1
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Wagenaar GTM, Moll GN. Evolving views on the first two ligands of the angiotensin II type 2 receptor. From putative antagonists to potential agonists? Eur J Pharmacol 2023; 961:176189. [PMID: 37951489 DOI: 10.1016/j.ejphar.2023.176189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/29/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023]
Abstract
The renin-angiotensin system is one of the most complex regulatory systems that controls multiple organ functions. One of its key components, angiotensin II (Ang II), stimulates two G-protein coupled class A receptors: the Ang II type 1 (AT1) receptor and the Ang II type 2 (AT2) receptor. While stimulation of the AT1 receptor causes G-protein-dependent signaling and arrestin recruitment, the AT2 receptor seems to have a constitutively active-like conformation and appears to act via G-protein-dependent and -independent pathways. Overstimulation of the AT1 receptor may lead to unwanted effects like inflammation and fibrosis. In contrast, stimulation of the AT2 receptor leads to opposite effects thus restoring the balance. However, the role of the AT2 receptor has become controversial due to beneficial effects of putative AT2 receptor antagonists. The two first synthetic AT2 receptor-selective ligands, peptide CGP42112 and small molecule PD123319, were initially both considered antagonists. CGP42112 was subsequently considered a partial agonist and it was recently demonstrated to be a full agonist. Based on the search-term PD123319 in Pubmed, 1652 studies have investigated putative AT2 receptor antagonist PD123319. Here, we put forward literature that shows beneficial effects of PD123319 alone, even at doses too low for antagonist efficacy. These beneficial effects appear compatible with agonist-like activity via the AT2 receptor. Taken together, a more consistent image of a therapeutic role of stimulated AT2 receptor emerges which may clarify current controversies.
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Affiliation(s)
| | - Gert N Moll
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, the Netherlands.
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2
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Hejenkowska ED, Mitash N, Donovan JE, Chandra A, Bertrand C, De Santi C, Greene CM, Mu F, Swiatecka-Urban A. TGF-β1 Inhibition of ACE2 Mediated by miRNA Uncovers Novel Mechanism of SARS-CoV-2 Pathogenesis. J Innate Immun 2023; 15:629-646. [PMID: 37579743 PMCID: PMC10601633 DOI: 10.1159/000533606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/11/2023] [Indexed: 08/16/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for COVID-19, utilizes receptor binding domain (RBD) of spike glycoprotein to interact with angiotensin (Ang)-converting enzyme 2 (ACE2). Altering ACE2 levels may affect entry of SARS-CoV-2 and recovery from COVID-19. Decreased cell surface density of ACE2 leads to increased local levels of Ang II and may contribute to mortality resulting from acute lung injury and fibrosis during COVID-19. Studies published early during the COVID-19 pandemic reported that people with cystic fibrosis (PwCF) had milder symptoms, compared to people without CF. This finding was attributed to elevated ACE2 levels and/or treatment with the high efficiency CFTR modulators. Subsequent studies did not confirm these findings reporting variable effects of CFTR gene mutations on ACE2 levels. Transforming growth factor (TGF)-β signaling is essential during SARS-CoV-2 infection and dominates the chronic immune response in severe COVID-19, leading to pulmonary fibrosis. TGF-β1 is a gene modifier associated with more severe lung disease in PwCF but its effects on the COVID-19 course in PwCF is unknown. To understand whether TGF-β1 affects ACE2 levels in the airway, we examined miRNAs and their gene targets affecting SARS-CoV-2 pathogenesis in response to TGF-β1. Small RNAseq and micro(mi)RNA profiling identified pathways uniquely affected by TGF-β1, including those associated with SARS-CoV-2 invasion, replication, and the host immune responses. TGF-β1 inhibited ACE2 expression by miR-136-3p and miR-369-5p mediated mechanism in CF and non-CF bronchial epithelial cells. ACE2 levels were higher in two bronchial epithelial cell models expressing the most common CF-causing mutation in CFTR gene F508del, compared to controls without the mutation. After TGF-β1 treatment, ACE2 protein levels were still higher in CF, compared to non-CF cells. TGF-β1 prevented the modulator-mediated rescue of F508del-CFTR function while the modulators did not prevent the TGF-β1 inhibition of ACE2 levels. Finally, TGF-β1 reduced the interaction between ACE2 and the recombinant spike RBD by lowering ACE2 levels and its binding to RBD. Our data demonstrate novel mechanism whereby TGF-β1 inhibition of ACE2 in CF and non-CF bronchial epithelial cells may modulate SARS-CoV-2 pathogenicity and COVID-19 severity. By reducing ACE2 levels, TGF-β1 may decrease entry of SARS-CoV-2 into the host cells while hindering the recovery from COVID-19 due to loss of the anti-inflammatory and regenerative effects of ACE2. The above outcomes may be modulated by other, miRNA-mediated effects exerted by TGF-β1 on the host immune responses, leading to a complex and yet incompletely understood circuitry.
