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Li Z, Barnaby R, Nymon A, Roche C, Koeppen K, Ashare A, Hogan DA, Gerber SA, Taatjes DJ, Hampton TH, Stanton BA. P. aeruginosa tRNA-fMet halves secreted in outer membrane vesicles suppress lung inflammation in cystic fibrosis. Am J Physiol Lung Cell Mol Physiol 2024; 326:L574-L588. [PMID: 38440830 DOI: 10.1152/ajplung.00018.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 03/06/2024] Open
Abstract
Although tobramycin increases lung function in people with cystic fibrosis (pwCF), the density of Pseudomonas aeruginosa (P. aeruginosa) in the lungs is only modestly reduced by tobramycin; hence, the mechanism whereby tobramycin improves lung function is not completely understood. Here, we demonstrate that tobramycin increases 5' tRNA-fMet halves in outer membrane vesicles (OMVs) secreted by laboratory and CF clinical isolates of P. aeruginosa. The 5' tRNA-fMet halves are transferred from OMVs into primary CF human bronchial epithelial cells (CF-HBEC), decreasing OMV-induced IL-8 and IP-10 secretion. In mouse lungs, increased expression of the 5' tRNA-fMet halves in OMVs attenuated KC (murine homolog of IL-8) secretion and neutrophil recruitment. Furthermore, there was less IL-8 and neutrophils in bronchoalveolar lavage fluid isolated from pwCF during the period of exposure to tobramycin versus the period off tobramycin. In conclusion, we have shown in mice and in vitro studies on CF-HBEC that tobramycin reduces inflammation by increasing 5' tRNA-fMet halves in OMVs that are delivered to CF-HBEC and reduce IL-8 and neutrophilic airway inflammation. This effect is predicted to improve lung function in pwCF receiving tobramycin for P. aeruginosa infection.NEW & NOTEWORTHY The experiments in this report identify a novel mechanism, whereby tobramycin reduces inflammation in two models of CF. Tobramycin increased the secretion of tRNA-fMet halves in OMVs secreted by P. aeruginosa, which reduced the OMV-LPS-induced inflammatory response in primary cultures of CF-HBEC and in mouse lung, an effect predicted to reduce lung damage in pwCF.
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Affiliation(s)
- Zhongyou Li
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States
| | - Roxanna Barnaby
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States
| | - Amanda Nymon
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States
| | - Carolyn Roche
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States
| | - Katja Koeppen
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States
| | - Alix Ashare
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States
- Pulmonary and Critical Care Medicine, Dartmouth Health Medical Center, Lebanon, New Hampshire, United States
| | - Deborah A Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States
| | - Scott A Gerber
- Dartmouth Health Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States
| | - Douglas J Taatjes
- Department of Pathology and Laboratory Medicine, Center for Biomedical Shared Resources, Larner College of Medicine, University of Vermont, Burlington, Vermont, United States
| | - Thomas H Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States
| | - Bruce A Stanton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States
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2
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Li Z, Barnaby R, Nymon A, Roche C, Koeppen K, Ashare A, Hogan DA, Gerber SA, Taatjes DJ, Hampton TH, Stanton BA. P. aeruginosa tRNA-fMet halves secreted in outer membrane vesicles suppress lung inflammation in Cystic Fibrosis. bioRxiv 2024:2024.02.03.578737. [PMID: 38352468 PMCID: PMC10862835 DOI: 10.1101/2024.02.03.578737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Although tobramycin increases lung function in people with cystic fibrosis (pwCF), the density of Pseudomonas aeruginosa (P. aeruginosa) in the lungs is only modestly reduced by tobramycin; hence, the mechanism whereby tobramycin improves lung function is not completely understood. Here, we demonstrate that tobramycin increases 5' tRNA-fMet halves in outer membrane vesicles (OMVs) secreted by laboratory and CF clinical isolates of P. aeruginosa . The 5' tRNA-fMet halves are transferred from OMVs into primary CF human bronchial epithelial cells (CF-HBEC), decreasing OMV-induced IL-8 and IP-10 secretion. In mouse lung, increased expression of the 5' tRNA-fMet halves in OMVs attenuated KC secretion and neutrophil recruitment. Furthermore, there was less IL-8 and neutrophils in bronchoalveolar lavage fluid isolated from pwCF during the period of exposure to tobramycin versus the period off tobramycin. In conclusion, we have shown in mice and in vitro studies on CF-HBEC that tobramycin reduces inflammation by increasing 5' tRNA-fMet halves in OMVs that are delivered to CF-HBEC and reduce IL-8 and neutrophilic airway inflammation. This effect is predicted to improve lung function in pwCF receiving tobramycin for P. aeruginosa infection. New and noteworthy The experiments in this report identify a novel mechanim whereby tobramycin reduces inflammation in two models of CF. Tobramycin increased the secretion of tRNA-fMet haves in OMVs secreted by P. aeruginiosa , which reduced the OMV-LPS induced inflammatory response in primary cultures of CF-HBEC and in mouse lung, an effect predicted to reduce lung damage in pwCF. Graphical abstract The anti-inflammatory effect of tobramycin mediated by 5' tRNA-fMet halves secreted in P. aeruginosa OMVs. (A) P. aeruginosa colonizes the CF lungs and secrets OMVs. OMVs diffuse through the mucus layer overlying bronchial epithelial cells and induce IL-8 secretion, which recruits neutrophils that causes lung damage. ( B ) Tobramycin increases 5' tRNA-fMet halves in OMVs secreted by P. aeruginosa . 5' tRNA-fMet halves are delivered into host cells after OMVs fuse with lipid rafts in CF-HBEC and down-regulate protein expression of MAPK10, IKBKG, and EP300, which suppresses IL-8 secretion and neutrophils in the lungs. A reduction in neutrophils in CF BALF is predicted to improve lung function and decrease lung damage.
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Neff SL, Hampton TH, Koeppen K, Sarkar S, Latario CJ, Ross BD, Stanton BA. Rocket-miR, a translational launchpad for miRNA-based antimicrobial drug development. mSystems 2023; 8:e0065323. [PMID: 37975659 PMCID: PMC10734502 DOI: 10.1128/msystems.00653-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/06/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Antimicrobial-resistant infections contribute to millions of deaths worldwide every year. In particular, the group of bacteria collectively known as ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter sp.) pathogens are of considerable medical concern due to their virulence and exceptional ability to develop antibiotic resistance. New kinds of antimicrobial therapies are urgently needed to treat patients for whom existing antibiotics are ineffective. The Rocket-miR application predicts targets of human miRNAs in bacterial and fungal pathogens, rapidly identifying candidate miRNA-based antimicrobials. The application's target audience are microbiologists that have the laboratory resources to test the application's predictions. The Rocket-miR application currently supports 24 recognized human pathogens that are relevant to numerous diseases including cystic fibrosis, chronic obstructive pulmonary disease (COPD), urinary tract infections, and pneumonia. Furthermore, the application code was designed to be easily extendible to other human pathogens that commonly cause hospital-acquired infections.
