呈现负相关。由此,TBX5的基因表达水平和甲基化程度是潜在的表证肺癌增殖和转移的生物标志物,具有作为肺癌治疗靶点的潜力。
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Affiliation(s)
- Weijia Huang
- West China School of Medicine, Sichuan University, Chengdu 610041, China
| | - Peiwei Li
- West China School of Medicine, Sichuan University, Chengdu 610041, China
| | - Xiaoming Qiu
- Department of Lung Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
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62
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Conway RF, Frum T, Conchola AS, Spence JR. Understanding Human Lung Development through In Vitro Model Systems. Bioessays 2020; 42:e2000006. [PMID: 32310312 PMCID: PMC7433239 DOI: 10.1002/bies.202000006] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/28/2020] [Indexed: 12/19/2022]
Abstract
An abundance of information about lung development in animal models exists; however, comparatively little is known about lung development in humans. Recent advances using primary human lung tissue combined with the use of human in vitro model systems, such as human pluripotent stem cell-derived tissue, have led to a growing understanding of the mechanisms governing human lung development. They have illuminated key differences between animal models and humans, underscoring the need for continued advancements in modeling human lung development and utilizing human tissue. This review discusses the use of human tissue and the use of human in vitro model systems that have been leveraged to better understand key regulators of human lung development and that have identified uniquely human features of development. This review also examines the implementation and challenges of human model systems and discusses how they can be applied to address knowledge gaps.
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Affiliation(s)
- Renee F Conway
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48104, USA
| | - Tristan Frum
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, 48104, USA
| | - Ansley S Conchola
- Cell and Molecular Biology (CMB) Training Program, University of Michigan Medical School, Ann Arbor, MI, 48104, USA
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48104, USA
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, 48104, USA
- Cell and Molecular Biology (CMB) Training Program, University of Michigan Medical School, Ann Arbor, MI, 48104, USA
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI, 48104, USA
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63
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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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64
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Swietlik EM, Gräf S, Morrell NW. The role of genomics and genetics in pulmonary arterial hypertension. Glob Cardiol Sci Pract 2020; 2020:e202013. [PMID: 33150157 PMCID: PMC7590931 DOI: 10.21542/gcsp.2020.13] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Emilia M Swietlik
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom.,Addenbrooke's Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom.,Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Stefan Gräf
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom.,Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom.,NIHR BioResource for Translational Research, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Nicholas W Morrell
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom.,Addenbrooke's Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom.,Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom.,NIHR BioResource for Translational Research, Cambridge Biomedical Campus, Cambridge, United Kingdom
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65
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Onimaru K. The evolutionary origin of developmental enhancers in vertebrates: Insights from non‐model species. Dev Growth Differ 2020; 62:326-333. [DOI: 10.1111/dgd.12662] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Koh Onimaru
- Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research (BDR) Wako CitySaitama Japan
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66
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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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67
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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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68
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Thoré P, Girerd B, Jaïs X, Savale L, Ghigna MR, Eyries M, Levy M, Ovaert C, Servettaz A, Guillaumot A, Dauphin C, Chabanne C, Boiffard E, Cottin V, Perros F, Simonneau G, Sitbon O, Soubrier F, Bonnet D, Remy-Jardin M, Chaouat A, Humbert M, Montani D. Phenotype and outcome of pulmonary arterial hypertension patients carrying a TBX4 mutation. Eur Respir J 2020; 55:13993003.02340-2019. [DOI: 10.1183/13993003.02340-2019] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/05/2020] [Indexed: 12/16/2022]
Abstract
IntroductionTBX4 mutation causes small patella syndrome (SPS) and/or pulmonary arterial hypertension (PAH). The characteristics and outcomes of PAH associated with TBX4 mutations are largely unknown.MethodsWe report the clinical, functional, radiologic, histologic and haemodynamic characteristics and outcomes of heritable PAH patients carrying a TBX4 mutation from the French pulmonary hypertension (PH) network.Results20 patients were identified in 17 families. They were characterised by a median age at diagnosis of 29 years (0–76 years) and a female to male ratio of three. Most of the patients (70%) were in New York Heart Association (NYHA) functional class III or IV with a severe haemodynamic impairment (median pulmonary vascular resistance (PVR) of 13.6 (6.2–41.8) Wood units). Skeletal signs of SPS were present in 80% of cases. Half of the patients had mild restrictive or obstructive limitation and diffusing capacity of the lung for carbon monoxide (DLCO) was decreased in all patients. High-resolution computed tomography (HRCT) showed bronchial abnormalities, peri-bronchial cysts, mosaic distribution and mediastinal lymphadenopathies. PAH therapy was associated with significant clinical improvement. At follow-up (median 76 months), two patients had died and two had undergone lung transplantation. One-year, three-year and five-year event-free survival rates were 100%, 94% and 83%, respectively. Histologic examination of explanted lungs revealed alveolar growth abnormalities, major pulmonary vascular remodelling similar to that observed in idiopathic pulmonary arterial hypertension (IPAH) and accumulation of cholesterol crystals within the lung parenchyma.ConclusionPAH due to TBX4 mutations may occur with or without skeletal abnormalities across a broad age range from birth to late adulthood. PAH is usually severe and associated with bronchial and parenchymal abnormalities.
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69
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Teramoto M, Sugawara R, Minegishi K, Uchikawa M, Takemoto T, Kuroiwa A, Ishii Y, Kondoh H. The absence of SOX2 in the anterior foregut alters the esophagus into trachea and bronchi in both epithelial and mesenchymal components. Biol Open 2020; 9:bio048728. [PMID: 31988094 PMCID: PMC7044460 DOI: 10.1242/bio.048728] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/09/2020] [Indexed: 11/20/2022] Open
Abstract
In the anterior foregut (AFG) of mouse embryos, the transcription factor SOX2 is expressed in the epithelia of the esophagus and proximal branches of respiratory organs comprising the trachea and bronchi, whereas NKX2.1 is expressed only in the epithelia of respiratory organs. Previous studies using hypomorphic Sox2 alleles have indicated that reduced SOX2 expression causes the esophageal epithelium to display some respiratory organ characteristics. In the present study, we produced mouse embryos with AFG-specific SOX2 deficiency. In the absence of SOX2 expression, a single NKX2.1-expressing epithelial tube connected the pharynx and the stomach, and a pair of bronchi developed in the middle of the tube. Expression patterns of NKX2.1 and SOX9 revealed that the anterior and posterior halves of SOX2-deficient AFG epithelial tubes assumed the characteristics of the trachea and bronchus, respectively. In addition, we found that mesenchymal tissues surrounding the SOX2-deficient NKX2.1-expressing epithelial tube changed to those surrounding the trachea and bronchi in the anterior and posterior halves, as indicated by the arrangement of smooth muscle cells and SOX9-expressing cells and by the expression of Wnt4 (esophagus specific), Tbx4 (respiratory organ specific), and Hoxb6 (distal bronchus specific). The impact of mesenchyme-derived signaling on the early stage of AFG epithelial specification has been indicated. Our study demonstrated an opposite trend where epithelial tissue specification causes concordant changes in mesenchymal tissues, indicating a reciprocity of epithelial-mesenchymal interactions.
