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Hodos RA, Strub MD, Ramachandran S, Li L, McCray PB, Dudley JT. Integrative genomic meta-analysis reveals novel molecular insights into cystic fibrosis and ΔF508-CFTR rescue. Sci Rep 2020; 10:20553. [PMID: 33239626 PMCID: PMC7689470 DOI: 10.1038/s41598-020-76347-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
Cystic fibrosis (CF), caused by mutations to CFTR, leads to severe and progressive lung disease. The most common mutant, ΔF508-CFTR, undergoes proteasomal degradation, extinguishing its anion channel function. Numerous in vitro interventions have been identified to partially rescue ΔF508-CFTR function yet remain poorly understood. Improved understanding of both the altered state of CF cells and the mechanisms of existing rescue strategies could reveal novel therapeutic strategies. Toward this aim, we measured transcriptional profiles of established temperature, genetic, and chemical interventions that rescue ΔF508-CFTR and also re-analyzed public datasets characterizing transcription in human CF vs. non-CF samples from airway and whole blood. Meta-analysis yielded a core disease signature and two core rescue signatures. To interpret these through the lens of prior knowledge, we compiled a "CFTR Gene Set Library" from literature. The core disease signature revealed remarkably strong connections to genes with established effects on CFTR trafficking and function and suggested novel roles of EGR1 and SGK1 in the disease state. Our data also revealed an unexpected mechanistic link between several genetic rescue interventions and the unfolded protein response. Finally, we found that C18, an analog of the CFTR corrector compound Lumacaftor, induces almost no transcriptional perturbation despite its rescue activity.
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Affiliation(s)
- Rachel A Hodos
- Mount Sinai School of Medicine, Institute for Next Generation Healthcare, New York, NY, USA
- Courant Institute for Mathematical Sciences, New York University, New York, NY, USA
- BenevolentAI, Brooklyn, NY, USA
| | - Matthew D Strub
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, USA
| | - Shyam Ramachandran
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Editas Medicine, Cambridge, MA, USA
| | - Li Li
- Mount Sinai School of Medicine, Institute for Next Generation Healthcare, New York, NY, USA
- Sema4, Stamford, CT, USA
| | - Paul B McCray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, USA.
| | - Joel T Dudley
- Mount Sinai School of Medicine, Institute for Next Generation Healthcare, New York, NY, USA.
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Ahsan MK, Figueroa-Hall L, Baratta V, Garcia-Milian R, Lam TT, Hoque K, Salas PJ, Ameen NA. Glucocorticoids and serum- and glucocorticoid-inducible kinase 1 are potent regulators of CFTR in the native intestine: implications for stress-induced diarrhea. Am J Physiol Gastrointest Liver Physiol 2020; 319:G121-G132. [PMID: 32567324 PMCID: PMC7500270 DOI: 10.1152/ajpgi.00076.2020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Nongenomic glucocorticoid (GC) and serum- and glucocorticoid-inducible kinase 1 (SGK1) signaling regulate ion transport, but CFTR has not been investigated in the intestine. We examined GC, SGK1, and phosphatidylinositol 3-kinase (PI3K) kinase signaling of CFTR ion transport in native intestine and the role of GCs on mRNA, protein, surface expression, and cyclic guanosine monophosphate (cGMP)-elicited diarrhea. Rats were treated with dexamethasone (DEXA; 2 mg/kg ip) or DMSO for 1, 4, and 24 h. Cyclic adenosine monophosphate (cAMP)-activated ion transport was examined in the presence or absence of SGK1 and PI3K inhibitors. Phosphorylation of SGK1, phosphoinositide-dependent kinase 1, and Akt kinases was confirmed by immunoblots using phosphor-specific antibodies. Tissue lysates were analyzed by mass spectrometry. CFTR and SGK1 mRNA were measured by quantitative PCR. Changes in total and surface CFTR protein were determined. The role of GC in cGMP-activated CFTR ion transport was examined. GC synergistically increased CFTR ion transport by SGK1 and PI3K signaling and increased CFTR protein without altering SGK1 or CFTR mRNA. GC induced highest levels of CFTR protein at 4 h that were associated with marked increase in surface CFTR, phosphorylation of the ubiquitin ligase neural precursor cell expressed developmentally downregulated 4-like (Nedd4-2), and 14-3-3ε, supporting their roles in surface retention and stability. Coimmunoprecipitation of CFTR, Nedd4-2, and 14-3-3ε indicated that assembly of this complex is a likely effector of the SGK and Akt pathways. Mass spectrometry identified phosphorylated peptides in relevant proteins. GC-SGK1 potently regulates CFTR in the intestine and is implicated in diarrheal disease.NEW & NOTEWORTHY This is the first study to examine the mechanisms of glucocorticoid, serum- and glucocorticoid-inducible kinase 1, and nongenomic kinase signaling of CFTR in the native intestine. We identified unique and druggable intestine-specific factors of the pathway that are targets for treating stress-induced diarrhea.
