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Lei L, Pan W, Shou X, Shao Y, Ye S, Zhang J, Kolliputi N, Shi L. Nanomaterials-assisted gene editing and synthetic biology for optimizing the treatment of pulmonary diseases. J Nanobiotechnology 2024; 22:343. [PMID: 38890749 PMCID: PMC11186260 DOI: 10.1186/s12951-024-02627-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 06/06/2024] [Indexed: 06/20/2024] Open
Abstract
The use of nanomaterials in gene editing and synthetic biology has emerged as a pivotal strategy in the pursuit of refined treatment methodologies for pulmonary disorders. This review discusses the utilization of nanomaterial-assisted gene editing tools and synthetic biology techniques to promote the development of more precise and efficient treatments for pulmonary diseases. First, we briefly outline the characterization of the respiratory system and succinctly describe the principal applications of diverse nanomaterials in lung ailment treatment. Second, we elaborate on gene-editing tools, their configurations, and assorted delivery methods, while delving into the present state of nanomaterial-facilitated gene-editing interventions for a spectrum of pulmonary diseases. Subsequently, we briefly expound on synthetic biology and its deployment in biomedicine, focusing on research advances in the diagnosis and treatment of pulmonary conditions against the backdrop of the coronavirus disease 2019 pandemic. Finally, we summarize the extant lacunae in current research and delineate prospects for advancement in this domain. This holistic approach augments the development of pioneering solutions in lung disease treatment, thereby endowing patients with more efficacious and personalized therapeutic alternatives.
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Affiliation(s)
- Lanjie Lei
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Institute of Translational Medicine, Zhejiang Shuren University, Hangzhou, Zhejiang, 310015, China
| | - Wenjie Pan
- Department of Pharmacy, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325200, China
| | - Xin Shou
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Institute of Translational Medicine, Zhejiang Shuren University, Hangzhou, Zhejiang, 310015, China
| | - Yunyuan Shao
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Institute of Translational Medicine, Zhejiang Shuren University, Hangzhou, Zhejiang, 310015, China
| | - Shuxuan Ye
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Institute of Translational Medicine, Zhejiang Shuren University, Hangzhou, Zhejiang, 310015, China
| | - Junfeng Zhang
- Department of Immunology and Medical Microbiology, Nanjing University of Chinese Medicine, Nanjing, 210046, China
| | - Narasaiah Kolliputi
- Division of Allergy and Immunology, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Liyun Shi
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Institute of Translational Medicine, Zhejiang Shuren University, Hangzhou, Zhejiang, 310015, China.
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Stanke F, Pallenberg ST, Tamm S, Hedtfeld S, Eichhorn EM, Minso R, Hansen G, Welte T, Sauer-Heilborn A, Ringshausen FC, Junge S, Tümmler B, Dittrich AM. Changes in cystic fibrosis transmembrane conductance regulator protein expression prior to and during elexacaftor-tezacaftor-ivacaftor therapy. Front Pharmacol 2023; 14:1114584. [PMID: 36778025 PMCID: PMC9911415 DOI: 10.3389/fphar.2023.1114584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 01/16/2023] [Indexed: 01/28/2023] Open
Abstract
Background: Defects in expression, maturation or function of the epithelial membrane glycoprotein CFTR are causative for the progressive disease cystic fibrosis. Recently, molecular therapeutics that improve CFTR maturation and functional defects have been approved. We aimed to verify whether we could detect an improvement of CFTR protein expression and maturation by triple therapy with elexacaftor-tezacaftor-ivacaftor (ELX/TEZ/IVA). Methods: Rectal suction biopsies of 21 p.Phe508del homozygous or compound heterozygous CF patients obtained pre- and during treatment with ELX/TEZ/IVA were analyzed by CFTR Western blot that was optimized to distinguish CFTR glycoisoforms. Findings: CFTR western immunoblot analysis revealed that-compared to baseline-the levels of CFTR protein increased by at least twofold in eight out of 12 patients upon treatment with ELX/TEZ/IVA compared to baseline (p < 0.02). However, polydispersity of the mutant CFTR protein was lower than that of the fully glycosylated wild type CFTR Golgi isoform, indicating an incompletely glycosylated p.Phe508el CFTR protein isoform C* in patients with CF which persists after ELX/TEZ/IVA treatment. Interpretation: Treatment with ELX/TEZ/IVA increased protein expression by facilitating the posttranslational processing of mutant CFTR but apparently did not succeed in generating the polydisperse spectrum of N-linked oligosaccharides that is characteristic for the wild type CFTR band C glycoisoform. Our results caution that the lower amounts or immature glycosylation of the C* glycoisoform observed in patients' biomaterial might not translate to fully restored function of mutant CFTR necessary for long-term provision of clinical benefit.
