1
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Doughty ES, Norvik C, Levin A, Bodmer J, Tran-Lundmark K, Abman SH, Galambos C. Long-Term Effect of TBX4 Germline Mutation on Pulmonary Clinico-Histopathologic Phenotype. Pediatr Dev Pathol 2024; 27:83-89. [PMID: 37801629 DOI: 10.1177/10935266231199933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/08/2023]
Abstract
Tbx4 protein, expressed in mesenchyme of the developing lung, contributes to airway branching and distal lung growth. An association between pediatric onset of pulmonary arterial hypertension (PAH) and genetic variations coding for the T-box transcription factor 4 gene (TBX4) has been increasingly recognized. Tbx4-related PAH onset has a bimodal age distribution, including severe to lethal PAH in newborns and later onset PAH. We present an autopsy study of a 24-year-old male with a heterozygous TBX4 variant, who developed pulmonary arterial hypertension at age 12 years. This unique case highlights the complex pulmonary histopathology leading to lethal cardiopulmonary failure in the setting of TBX4 mutation.
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Affiliation(s)
- Elizabeth S Doughty
- Department of Pathology and Laboratory Medicine, The University of Colorado Hospital, Aurora, CO, USA
| | - Christian Norvik
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
| | - Alice Levin
- Department of Pathology and Laboratory Medicine, Children's Hospital Colorado, Aurora, CO, USA
| | - Jenna Bodmer
- Department of Pathology and Laboratory Medicine, The University of Colorado Hospital, Aurora, CO, USA
- Department of Pathology and Laboratory Medicine, Children's Hospital Colorado, Aurora, CO, USA
| | - Karin Tran-Lundmark
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
| | - Steven H Abman
- Pediatric Heart Lung Center, Children's Hospital Colorado, Aurora, CO, USA
| | - Csaba Galambos
- Department of Pathology and Laboratory Medicine, The University of Colorado Hospital, Aurora, CO, USA
- Department of Pathology and Laboratory Medicine, Children's Hospital Colorado, Aurora, CO, USA
- Pediatric Heart Lung Center, Children's Hospital Colorado, Aurora, CO, USA
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2
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Guo M, Wikenheiser-Brokamp KA, Kitzmiller JA, Jiang C, Wang G, Wang A, Preissl S, Hou X, Buchanan J, Karolak JA, Miao Y, Frank DB, Zacharias WJ, Sun X, Xu Y, Gu M, Stankiewicz P, Kalinichenko VV, Wambach JA, Whitsett JA. Single Cell Multiomics Identifies Cells and Genetic Networks Underlying Alveolar Capillary Dysplasia. Am J Respir Crit Care Med 2023; 208:709-725. [PMID: 37463497 PMCID: PMC10515568 DOI: 10.1164/rccm.202210-2015oc] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 07/18/2023] [Indexed: 07/20/2023] Open
Abstract
Rationale: Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a lethal developmental disorder of lung morphogenesis caused by insufficiency of FOXF1 (forkhead box F1) transcription factor function. The cellular and transcriptional mechanisms by which FOXF1 deficiency disrupts human lung formation are unknown. Objectives: To identify cell types, gene networks, and cell-cell interactions underlying the pathogenesis of ACDMPV. Methods: We used single-nucleus RNA and assay for transposase-accessible chromatin sequencing, immunofluorescence confocal microscopy, and RNA in situ hybridization to identify cell types and molecular networks influenced by FOXF1 in ACDMPV lungs. Measurements and Main Results: Pathogenic single-nucleotide variants and copy-number variant deletions involving the FOXF1 gene locus in all subjects with ACDMPV (n = 6) were accompanied by marked changes in lung structure, including deficient alveolar development and a paucity of pulmonary microvasculature. Single-nucleus RNA and assay for transposase-accessible chromatin sequencing identified alterations in cell number and gene expression in endothelial cells (ECs), pericytes, fibroblasts, and epithelial cells in ACDMPV lungs. Distinct cell-autonomous roles for FOXF1 in capillary ECs and pericytes were identified. Pathogenic variants involving the FOXF1 gene locus disrupt gene expression in EC progenitors, inhibiting the differentiation or survival of capillary 2 ECs and cell-cell interactions necessary for both pulmonary vasculogenesis and alveolar type 1 cell differentiation. Loss of the pulmonary microvasculature was associated with increased VEGFA (vascular endothelial growth factor A) signaling and marked expansion of systemic bronchial ECs expressing COL15A1 (collagen type XV α 1 chain). Conclusions: Distinct FOXF1 gene regulatory networks were identified in subsets of pulmonary endothelial and fibroblast progenitors, providing both cellular and molecular targets for the development of therapies for ACDMPV and other diffuse lung diseases of infancy.