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Affiliation(s)
| | - Nilay Mitash
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joshua E. Donovan
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | - Anvita Chandra
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | - Carol Bertrand
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Chiara De Santi
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Catherine M. Greene
- Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Fangping Mu
- Center for Research Computing, University of Pittsburgh, Pittsburgh, PA, USA
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3
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Zhou YH, Gallins PJ, Pace RG, Dang H, Aksit MA, Blue EE, Buckingham KJ, Collaco JM, Faino AV, Gordon WW, Hetrick KN, Ling H, Liu W, Onchiri FM, Pagel K, Pugh EW, Raraigh KS, Rosenfeld M, Sun Q, Wen J, Li Y, Corvol H, Strug LJ, Bamshad MJ, Blackman SM, Cutting GR, Gibson RL, O’Neal WK, Wright FA, Knowles MR. Genetic Modifiers of Cystic Fibrosis Lung Disease Severity: Whole-Genome Analysis of 7,840 Patients. Am J Respir Crit Care Med 2023; 207:1324-1333. [PMID: 36921087 PMCID: PMC10595435 DOI: 10.1164/rccm.202209-1653oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 02/27/2023] [Indexed: 03/17/2023] Open
Abstract
Rationale: Lung disease is the major cause of morbidity and mortality in persons with cystic fibrosis (pwCF). Variability in CF lung disease has substantial non-CFTR (CF transmembrane conductance regulator) genetic influence. Identification of genetic modifiers has prognostic and therapeutic importance. Objectives: Identify genetic modifier loci and genes/pathways associated with pulmonary disease severity. Methods: Whole-genome sequencing data on 4,248 unique pwCF with pancreatic insufficiency and lung function measures were combined with imputed genotypes from an additional 3,592 patients with pancreatic insufficiency from the United States, Canada, and France. This report describes association of approximately 15.9 million SNPs using the quantitative Kulich normal residual mortality-adjusted (KNoRMA) lung disease phenotype in 7,840 pwCF using premodulator lung function data. Measurements and Main Results: Testing included common and rare SNPs, transcriptome-wide association, gene-level, and pathway analyses. Pathway analyses identified novel associations with genes that have key roles in organ development, and we hypothesize that these genes may relate to dysanapsis and/or variability in lung repair. Results confirmed and extended previous genome-wide association study findings. These whole-genome sequencing data provide finely mapped genetic information to support mechanistic studies. No novel primary associations with common single variants or rare variants were found. Multilocus effects at chr5p13 (SLC9A3/CEP72) and chr11p13 (EHF/APIP) were identified. Variant effect size estimates at associated loci were consistently ordered across the cohorts, indicating possible age or birth cohort effects. Conclusions: This premodulator genomic, transcriptomic, and pathway association study of 7,840 pwCF will facilitate mechanistic and postmodulator genetic studies and the development of novel therapeutics for CF lung disease.