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Affiliation(s)
- Frauke Stanke
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany,*Correspondence: Frauke Stanke,
| | - Sophia T. Pallenberg
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Stephanie Tamm
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
| | - Silke Hedtfeld
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Ella M. Eichhorn
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Rebecca Minso
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Gesine Hansen
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
| | - Tobias Welte
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany,Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany
| | | | - Felix C. Ringshausen
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany,Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany
| | - Sibylle Junge
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Burkhard Tümmler
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
| | - Anna-Maria Dittrich
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
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3
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Corcoran TE, Bertrand CA, Myerburg MM, Weiner DJ, Frizzell SA, Li A, Agostini B, Parker RS, Shapiro ME, Muthukrishnan A, Hages ND, Mulhern BP, Pilewski JM. Nasal epithelial cell culture fluorescence recovery after photobleaching predicts cystic fibrosis therapeutic response. ERJ Open Res 2022; 8:00382-2022. [PMID: 36655223 PMCID: PMC9835985 DOI: 10.1183/23120541.00382-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/23/2022] [Indexed: 11/12/2022] Open
Abstract
Background Human nasal epithelial (HNE) cells can be sampled noninvasively and cultured to provide a model of the airway epithelium that reflects cystic fibrosis (CF) pathophysiology. We hypothesised that in vitro measures of HNE cell physiology would correlate directly with in vivo measures of lung physiology and therapeutic response, providing a framework for using HNE cells for therapeutic development and precision medicine. Methods We sampled nasal cells from participants with CF (CF group, n=26), healthy controls (HC group, n=14) and single CF transmembrane conductance regulator (CFTR) mutation carrier parents of the CF group (CR group, n=16). Participants underwent lung physiology and sweat chloride testing, and nuclear imaging-based measurement of mucociliary clearance (MCC) and small-molecule absorption (ABS). CF participants completed a second imaging day that included hypertonic saline (HS) inhalation to assess therapeutic response in terms of MCC. HNE measurements included Ussing chamber electrophysiology, small-molecule and liquid absorption rates, and particle diffusion rates through the HNE airway surface liquid (ASL) measured using fluorescence recovery after photobleaching (FRAP). Results Long FRAP diffusion times were associated with increased MCC response to HS in CF. This implies a strong relationship between inherent factors affecting ASL mucin concentration and therapeutic response to a hydrating therapy. MCC decreased with age in the CR group, which had a larger range of ages than the other two groups. Likely this indicates a general age-related effect that may be accentuated in this group. Measures of lung ABS correlated with sweat chloride in both the HC and CF groups, indicating that CFTR function drives this measure of paracellular small-molecule probe absorption. Conclusions Our results demonstrate the utility of HNE cultures for assessing therapeutic response for hydrating therapies. In vitro measurements of FRAP were particularly useful for predicting response and for characterising important properties of ASL mucus that were ultimately reflected in lung physiology.
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Affiliation(s)
- Timothy E. Corcoran
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Carol A. Bertrand
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael M. Myerburg
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel J. Weiner
- Division of Pediatric Pulmonology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sheila A. Frizzell
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Anna Li
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Brittani Agostini
- Division of Pediatric Pulmonology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Robert S. Parker
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Monica E. Shapiro
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Nicholas D. Hages
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Brian P. Mulhern
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joseph M. Pilewski
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
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Schmidt H, Gutjahr L, Sauter A, Zech F, Nchioua R, Stenger S, Frick M, Kirchhoff F, Dietl P, Wittekindt OH. Serially passaged, conditionally reprogrammed nasal epithelial cells as a model to study epithelial functions and SARS-CoV-2 infection. Am J Physiol Cell Physiol 2022; 322:C591-C604. [PMID: 35196166 PMCID: PMC8977148 DOI: 10.1152/ajpcell.00363.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Primary airway epithelial cells (pAECs) cultivated at air-liquid interface (ALI) conditions are widely used as surrogates for human in vivo epithelia. To extend the proliferative capacity and to enable serially passaging of pAECs, conditional reprogramming (cr) has been employed in recent years. However, ALI epithelia derived from cr cells often display functional changes with increasing passages. This highlights the need for thorough validation of the ALI cultures for the respective application. In our study, we evaluated the use of serially passaged cr nasal epithelial cells (crNECs) as a model to study SARS-CoV-2 infection and effects on ion and water transport. NECs were obtained from healthy individuals and cultivated as ALI epithelia derived from passages 1, 2, 3, and 5. We compared epithelial differentiation, ion and water transport, and infection with SARS-CoV-2 between passages. Our results show that epithelia maintained major differentiation characteristics and physiological ion and water transport properties through all passages. However, the frequency of ciliated cells, short circuit currents reflecting epithelial Na+ channel (ENaC) and cystic fibrosis transmembrane conductance regulator (CFTR) activity and expression of aquaporin 3 and 5 decreased gradually over passages. crNECs also expressed SARS-CoV-2 receptors angiotensin converting enzyme 2 (ACE2) and transmembrane serin2 protease 2 (TMPRSS2) across all passages and allowed SARS-CoV-2 replication in all passages. In summary, we provide evidence that passaged crNECs provide an appropriate model to study SARS-CoV-2 infection and also epithelial transport function when considering some limitations that we defined herein.