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Affiliation(s)
- Minzhe Guo
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology
- Department of Pediatrics and
| | - Kathryn A. Wikenheiser-Brokamp
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology
- Division of Pathology and Laboratory Medicine
- Department of Pathology & Laboratory Medicine, College of Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Joseph A. Kitzmiller
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology
| | - Cheng Jiang
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology
| | - Guolun Wang
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology
- Center for Lung Regenerative Medicine
| | - Allen Wang
- Center for Epigenomics & Department of Cellular & Molecular Medicine
| | - Sebastian Preissl
- Center for Epigenomics & Department of Cellular & Molecular Medicine
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Xiaomeng Hou
- Center for Epigenomics & Department of Cellular & Molecular Medicine
| | - Justin Buchanan
- Center for Epigenomics & Department of Cellular & Molecular Medicine
| | - Justyna A. Karolak
- Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Yifei Miao
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology
- Division of Developmental Biology, and
- Center for Stem Cell and Organoid Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
- Department of Pediatrics and
| | - David B. Frank
- Penn-CHOP Lung Biology Institute and
- Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania
- Division of Cardiology, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - William J. Zacharias
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology
- Department of Pediatrics and
| | - Xin Sun
- Department of Pediatrics, and
- Department of Biological Sciences, University of California, San Diego, La Jolla, California
| | - Yan Xu
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology
- Division of Biomedical Informatics
- Department of Pediatrics and
| | - Mingxia Gu
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology
- Division of Developmental Biology, and
- Center for Stem Cell and Organoid Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
- Department of Pediatrics and
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas; and
| | - Vladimir V. Kalinichenko
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology
- Center for Lung Regenerative Medicine
- Department of Pediatrics and
| | - Jennifer A. Wambach
- Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine and St. Louis Children’s Hospital, St. Louis, Missouri
| | - Jeffrey A. Whitsett
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology
- Department of Pediatrics and
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3
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Karolak JA, Welch CL, Mosimann C, Bzdęga K, West JD, Montani D, Eyries M, Mullen MP, Abman SH, Prapa M, Gräf S, Morrell NW, Hemnes AR, Perros F, Hamid R, Logan MPO, Whitsett J, Galambos C, Stankiewicz P, Chung WK, Austin ED. Molecular Function and Contribution of TBX4 in Development and Disease. Am J Respir Crit Care Med 2023; 207:855-864. [PMID: 36367783 PMCID: PMC10111992 DOI: 10.1164/rccm.202206-1039tr] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/10/2022] [Indexed: 11/13/2022] Open
Abstract
Over the past decade, recognition of the profound impact of the TBX4 (T-box 4) gene, which encodes a member of the evolutionarily conserved family of T-box-containing transcription factors, on respiratory diseases has emerged. The developmental importance of TBX4 is emphasized by the association of TBX4 variants with congenital disorders involving respiratory and skeletal structures; however, the exact role of TBX4 in human development remains incompletely understood. Here, we discuss the developmental, tissue-specific, and pathological TBX4 functions identified through human and animal studies and review the published TBX4 variants resulting in variable disease phenotypes. We also outline future research directions to fill the gaps in our understanding of TBX4 function and of how TBX4 disruption affects development.