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Affiliation(s)
- Samuel L. Neff
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Thomas H. Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Katja Koeppen
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Sharanya Sarkar
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Casey J. Latario
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Benjamin D. Ross
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Bruce A. Stanton
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
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Koeppen K, Hampton TH, Barnaby R, Roche C, Gerber SA, Goo YA, Cho BK, Vermilyea DM, Hogan DA, Stanton BA. An rRNA fragment in extracellular vesicles secreted by human airway epithelial cells increases the fluoroquinolone sensitivity of P. aeruginosa. Am J Physiol Lung Cell Mol Physiol 2023. [PMID: 37256658 PMCID: PMC10390050 DOI: 10.1152/ajplung.00150.2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
Abstract
Lung infections caused by antibiotic resistant strains of Pseudomonas aeruginosa are difficult to eradicate in immunocompromised hosts such as those with cystic fibrosis. We previously demonstrated that extracellular vesicles (EVs) secreted by primary human airway epithelial cells (AEC) delivermiRNA let-7b-5p to P. aeruginosa to suppress biofilm formation and increase sensitivity to beta-lactam antibiotics. In this study, we show that EVs secreted by AEC transfer multiple distinct sRNA fragments to P. aeruginosa that are predicted to target the three subunits of the fluoroquinolone efflux pump MexHI-OpmD, thus increasing antibiotic sensitivity. Exposure of P. aeruginosa to EVs resulted in a significant reduction in the protein levels of MexH (-48%), MexI (-50%) and OpmD (-35%). Moreover, EVs reduced planktonic growth of P. aeruginosa in the presence of the fluoroquinolone antibiotic ciprofloxacin by 20%. A mexGHI-opmD deletion mutant of P. aeruginosa phenocopied this increased sensitivity to ciprofloxacin. Finally, we found that a fragment of an 18S rRNA external transcribed spacer that was transferred to P. aeruginosa by EVs reduced planktonic growth of P. aeruginosa in the presence of ciprofloxacin, reduced the minimum inhibitory concentration (MIC) of P. aeruginosa for ciprofloxacin by over 50%, and significantly reduced protein levels of both MexH and OpmD. In conclusion, an rRNA fragment secreted by AEC in EVs that targets the fluoroquinolone efflux pump MexHI-OpmD down-regulated these proteins and increased the ciprofloxacin sensitivity of P. aeruginosa. A combination of rRNA fragments and ciprofloxacin packaged in nanoparticles or EVs may benefit patients with antibiotic-resistant P. aeruginosa infections.
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Affiliation(s)
- Katja Koeppen
- Department of Microbiology and Immunology, Dartmouth College, Hanover, NH, United States
| | - Thomas H Hampton
- Department of Microbiology and Immunology, Dartmouth College, Hanover, NH, United States
| | - Roxanna Barnaby
- Department of Microbiology and Immunology, Dartmouth College, Hanover, NH, United States
| | - Carolyn Roche
- Department of Microbiology and Immunology, Dartmouth College, Hanover, NH, United States
| | - Scott A Gerber
- Norris Cotton Cancer Center, Dartmouth College, Lebanon, NH, United States
| | - Young Ah Goo
- Mass Spectrometry Technology Access Center, McDonnell Genome Institute, Washington University in St. Louis School of Medicine, St. Louis, MO, United States
| | - Byoung-Kyu Cho
- Mass Spectrometry Technology Access Center, McDonnell Genome Institute, Washington University in St. Louis School of Medicine, St. Louis, MO, United States
| | - Danielle M Vermilyea
- Department of Microbiology and Immunology, Dartmouth College, Hanover, NH, United States
| | - Deborah A Hogan
- Department of Microbiology and Immunology, Dartmouth College, Hanover, NH, United States
| | - Bruce A Stanton
- Department of Microbiology and Immunology, Dartmouth College, Hanover, NH, United States
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Abstract
The last 20 years have witnessed an explosion in publicly available gene expression and proteomic data and new tools to help researchers analyze these data. Tools typically include statistical approaches to identify differential expression, integrate prior knowledge, visualize results, and suggest how differential expression relates to changes in phenotype. Here, we provide a simple web-based tool that bridges some of the gaps between the functionality available to those studying eukaryotes and those studying prokaryotes. Specifically, our Shiny web application ESKAPE Act PLUS allows researchers to upload results of high-throughput bacterial gene or protein expression experiments from 13 species, including the six ESKAPE pathogens, to our system and receive (i) an analysis of which KEGG pathways or GO terms are significantly activated or repressed, (ii) visual representations of the magnitude of activation or repression in each category, and (iii) detailed diagrams showing known relationships between genes in each regulated KEGG pathway and fold changes of individual genes. Importantly, our statistical approach does not require users to identify which genes or proteins are differentially expressed. ESKAPE Act PLUS provides high-quality statistics and graphical representations not available using other web-based systems to assess whether prokaryotic biological functions are activated or repressed by experimental conditions. To our knowledge, ESKAPE Act PLUS is the first application that provides pathway activation analysis and pathway-level visualization of gene or protein expression for prokaryotes. IMPORTANCE ESKAPE pathogens are bacteria of concern because they develop antibiotic resistance and can cause life-threatening infections, particularly in more susceptible immunocompromised people. ESKAPE Act PLUS is a user-friendly web application that will advance research on ESKAPE and other pathogens commonly studied by the biomedical community by allowing scientists to infer biological phenotypes from the results from high-throughput bacterial gene or protein expression experiments. ESKAPE Act PLUS currently supports analysis of 23 strains of bacteria from 13 species and can also be used to re-analyze publicly available data to generate new findings and hypotheses for follow-up experiments.
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Affiliation(s)
- Katja Koeppen
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Thomas H. Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Samuel L. Neff
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Bruce A. Stanton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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Neff SL, Hampton TH, Puerner C, Cengher L, Doing G, Lee AJ, Koeppen K, Cheung AL, Hogan DA, Cramer RA, Stanton BA. CF-Seq, an accessible web application for rapid re-analysis of cystic fibrosis pathogen RNA sequencing studies. Sci Data 2022; 9:343. [PMID: 35710652 PMCID: PMC9203545 DOI: 10.1038/s41597-022-01431-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/25/2022] [Indexed: 01/13/2023] Open
Abstract
Researchers studying cystic fibrosis (CF) pathogens have produced numerous RNA-seq datasets which are available in the gene expression omnibus (GEO). Although these studies are publicly available, substantial computational expertise and manual effort are required to compare similar studies, visualize gene expression patterns within studies, and use published data to generate new experimental hypotheses. Furthermore, it is difficult to filter available studies by domain-relevant attributes such as strain, treatment, or media, or for a researcher to assess how a specific gene responds to various experimental conditions across studies. To reduce these barriers to data re-analysis, we have developed an R Shiny application called CF-Seq, which works with a compendium of 128 studies and 1,322 individual samples from 13 clinically relevant CF pathogens. The application allows users to filter studies by experimental factors and to view complex differential gene expression analyses at the click of a button. Here we present a series of use cases that demonstrate the application is a useful and efficient tool for new hypothesis generation. (CF-Seq: http://scangeo.dartmouth.edu/CFSeq/ ).