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Affiliation(s)
- Hanna Schmidt
- Department of Pediatric and Adolescent Medicine, Ulm University Medical Cente, Ulm, Germany.,Institute of General Physiology, Ulm University, Ulm, Germany
| | - Lara Gutjahr
- Institute of General Physiology, Ulm University, Ulm, Germany
| | | | - Fabian Zech
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Rayhane Nchioua
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Steffen Stenger
- Institute of Medical Microbiology and Hygiene, Ulm University Medical Center, Ulm, Germany
| | - Manfred Frick
- Institute of General Physiology, Ulm University, Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Paul Dietl
- Institute of General Physiology, Ulm University, Ulm, Germany
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Sato Y, Mustafina KR, Luo Y, Martini C, Thomas DY, Wiseman PW, Hanrahan JW. Nonspecific binding of common anti-CFTR antibodies in ciliated cells of human airway epithelium. Sci Rep 2021; 11:23256. [PMID: 34853321 PMCID: PMC8636639 DOI: 10.1038/s41598-021-02420-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/11/2021] [Indexed: 11/10/2022] Open
Abstract
There is evidence that the cystic fibrosis transmembrane conductance regulator (CFTR) anion channel is highly expressed at the apical pole of ciliated cells in human bronchial epithelium (HBE), however recent studies have detected little CFTR mRNA in those cells. To understand this discrepancy we immunostained well differentiated primary HBE cells using CFTR antibodies. We confirmed apical immunofluorescence in ciliated cells and quantified the covariance of the fluorescence signals and that of an antibody against the ciliary marker centrin-2 using image cross-correlation spectroscopy (ICCS). Super-resolution stimulated emission depletion (STED) imaging localized the immunofluorescence in distinct clusters at the bases of the cilia. However, similar apical fluorescence was observed when the monoclonal CFTR antibodies 596, 528 and 769 were used to immunostain ciliated cells expressing F508del-CFTR, or cells lacking CFTR due to a Class I mutation. A BLAST search using the CFTR epitope identified a similar amino acid sequence in the ciliary protein rootletin X1. Its expression level correlated with the intensity of immunostaining by CFTR antibodies and it was detected by 596 antibody after transfection into CFBE cells. These results may explain the high apparent expression of CFTR in ciliated cells and reports of anomalous apical immunofluorescence in well differentiated cells that express F508del-CFTR.
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Affiliation(s)
- Yukiko Sato
- Department of Physiology, McGill University, McIntyre Medical Sciences Building, 3655 Promenade Sir William Osler, Montréal, QC, H3G 1Y6, Canada.,Cystic Fibrosis Translational Research Centre, McGill University, Montréal, Canada
| | - Kamila R Mustafina
- Cystic Fibrosis Translational Research Centre, McGill University, Montréal, Canada.,Department of Chemistry, McGill University, Montréal, Canada
| | - Yishan Luo
- Department of Physiology, McGill University, McIntyre Medical Sciences Building, 3655 Promenade Sir William Osler, Montréal, QC, H3G 1Y6, Canada.,Cystic Fibrosis Translational Research Centre, McGill University, Montréal, Canada
| | - Carolina Martini
- Department of Physiology, McGill University, McIntyre Medical Sciences Building, 3655 Promenade Sir William Osler, Montréal, QC, H3G 1Y6, Canada.,Cystic Fibrosis Translational Research Centre, McGill University, Montréal, Canada
| | - David Y Thomas
- Cystic Fibrosis Translational Research Centre, McGill University, Montréal, Canada.,Department of Biochemistry, McGill University, Montréal, Canada
| | - Paul W Wiseman
- Cystic Fibrosis Translational Research Centre, McGill University, Montréal, Canada.,Department of Chemistry, McGill University, Montréal, Canada.,Department of Physics, McGill University, Montréal, Canada
| | - John W Hanrahan
- Department of Physiology, McGill University, McIntyre Medical Sciences Building, 3655 Promenade Sir William Osler, Montréal, QC, H3G 1Y6, Canada. .,Cystic Fibrosis Translational Research Centre, McGill University, Montréal, Canada. .,Research Institute - McGill University Health Centre, Montréal, Canada.