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Affiliation(s)
- Md Kaimul Ahsan
- Department of Pediatrics/Gastroenterology and Hepatology, Yale School of Medicine, New Haven, Connecticut
| | - Leandra Figueroa-Hall
- Department of Pediatrics/Gastroenterology and Hepatology, Yale School of Medicine, New Haven, Connecticut
| | - Vanessa Baratta
- Department of Surgery, Yale School of Medicine, New Haven, Connecticut
| | - Rolando Garcia-Milian
- Bioinformatics Support Program, Cushing/Whitney Medical Library, Yale School of Medicine, New Haven, Connecticut
| | - TuKiet T Lam
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.,Mass Spectrometry and Proteomics Resource, W. M. Keck Biotechnology Resource Laboratory, Yale University, New Haven, Connecticut
| | - Kazi Hoque
- Department of Physiology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Pedro J Salas
- Department of Cell Biology, Miller School of Medicine, University of Miami, Miami, Florida
| | - Nadia A Ameen
- Department of Pediatrics/Gastroenterology and Hepatology, Yale School of Medicine, New Haven, Connecticut.,Department of Pediatrics, Cellular and Molecular Physiology, Yale School of Medicine, New Haven, Connecticut
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Bertrams W, Griss K, Han M, Seidel K, Klemmer A, Sittka-Stark A, Hippenstiel S, Suttorp N, Finkernagel F, Wilhelm J, Greulich T, Vogelmeier CF, Vera J, Schmeck B. Transcriptional analysis identifies potential biomarkers and molecular regulators in pneumonia and COPD exacerbation. Sci Rep 2020; 10:241. [PMID: 31937830 PMCID: PMC6959367 DOI: 10.1038/s41598-019-57108-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/20/2019] [Indexed: 01/16/2023] Open
Abstract
Lower respiratory infections, such as community-acquired pneumonia (CAP), and chronic obstructive pulmonary disease (COPD) rank among the most frequent causes of death worldwide. Improved diagnostics and profound pathophysiological insights are urgent clinical needs. In our cohort, we analysed transcriptional networks of peripheral blood mononuclear cells (PBMCs) to identify central regulators and potential biomarkers. We investigated the mRNA- and miRNA-transcriptome of PBMCs of healthy subjects and patients suffering from CAP or AECOPD by microarray and Taqman Low Density Array. Genes that correlated with PBMC composition were eliminated, and remaining differentially expressed genes were grouped into modules. One selected module (120 genes) was particularly suitable to discriminate AECOPD and CAP and most notably contained a subset of five biologically relevant mRNAs that differentiated between CAP and AECOPD with an AUC of 86.1%. Likewise, we identified several microRNAs, e.g. miR-545-3p and miR-519c-3p, which separated AECOPD and CAP. We furthermore retrieved an integrated network of differentially regulated mRNAs and microRNAs and identified HNF4A, MCC and MUC1 as central network regulators or most important discriminatory markers. In summary, transcriptional analysis retrieved potential biomarkers and central molecular features of CAP and AECOPD.