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Affiliation(s)
- Machiko Teramoto
- Faculty of Life Sciences and Institutes for Protein Dynamics and Comprehensive Research, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Ryo Sugawara
- Faculty of Life Sciences and Institutes for Protein Dynamics and Comprehensive Research, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Katsura Minegishi
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Masanori Uchikawa
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Tatsuya Takemoto
- Institute of Advanced Medical Sciences, Tokushima University, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| | - Atsushi Kuroiwa
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Yasuo Ishii
- Faculty of Life Sciences and Institutes for Protein Dynamics and Comprehensive Research, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
- Department of Biology, School of Medicine, Tokyo Women's Medical University, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Hisato Kondoh
- Faculty of Life Sciences and Institutes for Protein Dynamics and Comprehensive Research, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
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70
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Southgate L, Machado RD, Gräf S, Morrell NW. Molecular genetic framework underlying pulmonary arterial hypertension. Nat Rev Cardiol 2020; 17:85-95. [PMID: 31406341 DOI: 10.1038/s41569-019-0242-x] [Citation(s) in RCA: 172] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/12/2019] [Indexed: 02/02/2023]
Abstract
Pulmonary arterial hypertension (PAH) is a rare, progressive disorder typified by occlusion of the pulmonary arterioles owing to endothelial dysfunction and uncontrolled proliferation of pulmonary artery smooth muscle cells and fibroblasts. Vascular occlusion can lead to increased pressure in the pulmonary arteries, often resulting in right ventricular failure with shortness of breath and syncope. Since the identification of BMPR2, which encodes a receptor in the transforming growth factor-β superfamily, the development of high-throughput sequencing approaches to identify novel causal genes has substantially advanced our understanding of the molecular genetics of PAH. In the past 6 years, additional pathways involved in PAH susceptibility have been described through the identification of deleterious genetic variants in potassium channels (KCNK3 and ABCC8) and transcription factors (TBX4 and SOX17), among others. Although familial PAH most often has an autosomal-dominant pattern of inheritance, cases of incomplete penetrance and evidence of genetic heterogeneity support a model of PAH as a Mendelian disorder with complex disease features. In this Review, we outline the latest advances in the detection of rare and common genetic variants underlying PAH susceptibility and disease progression. These findings have clinical implications for lung vascular function and can help to identify mechanistic pathways amenable to pharmacological intervention.
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Affiliation(s)
- Laura Southgate
- Molecular and Clinical Sciences Research Institute, St George's University of London, London, UK.,Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Rajiv D Machado
- Molecular and Clinical Sciences Research Institute, St George's University of London, London, UK
| | - Stefan Gräf
- Department of Medicine, University of Cambridge, Cambridge, UK.,Department of Haematology, University of Cambridge, Cambridge, UK.,NIHR BioResource, Cambridge, UK
| | - Nicholas W Morrell
- Department of Medicine, University of Cambridge, Cambridge, UK. .,NIHR BioResource, Cambridge, UK.
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71
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Genetics and Other Omics in Pediatric Pulmonary Arterial Hypertension. Chest 2020; 157:1287-1295. [PMID: 32006592 DOI: 10.1016/j.chest.2020.01.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/09/2019] [Accepted: 01/07/2020] [Indexed: 12/15/2022] Open
Abstract
Pulmonary arterial hypertension (PAH) is a rare disease with high mortality despite therapeutic advances. Clinical management of children with PAH is particularly challenging because of increased complexity of disease etiology and clinical presentation, and the lack of data from pediatric-specific clinical trials. In children, PAH often develops in association with congenital heart disease and other developmental disorders. Emerging data from genetic studies of pediatric-onset PAH indicate that the genetic basis is different than that of adults. There is a greater genetic burden in children, with rare genetic factors contributing to at least 35% of pediatric-onset idiopathic PAH (IPAH) compared with approximately 11% of adult-onset IPAH. De novo variants are the most frequent monogenetic cause of PAH in children, likely contributing to approximately 15% of all cases. Rare deleterious variants in BMPR2 contribute to pediatric-onset IPAH and familial PAH with similar frequency as adult-onset disease but rarely explain cases of PAH associated with other diseases. Rare deleterious variants in developmental genes-including TBX4, SOX17, and other genes requiring confirmation in larger cohorts-are emerging as important contributors to pediatric-onset disease. Because each causal gene contributes to only a small number of cases, large cohorts of pediatric-onset PAH are needed to further identify the unique etiologic differences of PAH in children. We propose a genetics-first approach followed by focused phenotyping of pediatric patients grouped by genetic diagnosis to define endophenotypes that can be used to improve risk stratification and treatment.
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72
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Yue H, Ji X, Li G, Hu M, Sang N. Maternal Exposure to PM 2.5 Affects Fetal Lung Development at Sensitive Windows. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:316-324. [PMID: 31872757 DOI: 10.1021/acs.est.9b04674] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Lung development continues from the embryonic period to adulthood. Previous epidemiological studies have noted that maternal exposure of atmospheric pollutants during the sensitive windows disturbed the lung development and increased the risk of lung diseases after birth, but the experimental evidence was insufficient. In the present study, we exposed plug-positive mice to PM2.5 (3 mg/kg b.w.) by oropharyngeal aspiration every other day, and intended to test whether maternal PM2.5 exposure affected prenatal lung development in the offspring. First, maternal PM2.5 exposure decreased embryo weight and crown-rump length at E18.5 but not in earlier developmental stages (E0-E16.5). Second, maternal PM2.5 exposure did not prevent lung-bud and tracheal specification, and did not cause abnormalities in branching morphogenesis, distal lung epithelium, and mesenchyme differentiation in earlier stages of lung development (E0-E16.5). However, the exposure significantly disturbed the distal lung epithelium and mesenchyme differentiation of lung, led to reduced intact rings of trachea, and suppressed the expression of lung development-related genes (Nkx2.1, Tbx4, Tbx5, and Sox9) at E18.5. Finally, we found that the exposure not only increased PM2.5-bound metal content (Pb and Cu) but also caused inflammatory response in the placenta, which transmitted from the mother to the fetus and contributed to the developmental abnormalities.