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Affiliation(s)
- Samuel L Neff
- Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | | | - Charles Puerner
- Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Liviu Cengher
- Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Georgia Doing
- Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | | | - Katja Koeppen
- Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | | | - Deborah A Hogan
- Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Robert A Cramer
- Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Bruce A Stanton
- Geisel School of Medicine, Dartmouth College, Hanover, NH, USA.
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Hollomon JM, Liu Z, Rusin SF, Jenkins NP, Smith AK, Koeppen K, Kettenbach AN, Myers LC, Hogan DA. The Candida albicans Cdk8-dependent phosphoproteome reveals repression of hyphal growth through a Flo8-dependent pathway. PLoS Genet 2022; 18:e1009622. [PMID: 34982775 PMCID: PMC8769334 DOI: 10.1371/journal.pgen.1009622] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 01/19/2022] [Accepted: 12/06/2021] [Indexed: 12/26/2022] Open
Abstract
Ssn3, also known as Cdk8, is a member of the four protein Cdk8 submodule within the multi-subunit Mediator complex involved in the co-regulation of transcription. In Candida albicans, the loss of Ssn3 kinase activity affects multiple phenotypes including cellular morphology, metabolism, nutrient acquisition, immune cell interactions, and drug resistance. In these studies, we generated a strain in which Ssn3 was replaced with a functional variant of Ssn3 that can be rapidly and selectively inhibited by the ATP analog 3-MB-PP1. Consistent with ssn3 null mutant and kinase dead phenotypes, inhibition of Ssn3 kinase activity promoted hypha formation. Furthermore, the increased expression of hypha-specific genes was the strongest transcriptional signal upon inhibition of Ssn3 in transcriptomics analyses. Rapid inactivation of Ssn3 was used for phosphoproteomic studies performed to identify Ssn3 kinase substrates associated with filamentation potential. Both previously validated and novel Ssn3 targets were identified. Protein phosphorylation sites that were reduced specifically upon Ssn3 inhibition included two sites in Flo8 which is a transcription factor known to positively regulate C. albicans morphology. Mutation of the two Flo8 phosphosites (threonine 589 and serine 620) was sufficient to increase Flo8-HA levels and Flo8 dependent transcriptional and morphological changes, suggesting that Ssn3 kinase activity negatively regulates Flo8.Under embedded conditions, when ssn3Δ/Δ and efg1Δ/Δ mutants were hyperfilamentous, FLO8 was essential for hypha formation. Previous work has also shown that loss of Ssn3 activity leads to increased alkalinization of medium with amino acids. Here, we show that the ssn3Δ/Δ medium alkalinization phenotype, which is dependent on STP2, a transcription factor involved in amino acid utilization, also requires FLO8 and EFG1. Together, these data show that Ssn3 activity can modulate Flo8 and its direct and indirect interactions in different ways, and underscores the potential importance of considering Ssn3 function in the control of transcription factor activities. In Candida albicans, Ssn3 kinase activity co-regulates the transcription of numerous genes involved in hyphal growth, metabolism and nutrient acquisition, immune cell interactions, and drug resistance. Using a strain in which Ssn3 could be rapidly and selectively inhibited, we identified both known and novel Ssn3 targets. We identified two phosphosites in Flo8, a regulator of morphology and virulence, that were shown to negatively regulate Flo8 levels and activity. The data and tools presented here will enable a better understanding of how Ssn3 impacts transcriptional and post-transcriptional regulation in order to coordinate processes during physiological and morphological transitions as well as during steady state growth.
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Affiliation(s)
- Jeffrey M. Hollomon
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Zhongle Liu
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Scott F. Rusin
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- Norris Cotton Cancer Center, Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center at Dartmouth, Lebanon, New Hampshire, United States of America
| | - Nicole P. Jenkins
- Norris Cotton Cancer Center, Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center at Dartmouth, Lebanon, New Hampshire, United States of America
| | - Allia K. Smith
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Katja Koeppen
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Arminja N. Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- Norris Cotton Cancer Center, Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center at Dartmouth, Lebanon, New Hampshire, United States of America
| | - Lawrence C. Myers
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- Department of Medical Education, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- * E-mail: (LCM); (DAH)
| | - Deborah A. Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- * E-mail: (LCM); (DAH)
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Koeppen K, Hampton T, Kolling F, Gerber S, Stanton B. 471: Short RNAs in extracellular vesicles secreted by human airway epithelial cells increase antibiotic sensitivity of Pseudomonas aeruginosa. J Cyst Fibros 2021. [DOI: 10.1016/s1569-1993(21)01895-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Koeppen K, Nymon A, Barnaby R, Li Z, Hampton TH, Ashare A, Stanton BA. CF monocyte-derived macrophages have an attenuated response to extracellular vesicles secreted by airway epithelial cells. Am J Physiol Lung Cell Mol Physiol 2021; 320:L530-L544. [PMID: 33471607 PMCID: PMC8238154 DOI: 10.1152/ajplung.00621.2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/13/2021] [Accepted: 01/19/2021] [Indexed: 01/08/2023] Open
Abstract
Mutations in CFTR alter macrophage responses, for example, by reducing their ability to phagocytose and kill bacteria. Altered macrophage responses may facilitate bacterial infection and inflammation in the lungs, contributing to morbidity and mortality in cystic fibrosis (CF). Extracellular vesicles (EVs) are secreted by multiple cell types in the lungs and participate in the host immune response to bacterial infection, but the effect of EVs secreted by CF airway epithelial cells (AEC) on CF macrophages is unknown. This report examines the effect of EVs secreted by primary AEC on monocyte-derived macrophages (MDM) and contrasts responses of CF and wild type (WT) MDM. We found that EVs generally increase pro-inflammatory cytokine secretion and expression of innate immune genes in MDM, especially when EVs are derived from AEC exposed to Pseudomonas aeruginosa and that this effect is attenuated in CF MDM. Specifically, EVs secreted by P. aeruginosa exposed AEC (EV-PA) induced immune response genes and increased secretion of proinflammatory cytokines, chemoattractants, and chemokines involved in tissue repair by WT MDM, but these effects were less robust in CF MDM. We attribute attenuated responses by CF MDM to differences between CF and WT macrophages because EVs secreted by CF AEC or WT AEC elicited similar responses in CF MDM. Our findings demonstrate the importance of AEC EVs in macrophage responses and show that the Phe508del mutation in CFTR attenuates the innate immune response of MDM to EVs.