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Affiliation(s)
- Yi-Hui Zhou
- Bioinformatics Research Center
- Department of Biological Sciences, and
| | | | - Rhonda G. Pace
- Marsico Lung Institute/UNC CF Research Center, School of Medicine
| | - Hong Dang
- Marsico Lung Institute/UNC CF Research Center, School of Medicine
| | | | - Elizabeth E. Blue
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Division of Medical Genetics, Department of Medicine
| | | | | | - Anna V. Faino
- Children’s Core for Biostatistics, Epidemiology and Analytics in Research and
| | | | - Kurt N. Hetrick
- Department of Genetic Medicine, Center for Inherited Disease Research, and
| | - Hua Ling
- Department of Genetic Medicine, Center for Inherited Disease Research, and
| | | | | | - Kymberleigh Pagel
- The Institute for Computational Medicine, The Johns Hopkins University, Baltimore, Maryland
| | - Elizabeth W. Pugh
- Department of Genetic Medicine, Center for Inherited Disease Research, and
| | | | - Margaret Rosenfeld
- Department of Pediatrics, and
- Center for Clinical and Translational Research, Seattle Children’s Research Institute, Seattle, Washington
| | | | | | - Yun Li
- Department of Biostatistics
- Department of Genetics, and
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Harriet Corvol
- Pediatric Pulmonary Department, Assistance Publique-Hôpitaux de Paris, Hôpital Trousseau, Paris, France
- Centre de Recherche Saint Antoine, Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Paris, France
| | - Lisa J. Strug
- Division of Biostatistics, Dalla Lana School of Public Health
- Department of Statistical Sciences, and
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada; and
- Program in Genetics and Genome Biology and
- The Center for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael J. Bamshad
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Division of Genetic Medicine, Department of Pediatrics
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Scott M. Blackman
- McKusick-Nathans Department of Genetic Medicine
- Division of Pediatric Endocrinology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Ronald L. Gibson
- Department of Pediatrics, and
- Center for Clinical and Translational Research, Seattle Children’s Research Institute, Seattle, Washington
| | - Wanda K. O’Neal
- Marsico Lung Institute/UNC CF Research Center, School of Medicine
| | - Fred A. Wright
- Bioinformatics Research Center
- Department of Biological Sciences, and
- Department of Statistics, North Carolina State University, Raleigh, North Carolina
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4
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Abstract
Cystic fibrosis (CF) pathophysiology is hallmarked by excessive inflammation and the inability to resolve lung infections, contributing to morbidity and eventually mortality. Paradoxically, despite a robust inflammatory response, CF lungs fail to clear bacteria and are susceptible to chronic infections. Impaired mucociliary transport plays a critical role in chronic infection but the immune mechanisms contributing to the adaptation of bacteria to the lung microenvironment is not clear. CFTR modulator therapy has advanced CF life expectancy opening up the need to understand changes in immunity as CF patients age. Here, we have summarized the current understanding of immune dysregulation in CF.
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Affiliation(s)
- Emanuela M Bruscia
- Department of Pediatrics, Section of Pulmonology, Allergy, Immunology and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA.
| | - Tracey L Bonfield
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
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5
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Wine JJ. How the sweat gland reveals levels of CFTR activity. J Cyst Fibros 2022; 21:396-406. [DOI: 10.1016/j.jcf.2022.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 02/05/2022] [Accepted: 02/05/2022] [Indexed: 10/19/2022]
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6
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Shah VS, Chivukula RR, Lin B, Waghray A, Rajagopal J. Cystic Fibrosis and the Cells of the Airway Epithelium: What Are Ionocytes and What Do They Do? ANNUAL REVIEW OF PATHOLOGY 2022; 17:23-46. [PMID: 34437820 PMCID: PMC10837786 DOI: 10.1146/annurev-pathol-042420-094031] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cystic fibrosis (CF) is caused by defects in an anion channel, the cystic fibrosis transmembrane conductance regulator (CFTR). Recently, a new airway epithelial cell type has been discovered and dubbed the pulmonary ionocyte. Unexpectedly, these ionocytes express higher levels of CFTR than any other airway epithelial cell type. However, ionocytes are not the sole CFTR-expressing airway epithelial cells, and CF-associated disease genes are in fact expressed in multiple airway epithelial cell types. The experimental depletion of ionocytes perturbs epithelial physiology in the mouse trachea, but the role of these rare cells in the pathogenesis of human CF remains mysterious. Ionocytes have been described in diverse tissues(kidney and inner ear) and species (frog and fish). We draw on these prior studies to suggest potential roles of airway ionocytes in health and disease. A complete understanding of ionocytes in the mammalian airway will ultimately depend on cell type-specific genetic manipulation.