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Affiliation(s)
- Huifeng Yue
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, P. R. China
| | - Xiaotong Ji
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, P. R. China
| | - Guangke Li
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, P. R. China
| | - Meng Hu
- School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, P. R. China
| | - Nan Sang
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, P. R. China
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73
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Ma J, Meng C, Feng Z, Han X, Liu S, Liu N, Zhu W. Clinical Analysis of Congenital Deficient Tracheal Cartilage Rings: Six Case Reports and a Literature Review. Front Pediatr 2020; 8:548089. [PMID: 33194888 PMCID: PMC7606407 DOI: 10.3389/fped.2020.548089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/26/2020] [Indexed: 02/02/2023] Open
Abstract
Congenital deficiency of tracheal rings is a rare tracheal malformation that can cause central airway obstruction. Herein we reported the clinical data of six patients with symptomatic congenital deficient tracheal rings. There were five cases, with isolated short-segment absent cartilage ring located on the distal trachea (three cases), cervical trachea (one case), and distal trachea combined with bilateral bronchi (one case). Among them, four (4/5) received surgical tracheal resection, three fully recovered, and one died of severe infection. Besides that, one patient, who could not be weaned off the mechanical ventilation, died after rejecting surgery. One case had episodes of recurrent dyspnea and extubation failure due to long-segment tracheomalacia after repair of esophageal atresia and tracheoesophageal fistula. For this patient, deficient cartilage rings were suspected and confirmed at the age of 26 months. Moreover, the clinical characteristics of 12 cases with congenital deficient tracheal cartilage rings reported in previous literature were reviewed. The different characteristics between short- and long-segment deficient cartilage rings were discussed.
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Affiliation(s)
- Jing Ma
- Department of Pediatrics, Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Respiratory Intervention, Qilu Children's Hospital of Shandong University, Jinan, China
| | - Chen Meng
- Department of Respiratory Intervention, Qilu Children's Hospital of Shandong University, Jinan, China
| | - Zhiyu Feng
- Department of Cardiac Surgery, Qilu Children's Hospital of Shandong University, Jinan, China
| | - Xiaorong Han
- Department of Respiratory Intervention, Qilu Children's Hospital of Shandong University, Jinan, China
| | - Shuaishuai Liu
- Department of Respiratory Intervention, Qilu Children's Hospital of Shandong University, Jinan, China
| | - Na Liu
- Department of Respiratory Intervention, Qilu Children's Hospital of Shandong University, Jinan, China
| | - Weiwei Zhu
- Department of Pediatrics, Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
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74
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Wojahn I, Lüdtke TH, Christoffels VM, Trowe MO, Kispert A. TBX2-positive cells represent a multi-potent mesenchymal progenitor pool in the developing lung. Respir Res 2019; 20:292. [PMID: 31870435 PMCID: PMC6929292 DOI: 10.1186/s12931-019-1264-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 12/18/2019] [Indexed: 12/18/2022] Open
Abstract
Background In the embryonic mammalian lung, mesenchymal cells act both as a signaling center for epithelial proliferation, differentiation and morphogenesis as well as a source for a multitude of differentiated cell types that support the structure of the developing and mature organ. Whether the embryonic pulmonary mesenchyme is a homogenous precursor pool and how it diversifies into different cell lineages is poorly understood. We have previously shown that the T-box transcription factor gene Tbx2 is expressed in the pulmonary mesenchyme of the developing murine lung and is required therein to maintain branching morphogenesis. Methods We determined Tbx2/TBX2 expression in the developing murine lung by in situ hybridization and immunofluorescence analyses. We used a genetic lineage tracing approach with a Cre line under the control of endogenous Tbx2 control elements (Tbx2cre), and the R26mTmG reporter line to trace TBX2-positive cells in the murine lung. We determined the fate of the TBX2 lineage by co-immunofluorescence analysis of the GFP reporter and differentiation markers in normal murine lungs and in lungs lacking or overexpressing TBX2 in the pulmonary mesenchyme. Results We show that TBX2 is strongly expressed in mesenchymal progenitors in the developing murine lung. In differentiated smooth muscle cells and in fibroblasts, expression of TBX2 is still widespread but strongly reduced. In mesothelial and endothelial cells expression is more variable and scattered. All fetal smooth muscle cells, endothelial cells and fibroblasts derive from TBX2+ progenitors, whereas half of the mesothelial cells have a different descent. The fate of TBX2-expressing cells is not changed in Tbx2-deficient and in TBX2-constitutively overexpressing mice but the distribution and abundance of endothelial and smooth muscle cells is changed in the overexpression condition. Conclusion The fate of pulmonary mesenchymal progenitors is largely independent of TBX2. Nevertheless, a successive and precisely timed downregulation of TBX2 is necessary to allow proper differentiation and functionality of bronchial smooth muscle cells and to limit endothelial differentiation. Our work suggests expression of TBX2 in an early pulmonary mesenchymal progenitor and supports a role of TBX2 in maintaining the precursor state of these cells.
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Affiliation(s)
- Irina Wojahn
- Institut für Molekularbiologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Timo H Lüdtke
- Institut für Molekularbiologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Vincent M Christoffels
- Department of Anatomy, Embryology and Physiology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Mark-Oliver Trowe
- Institut für Molekularbiologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Andreas Kispert
- Institut für Molekularbiologie, Medizinische Hochschule Hannover, Hannover, Germany.
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75
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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: 17] [Impact Index Per Article: 3.4] [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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76
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Sinner DI, Carey B, Zgherea D, Kaufman KM, Leesman L, Wood RE, Rutter MJ, de Alarcon A, Elluru RG, Harley JB, Whitsett JA, Trapnell BC. Complete Tracheal Ring Deformity. A Translational Genomics Approach to Pathogenesis. Am J Respir Crit Care Med 2019; 200:1267-1281. [PMID: 31215789 PMCID: PMC6857493 DOI: 10.1164/rccm.201809-1626oc] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 06/17/2019] [Indexed: 12/12/2022] Open
Abstract
Rationale: Complete tracheal ring deformity (CTRD) is a rare congenital abnormality of unknown etiology characterized by circumferentially continuous or nearly continuous cartilaginous tracheal rings, variable degrees of tracheal stenosis and/or shortening, and/or pulmonary arterial sling anomaly.Objectives: To test the hypothesis that CTRD is caused by inherited or de novo mutations in genes required for normal tracheal development.Methods: CTRD and normal tracheal tissues were examined microscopically to define the tracheal abnormalities present in CTRD. Whole-exome sequencing was performed in children with CTRD and their biological parents ("trio analysis") to identify gene variants in patients with CTRD. Mutations were confirmed by Sanger sequencing, and their potential impact on structure and/or function of encoded proteins was examined using human gene mutation databases. Relevance was further examined by comparison with the effects of targeted deletion of murine homologs important to tracheal development in mice.Measurements and Main Results: The trachealis muscle was absent in all of five patients with CTRD. Exome analysis identified six de novo, three recessive, and multiple compound-heterozygous or rare hemizygous variants in children with CTRD. De novo variants were identified in SHH (Sonic Hedgehog), and inherited variants were identified in HSPG2 (perlecan), ROR2 (receptor tyrosine kinase-like orphan receptor 2), and WLS (Wntless), genes involved in morphogenetic pathways known to mediate tracheoesophageal development in mice.Conclusions: The results of the present study demonstrate that absence of the trachealis muscle is associated with CTRD. Variants predicted to cause disease were identified in genes encoding Hedgehog and Wnt signaling pathway molecules, which are critical to cartilage formation and normal upper airway development in mice.