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Affiliation(s)
- Katja Koeppen
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Amanda Nymon
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Roxanna Barnaby
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Zhongyou Li
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Thomas H Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Alix Ashare
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
- Pulmonary and Critical Care Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
| | - Bruce A Stanton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
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Hampton TH, Koeppen K, Bashor L, Stanton BA. Selection of reference genes for quantitative PCR: identifying reference genes for airway epithelial cells exposed to Pseudomonas aeruginosa. Am J Physiol Lung Cell Mol Physiol 2020; 319:L256-L265. [PMID: 32521165 PMCID: PMC7473940 DOI: 10.1152/ajplung.00158.2020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 12/30/2022] Open
Abstract
Most quantitative PCR (qPCR) experiments report differential expression relative to the expression of one or more reference genes. Therefore, when experimental conditions alter reference gene expression, qPCR results may be compromised. Little is known about the magnitude of this problem in practice. We found that reference gene responses are common and hard to predict and that their stability should be demonstrated in each experiment. Our reanalysis of 15 airway epithelia microarray data sets retrieved from the National Center for Biotechnology Information (NCBI) identified no common reference gene that was reliable in all 15 studies. Reanalysis of published RNA sequencing (RNA-seq) data in which human bronchial epithelial cells (HBEC) were exposed to Pseudomonas aeruginosa revealed that minor experimental details, including bacterial strain, may alter reference gene responses. Direct measurement of 32 TaqMan reference genes in primary cultures of HBEC exposed to P. aeruginosa (strain PA14) demonstrated that choosing an unstable reference gene could make it impossible to observe statistically significant changes in IL8 gene expression. We found that reference gene instability is a general phenomenon and not limited to studies of airway epithelial cells. In a diverse compendium of 986 human microarray experiments retrieved from the NCBI, reference genes were differentially expressed in 42% of studies. Experimentally induced changes in reference gene expression ranged from 21% to 212%. These results highlight the importance of identifying adequate reference genes for each experimental system and documenting their response to treatment in each experiment. This will enhance experimental rigor and reproducibility in qPCR studies.
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Affiliation(s)
- Thomas H Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Katja Koeppen
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Laura Bashor
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Bruce A Stanton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
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11
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Matissek SJ, Koeppen K, Elsawa SF. TLR-TRIF signaling induces GLI3 to modulate inflammation. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.152.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Chronic inflammation is associated with several disorders and therefore the identification of novel regulators of inflammation is needed. We identified GLI3 as a novel component of the TLR-TRIF signaling. Stimulation of monocytes with LPS increased GLI3 expression in a hedgehog-independent mechanism. We stimulated cells with MPLA, (TLR4 ligand that signals through TRIF) and polyI:C (TLR3 ligand) and found that IRF3 directly binds to the GLI3 promoter and IRF3 increased GLI3 expression. We generated a conditional knockout (cko) mouse where GLI3 was deleted in myeloid cells using LysM-Cre mediated recombination. IFA-elicited macrophages from cko mice stimulated with LPS showed reduced IL-6, CCL2 and TNF-a secretion compared to macrophages from wild-type (wt) littermates. We also performed RNA sequencing of LPS treated or untreated macrophages from GLI3 cko or wt mice. Using a generalized linear model in edgeR, we identified 495 genes with significant interaction effects between genotype and LPS treatment. Ingenuity Pathway Analysis of the interaction genes revealed “Inflammatory Response” and “Immune Cell Trafficking” pathways as most significantly enriched. The 25 significant interaction genes on these pathways included 9 with a positive interaction (Ccl25, Cd226, Cgas, Hmgn5, Il12b, Lrrc8a, Rapgef3, Rnf122, and Tlr8) and 16 with a negative interaction (Acacb, Adipoq, Ccl1, Ccne1, Cx3cl1, Fry, Gstk1, Mertk, Nqo2, Slc6a4, Sort1, Timd4, Tnfrsf18/GITR, Tnfsf13/APRIL, Tnfsf13b/BAFF, and Trem2). Taken together, these results identify a novel role for GLI3 in mediating TLR-TRIF-induced inflammation and identify a novel set of inflammatory genes that are dependent on GLI3 in response to TLR-TRIF signaling.
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Affiliation(s)
| | - Katja Koeppen
- 2Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth, Lebanon New Hampshire
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Koeppen K, Barnaby R, Jackson AA, Gerber SA, Hogan DA, Stanton BA. Tobramycin reduces key virulence determinants in the proteome of Pseudomonas aeruginosa outer membrane vesicles. PLoS One 2019; 14:e0211290. [PMID: 30682135 PMCID: PMC6347270 DOI: 10.1371/journal.pone.0211290] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/10/2019] [Indexed: 12/20/2022] Open
Abstract
Tobramycin is commonly used to treat Pseudomonas aeruginosa lung infections in patients with Cystic Fibrosis (CF). Tobramycin treatment leads to increased lung function and fewer clinical exacerbations in CF patients, and modestly reduces the density of P. aeruginosa in the lungs. P. aeruginosa resides primarily in the mucus overlying lung epithelial cells and secretes outer membrane vesicles (OMVs) that diffuse through the mucus and fuse with airway epithelial cells, thus delivering virulence factors into the cytoplasm that modify the innate immune response. The goal of this study was to test the hypothesis that Tobramycin reduces the abundance of virulence factors in OMVs secreted by P. aeruginosa. Characterization of the proteome of OMVs isolated from control or Tobramycin-exposed P. aeruginosa strain PAO1 revealed that Tobramycin reduced several OMV-associated virulence determinants, including AprA, an alkaline protease that enhances P. aeruginosa survival in the lung, and is predicted to contribute to the inhibitory effect of P. aeruginosa on Phe508del-CFTR Cl- secretion by primary human bronchial epithelial cells. Deletion of the gene encoding AprA reduced the inhibitory effect of P. aeruginosa on Phe508del-CFTR Cl- secretion. Moreover, as predicted by our proteomic analysis, OMVs isolated from Tobramycin treated P. aeruginosa had a diminished inhibitory effect on Phe508del-CFTR Cl- secretion compared to OMVs isolated from control P. aeruginosa. Taken together, our proteomic analysis of OMVs and biological validation suggest that Tobramycin may improve lung function in CF patients infected with P. aeruginosa by reducing several key virulence factors in OMVs that reduce CFTR Cl- secretion, which is essential for bacterial clearance from the lungs.