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Affiliation(s)
- Viral S Shah
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA; , , , ,
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Raghu R Chivukula
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA; , , , ,
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
| | - Brian Lin
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA; , , , ,
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
| | - Avinash Waghray
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA; , , , ,
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
| | - Jayaraj Rajagopal
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA; , , , ,
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
- Klarman Cell Observatory, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
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7
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Fallerini C, Picchiotti N, Baldassarri M, Zguro K, Daga S, Fava F, Benetti E, Amitrano S, Bruttini M, Palmieri M, Croci S, Lista M, Beligni G, Valentino F, Meloni I, Tanfoni M, Minnai F, Colombo F, Cabri E, Fratelli M, Gabbi C, Mantovani S, Frullanti E, Gori M, Crawley FP, Butler-Laporte G, Richards B, Zeberg H, Lipcsey M, Hultström M, Ludwig KU, Schulte EC, Pairo-Castineira E, Baillie JK, Schmidt A, Frithiof R, Mari F, Renieri A, Furini S. Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity. Hum Genet 2022; 141:147-173. [PMID: 34889978 PMCID: PMC8661833 DOI: 10.1007/s00439-021-02397-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/26/2021] [Indexed: 12/13/2022]
Abstract
The combined impact of common and rare exonic variants in COVID-19 host genetics is currently insufficiently understood. Here, common and rare variants from whole-exome sequencing data of about 4000 SARS-CoV-2-positive individuals were used to define an interpretable machine-learning model for predicting COVID-19 severity. First, variants were converted into separate sets of Boolean features, depending on the absence or the presence of variants in each gene. An ensemble of LASSO logistic regression models was used to identify the most informative Boolean features with respect to the genetic bases of severity. The Boolean features selected by these logistic models were combined into an Integrated PolyGenic Score that offers a synthetic and interpretable index for describing the contribution of host genetics in COVID-19 severity, as demonstrated through testing in several independent cohorts. Selected features belong to ultra-rare, rare, low-frequency, and common variants, including those in linkage disequilibrium with known GWAS loci. Noteworthily, around one quarter of the selected genes are sex-specific. Pathway analysis of the selected genes associated with COVID-19 severity reflected the multi-organ nature of the disease. The proposed model might provide useful information for developing diagnostics and therapeutics, while also being able to guide bedside disease management.