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Affiliation(s)
- Debora I. Sinner
- Division of Neonatology
- Division of Pulmonary Biology
- Department of Pediatrics and
| | | | | | - K. M. Kaufman
- Center for Autoimmune Genomics and Etiology, and
- Department of Pediatrics and
- U.S. Department of Veterans Affairs Medical Center, Cincinnati, Ohio
| | - Lauren Leesman
- Division of Neonatology
- Division of Pulmonary Biology
- Department of Pediatrics and
| | | | - Michael J. Rutter
- Division of Ear Nose and Throat Surgery, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Alessandro de Alarcon
- Division of Ear Nose and Throat Surgery, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Ravindhra G. Elluru
- Division of Ear Nose and Throat Surgery, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - John B. Harley
- Center for Autoimmune Genomics and Etiology, and
- Department of Pediatrics and
- U.S. Department of Veterans Affairs Medical Center, Cincinnati, Ohio
| | - Jeffrey A. Whitsett
- Division of Neonatology
- Division of Pulmonary Biology
- Department of Pediatrics and
| | - Bruce C. Trapnell
- Division of Neonatology
- Division of Pulmonary Biology
- Translational Pulmonary Science Center
- Department of Pediatrics and
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio; and
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77
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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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78
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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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79
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Ding J, Ahangari F, Espinoza CR, Chhabra D, Nicola T, Yan X, Lal CV, Hagood JS, Kaminski N, Bar-Joseph Z, Ambalavanan N. Integrating multiomics longitudinal data to reconstruct networks underlying lung development. Am J Physiol Lung Cell Mol Physiol 2019; 317:L556-L568. [PMID: 31432713 DOI: 10.1152/ajplung.00554.2018] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
A comprehensive understanding of the dynamic regulatory networks that govern postnatal alveolar lung development is still lacking. To construct such a model, we profiled mRNA, microRNA, DNA methylation, and proteomics of developing murine alveoli isolated by laser capture microdissection at 14 predetermined time points. We developed a detailed comprehensive and interactive model that provides information about the major expression trajectories, the regulators of specific key events, and the impact of epigenetic changes. Intersecting the model with single-cell RNA-Seq data led to the identification of active pathways in multiple or individual cell types. We then constructed a similar model for human lung development by profiling time-series human omics data sets. Several key pathways and regulators are shared between the reconstructed models. We experimentally validated the activity of a number of predicted regulators, leading to new insights about the regulation of innate immunity during lung development.
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Affiliation(s)
- Jun Ding
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Farida Ahangari
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Celia R Espinoza
- Division of Respiratory Medicine, Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Divya Chhabra
- Division of Respiratory Medicine, Department of Pediatrics, University of California, San Diego, La Jolla, California.,Rady Children's Hospital of San Diego, San Diego California
| | - Teodora Nicola
- Division of Neonatology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Xiting Yan
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Charitharth V Lal
- Division of Neonatology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - James S Hagood
- Division of Respiratory Medicine, Department of Pediatrics, University of California, San Diego, La Jolla, California.,Rady Children's Hospital of San Diego, San Diego California
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Ziv Bar-Joseph
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Namasivayam Ambalavanan
- Division of Neonatology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
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80
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Liu X, Mei M, Chen X, Lu Y, Dong X, Hu L, Hu X, Cheng G, Cao Y, Yang L, Zhou W. Identification of genetic factors underlying persistent pulmonary hypertension of newborns in a cohort of Chinese neonates. Respir Res 2019; 20:174. [PMID: 31382961 PMCID: PMC6683566 DOI: 10.1186/s12931-019-1148-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/29/2019] [Indexed: 01/02/2023] Open
Abstract
Background Persistent pulmonary hypertension of the newborn (PPHN) is a severe clinical problem among neonatal intensive care unit (NICU) patients. The genetic pathogenesis of PPHN is unclear. Only a few genetic polymorphisms have been identified in infants with PPHN. Our study aimed to investigate the potential genetic etiology of PPHN. Methods This study recruited PPHN patients admitted to the NICU of the Children’s Hospital of Fudan University from Jan 2016 to Dec 2017. Exome sequencing was performed for all patients. Variants in reported PPHN/pulmonary arterial hypertension (PAH)-related genes were assessed. Single nucleotide polymorphism (SNP) association and gene-level analyses were carried out in 74 PPHN cases and 115 non-PPHN controls with matched baseline characteristics. Results Among the patient cohort, 74 (64.3%) patients were late preterm and term infants (≥ 34 weeks gestation) and 41 (35.7%) were preterm infants (< 34 weeks gestation). Preterm infants with PPHN exhibited low birth weight and a high frequency of bronchopulmonary dysplasia, respiratory distress syndrome (RDS) and mortality. Nine patients (only one preterm infant) were identified as harboring genetic variants, including three with pathogenic/likely pathogenic variants in TBX4 and BMPR2 and six with variants of unknown significance in BMPR2, SMAD9, TGFB1, KCNA5 and TRPC6. Three SNPs (rs192759073, rs1047883 and rs2229589) in CPS1 and one SNP (rs1044008) in NOTCH3 were significantly associated with PPHN (p < 0.05). CPS1 and SMAD9 were identified as risk genes for PPHN (p < 0.05). Conclusions In this study, we identified genetic variants in PPHN patients, and we reported CPS1, NOTCH3 and SMAD9 as risk genes for late preterm and term PPHN in a single-center Chinese cohort. Our findings provide additional genetic evidence of the pathogenesis of PPHN and new insight into potential strategies for disease treatment. Electronic supplementary material The online version of this article (10.1186/s12931-019-1148-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xu Liu
- Clinical Genetic Center, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China.,Department of Neonatology, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Mei Mei
- Department of Pulmonology, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Xiang Chen
- Department of Neonatology, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Yulan Lu
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Xinran Dong
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Liyuan Hu
- Department of Neonatology, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Xiaojing Hu
- Department of Neonatology, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Guoqiang Cheng
- Department of Neonatology, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Yun Cao
- Department of Neonatology, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Lin Yang
- Clinical Genetic Center, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China. .,Key Laboratory of Birth Defects, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China.
| | - Wenhao Zhou
- Clinical Genetic Center, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China. .,Department of Neonatology, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China. .,Key Laboratory of Birth Defects, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China.
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81
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Callahan ZM, Shi Z, Su B, Xu J, Ujiki M. Genetic variants in Barrett's esophagus and esophageal adenocarcinoma: a literature review. Dis Esophagus 2019; 32:5393313. [PMID: 30888413 DOI: 10.1093/dote/doz017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Surveillance of Barrett's esophagus (BE) is a clinical challenge; metaplasia of the distal esophagus increases a patient's risk of esophageal adenocarcinoma (EAC) significantly but the actual percentage of patients who progress is low. The current screening recommendations require frequent endoscopy and biopsy, which has inherent risk, high cost, and operator variation. Identifying BE patients genetically who are at high risk of progressing could deemphasize the role of endoscopic screening and create an opportunity for early therapeutic intervention. Genetic alterations in germline DNA have been identified in other disease processes and allow for early intervention or surveillance well before disease develops. The genetic component of BE remains mostly unknown and only a few genome-wide association studies exist on this topic. This review summarizes the current literature available that examines genetic alterations in BE and EAC with a particular emphasis on clinical implications.