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Affiliation(s)
- Katja Koeppen
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- * E-mail:
| | - Roxanna Barnaby
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Angelyca A. Jackson
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Scott A. Gerber
- Department of Molecular and Systems Biology, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Deborah A. Hogan
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Bruce A. Stanton
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
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Barnaby R, Koeppen K, Stanton BA. Cyclodextrins reduce the ability of Pseudomonas aeruginosa outer-membrane vesicles to reduce CFTR Cl - secretion. Am J Physiol Lung Cell Mol Physiol 2018; 316:L206-L215. [PMID: 30358440 DOI: 10.1152/ajplung.00316.2018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Pseudomonas aeruginosa secretes outer-membrane vesicles (OMVs) that fuse with cholesterol-rich lipid rafts in the apical membrane of airway epithelial cells and decrease wt-CFTR Cl- secretion. Herein, we tested the hypothesis that a reduction of the cholesterol content of CF human airway epithelial cells by cyclodextrins reduces the inhibitory effect of OMVs on VX-809 (lumacaftor)-stimulated Phe508del CFTR Cl- secretion. Primary CF bronchial epithelial cells and CFBE cells were treated with vehicle, hydroxypropyl-β-cyclodextrin (HPβCD), or methyl-β-cyclodextrin (MβCD), and the effects of OMVs secreted by P. aeruginosa on VX-809 stimulated Phe508del CFTR Cl- secretion were measured in Ussing chambers. Neither HPβCD nor MβCD were cytotoxic, and neither altered Phe508del CFTR Cl- secretion. Both cyclodextrins reduced OMV inhibition of VX-809-stimulated Phe508del-CFTR Cl- secretion when added to the apical side of CF monolayers. Both cyclodextrins also reduced the ability of P. aeruginosa to form biofilms and suppressed planktonic growth of P. aeruginosa. Our data suggest that HPβCD, which is in clinical trials for Niemann-Pick Type C disease, and MβCD, which has been approved by the U.S. Food and Drug Administration for use in solubilizing lipophilic drugs, may enhance the clinical efficacy of VX-809 in CF patients when added to the apical side of airway epithelial cells, and reduce planktonic growth and biofilm formation by P. aeruginosa. Both effects would be beneficial to CF patients.
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Affiliation(s)
- Roxanna Barnaby
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Katja Koeppen
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Bruce A Stanton
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
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Koeppen K, Stanton BA, Hampton TH. ScanGEO: parallel mining of high-throughput gene expression data. Bioinformatics 2018; 33:3500-3501. [PMID: 29036513 DOI: 10.1093/bioinformatics/btx452] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 07/11/2017] [Indexed: 11/14/2022] Open
Abstract
Summary Current options to mine publicly available gene expression data deposited in NCBI's gene expression omnibus (GEO), such as the GEO web portal and related applications, are optimized to reanalyze a single study, or search for a single gene, and therefore require manual intervention to reanalyze multiple studies for user-specified gene sets. ScanGEO is a simple, user-friendly Shiny web application designed to identify differentially expressed genes across all GEO studies matching user-specified criteria, for a flexible set of genes, visualize results and provide summary statistics and other reports using a single command. Availability and implementation The ScanGEO source code is written in R and implemented as a Shiny app that can be freely accessed at http://scangeo.dartmouth.edu/ScanGEO/. For users who would like to run a local instantiation of the app, the R source code is available under a GNU GPLv3 license at https://github.com/StantonLabDartmouth/AppScanGEO. Contact katja.koeppen@dartmouth.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Katja Koeppen
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Bruce A Stanton
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Thomas H Hampton
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
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Barnaby R, Koeppen K, Nymon A, Hampton TH, Berwin B, Ashare A, Stanton BA. Lumacaftor (VX-809) restores the ability of CF macrophages to phagocytose and kill Pseudomonas aeruginosa. Am J Physiol Lung Cell Mol Physiol 2017; 314:L432-L438. [PMID: 29146575 DOI: 10.1152/ajplung.00461.2017] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Cystic fibrosis (CF), the most common lethal genetic disease in Caucasians, is characterized by chronic bacterial lung infection and excessive inflammation, which lead to progressive loss of lung function and premature death. Although ivacaftor (VX-770) alone and ivacaftor in combination with lumacaftor (VX-809) improve lung function in CF patients with the Gly551Asp and del508Phe mutations, respectively, the effects of these drugs on the function of human CF macrophages are unknown. Thus studies were conducted to examine the effects of lumacaftor alone and lumacaftor in combination with ivacaftor (i.e., ORKAMBI) on the ability of human CF ( del508Phe/ del508Phe) monocyte-derived macrophages (MDMs) to phagocytose and kill Pseudomonas aeruginosa. Lumacaftor alone restored the ability of CF MDMs to phagocytose and kill P. aeruginosa to levels observed in MDMs obtained from non-CF (WT-CFTR) donors. This effect contrasts with the partial (~15%) correction of del508Phe Cl- secretion of airway epithelial cells by lumacaftor. Ivacaftor reduced the ability of lumacaftor to stimulate phagocytosis and killing of P. aeruginosa. Lumacaftor had no effect on P. aeruginosa-stimulated cytokine secretion by CF MDMs. Ivacaftor (5 µM) alone and ivacaftor in combination with lumacaftor reduced secretion of several proinflammatory cytokines. The clinical efficacy of ORKAMBI may be related in part to the ability of lumacaftor to stimulate phagocytosis and killing of P. aeruginosa by macrophages.
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Affiliation(s)
- Roxanna Barnaby
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Katja Koeppen
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Amanda Nymon
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire.,Section of Pulmonary and Critical Care Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
| | - Thomas H Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Brent Berwin
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Alix Ashare
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire.,Section of Pulmonary and Critical Care Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
| | - Bruce A Stanton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
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Seidler D, Griffin M, Nymon A, Koeppen K, Ashare A. Throat Swabs and Sputum Culture as Predictors of P. aeruginosa or S. aureus Lung Colonization in Adult Cystic Fibrosis Patients. PLoS One 2016; 11:e0164232. [PMID: 27711152 PMCID: PMC5053402 DOI: 10.1371/journal.pone.0164232] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/21/2016] [Indexed: 01/22/2023] Open
Abstract
Background Due to frequent infections in cystic fibrosis (CF) patients, repeated respiratory cultures are obtained to inform treatment. When patients are unable to expectorate sputum, clinicians obtain throat swabs as a surrogate for lower respiratory cultures. There is no clear data in adult subjects demonstrating the adequacy of throat swabs as a surrogate for sputum or BAL. Our study was designed to determine the utility of throat swabs in identifying lung colonization with common organisms in adults with CF. Methods Adult CF subjects (n = 20) underwent bronchoscopy with BAL. Prior to bronchoscopy, a throat swab was obtained. A sputum sample was obtained from subjects who were able to spontaneously expectorate. All samples were sent for standard microbiology culture. Results Using BAL as the gold standard, we found the positive predictive value for Pseudomonas aeruginosa to be 100% in both sputum and throat swab compared to BAL. However, the negative predictive value for P. aeruginosa was 60% and 50% in sputum and throat swab, respectively. Conversely, the positive predictive value for Staphylococcus aureus was 57% in sputum and only 41% in throat swab and the negative predictive value of S. aureus was 100% in sputum and throat swab compared to BAL. Conclusions Our data show that positive sputum and throat culture findings of P. aeruginosa reflect results found on BAL fluid analysis, suggesting these are reasonable surrogates to determine lung colonization with P. aeruginosa. However, sputum and throat culture findings of S. aureus do not appear to reflect S. aureus colonization of the lung.