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Affiliation(s)
- Justyna A. Karolak
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | | | | | - Katarzyna Bzdęga
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - James D. West
- Division of Allergy, Pulmonary and Critical Care Medicine, and
| | - David Montani
- Université Paris-Saclay, Assistance Publique–Hôpitaux de Paris, Service de Pneumologie et Soins Intensifs Respiratoires, Hôpital de Bicêtre, DMU 5 Thorinno, Inserm UMR_S999, Le Kremlin-Bicêtre, France
| | - Mélanie Eyries
- Sorbonne Université, AP-HP, Département de Génétique, Hôpital Pitié-Salpêtrière, Paris, France
| | - Mary P. Mullen
- Department of Cardiology, Boston Children’s Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | | | - Matina Prapa
- St. George’s University Hospitals NHS Foundation Trust, London, United Kingdom
| | - Stefan Gräf
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Heart and Lung Research Institute, Cambridge, United Kingdom
| | - Nicholas W. Morrell
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Heart and Lung Research Institute, Cambridge, United Kingdom
| | - Anna R. Hemnes
- Division of Allergy, Pulmonary and Critical Care Medicine, and
| | - Frédéric Perros
- Université Paris-Saclay, Assistance Publique–Hôpitaux de Paris, Service de Pneumologie et Soins Intensifs Respiratoires, Hôpital de Bicêtre, DMU 5 Thorinno, Inserm UMR_S999, Le Kremlin-Bicêtre, France
| | - Rizwan Hamid
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Malcolm P. O. Logan
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, United Kingdom
| | - Jeffrey Whitsett
- Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Perinatal Institute, Cincinnati, Ohio
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio; and
| | - Csaba Galambos
- Department of Pathology, University of Colorado School of Medicine, and Children’s Hospital Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Wendy K. Chung
- Department of Pediatrics and
- Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Eric D. Austin
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
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4
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Otálora-Otálora BA, López-Kleine L, Rojas A. Lung Cancer Gene Regulatory Network of Transcription Factors Related to the Hallmarks of Cancer. Curr Issues Mol Biol 2023; 45:434-464. [PMID: 36661515 PMCID: PMC9857713 DOI: 10.3390/cimb45010029] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 01/06/2023] Open
Abstract
The transcriptomic analysis of microarray and RNA-Seq datasets followed our own bioinformatic pipeline to identify a transcriptional regulatory network of lung cancer. Twenty-six transcription factors are dysregulated and co-expressed in most of the lung cancer and pulmonary arterial hypertension datasets, which makes them the most frequently dysregulated transcription factors. Co-expression, gene regulatory, coregulatory, and transcriptional regulatory networks, along with fibration symmetries, were constructed to identify common connection patterns, alignments, main regulators, and target genes in order to analyze transcription factor complex formation, as well as its synchronized co-expression patterns in every type of lung cancer. The regulatory function of the most frequently dysregulated transcription factors over lung cancer deregulated genes was validated with ChEA3 enrichment analysis. A Kaplan-Meier plotter analysis linked the dysregulation of the top transcription factors with lung cancer patients' survival. Our results indicate that lung cancer has unique and common deregulated genes and transcription factors with pulmonary arterial hypertension, co-expressed and regulated in a coordinated and cooperative manner by the transcriptional regulatory network that might be associated with critical biological processes and signaling pathways related to the acquisition of the hallmarks of cancer, making them potentially relevant tumor biomarkers for lung cancer early diagnosis and targets for the development of personalized therapies against lung cancer.
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Affiliation(s)
- Beatriz Andrea Otálora-Otálora
- Grupo de Investigación INPAC, Unidad de Investigación, Fundación Universitaria Sanitas, Bogotá 110131, Colombia
- Facultad de Medicina, Universidad Nacional de Colombia, Bogotá 11001, Colombia
| | - Liliana López-Kleine
- Departamento de Estadística, Universidad Nacional de Colombia, Bogotá 11001, Colombia
- Correspondence: (L.L.-K.); (A.R.)
| | - Adriana Rojas
- Facultad de Medicina, Instituto de Genética Humana, Pontificia Universidad Javeriana, Bogotá 110211, Colombia
- Correspondence: (L.L.-K.); (A.R.)