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Affiliation(s)
| | - Zhuqing Shi
- NorthShore University HealthSystem Research Institute
| | - Bailey Su
- Department of General Surgery, NorthShore University HealthSystem.,Department of General Surgery, University of Chicago, Chicago, USA
| | - Jianfeng Xu
- NorthShore University HealthSystem Research Institute
| | - Michael Ujiki
- Department of General Surgery, NorthShore University HealthSystem
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Li W, Wang M, Zhou R, Wang S, Zheng H, Liu D, Zhou Z, Zhu H, Wu T, Beaty TH. Exploring the interaction between FGF Genes and T-box genes among chinese nonsyndromic cleft lip with or without cleft palate case-parent trios. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2019; 60:602-606. [PMID: 30848863 DOI: 10.1002/em.22286] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 02/17/2019] [Accepted: 03/05/2019] [Indexed: 06/09/2023]
Abstract
Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect. Genetic variants causing syndromic orofacial clefts can also contribute to the etiology of NSCL/P. The purpose of the present study was to explore gene-gene (G × G) interaction using common single nucleotide polymorphic (SNP) markers in fibroblast growth factor (FGF) family and its receptors and T-box genes, which were associated with syndromic orofacial clefts. Our study was conducted in 806 Chinese NSCL/P case-parent trios drawn from an international consortium. A total of 252 SNPs in FGF8, FGF10, FGFR1, FGFR2, and TBX5 passed the quality control criteria and were included in the analysis. The interactions between SNPs in different genes were assessed using Cordell's method, which fitted a conditional logistic regression model. The analysis was performed using the R-package trio (Version 3.8.0). Bonferroni correction was used to adjust for multiple comparisons, and the overall significance threshold was set as P = 1.98 × 10-4 (0.05/252). Conditional logistic regression revealed the most significant interaction between rs2330542 in FGF10 and rs1946295 in TBX5, which remained significant (P = 9.63 × 10-6 ) after Bonferroni correction. The relative risk of allele C in rs2330542 (FGF10) was 1.02 (95%CI 0.81-1.28), while the relative risk was 1.42 (95%CI 1.03-1.97) when the exposure was a combination of allele C in rs2330542 and allele A in rs1946295 (TBX5). Our findings confirmed the importance of considering G × G interaction when exploring the genetic risk factors of NSCL/P. Further investigations are warranted to validate the potential interaction and reveal the biological function of FGF10/FGFR2/TBX5. Environ. Mol. Mutagen. 2019. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Wenyong Li
- School of Public Health, Peking University, Beijing, China
| | - Mengying Wang
- School of Public Health, Peking University, Beijing, China
| | - Ren Zhou
- School of Public Health, Peking University, Beijing, China
| | - Siyue Wang
- School of Public Health, Peking University, Beijing, China
| | - Hongchen Zheng
- School of Public Health, Peking University, Beijing, China
| | - Dongjing Liu
- School of Public Health, Peking University, Beijing, China
| | - Zhibo Zhou
- School of Stomatology, Peking University, Beijing, China
| | - Hongping Zhu
- School of Stomatology, Peking University, Beijing, China
| | - Tao Wu
- School of Public Health, Peking University, Beijing, China
- Key Laboratory of Reproductive Health, Ministry of Health, Beijing, China
| | - Terri H Beaty
- School of Public Health, Johns Hopkins University, Baltimore, Maryland
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83
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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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84
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Male-Specific Long Noncoding RNA TTTY15 Inhibits Non-Small Cell Lung Cancer Proliferation and Metastasis via TBX4. Int J Mol Sci 2019; 20:ijms20143473. [PMID: 31311130 PMCID: PMC6678590 DOI: 10.3390/ijms20143473] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/11/2019] [Accepted: 07/13/2019] [Indexed: 12/20/2022] Open
Abstract
Gender affects cancer susceptibility. Currently, there are only a few studies on Y chromosome-linked long noncoding RNAs (lncRNAs), and the potential association between lncRNAs and cancers in males has not been fully elucidated. Here, we examined the expression of testis-specific transcript Y-linked 15 (TTTY15) in 37 males with non-small cell lung cancer (NSCLC), and performed circular chromosome conformation capture with next-generation sequencing to determine the genomic interaction regions of the TTTY15 gene. Our results showed that the expression levels of TTTY15 were lower in NSCLC tissues. Lower TTTY15 expression levels were associated with Tumor-Node-Metastasis (TNM) stage. A TTTY15 knockdown promoted malignant transformation of NSCLC cells. Based on the bioinformatics analysis of circular chromosome conformation capture data, we found that T-box transcription factor 4 (TBX4) may be a potential target gene of TTTY15. The RNA immunoprecipitation and chromatin immunoprecipitation results showed that TTTY15 may interact with DNA (cytosine-5)-methyltransferase 3A (DNMT3A), and the TTTY15 knockdown increased the binding of DNMT3A to the TBX4 promoter. We concluded that low TTTY15 expression correlates with worse prognosis among patients with NSCLC. TTTY15 promotes TBX4 expression via DNMT3A-mediated regulation. The identification of lncRNAs encoded by male-specific genes may help to identify potential targets for NSCLC therapy.
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85
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Cellular crosstalk in the development and regeneration of the respiratory system. Nat Rev Mol Cell Biol 2019; 20:551-566. [PMID: 31217577 DOI: 10.1038/s41580-019-0141-3] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2019] [Indexed: 12/14/2022]
Abstract
The respiratory system, including the peripheral lungs, large airways and trachea, is one of the most recently evolved adaptations to terrestrial life. To support the exchange of respiratory gases, the respiratory system is interconnected with the cardiovascular system, and this interconnective nature requires a complex interplay between a myriad of cell types. Until recently, this complexity has hampered our understanding of how the respiratory system develops and responds to postnatal injury to maintain homeostasis. The advent of new single-cell sequencing technologies, developments in cellular and tissue imaging and advances in cell lineage tracing have begun to fill this gap. The view that emerges from these studies is that cellular and functional heterogeneity of the respiratory system is even greater than expected and also highly adaptive. In this Review, we explore the cellular crosstalk that coordinates the development and regeneration of the respiratory system. We discuss both the classic cell and developmental biology studies and recent single-cell analysis to provide an integrated understanding of the cellular niches that control how the respiratory system develops, interacts with the external environment and responds to injury.
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86
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German K, Deutsch GH, Freed AS, Dipple KM, Chabra S, Bennett JT. Identification of a deletion containing TBX4 in a neonate with acinar dysplasia by rapid exome sequencing. Am J Med Genet A 2019; 179:842-845. [PMID: 30828993 PMCID: PMC7738195 DOI: 10.1002/ajmg.a.61096] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/31/2019] [Accepted: 02/01/2019] [Indexed: 01/14/2023]
Abstract
We describe a neonate with severe respiratory failure due to acinar dysplasia found by rapid exome sequencing (rES), to have a deletion containing the TBX4 gene. rES can affect patient management in the intensive care unit and should be considered in concert with lung biopsy in neonates with undifferentiated respiratory failure.