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Affiliation(s)
- Darius Seidler
- Pulmonary and Critical Care Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, United States of America
| | - Mary Griffin
- Pulmonary and Critical Care Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, United States of America
| | - Amanda Nymon
- Pulmonary and Critical Care Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, United States of America
| | - Katja Koeppen
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States of America
| | - Alix Ashare
- Pulmonary and Critical Care Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, United States of America
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States of America
- * E-mail:
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Koeppen K, Hampton TH, Jarek M, Scharfe M, Gerber SA, Mielcarz DW, Demers EG, Dolben EL, Hammond JH, Hogan DA, Stanton BA. A Novel Mechanism of Host-Pathogen Interaction through sRNA in Bacterial Outer Membrane Vesicles. PLoS Pathog 2016; 12:e1005672. [PMID: 27295279 PMCID: PMC4905634 DOI: 10.1371/journal.ppat.1005672] [Citation(s) in RCA: 278] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 05/10/2016] [Indexed: 12/20/2022] Open
Abstract
Bacterial outer membrane vesicle (OMV)-mediated delivery of proteins to host cells is an important mechanism of host-pathogen communication. Emerging evidence suggests that OMVs contain differentially packaged short RNAs (sRNAs) with the potential to target host mRNA function and/or stability. In this study, we used RNA-Seq to characterize differentially packaged sRNAs in Pseudomonas aeruginosa OMVs, and to show transfer of OMV sRNAs to human airway cells. We selected one sRNA for further study based on its stable secondary structure and predicted mRNA targets. Our candidate sRNA (sRNA52320), a fragment of a P. aeruginosa methionine tRNA, was abundant in OMVs and reduced LPS-induced as well as OMV-induced IL-8 secretion by cultured primary human airway epithelial cells. We also showed that sRNA52320 attenuated OMV-induced KC cytokine secretion and neutrophil infiltration in mouse lung. Collectively, these findings are consistent with the hypothesis that sRNA52320 in OMVs is a novel mechanism of host-pathogen interaction whereby P. aeruginosa reduces the host immune response. Pseudomonas aeruginosa is a gram-negative, opportunistic pathogen that accounts for about 10% of all hospital-acquired infections in the US and primarily infects immunocompromised hosts, including patients with chronic obstructive pulmonary disease and cystic fibrosis. Gram-negative bacteria like P. aeruginosa produce outer membrane vesicles (OMVs), which constitute an important mechanism for host colonization. In this study we demonstrate a novel mechanism of pathogen-host interaction that attenuates the innate immune response in human airway epithelial cells and in mouse lung through a regulatory sRNA contained inside OMVs secreted by P. aeruginosa.
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Affiliation(s)
- Katja Koeppen
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- * E-mail:
| | - Thomas H. Hampton
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Michael Jarek
- Genome Analytics Helmholtz Centre for Infection Research, Braunschweig, Lower Saxony, Germany
| | - Maren Scharfe
- Genome Analytics Helmholtz Centre for Infection Research, Braunschweig, Lower Saxony, Germany
| | - Scott A. Gerber
- Departments of Genetics and Biochemistry, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- Norris Cotton Cancer Center, Lebanon, New Hampshire, United States of America
| | - Daniel W. Mielcarz
- Norris Cotton Cancer Center, Lebanon, New Hampshire, United States of America
| | - Elora G. Demers
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Emily L. Dolben
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - John H. Hammond
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Deborah A. Hogan
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Bruce A. Stanton
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
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Koeppen K, Coutermarsh BA, Madden DR, Stanton BA. Serum- and glucocorticoid-induced protein kinase 1 (SGK1) increases the cystic fibrosis transmembrane conductance regulator (CFTR) in airway epithelial cells by phosphorylating Shank2E protein. J Biol Chem 2014; 289:17142-50. [PMID: 24811177 DOI: 10.1074/jbc.m114.555599] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The glucocorticoid dexamethasone increases cystic fibrosis transmembrane conductance regulator (CFTR) abundance in human airway epithelial cells by a mechanism that requires serum- and glucocorticoid-induced protein kinase 1 (SGK1) activity. The goal of this study was to determine whether SGK1 increases CFTR abundance by phosphorylating Shank2E, a PDZ domain protein that contains two SGK1 phosphorylation consensus sites. We found that SGK1 phosphorylates Shank2E as well as a peptide containing the first SGK1 consensus motif of Shank2E. The dexamethasone-induced increase in CFTR abundance was diminished by overexpression of a dominant-negative Shank2E in which the SGK1 phosphorylation sites had been mutated. siRNA-mediated reduction of Shank2E also reduced the dexamethasone-induced increase in CFTR abundance. Taken together, these data demonstrate that the glucocorticoid-induced increase in CFTR abundance requires phosphorylation of Shank2E at an SGK1 consensus site.
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Affiliation(s)
- Katja Koeppen
- From the Department of Microbiology and Immunology and
| | | | - Dean R Madden
- Department of Biochemistry, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755
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Koeppen K, Coutermarsh B, Bomberger JM, Stanton BA. Shank2E mediates dexamethasone‐induced increase in membrane CFTR in human airway cells. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.913.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Katja Koeppen
- Department of Microbiology & Immunology and of PhysiologyThe Geisel School of Medicine at DartmouthHanoverNH
| | - Bonita Coutermarsh
- Department of Microbiology & Immunology and of PhysiologyThe Geisel School of Medicine at DartmouthHanoverNH
| | - Jennifer M Bomberger
- Department of Microbiology & Immunology and of PhysiologyThe Geisel School of Medicine at DartmouthHanoverNH
- Department of Microbiology & Molecular GeneticsUniversity of PittsburghPittsburghPA
| | - Bruce A Stanton
- Department of Microbiology & Immunology and of PhysiologyThe Geisel School of Medicine at DartmouthHanoverNH
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Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR), a Cl(-) channel in airway epithelial cells, plays an important role in maintaining the volume of the airway surface liquid and therefore mucociliary clearance of respiratory pathogens. A recent study has shown that the E3 ubiquitin ligase Neural precursor cells expressed developmentally downregulated (Nedd4-2) ubiquitinates ΔF508-CFTR in pancreatic epithelial cells and that siRNA-mediated silencing of Nedd4-2 increases plasma membrane ΔF508-CFTR. Because the role of Nedd4-2 in regulating wild-type (wt)-CFTR in airway epithelial cells is unknown, studies were conducted to test the hypothesis that Nedd4-2 also ubiquitinates wt-CFTR and regulates its plasma membrane abundance. We found that Nedd4-2 did not affect wt-CFTR Cl(-) currents in Xenopus oocytes. Likewise, overexpression of Nedd4-2 in human airway epithelial cells did not alter the amount of ubiquitinated wt-CFTR. siRNA knockdown of Nedd4-2 in human airway epithelial cells had no effect on ubiquitination or apical plasma membrane abundance of wt-CFTR. Thus Nedd4-2 does not ubiquitinate and thereby regulate wt-CFTR in human airway epithelial cells.
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Affiliation(s)
- Katja Koeppen
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, 604 Remsen, Hanover, NH 03755, USA.