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Affiliation(s)
- Chiara Fallerini
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Nicola Picchiotti
- grid.9024.f0000 0004 1757 4641University of Siena, DIISM-SAILAB, Siena, Italy ,grid.8982.b0000 0004 1762 5736Department of Mathematics, University of Pavia, Pavia, Italy
| | - Margherita Baldassarri
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Kristina Zguro
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
| | - Sergio Daga
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Francesca Fava
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy ,grid.411477.00000 0004 1759 0844Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Elisa Benetti
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
| | - Sara Amitrano
- grid.411477.00000 0004 1759 0844Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Mirella Bruttini
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy ,grid.411477.00000 0004 1759 0844Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Maria Palmieri
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Susanna Croci
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Mirjam Lista
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Giada Beligni
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Floriana Valentino
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Ilaria Meloni
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Marco Tanfoni
- grid.9024.f0000 0004 1757 4641University of Siena, DIISM-SAILAB, Siena, Italy
| | - Francesca Minnai
- grid.429135.80000 0004 1756 2536Istituto di Tecnologie Biomediche-Consiglio Nazionale delle Ricerche, Segrate, MI Italy
| | - Francesca Colombo
- grid.429135.80000 0004 1756 2536Istituto di Tecnologie Biomediche-Consiglio Nazionale delle Ricerche, Segrate, MI Italy
| | - Enrico Cabri
- grid.4527.40000000106678902Pharmacogenomics Unit, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Maddalena Fratelli
- grid.4527.40000000106678902Pharmacogenomics Unit, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Chiara Gabbi
- grid.4714.60000 0004 1937 0626Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Stefania Mantovani
- grid.419425.f0000 0004 1760 3027Department of Medicine, Clinical Immunology and Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Elisa Frullanti
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Marco Gori
- grid.9024.f0000 0004 1757 4641University of Siena, DIISM-SAILAB, Siena, Italy ,grid.503321.60000 0001 0561 3840Models and Algorithms for Artificial Intelligence (MAASAI) Research Group, Université Côte d’Azur, Inria, CNRS, I3S, Biot, France
| | - Francis P. Crawley
- Good Clinical Practice Alliance-Europe (GCPA) and Strategic Initiative for Developing Capacity in Ethical Review (SIDCER), Leuven, Belgium
| | - Guillaume Butler-Laporte
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC Canada ,grid.14709.3b0000 0004 1936 8649Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC Canada
| | - Brent Richards
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC Canada ,grid.14709.3b0000 0004 1936 8649Department of Human Genetics, McGill University, Montreal, QC Canada ,grid.13097.3c0000 0001 2322 6764Department of Twin Research, King’s College London, London, UK
| | - Hugo Zeberg
- grid.4714.60000 0004 1937 0626Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Miklos Lipcsey
- grid.8993.b0000 0004 1936 9457Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden ,grid.8993.b0000 0004 1936 9457Hedenstierna Laboratory, CIRRUS, Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Michael Hultström
- grid.8993.b0000 0004 1936 9457Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden ,grid.8993.b0000 0004 1936 9457Integrative Physiology, Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Kerstin U. Ludwig
- grid.10388.320000 0001 2240 3300Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Eva C. Schulte
- grid.411095.80000 0004 0477 2585Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, 80336 Munich, Germany ,grid.5252.00000 0004 1936 973XDepartment of Psychiatry and Psychotherapy, University Hospital, LMU Munich, 80336 Munich, Germany ,grid.6936.a0000000123222966Institute of Virology, Technical University Munich/Helmholtz Zentrum München, Munich, Germany
| | - Erola Pairo-Castineira
- grid.4305.20000 0004 1936 7988MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU UK ,grid.4305.20000 0004 1936 7988Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG UK
| | - John Kenneth Baillie
- grid.4305.20000 0004 1936 7988MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU UK ,grid.4305.20000 0004 1936 7988Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG UK ,grid.418716.d0000 0001 0709 1919Intensive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, H16 5SA UK
| | - Axel Schmidt
- grid.10388.320000 0001 2240 3300Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Robert Frithiof
- grid.8993.b0000 0004 1936 9457Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | | | | | | | - Francesca Mari
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy ,grid.411477.00000 0004 1759 0844Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Alessandra Renieri
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy. .,Medical Genetics, University of Siena, Siena, Italy. .,Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy. .,Medical Genetics Unit, University of Siena, Policlinico Le Scotte, Viale Bracci, 2, 53100, Siena, Italy.