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Affiliation(s)
- Kendell German
- Department of Pediatrics, University of Washington, Seattle, Washington
| | - Gail H Deutsch
- Department of Pathology, Seattle Children's Hospital and University of Washington, Seattle, Washington
| | - Amanda S Freed
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington
| | - Katrina M Dipple
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, Washington
- Center for Clinical and Translational Research, Seattle Children's Research Institute, Seattle, Washington
| | - Shilpi Chabra
- Department of Pediatrics, University of Washington, Seattle, Washington
| | - James T Bennett
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, Washington
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, Washington
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87
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Epigenetic Suppression of the T-box Subfamily 2 ( TBX2) in Human Non-Small Cell Lung Cancer. Int J Mol Sci 2019; 20:ijms20051159. [PMID: 30866410 PMCID: PMC6429281 DOI: 10.3390/ijms20051159] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/15/2019] [Accepted: 02/18/2019] [Indexed: 12/25/2022] Open
Abstract
(1) The TBX2 subfamily of transcription factors (TBXs 2, 3, 4 and 5) are markedly down-regulated in human non-small cell lung cancer (NSCLC) and exert tumor suppressor effects in lung malignancy. Yet, mechanisms underlying suppressed expression of the TBX2 subfamily in NSCLC are elusive. Here, we interrogated probable epigenetic mechanisms in suppressed expression of the TBX2 subfamily in human NSCLC. (2) TBX2 subfamily gene expression and methylation levels in NSCLC and normal lung tissues were surveyed using publicly available RNA-sequence and genome-wide methylation datasets. Methylation β-values of the four genes were statistically compared between NSCLCs and normal lung tissues, correlated with gene expression levels, and interrogated with clinicopathological variables. Expression and methylation levels of TBXs were quantified in NSCLC cells using real-time PCR and methylation-specific PCR assays, respectively. Effects of the DNA methyltransferase inhibitor 5-azacytidine (Aza) on TBX2 subfamily expression were assessed in NSCLC cells. Impact of TBX2 subfamily expression on Aza-treated cells was evaluated by RNA interference. (3) All four TBXs were significantly hypermethylated in NSCLCs relative to normal lung tissues (p < 0.05). Methylation β-values of the genes, with exception of TBX2, were significantly inversely correlated with corresponding mRNA expression levels (p < 0.05). We found no statistically significant differences in hypermethylation levels of the TBX2 subfamily by clinicopathological features including stage and tobacco history. Expression levels of the TBX genes were overall suppressed in NSCLC cells relative to normal alveolar cells. Members of the subfamily were significantly hypermethylated in all tested NSCLC cell lines relative to normal alveolar cells. Treatment with Aza induced the expression of the TBX2 subfamily concomitant with NSCLC cell growth inhibition. Further, simultaneous knockdown of the four TBX genes markedly reduced anti-growth effects of Aza in NSCLC cells. (4) Our study sheds light on new epigenetic profiles in the molecular pathogenesis of human NSCLC.
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88
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Neonatal Lung Disease Associated with TBX4 Mutations. J Pediatr 2019; 206:286-292.e1. [PMID: 30413314 PMCID: PMC6389379 DOI: 10.1016/j.jpeds.2018.10.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 01/06/2023]
Abstract
Variable lung disease was documented in 2 infants with heterozygous TBX4 mutations; their clinical presentations, pathology, and outcomes were distinct. These findings demonstrate that TBX4 gene mutations are associated with neonatal respiratory failure and highlight the wide spectrum of clinicopathological outcomes that have implications for patient diagnosis and management.
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89
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Zhang K, Wang M, Zhao Y, Wang W. Taiji: System-level identification of key transcription factors reveals transcriptional waves in mouse embryonic development. SCIENCE ADVANCES 2019; 5:eaav3262. [PMID: 30944857 PMCID: PMC6436936 DOI: 10.1126/sciadv.aav3262] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 01/30/2019] [Indexed: 05/20/2023]
Abstract
Transcriptional regulation is pivotal to the specification of distinct cell types during embryonic development. However, it still lacks a systematic way to identify key transcription factors (TFs) orchestrating the temporal and tissue specificity of gene expression. Here, we integrated epigenomic and transcriptomic data to reveal key regulators from two cells to postnatal day 0 in mouse embryogenesis. We predicted three-dimensional chromatin interactions in 12 tissues across eight developmental stages, which facilitates linking TFs to their target genes for constructing transcriptional regulatory networks. To identify driver TFs, we developed a new algorithm, dubbed Taiji, to assess the global influence of each TF and systematically uncovered TFs critical for lineage-specific and stage-dependent tissue specification. We have also identified TF combinations that function in spatiotemporal order to form transcriptional waves regulating developmental progress. Furthermore, lacking stage-specific TF combinations suggests a distributed timing strategy to orchestrate the coordination between tissues during embryonic development.
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Affiliation(s)
- Kai Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Mengchi Wang
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Ying Zhao
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Corresponding author.
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90
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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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91
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Whitsett JA, Kalin TV, Xu Y, Kalinichenko VV. Building and Regenerating the Lung Cell by Cell. Physiol Rev 2019; 99:513-554. [PMID: 30427276 DOI: 10.1152/physrev.00001.2018] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The unique architecture of the mammalian lung is required for adaptation to air breathing at birth and thereafter. Understanding the cellular and molecular mechanisms controlling its morphogenesis provides the framework for understanding the pathogenesis of acute and chronic lung diseases. Recent single-cell RNA sequencing data and high-resolution imaging identify the remarkable heterogeneity of pulmonary cell types and provides cell selective gene expression underlying lung development. We will address fundamental issues related to the diversity of pulmonary cells, to the formation and function of the mammalian lung, and will review recent advances regarding the cellular and molecular pathways involved in lung organogenesis. What cells form the lung in the early embryo? How are cell proliferation, migration, and differentiation regulated during lung morphogenesis? How do cells interact during lung formation and repair? How do signaling and transcriptional programs determine cell-cell interactions necessary for lung morphogenesis and function?