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Affiliation(s)
- Wilhelm Bertrams
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center, German Center for Lung Research (DZL), Marburg, Germany
| | - Kathrin Griss
- Department of Internal Medicine/Infectious Diseases and Respiratory Medicine, Charité - University Medicine Berlin, Berlin, Germany
| | - Maria Han
- Department of Internal Medicine/Infectious Diseases and Respiratory Medicine, Charité - University Medicine Berlin, Berlin, Germany
| | - Kerstin Seidel
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center, German Center for Lung Research (DZL), Marburg, Germany
| | - Andreas Klemmer
- Pulmonary and Critical Care Medicine, University Medical Center Giessen and Marburg, German Center for Lung Research (DZL), Marburg, Germany
| | - Alexandra Sittka-Stark
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center, German Center for Lung Research (DZL), Marburg, Germany
| | - Stefan Hippenstiel
- Department of Internal Medicine/Infectious Diseases and Respiratory Medicine, Charité - University Medicine Berlin, Berlin, Germany
| | - Norbert Suttorp
- Department of Internal Medicine/Infectious Diseases and Respiratory Medicine, Charité - University Medicine Berlin, Berlin, Germany
| | - Florian Finkernagel
- Institute of Molecular Biology and Tumor Research (IMT), Genomics Core Facility, Philipps-University of Marburg, Marburg, Germany
| | - Jochen Wilhelm
- Justus-Liebig-University, Universities Giessen & Marburg Lung Center, German Center for Lung Research (DZL), Giessen, Germany
| | - Timm Greulich
- Pulmonary and Critical Care Medicine, University Medical Center Giessen and Marburg, German Center for Lung Research (DZL), Marburg, Germany
| | - Claus F Vogelmeier
- Pulmonary and Critical Care Medicine, University Medical Center Giessen and Marburg, German Center for Lung Research (DZL), Marburg, Germany
| | - Julio Vera
- Laboratory of Systems Tumor Immunology, Department of Dermatology, Universitätsklinikum Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Bernd Schmeck
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center, German Center for Lung Research (DZL), Marburg, Germany. .,Pulmonary and Critical Care Medicine, University Medical Center Giessen and Marburg, German Center for Lung Research (DZL), Marburg, Germany. .,Center for Synthetic Microbiology (SYNMIKRO), Philipps-University of Marburg, Marburg, Germany. .,German Center for Infection Research (DZIF), partner site Giessen-Marburg-Langen, Marburg, Germany.
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Stanton BA. Effects of Pseudomonas aeruginosa on CFTR chloride secretion and the host immune response. Am J Physiol Cell Physiol 2017; 312:C357-C366. [PMID: 28122735 DOI: 10.1152/ajpcell.00373.2016] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 01/20/2017] [Accepted: 01/21/2017] [Indexed: 12/18/2022]
Abstract
In the healthy lung the opportunistic pathogen, Pseudomonas aeruginosa, is rapidly eliminated by mucociliary clearance, a process that is dependent on the activity of the CFTR anion channel that, in concert with a number of other transport proteins, regulates the volume and composition of the periciliary surface liquid. This fluid layer is essential to enable cilia to clear pathogens from the lungs. However, in cystic fibrosis (CF), mutations in the CFTR gene reduce Cl- and [Formula: see text] secretion, thereby decreasing periciliary surface liquid volume and mucociliary clearance of bacteria. In CF this leads to persistent infection with the opportunistic pathogen, P. aeruginosa, which is the cause of reduced lung function and death in ~95% of CF patients. Others and we have conducted studies to elucidate the effects of P. aeruginosa on wild-type and Phe508del-CFTR Cl- secretion as well as on the host immune response. These studies have demonstrated that Cif (CFTR inhibitory factor), a virulence factor secreted by P. aeruginosa, is associated with reduced lung function in CF and induces the ubiquitination and degradation of wt-CFTR as well as TAP1, which plays a key role in viral and bacterial antigen presentation. Cif also enhances the degradation of Phe508del-CFTR that has been rescued by ORKAMBI, a drug approved for CF patients homozygous for the Phe508del-CFTR mutation, thereby reducing drug efficacy. This review is based on the Hans Ussing Distinguished Lecture at the 2016 Experimental Biology Meeting given by the author.
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Affiliation(s)
- Bruce A Stanton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
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Pesce E, Gorrieri G, Sirci F, Napolitano F, Carrella D, Caci E, Tomati V, Zegarra-Moran O, di Bernardo D, Galietta LJV. Evaluation of a systems biology approach to identify pharmacological correctors of the mutant CFTR chloride channel. J Cyst Fibros 2016; 15:425-35. [PMID: 26971626 DOI: 10.1016/j.jcf.2016.02.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 01/21/2016] [Accepted: 02/22/2016] [Indexed: 11/28/2022]
Abstract
BACKGROUND Mistrafficking of CFTR protein caused by F508del, the most frequent mutation in cystic fibrosis (CF), can be corrected by cell incubation at low temperature, an effect that may be mediated by altered expression of proteostasis genes. METHODS To identify small molecules mimicking low temperature, we compared gene expression profiles of cells kept at 27°C with those previously generated from more than 1300 compounds. The resulting candidates were tested with a functional assay on a bronchial epithelial cell line. RESULTS We found that anti-inflammatory glucocorticoids, such as mometasone, budesonide, and fluticasone, increased mutant CFTR function. However, this activity was not confirmed in primary bronchial epithelial cells. Actually, glucocorticoids enhanced Na(+) absorption, an effect that could further impair mucociliary clearance in CF airways. CONCLUSIONS Our results suggest that rescue of F508del-CFTR by low temperature cannot be easily mimicked by small molecules and that compounds with closer transcriptional and functional effects need to be found.