| | - Simone Furini
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
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8
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Rivas-Barragan D, Mubeen S, Guim Bernat F, Hofmann-Apitius M, Domingo-Fernández D. Drug2ways: Reasoning over causal paths in biological networks for drug discovery. PLoS Comput Biol 2020; 16:e1008464. [PMID: 33264280 PMCID: PMC7735677 DOI: 10.1371/journal.pcbi.1008464] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 12/14/2020] [Accepted: 10/23/2020] [Indexed: 12/24/2022] Open
Abstract
Elucidating the causal mechanisms responsible for disease can reveal potential therapeutic targets for pharmacological intervention and, accordingly, guide drug repositioning and discovery. In essence, the topology of a network can reveal the impact a drug candidate may have on a given biological state, leading the way for enhanced disease characterization and the design of advanced therapies. Network-based approaches, in particular, are highly suited for these purposes as they hold the capacity to identify the molecular mechanisms underlying disease. Here, we present drug2ways, a novel methodology that leverages multimodal causal networks for predicting drug candidates. Drug2ways implements an efficient algorithm which reasons over causal paths in large-scale biological networks to propose drug candidates for a given disease. We validate our approach using clinical trial information and demonstrate how drug2ways can be used for multiple applications to identify: i) single-target drug candidates, ii) candidates with polypharmacological properties that can optimize multiple targets, and iii) candidates for combination therapy. Finally, we make drug2ways available to the scientific community as a Python package that enables conducting these applications on multiple standard network formats.
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Affiliation(s)
- Daniel Rivas-Barragan
- Barcelona Supercomputing Center, Barcelona, Spain
- Computer Architecture Department, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Sarah Mubeen
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany
- Fraunhofer Center for Machine Learning, Germany
| | | | - Martin Hofmann-Apitius
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany
| | - Daniel Domingo-Fernández
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany
- Fraunhofer Center for Machine Learning, Germany
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9
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Barbato E, Daly B, Douglas S, Kerr M, Litman P, Darrah R. Genetic Variation Near chrXq22-q23 Is Linked to Emotional Functioning in Cystic Fibrosis. Biol Res Nurs 2020; 22:319-325. [PMID: 32390518 DOI: 10.1177/1099800420924125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
INTRODUCTION Cystic fibrosis (CF) is an autosomal recessive disease that affects many organ systems, most notably the pulmonary and gastrointestinal systems. Through genome-wide association studies, multiple genetic regions modifying CF-related pulmonary and gastrointestinal symptoms have been identified, but translation of these findings to clinical benefit remains elusive. Symptom variation in CF patients has been associated with changes in health-related quality of life (HRQOL), but the relationship between CF symptom-modifying genetic loci and HRQOL has not been explored. The purpose of this study was to determine whether two previously identified genetic modifiers of CF-related pathology also modify the subscales of HRQOL. METHODS HRQOL and genotype data were obtained and analyzed. Linear regressions were used to examine the amount of variance in HRQOL subscales that could be explained by genotype for each modifier locus. RESULTS A significant regression equation was found between genotype for rs5952223, a variant near chrXq22-q23, and emotional functioning in a sample of 129 CF patients. DISCUSSION These data suggest that genotype for this single-nucleotide polymorphism is associated with emotional functioning in CF patients and highlight this genetic region as a potential therapeutic target, irrespective of CF transmembrane conductance regulator genotype.