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Affiliation(s)
- Jeffrey A Whitsett
- Perinatal Institute, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati, Ohio
| | - Tanya V Kalin
- Perinatal Institute, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati, Ohio
| | - Yan Xu
- Perinatal Institute, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati, Ohio
| | - Vladimir V Kalinichenko
- Perinatal Institute, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati, Ohio
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92
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Shichino S, Ueha S, Hashimoto S, Otsuji M, Abe J, Tsukui T, Deshimaru S, Nakajima T, Kosugi-Kanaya M, Shand FH, Inagaki Y, Shimano H, Matsushima K. Transcriptome network analysis identifies protective role of the LXR/SREBP-1c axis in murine pulmonary fibrosis. JCI Insight 2019; 4:122163. [PMID: 30626759 DOI: 10.1172/jci.insight.122163] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 12/05/2018] [Indexed: 12/13/2022] Open
Abstract
Pulmonary fibrosis (PF) is an intractable disorder with a poor prognosis. Although lung fibroblasts play a central role in PF, the key regulatory molecules involved in this process remain unknown. To address this issue, we performed a time-course transcriptome analysis on lung fibroblasts of bleomycin- and silica-treated murine lungs. We found gene modules whose expression kinetics were associated with the progression of PF and human idiopathic PF (IPF). Upstream analysis of a transcriptome network helped in identifying 55 hub transcription factors that were highly connected with PF-associated gene modules. Of these hubs, the expression of Srebf1 decreased in line with progression of PF and human IPF, suggesting its suppressive role in fibroblast activation. Consistently, adoptive transfer and genetic modification studies revealed that the hub transcription factor SREBP-1c suppressed PF-associated gene expression changes in lung fibroblasts and PF pathology in vivo. Moreover, therapeutic pharmacological activation of LXR, an SREBP-1c activator, suppressed the Srebf1-dependent activation of fibroblasts and progression of PF. Thus, SREBP-1c acts as a protective hub of lung fibroblast activation in PF. Collectively, the findings of the current study may prove to be valuable in the development of effective therapeutic strategies for PF.
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Affiliation(s)
- Shigeyuki Shichino
- Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Satoshi Ueha
- Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Shinichi Hashimoto
- Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Chiba, Japan.,Department of Integrative Medicine for Longevity, Graduate School of Medical Sciences, Kanazawa University, Ishikawa, Japan
| | - Mikiya Otsuji
- Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Jun Abe
- Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Theodor Kocher Institute, University of Bern, Bern, Switzerland
| | - Tatsuya Tsukui
- Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shungo Deshimaru
- Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Takuya Nakajima
- Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Mizuha Kosugi-Kanaya
- Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Francis Hw Shand
- Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yutaka Inagaki
- Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, Kanagawa, Japan
| | - Hitoshi Shimano
- Department of Endocrinology and Metabolism, Faculty of Medicine, University of Tsukuba, Chiba, Japan
| | - Kouji Matsushima
- Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Chiba, Japan
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93
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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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94
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Holt-Oram syndrome: clinical and molecular description of 78 patients with TBX5 variants. Eur J Hum Genet 2018; 27:360-368. [PMID: 30552424 DOI: 10.1038/s41431-018-0303-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 10/12/2018] [Accepted: 10/25/2018] [Indexed: 12/24/2022] Open
Abstract
Holt-Oram syndrome (HOS) is an autosomal dominant condition characterised by the association of congenital heart defect (CHD), with or without rhythm disturbances and radial defects, due to TBX5 variants. The diagnosis is challenged by the variability of expression and the large phenotypic overlap with other conditions, like Okihiro syndrome, TAR syndrome or Fanconi disease. We retrospectively reviewed 212 patients referred for suspicion of HOS between 2002 and 2014, who underwent TBX5 screening. A TBX5 variant has been identified in 78 patients, representing the largest molecular series ever described. In the cohort, 61 met the previously described diagnostic criteria and 17 have been considered with an uncertain HOS diagnosis. A CHD was present in 91% of the patients with a TBX5 variant, atrial septal defects being the most common (61.5%). The genotype-phenotype study highlights the importance of some critical features in HOS: the septal characteristic of the CHD, the bilateral and asymmetric characteristics of the radial defect and the presence of shoulder or elbow mobility defect. Besides, 21 patients presented with an overlapping condition. Among them, 13 had a typical HOS presentation. We discuss the strategies that could be adopted to improve the molecular delineation of the remaining typical patients.
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95
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Khalil A, Dekmak B, Boulos F, Kantrowitz J, Spira A, Fujimoto J, Kadara H, El-Hachem N, Nemer G. Transcriptomic Alterations in Lung Adenocarcinoma Unveil New Mechanisms Targeted by the TBX2 Subfamily of Tumor Suppressor Genes. Front Oncol 2018; 8:482. [PMID: 30425966 PMCID: PMC6218583 DOI: 10.3389/fonc.2018.00482] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 10/09/2018] [Indexed: 12/22/2022] Open
Abstract
T-box (TBX) transcription factors are evolutionary conserved genes and master transcriptional regulators. In mammals, TBX2 subfamily (TBX2, TBX3, TBX4, and TBX5) genes are expressed in the developing lung bud and tracheae. Our group previously showed that the expression of TBX2 subfamily was significantly high in human normal lungs, but markedly suppressed in lung adenocarcinoma (LUAD). To further elucidate their role in LUAD pathogenesis, we first confirmed abundant expression of protein products of the four members by immunostaining in adult human normal lung tissues. We also found overall suppressed expression of these genes and their corresponding proteins in a panel of human LUAD cell lines. Transient over-expression of each of the genes in human (NCI-H1299), and mouse (MDA-F471) derived lung cancer cells was found to significantly inhibit growth and proliferation as well as induce apoptosis. Genome-wide transcriptomic analyses on NCI-H1299 cells, overexpressing TBX2 gene subfamily, unraveled novel regulatory pathways. These included, among others, inhibition of cell cycle progression but more importantly activation of the histone demethylase pathway. When using a pattern-matching algorithm, we showed that TBX's overexpression mimic molecular signatures from azacitidine treated NCI-H1299 cells which in turn are inversely correlated to expression profiles of both human and murine lung tumors relative to matched normal lung. In conclusion, we showed that the TBX2 subfamily genes play a critical tumor suppressor role in lung cancer pathogenesis through regulating its methylating pattern, making them putative candidates for epigenetic therapy in LUAD.
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Affiliation(s)
- Athar Khalil
- Departments of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Batoul Dekmak
- Departments of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Fouad Boulos
- Department of Pathology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Jake Kantrowitz
- Section of Computational Biomedicine, Boston University, Boston, MA, United States
| | - Avrum Spira
- Section of Computational Biomedicine, Boston University, Boston, MA, United States
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Humam Kadara
- Departments of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.,Division of Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Nehme El-Hachem
- Faculty of Medicine and Genome Innovation Centre, McGill University, Montreal, QC, Canada
| | - Georges Nemer
- Departments of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
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96
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Evolutionarily conserved Tbx5- Wnt2/2b pathway orchestrates cardiopulmonary development. Proc Natl Acad Sci U S A 2018; 115:E10615-E10624. [PMID: 30352852 DOI: 10.1073/pnas.1811624115] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Codevelopment of the lungs and heart underlies key evolutionary innovations in the transition to terrestrial life. Cardiac specializations that support pulmonary circulation, including the atrial septum, are generated by second heart field (SHF) cardiopulmonary progenitors (CPPs). It has been presumed that transcription factors required in the SHF for cardiac septation, e.g., Tbx5, directly drive a cardiac morphogenesis gene-regulatory network. Here, we report instead that TBX5 directly drives Wnt ligands to initiate a bidirectional signaling loop between cardiopulmonary mesoderm and the foregut endoderm for endodermal pulmonary specification and, subsequently, atrial septation. We show that Tbx5 is required for pulmonary specification in mice and amphibians but not for swim bladder development in zebrafish. TBX5 is non-cell-autonomously required for pulmonary endoderm specification by directly driving Wnt2 and Wnt2b expression in cardiopulmonary mesoderm. TBX5 ChIP-sequencing identified cis-regulatory elements at Wnt2 sufficient for endogenous Wnt2 expression domains in vivo and required for Wnt2 expression in precardiac mesoderm in vitro. Tbx5 cooperated with Shh signaling to drive Wnt2b expression for lung morphogenesis. Tbx5 haploinsufficiency in mice, a model of Holt-Oram syndrome, caused a quantitative decrement of mesodermal-to-endodermal Wnt signaling and subsequent endodermal-to-mesodermal Shh signaling required for cardiac morphogenesis. Thus, Tbx5 initiates a mesoderm-endoderm-mesoderm signaling loop in lunged vertebrates that provides a molecular basis for the coevolution of pulmonary and cardiac structures required for terrestrial life.