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5
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Kruk D, Yeung ACY, Faiz A, ten Hacken NHT, Timens W, van Kuppevelt TH, Daamen W, Hof D, Harmsen MC, Rojas M, Heijink IH. Gene expression profiles in mesenchymal stromal cells from bone marrow, adipose tissue and lung tissue of COPD patients and controls. Respir Res 2023; 24:22. [PMID: 36681830 PMCID: PMC9863276 DOI: 10.1186/s12931-023-02314-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/03/2023] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) is characterized by irreversible lung tissue damage. Novel regenerative strategies are urgently awaited. Cultured mesenchymal stem/stromal cells (MSCs) have shown promising results in experimental models of COPD, but differences between sources may impact on their potential use in therapeutic strategies in patients. AIM To assess the transcriptome of lung-derived MSCs (LMSCs), bone marrow-derived MSCs (BM-MSC) and adipose-derived MSCs (AD-MSCs) from COPD patients and non-COPD controls. METHODS We studied differences in gene expression profiles between the MSC-subtypes, as well as between COPD and control using RNA sequencing (RNA-seq). RESULTS We show that besides heterogeneity between donors, MSCs from different sources have strongly divergent gene signatures. The growth factors FGF10 and HGF were predominantly expressed in LMSCs. MSCs from all sources displayed altered expression profiles in COPD, with most pronounced significantly up- and downregulated genes in MSCs from adipose tissue. Pathway analysis revealed that the most differentially expressed genes in COPD-derived AD-MSCs are involved in extracellular matrix (ECM) binding and expression. In LMSCs, the gene that differed most strongly between COPD and control was CSGALNACT1, an ECM modulating gene. CONCLUSION Autologous MSCs from COPD patients display abnormalities with respect to their transcriptome, which were surprisingly most profound in MSCs from extrapulmonary sources. LMSCs may be optimally equipped for lung tissue repair because of the expression of specific growth factor genes.
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Affiliation(s)
- Dennis Kruk
- grid.4494.d0000 0000 9558 4598Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, Groningen The Netherlands ,grid.4494.d0000 0000 9558 4598Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Anna C. Y. Yeung
- grid.117476.20000 0004 1936 7611Respiratory Bioinformatics and Molecular Biology (RBMB) Group, The University of Technology Sydney, Ultimo, NSW Australia ,grid.1013.30000 0004 1936 834XWoolcock Institute of Medical Research, The University of Sydney, Glebe, NSW Australia
| | - Alen Faiz
- grid.117476.20000 0004 1936 7611Respiratory Bioinformatics and Molecular Biology (RBMB) Group, The University of Technology Sydney, Ultimo, NSW Australia
| | - Nick H. T. ten Hacken
- grid.4494.d0000 0000 9558 4598Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands ,grid.4494.d0000 0000 9558 4598Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Wim Timens
- grid.4494.d0000 0000 9558 4598Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, Groningen The Netherlands ,grid.4494.d0000 0000 9558 4598Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Toin H. van Kuppevelt
- grid.5590.90000000122931605Department of Biochemistry, University of Nijmegen, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Willeke Daamen
- grid.5590.90000000122931605Department of Biochemistry, University of Nijmegen, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Danique Hof
- grid.5590.90000000122931605Department of Biochemistry, University of Nijmegen, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Martin C. Harmsen
- grid.4494.d0000 0000 9558 4598Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, Groningen The Netherlands
| | - Mauricio Rojas
- grid.261331.40000 0001 2285 7943Division of Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, OH USA
| | - Irene H. Heijink
- grid.4494.d0000 0000 9558 4598Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, Groningen The Netherlands ,grid.4494.d0000 0000 9558 4598Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands ,grid.4494.d0000 0000 9558 4598Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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6
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Prapa M, Lago-Docampo M, Swietlik EM, Montani D, Eyries M, Humbert M, Welch CL, Chung WK, Berger RMF, Bogaard HJ, Danhaive O, Escribano-Subías P, Gall H, Girerd B, Hernandez-Gonzalez I, Holden S, Hunt D, Jansen SMA, Kerstjens-Frederikse W, Kiely DG, Lapunzina P, McDermott J, Moledina S, Pepke-Zaba J, Polwarth GJ, Schotte G, Tenorio-Castaño J, Thompson AAR, Wharton J, Wort SJ, Megy K, Mapeta R, Treacy CM, Martin JM, Li W, Swift AJ, Upton PD, Morrell NW, Gräf S, Valverde D. First Genotype-Phenotype Study in TBX4 Syndrome: Gain-of-Function Mutations Causative for Lung Disease. Am J Respir Crit Care Med 2022; 206:1522-1533. [PMID: 35852389 PMCID: PMC9757087 DOI: 10.1164/rccm.202203-0485oc] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/18/2022] [Indexed: 02/02/2023] Open