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Affiliation(s)
- Emanuela Pesce
- Istituto Giannina Gaslini, via Gerolamo Gaslini 5, 16147 Genova, Italy
| | - Giulia Gorrieri
- Istituto Giannina Gaslini, via Gerolamo Gaslini 5, 16147 Genova, Italy
| | - Francesco Sirci
- Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Francesco Napolitano
- Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Diego Carrella
- Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Emanuela Caci
- Istituto Giannina Gaslini, via Gerolamo Gaslini 5, 16147 Genova, Italy
| | - Valeria Tomati
- Istituto Giannina Gaslini, via Gerolamo Gaslini 5, 16147 Genova, Italy
| | | | - Diego di Bernardo
- Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Luis J V Galietta
- Istituto Giannina Gaslini, via Gerolamo Gaslini 5, 16147 Genova, Italy
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Dong ZW, Chen J, Ruan YC, Zhou T, Chen Y, Chen Y, Tsang LL, Chan HC, Peng YZ. CFTR-regulated MAPK/NF-κB signaling in pulmonary inflammation in thermal inhalation injury. Sci Rep 2015; 5:15946. [PMID: 26515683 PMCID: PMC4626762 DOI: 10.1038/srep15946] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 09/30/2015] [Indexed: 12/17/2022] Open
Abstract
The mechanism underlying pulmonary inflammation in thermal inhalation injury remains elusive. Cystic fibrosis, also hallmarked with pulmonary inflammation, is caused by mutations in CFTR, the expression of which is temperature-sensitive. We investigated whether CFTR is involved in heat-induced pulmonary inflammation. We applied heat-treatment in 16HBE14o- cells with CFTR knockdown or overexpression and heat-inhalation in rats in vivo. Heat-treatment caused significant reduction in CFTR and, reciprocally, increase in COX-2 at early stages both in vitro and in vivo. Activation of ERK/JNK, NF-κB and COX-2/PGE2 were detected in heat-treated cells, which were mimicked by knockdown, and reversed by overexpression of CFTR or VX-809, a reported CFTR mutation corrector. JNK/ERK inhibition reversed heat-/CFTR-knockdown-induced NF-κB activation, whereas NF-κB inhibitor showed no effect on JNK/ERK. IL-8 was augmented by heat-treatment or CFTR-knockdown, which was abolished by inhibition of NF-κB, JNK/ERK or COX-2. Moreover, in vitro or in vivo treatment with curcumin, a natural phenolic compound, significantly enhanced CFTR expression and reversed the heat-induced increases in COX-2/PGE2/IL-8, neutrophil infiltration and tissue damage in the airway. These results have revealed a CFTR-regulated MAPK/NF-κB pathway leading to COX-2/PGE2/IL-8 activation in thermal inhalation injury, and demonstrated therapeutic potential of curcumin for alleviating heat-induced pulmonary inflammation.
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Affiliation(s)
- Zhi Wei Dong
- State Key Laboratory of Trauma, Burns and Combined Injury, Chongqing Key Laboratory for Proteomics Disease, Institute of Burn Research, Southwest Hospital, the Third Military Medical University, Chongqing, China
| | - Jing Chen
- State Key Laboratory of Trauma, Burns and Combined Injury, Chongqing Key Laboratory for Proteomics Disease, Institute of Burn Research, Southwest Hospital, the Third Military Medical University, Chongqing, China
| | - Ye Chun Ruan
- Epithelial Cell Biology Research Center, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Tao Zhou
- State Key Laboratory of Trauma, Burns and Combined Injury, Chongqing Key Laboratory for Proteomics Disease, Institute of Burn Research, Southwest Hospital, the Third Military Medical University, Chongqing, China
| | - Yu Chen
- State Key Laboratory of Trauma, Burns and Combined Injury, Chongqing Key Laboratory for Proteomics Disease, Institute of Burn Research, Southwest Hospital, the Third Military Medical University, Chongqing, China
| | - YaJie Chen
- State Key Laboratory of Trauma, Burns and Combined Injury, Chongqing Key Laboratory for Proteomics Disease, Institute of Burn Research, Southwest Hospital, the Third Military Medical University, Chongqing, China
| | - Lai Ling Tsang
- Epithelial Cell Biology Research Center, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Hsiao Chang Chan
- Epithelial Cell Biology Research Center, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Yi Zhi Peng
- State Key Laboratory of Trauma, Burns and Combined Injury, Chongqing Key Laboratory for Proteomics Disease, Institute of Burn Research, Southwest Hospital, the Third Military Medical University, Chongqing, China
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