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97
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Abstract
In its most basic conception, a novelty is simply something new. However, when many previously proposed evolutionary novelties have been illuminated by genetic, developmental, and fossil data, they have refined and narrowed our concept of biological "newness." For example, they show that these novelties can occur at one or multiple levels of biological organization. Here, we review the identity of structures in the avian vocal organ, the syrinx, and bring together developmental data on airway patterning, structural data from across tetrapods, and mathematical modeling to assess what is novel. In contrast with laryngeal cartilages that support vocal folds in other vertebrates, we find no evidence that individual cartilage rings anchoring vocal folds in the syrinx have homology with any specific elements in outgroups. Further, unlike all other vertebrate vocal organs, the syrinx is not derived from a known valve precursor, and its origin involves a transition from an evolutionary "spandrel" in the respiratory tract, the site where the trachea meets the bronchi, to a target for novel selective regimes. We find that the syrinx falls into an unusual category of novel structures: those having significant functional overlap with the structures they replace. The syrinx, along with other evolutionary novelties in sensory and signaling modalities, may more commonly involve structural changes that contribute to or modify an existing function rather than those that enable new functions.
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98
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Bertero T, Handen AL, Chan SY. Factors Associated with Heritable Pulmonary Arterial Hypertension Exert Convergent Actions on the miR-130/301-Vascular Matrix Feedback Loop. Int J Mol Sci 2018; 19:ijms19082289. [PMID: 30081553 PMCID: PMC6121519 DOI: 10.3390/ijms19082289] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 07/31/2018] [Accepted: 08/01/2018] [Indexed: 11/16/2022] Open
Abstract
Pulmonary arterial hypertension (PAH) is characterized by occlusion of lung arterioles, leading to marked increases in pulmonary vascular resistance. Although heritable forms of PAH are known to be driven by genetic mutations that share some commonality of function, the extent to which these effectors converge to regulate shared processes in this disease is unknown. We have causally connected extracellular matrix (ECM) remodeling and mechanotransduction to the miR-130/301 family in a feedback loop that drives vascular activation and downstream PAH. However, the molecular interconnections between factors genetically associated with PAH and this mechano-driven feedback loop remain undefined. We performed systematic manipulation of matrix stiffness, the miR-130/301 family, and factors genetically associated with PAH in primary human pulmonary arterial cells and assessed downstream and reciprocal consequences on their expression. We found that a network of factors linked to heritable PAH converges upon the matrix stiffening-miR-130/301-PPARγ-LRP8 axis in order to remodel the ECM. Furthermore, we leveraged a computational network biology approach to predict a number of additional molecular circuits functionally linking this axis to the ECM. These results demonstrate that multiple genes associated with heritable PAH converge to control the miR-130/301 circuit, triggering a self-amplifying feedback process central to pulmonary vascular stiffening and disease.
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Affiliation(s)
- Thomas Bertero
- Université Côte d'Azur, CNRS UMR7284, INSERM U1081, IRCAN, Nice 06100, France.
| | - Adam L Handen
- Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA.
| | - Stephen Y Chan
- Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA.
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99
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Marcu R, Choi YJ, Xue J, Fortin CL, Wang Y, Nagao RJ, Xu J, MacDonald JW, Bammler TK, Murry CE, Muczynski K, Stevens KR, Himmelfarb J, Schwartz SM, Zheng Y. Human Organ-Specific Endothelial Cell Heterogeneity. iScience 2018; 4:20-35. [PMID: 30240741 PMCID: PMC6147238 DOI: 10.1016/j.isci.2018.05.003] [Citation(s) in RCA: 168] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 04/24/2018] [Accepted: 05/03/2018] [Indexed: 12/20/2022] Open
Abstract
The endothelium first forms in the blood islands in the extra-embryonic yolk sac and then throughout the embryo to establish circulatory networks that further acquire organ-specific properties during development to support diverse organ functions. Here, we investigated the properties of endothelial cells (ECs), isolated from four human major organs-the heart, lung, liver, and kidneys-in individual fetal tissues at three months' gestation, at gene expression, and at cellular function levels. We showed that organ-specific ECs have distinct expression patterns of gene clusters, which support their specific organ development and functions. These ECs displayed distinct barrier properties, angiogenic potential, and metabolic rate and support specific organ functions. Our findings showed the link between human EC heterogeneity and organ development and can be exploited therapeutically to contribute in organ regeneration, disease modeling, as well as guiding differentiation of tissue-specific ECs from human pluripotent stem cells.
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Affiliation(s)
- Raluca Marcu
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Yoon Jung Choi
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Jun Xue
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Chelsea L Fortin
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Yuliang Wang
- Department of Computer Science & Engineering, University of Washington, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Ryan J Nagao
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Jin Xu
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - James W MacDonald
- Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Theo K Bammler
- Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Charles E Murry
- Department of Bioengineering, University of Washington, Seattle, WA, USA; Department of Pathology, University of Washington, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA; Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Kelly R Stevens
- Department of Bioengineering, University of Washington, Seattle, WA, USA; Department of Pathology, University of Washington, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Jonathan Himmelfarb
- Department of Medicine, University of Washington, Seattle, WA, USA; Kidney Research Institute, University of Washington, Seattle, WA, USA
| | | | - Ying Zheng
- Department of Bioengineering, University of Washington, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA; Kidney Research Institute, University of Washington, Seattle, WA, USA.
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100
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Cirulis MM, Ryan JJ. Who’s Who of Pulmonary Hypertension. Circ Genom Precis Med 2018; 11:e002116. [DOI: 10.1161/circgen.118.002116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 03/05/2018] [Indexed: 11/16/2022]
Affiliation(s)
- Meghan M. Cirulis
- Division of Pulmonary Medicine (M.M.C.) and Division of Cardiovascular Medicine (J.J.R.), Department of Medicine, University of Utah, Salt Lake City
| | - John J. Ryan
- Division of Pulmonary Medicine (M.M.C.) and Division of Cardiovascular Medicine (J.J.R.), Department of Medicine, University of Utah, Salt Lake City
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