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Bomberger JM, Ye S, Maceachran DP, Koeppen K, Barnaby RL, O'Toole GA, Stanton BA. A Pseudomonas aeruginosa toxin that hijacks the host ubiquitin proteolytic system. PLoS Pathog 2011; 7:e1001325. [PMID: 21455491 PMCID: PMC3063759 DOI: 10.1371/journal.ppat.1001325] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Accepted: 02/18/2011] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas aeruginosa (P. aeruginosa) is an opportunistic pathogen chronically infecting the lungs of patients with chronic obstructive pulmonary disease (COPD), pneumonia, cystic fibrosis (CF), and bronchiectasis. Cif (PA2934), a bacterial toxin secreted in outer membrane vesicles (OMV) by P. aeruginosa, reduces CFTR-mediated chloride secretion by human airway epithelial cells, a key driving force for mucociliary clearance. The aim of this study was to investigate the mechanism whereby Cif reduces CFTR-mediated chloride secretion. Cif redirected endocytosed CFTR from recycling endosomes to lysosomes by stabilizing an inhibitory effect of G3BP1 on the deubiquitinating enzyme (DUB), USP10, thereby reducing USP10-mediated deubiquitination of CFTR and increasing the degradation of CFTR in lysosomes. This is the first example of a bacterial toxin that regulates the activity of a host DUB. These data suggest that the ability of P. aeruginosa to chronically infect the lungs of patients with COPD, pneumonia, CF, and bronchiectasis is due in part to the secretion of OMV containing Cif, which inhibits CFTR-mediated chloride secretion and thereby reduces the mucociliary clearance of pathogens.
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Affiliation(s)
- Jennifer M Bomberger
- Microbiology and Immunology, Dartmouth Medical School, Hanover, New Hampshire, United States of America.
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Koeppen K, Reuter P, Ladewig T, Kohl S, Baumann B, Jacobson SG, Plomp AS, Hamel CP, Janecke AR, Wissinger B. Dissecting the pathogenic mechanisms of mutations in the pore region of the human cone photoreceptor cyclic nucleotide-gated channel. Hum Mutat 2010; 31:830-9. [PMID: 20506298 DOI: 10.1002/humu.21283] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The CNGA3 gene encodes the A3 subunit of the cone photoreceptor cyclic nucleotide-gated (CNG) channel, an essential component of the phototransduction cascade. Certain mutations in CNGA3 cause autosomal recessive achromatopsia, a retinal disorder characterized by severely reduced visual acuity, lack of color discrimination, photophobia, and nystagmus. We identified three novel mutations in the pore-forming region of CNGA3 (L363P, G367V, and E376K) in patients diagnosed with achromatopsia. We assessed the expression and function of channels with these three new and two previously described mutations (S341P and P372S) in a heterologous HEK293 cell expression system using Western blot, subcellular localization on the basis of immunocytochemistry, calcium imaging, and patch clamp recordings. In this first comparative functional analysis of disease-associated mutations in the pore of a CNG channel, we found impaired surface expression of S341P, L363P, and P372S mutants and reduced macroscopic currents for channels with the mutations S341P, G367V, and E376K. Calcium imaging and patch clamp experiments after incubation at 37 degrees C revealed nonfunctional homo- and heteromeric channels in all five mutants, but incubation at 27 degrees C combined with coexpression of the B3 subunit restored residual function of channels with the mutations S341P, G367V, and E376K.
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Affiliation(s)
- Katja Koeppen
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Tuebingen, Germany.
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Danielyan L, Schäfer R, Schulz A, Ladewig T, Lourhmati A, Buadze M, Schmitt AL, Verleysdonk S, Kabisch D, Koeppen K, Siegel G, Proksch B, Kluba T, Eckert A, Köhle C, Schöneberg T, Northoff H, Schwab M, Gleiter CH. Survival, neuron-like differentiation and functionality of mesenchymal stem cells in neurotoxic environment: the critical role of erythropoietin. Cell Death Differ 2009; 16:1599-614. [PMID: 19609278 DOI: 10.1038/cdd.2009.95] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Mesenchymal stem cells (MSCs) can ameliorate symptoms in several neurodegenerative diseases. However, the toxic environment of a degenerating central nervous system (CNS) characterized by hypoxia, glutamate (Glu) excess and amyloid beta (Abeta) pathology may hamper the survival and regenerative/replacing capacities of engrafted stem cells. Indeed, human MSC (hMSC) exposed to hypoxia were disabled in (i) the capacity of their muscarinic receptors (mAChRs) to respond to acetylcholine (ACh) with a transient increase in intracellular [Ca(2+)], (ii) their capacity to metabolize Glu, reflected by a strong decrease in glutamine synthetase activity, and (iii) their survival on exposure to Glu. Cocultivation of MSC with PC12 cells expressing the amyloid precursor protein gene (APPsw-PC12) increased the release of IL-6 from MSC. HMSC exposed to erythropoietin (EPO) showed a cholinergic neuron-like phenotype reflected by increased cellular levels of choline acetyltransferase, ACh and mAChR. All their functional deficits observed under hypoxia, Glu exposure and APPsw-PC12 cocultivation were reversed by the application of EPO, which increased the expression of Wnt3a. EPO also enhanced the metabolism of Abeta in MSC by increasing their neprilysin content. Our data show that cholinergic neuron-like differentiation of MSC, their functionality and resistance to a neurotoxic environment is regulated and can be improved by EPO, highlighting its potential for optimizing cellular therapies of the CNS.
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Affiliation(s)
- L Danielyan
- Department of Clinical Pharmacology, University Hospital of Tübingen, 72076 Tübingen, Germany.
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Reuter P, Koeppen K, Ladewig T, Kohl S, Baumann B, Wissinger B. Mutations in CNGA3 impair trafficking or function of cone cyclic nucleotide-gated channels, resulting in achromatopsia. Hum Mutat 2008; 29:1228-36. [PMID: 18521937 DOI: 10.1002/humu.20790] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
CNGA3 encodes the A-subunit of the cone photoreceptor cyclic nucleotide-gated (CNG) channel, which is a crucial component of the phototransduction cascade in cone outer segments. Mutations in the CNGA3 gene have been associated with complete and incomplete forms of achromatopsia (ACHR), a congenital, autosomal recessively inherited retinal disorder characterized by lack of color discrimination, reduced visual acuity, nystagmus, and photophobia. Here we report the identification of three novel CNGA3 missense mutations in ACHR patients: c.682G>A (p.E228 K), c.1315C>T (p.R439W), and c.1405G>A (p.A469 T), and the detailed functional analyses of these new as well as five previously reported mutations (R283Q, T291R, F547L, G557R, and E590 K), in conjunction with clinical data of patients carrying these mutations, to establish genotype-phenotype correlations. The functional characterization of mutant CNGA3 channels was performed with calcium imaging and patch clamp recordings in a heterologous HEK293 cell expression system. Results were corroborated by immunostaining and colocalization experiments of the channel protein with the plasma membrane. Several mutations evoked pronounced alterations of the apparent cGMP sensitivity of mutant channels. These functional defects were fully or partially compensated by coexpressing the mutant CNGA3 subunit with the wild-type CNGB3 subunit for channels with the mutations R439W, A469 T, F547L, and E590 K. We could show that several mutant channels with agonist dose-response relationships similar to the wild-type exhibited severely impaired membrane targeting. In addition, this study presents the positive effect of reduced cell culture temperature on surface expression and functional performance of mutant CNG channels with protein folding or trafficking defects.