Abstract
Rationale: Despite the increased recognition of TBX4 (T-BOX transcription factor 4)-associated pulmonary arterial hypertension (PAH), genotype-phenotype associations are lacking and may provide important insights. Objectives: To compile and functionally characterize all TBX4 variants reported to date and undertake a comprehensive genotype-phenotype analysis. Methods: We assembled a multicenter cohort of 137 patients harboring monoallelic TBX4 variants and assessed the pathogenicity of missense variation (n = 42) using a novel luciferase reporter assay containing T-BOX binding motifs. We sought genotype-phenotype correlations and undertook a comparative analysis with patients with PAH with BMPR2 (Bone Morphogenetic Protein Receptor type 2) causal variants (n = 162) or no identified variants in PAH-associated genes (n = 741) genotyped via the National Institute for Health Research BioResource-Rare Diseases. Measurements and Main Results: Functional assessment of TBX4 missense variants led to the novel finding of gain-of-function effects associated with older age at diagnosis of lung disease compared with loss-of-function effects (P = 0.038). Variants located in the T-BOX and nuclear localization domains were associated with earlier presentation (P = 0.005) and increased incidence of interstitial lung disease (P = 0.003). Event-free survival (death or transplantation) was shorter in the T-BOX group (P = 0.022), although age had a significant effect in the hazard model (P = 0.0461). Carriers of TBX4 variants were diagnosed at a younger age (P < 0.001) and had worse baseline lung function (FEV1, FVC) (P = 0.009) than the BMPR2 and no identified causal variant groups. Conclusions: We demonstrated that TBX4 syndrome is not strictly the result of haploinsufficiency but can also be caused by gain of function. The pleiotropic effects of TBX4 in lung disease may be in part explained by the differential effect of pathogenic mutations located in critical protein domains.
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Affiliation(s)
- Matina Prapa
- Department of Medicine and
- St. George’s University Hospitals National Health Service (NHS) Foundation Trust, London, United Kingdom
| | - Mauro Lago-Docampo
- CINBIO, Universidade de Vigo, Vigo, Spain
- Rare Diseases and Pediatric Medicine, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Emilia M. Swietlik
- Department of Medicine and
- Addenbrooke’s Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - David Montani
- Université Paris-Saclay, AP-HP, Service de Pneumologie, Centre de référence de l’hypertension pulmonaire, INSERM UMR_S 999, Hôpital Bicêtre, Le Kremlin-Bicêtre, Paris, France
| | - Mélanie Eyries
- Département de génétique, hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, and UMR_S 1166-ICAN, INSERM, UPMC Sorbonne Universités, Paris, France
| | - Marc Humbert
- Université Paris-Saclay, AP-HP, Service de Pneumologie, Centre de référence de l’hypertension pulmonaire, INSERM UMR_S 999, Hôpital Bicêtre, Le Kremlin-Bicêtre, Paris, France
| | | | - Wendy K. Chung
- Department of Pediatrics and
- Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Rolf M. F. Berger
- Centre for Congenital Heart Diseases, Pediatric Cardiology, Beatrix Children’s Hospital, and
| | - Harm Jan Bogaard
- Department of Pulmonary Medicine, Amsterdam University Medical Centre, Vrije Universiteit Amsterdam, Amsterdam Cardiovascular Sciences, the Netherlands
| | - Olivier Danhaive
- Division of Neonatology, St.-Luc University Hospital, Catholic University of Louvain, Brussels, Belgium
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Pilar Escribano-Subías
- Unidad Multidisciplinar de Hipertensión Pulmonar, Servicio de Cardiología, Hospital Universitario 12 de Octubre, Madrid, Spain
- CIBERCV, Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, ISCIII, Madrid, Spain
| | - Henning Gall
- Centre for Congenital Heart Diseases, Pediatric Cardiology, Beatrix Children’s Hospital, and
| | - Barbara Girerd
- Université Paris-Saclay, AP-HP, Service de Pneumologie, Centre de référence de l’hypertension pulmonaire, INSERM UMR_S 999, Hôpital Bicêtre, Le Kremlin-Bicêtre, Paris, France
| | | | - Simon Holden
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - David Hunt
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom
| | - Samara M. A. Jansen