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Affiliation(s)
- Eric Barbato
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Barbara Daly
- Frances Payne Bolton School of Nursing, Case Western Reserve University, Cleveland, OH, USA
| | - Sara Douglas
- Frances Payne Bolton School of Nursing, Case Western Reserve University, Cleveland, OH, USA
| | - Mary Kerr
- Frances Payne Bolton School of Nursing, Case Western Reserve University, Cleveland, OH, USA
| | - Paul Litman
- Frances Payne Bolton School of Nursing, Case Western Reserve University, Cleveland, OH, USA
| | - Rebecca Darrah
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA.,Frances Payne Bolton School of Nursing, Case Western Reserve University, Cleveland, OH, USA
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10
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Shanthikumar S, Neeland MN, Saffery R, Ranganathan S. Gene modifiers of cystic fibrosis lung disease: A systematic review. Pediatr Pulmonol 2019; 54:1356-1366. [PMID: 31140758 DOI: 10.1002/ppul.24366] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 05/03/2019] [Accepted: 05/05/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND Lung disease is the major source of morbidity and mortality in cystic fibrosis (CF), with large variability in severity between patients. Although accurate prediction of lung disease severity would be extremely useful, no robust methods exist. Twin and sibling studies have highlighted the importance of non-cystic fibrosis transmembrane conductance regulator (CFTR) genes in determining lung disease severity but how these impact on the severity in CF remains unclear. METHODS A systematic review was undertaken to answer the question "In patients with CF which non-CFTR genes modify the severity of lung disease?" The method for this systematic review was based upon the "Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA)" statement, with a narrative synthesis of results planned. RESULTS A total of 1168 articles were screened for inclusion, with 275 articles undergoing detailed assessment for inclusion. One hundred and forty articles were included. Early studies focused on candidate genes, whereas more recent studies utilized genome-wide approaches and also examined epigenetic mechanisms, gene expression, and therapeutic response. DISCUSSION A large body of evidence regarding non-CFTR gene modifiers of lung disease severity has been generated, examining a wide array of genes. Limitations to existing studies include heterogeneity in outcome measures used, limited replication, and relative lack of clinical impact. Future work examining non-CFTR gene modifiers will have to overcome these limitations if gene modifiers are to have a meaningful role in the care of patients with CF.
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Affiliation(s)
- Shivanthan Shanthikumar
- Respiratory and Sleep Medicine Department, Royal Children's Hospital, Melbourne, Australia.,Respiratory Diseases Department, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, The University of Melbourne, Australia
| | - Melanie N Neeland
- Department of Paediatrics, The University of Melbourne, Australia.,Centre of Food and Allergy Research, Murdoch Children's Research Institute, Melbourne, Australia
| | - Richard Saffery
- Department of Paediatrics, The University of Melbourne, Australia.,Cancer & Disease Epigenetics, Murdoch Children's Research Institute, Melbourne, Australia
| | - Sarath Ranganathan
- Respiratory and Sleep Medicine Department, Royal Children's Hospital, Melbourne, Australia.,Respiratory Diseases Department, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, The University of Melbourne, Australia
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11
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Strug LJ, Stephenson AL, Panjwani N, Harris A. Recent advances in developing therapeutics for cystic fibrosis. Hum Mol Genet 2018; 27:R173-R186. [PMID: 30060192 PMCID: PMC6061831 DOI: 10.1093/hmg/ddy188] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 05/07/2018] [Accepted: 05/10/2018] [Indexed: 12/23/2022] Open
Abstract
Despite hope that a cure was imminent when the causative gene was cloned nearly 30 years ago, cystic fibrosis (CF [MIM: 219700]) remains a life-shortening disease affecting more than 70 000 individuals worldwide. However, within the last 6 years the Food and Drug Administration's approval of Ivacaftor, the first drug that corrects the defective cystic fibrosis transmembrane conductance regulator protein [CFTR (MIM: 602421)] in patients with the G551D mutation, marks a watershed in the development of novel therapeutics for this devastating disease. Here we review recent progress in diverse research areas, which all focus on curing CF at the genetic, biochemical or physiological level. In the near future it seems probable that development of mutation-specific therapies will be the focus, since it is unlikely that any one approach will be efficient in correcting the more than 2000 disease-associated variants. We discuss the new drugs and combinations of drugs that either enhance delivery of misfolded CFTR protein to the cell membrane, where it functions as an ion channel, or that activate channel opening. Next we consider approaches to correct the causative genetic lesion at the DNA or RNA level, through repressing stop mutations and nonsense-mediated decay, modulating splice mutations, fixing errors by gene editing or using novel routes to gene replacement. Finally, we explore how modifier genes, loci elsewhere in the genome that modify CF disease severity, may be used to restore a normal phenotype. Progress in all of these areas has been dramatic, generating enthusiasm that CF may soon become a broadly treatable disease.
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Affiliation(s)
- Lisa J Strug
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Anne L Stephenson
- Department of Respirology, Adult Cystic Fibrosis Program, St. Michael’s Hospital, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Naim Panjwani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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