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Affiliation(s)
- Peggy Reuter
- Centre for Ophthalmology, Institute for Ophthalmic Research, Molecular Genetics Laboratory, Tuebingen, Germany
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Koeppen K, Reuter P, Kohl S, Baumann B, Ladewig T, Wissinger B. Functional analysis of human CNGA3 mutations associated with colour blindness suggests impaired surface expression of channel mutants A3(R427C) and A3(R563C). Eur J Neurosci 2008; 27:2391-401. [PMID: 18445228 DOI: 10.1111/j.1460-9568.2008.06195.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mutations in the CNGA3 gene have been associated with complete and incomplete forms of total colour blindness (achromatopsia), a disorder characterized by reduced visual acuity, lack of colour discrimination, photophobia and nystagmus. CNGA3 encodes the A-subunit of the cone photoreceptor cyclic nucleotide-gated (CNG) channel, an essential component of the phototransduction cascade. Here we report the identification of three new CNGA3 mutations in patients with achromatopsia. To assess the pathogenicity of these newly identified and four previously reported mutations, mutant CNGA3 channels were heterologously expressed in a human embryonic kidney cell line (HEK293 cells) and functionally analysed using calcium imaging. Channels with the mutations R427C and R563C showed a response in imaging experiments and were subsequently characterized in-depth with the patch-clamp technique. The mutant channels were analysed as homooligomers and also as heterooligomers with the wild-type B-subunit present in native channels. Overall, cyclic guanosine monophosphate (cGMP) maximum currents of mutant channels were profoundly reduced in homo- and heteromers. Treatment with the chemical chaperone glycerol effectively increased macroscopic currents, presumably by enhancing surface expression of mutant channels as confirmed by immunocytochemistry. These results suggest decreased channel density in the cell membrane due to impaired folding or trafficking of the channel protein as the main pathogenic effect of the mutations R427C and R563C. Moreover, A3(R427C) homomers showed distinctly increased cGMP and cyclic adenosine monophosphate (cAMP) sensitivities as well as cAMP fractional currents that were raised to over 90% of cGMP maximum currents. Co-expression of A3(R427C) with the B3 subunit compensated for most of these aberrant properties, apart from the reduced cGMP maximum currents.
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Affiliation(s)
- Katja Koeppen
- Centre for Ophthalmology, Institute for Ophthalmic Research, Molecular Genetics Laboratory, Tuebingen, Germany.
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Wissinger B, Dangel S, Ja¨gle H, Hansen L, Baumann B, Rudolph G, Wolf C, Bonin M, Koeppen K, Ladewig T, Kohl S, Zrenner E, Rosenberg T. Cone Dystrophy with Supernormal Rod Response Is Strictly Associated with Mutations inKCNV2. ACTA ACUST UNITED AC 2008; 49:751-7. [DOI: 10.1167/iovs.07-0471] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Bernd Wissinger
- From the Molecular Genetics Laboratory, Institute for Ophthalmic Research, Centre for Ophthalmology, University Clinics Tu¨bingen, Germany; the
| | - Susann Dangel
- From the Molecular Genetics Laboratory, Institute for Ophthalmic Research, Centre for Ophthalmology, University Clinics Tu¨bingen, Germany; the
| | - Herbert Ja¨gle
- University Eye Hospital, Centre for Ophthalmology, University Clinics Tu¨bingen, Germany
| | - Lars Hansen
- The Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Denmark; the
| | - Britta Baumann
- From the Molecular Genetics Laboratory, Institute for Ophthalmic Research, Centre for Ophthalmology, University Clinics Tu¨bingen, Germany; the
| | | | - Christiane Wolf
- From the Molecular Genetics Laboratory, Institute for Ophthalmic Research, Centre for Ophthalmology, University Clinics Tu¨bingen, Germany; the
| | - Michael Bonin
- Department of Medical Genetics, Institute for Human Genetics, University Tu¨bingen, Germany; and the
| | - Katja Koeppen
- From the Molecular Genetics Laboratory, Institute for Ophthalmic Research, Centre for Ophthalmology, University Clinics Tu¨bingen, Germany; the
| | - Thomas Ladewig
- From the Molecular Genetics Laboratory, Institute for Ophthalmic Research, Centre for Ophthalmology, University Clinics Tu¨bingen, Germany; the
| | - Susanne Kohl
- From the Molecular Genetics Laboratory, Institute for Ophthalmic Research, Centre for Ophthalmology, University Clinics Tu¨bingen, Germany; the
| | - Eberhart Zrenner
- University Eye Hospital, Centre for Ophthalmology, University Clinics Tu¨bingen, Germany
| | - Thomas Rosenberg
- Gordon Norrie Centre for Genetic Eye Diseases, Kennedy Institute–National Eye Clinic, Hellerup, Denmark
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Varsányi B, Wissinger B, Kohl S, Koeppen K, Farkas A. Clinical and genetic features of Hungarian achromatopsia patients. Mol Vis 2005; 11:996-1001. [PMID: 16319819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
PURPOSE To describe the clinical features and molecular genetic findings in a collection of Hungarian achromatopsia patients. METHODS Twelve patients with congenital achromatopsia from nine Hungarian families were analyzed in this study. The patients underwent standard ophthalmological examination including detailed full-field electroretinography and color vision testing. In two patients, dark adaptation and spectral luminosity tests were also performed. PCR/RFLP analysis and DNA sequencing was applied for mutation screening of CNGA3 and CNGB3. Heterologous minigene expression was used to evaluate transcript splicing of a new intronic mutation in CNGB3. RESULTS Mutations in CNGA3 were present in four families and mutations in CNGB3 in the remaining five families, including mutations known from Western European patient samples and two new CNGB3 mutations: c.112C>T/Gln38X and c.1663-5T>G. Heterologous expression in COS7 cells shows that the latter induces a splicing defect through the activation of a cryptic splice site 4 bases upstream of the genuine splice site. The patients presented with a clinical picture typical for congenital achromatopsia and there was no significant difference in the phenotype of subjects with either CNGA3 or CNGB3 mutations based on standard ophthalmological examination. However, we assume residual cone function in a subject homozygous for the Phe547Leu mutation in CNGA3 based on prior detailed psychophysical testing (i.e., dark adaptation and spectral luminosity). CONCLUSIONS Mutations in CNGA3 and CNGB3 account for achromatopsia in Hungarian patients including known mutations and a few new CNGB3 mutations. While standard ophthalmological examination revealed a phenotype of complete achromatopsia, we show that thorough psychophysical testing can help to identify subjects with some minute cone function.
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Affiliation(s)
- Balázs Varsányi
- Molecular Genetics Laboratory, University Eye Hospital, University of Tübingen, Tübingen, Germany.
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