- Department of Pulmonary Medicine, Amsterdam University Medical Centre, Vrije Universiteit Amsterdam, Amsterdam Cardiovascular Sciences, the Netherlands
| | | | - David G. Kiely
- Department of Infection, Immunity, and Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
- Sheffield Pulmonary Vascular Disease Unit, Royal Hallamshire Hospital, Sheffield, United Kingdom
| | - Pablo Lapunzina
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
- ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium
| | - John McDermott
- Manchester Centre for Genomic Medicine, St. Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | | | - Joanna Pepke-Zaba
- Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Gary J. Polwarth
- Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Gwen Schotte
- Department of Pulmonary Medicine, Amsterdam University Medical Centre, Vrije Universiteit Amsterdam, Amsterdam Cardiovascular Sciences, the Netherlands
| | - Jair Tenorio-Castaño
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
- ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium
| | - A. A. Roger Thompson
- Department of Infection, Immunity, and Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
- Sheffield Pulmonary Vascular Disease Unit, Royal Hallamshire Hospital, Sheffield, United Kingdom
| | - John Wharton
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Stephen J. Wort
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Karyn Megy
- Department of Medicine and
- Addenbrooke’s Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Rutendo Mapeta
- Department of Medicine and
- Addenbrooke’s Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | | | | | - Wei Li
- Department of Medicine and
| | - Andrew J. Swift
- Department of Infection, Immunity, and Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
| | | | - Nicholas W. Morrell
- Department of Medicine and
- Addenbrooke’s Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
- National Institute of Health Research (NIHR) BioResource for Translational Research, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Stefan Gräf
- Department of Medicine and
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- National Institute of Health Research (NIHR) BioResource for Translational Research, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Diana Valverde
- CINBIO, Universidade de Vigo, Vigo, Spain
- Rare Diseases and Pediatric Medicine, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
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Karolak JA, Deutsch G, Gambin T, Szafranski P, Popek E, Stankiewicz P. Transcriptome and Immunohistochemical Analyses in TBX4- and FGF10-Deficient Lungs Imply TMEM100 as a Mediator of Human Lung Development. Am J Respir Cell Mol Biol 2022; 66:694-697. [PMID: 35648090 PMCID: PMC9163642 DOI: 10.1165/rcmb.2021-0470le] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
| | - Gail Deutsch
- University of Washington School of MedicineSeattle, Washington
| | - Tomasz Gambin
- Baylor College of MedicineHouston, Texas
- Warsaw University of TechnologyWarsaw, Poland
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Szafranski P, Stankiewicz P. Long Non-Coding RNA FENDRR: Gene Structure, Expression, and Biological Relevance. Genes (Basel) 2021; 12:177. [PMID: 33513839 PMCID: PMC7911649 DOI: 10.3390/genes12020177] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/19/2021] [Accepted: 01/21/2021] [Indexed: 12/13/2022] Open
Abstract
The FOXF1 Adjacent Noncoding Developmental Regulatory RNA (Fendrr) plays an important role in the control of gene expression in mammals. It is transcribed in the opposite direction to the neighboring Foxf1 gene with which it shares a region containing promoters. In humans, FENDRR is located on chromosome 16q24.1, and is positively regulated both by the FOXF1 distant lung-specific cis-acting enhancer and by trans-acting FOXF1. Fendrr has been shown to function as a competing endogenous RNA, sponging microRNAs and protein factors that control stability of mRNAs, and as an epigenetic modifier of chromatin structure around gene promoters and other regulatory sites, targeting them with histone methyltrasferase complexes. In mice, Fendrr is essential for development of the heart, lungs, and gastrointestinal system; its homozygous loss causes embryonic or perinatal lethality. Importantly, deregulation of FENDRR expression has been causatively linked also to tumorigenesis, resistance to chemotherapy, fibrosis, and inflammatory diseases. Here, we review the current knowledge on the FENDRR structure, expression, and involvement in development and tissue maintenance.
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Affiliation(s)
- Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA;
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