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6
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Sala MA, Alexander M, Khuder B, Politanska Y, Abdala-Valencia H, Budinger GRS, Liu J, Jain M, Reyfman PA. The proteostatic network chaperome is downregulated in F508del homozygote cystic fibrosis. J Cyst Fibros 2021; 20:356-363. [PMID: 33495079 DOI: 10.1016/j.jcf.2020.12.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 12/16/2020] [Accepted: 12/20/2020] [Indexed: 11/15/2022]
Abstract
BACKGROUND CF patients demonstrate clinical heterogeneity and much remains unknown about how to risk stratify individuals for disease progression. The most common cystic fibrosis mutation, F508del, is a protein folding mutation that has been shown in vitro to negatively affect proteostasis and CFTR transcription. Since CFTR is expressed in the nasal epithelium, we hypothesized that by using unbiased transcriptomics we could gain clinically relevant insights about differential gene expression and heterogeneity in CF patients as well as assess proteostatic dysfunction in the nasal epithelium. METHODS Using nasal curettage and RNA-seq we assessed differential gene expression in F508del homozygotes compared to healthy volunteers. Gene set enrichment analysis was performed using a list of known chaperones. Pilot and validation cohorts were studied. RESULTS PCA analysis and gene expression heatmaps exhibited greater heterogeneity among CF than healthy volunteers. Differentially expressed genes were enriched for the downregulation of ciliary/microtubular genes and the upregulation of inflammatory/immune response genes in F508del homozygotes compared to healthy volunteers. Gene set analysis identified negative enrichment for chaperone genes and decreased CFTR transcription in the F508del homozygotes. We also found preliminary evidence for the recently identified ionocyte in the nasal specimens. CONCLUSION CF patients homozygous for F508del demonstrate heterogeneous gene expression profiles, proteostatic dysregulation, and reduced CFTR transcription. Larger studies are needed to determine whether nasal epithelial gene transcription profiles can be leveraged for insights into disease heterogeneity.
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Affiliation(s)
- Marc A Sala
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Michael Alexander
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Basil Khuder
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Yuliya Politanska
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Hiam Abdala-Valencia
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - G R Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Jing Liu
- Department of Surgery, College of Medicine, Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Manu Jain
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
| | - Paul A Reyfman
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
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Kanner SA, Shuja Z, Choudhury P, Jain A, Colecraft HM. Targeted deubiquitination rescues distinct trafficking-deficient ion channelopathies. Nat Methods 2020; 17:1245-1253. [PMID: 33169015 PMCID: PMC9335257 DOI: 10.1038/s41592-020-00992-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/07/2020] [Indexed: 12/11/2022]
Abstract
Impaired protein stability/trafficking underlies diverse ion channelopathies and represents an unexploited unifying principle to develop common treatments for otherwise dissimilar diseases. Ubiquitination limits ion channel surface density, but targeting this pathway for basic study or therapy is challenging because of its prevalent role in proteostasis. We developed engineered deubiquitinases (enDUBs) that enable ubiquitin chain removal selectively from target proteins to rescue functional expression of disparate mutant ion channels underlying Long QT syndrome (LQT1) and cystic fibrosis (CF). In a LQT1 cardiomyocyte model, enDUB treatment restored delayed rectifier K+ currents and normalized action potential duration. CF-targeted enDUBs synergistically rescued common (F508del) and pharmacotherapy-resistant (N1303K) CF mutations when combined with the FDA-approved drugs, Orkambi and Trikafta. Altogether, targeted deubiquitination via enDUBs provides a powerful protein stabilization method that not only corrects diverse diseases caused by impaired ion channel trafficking, but also introduces a new tool for deconstructing the ubiquitin code in situ.
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Affiliation(s)
- Scott A Kanner
- Doctoral Program in Neurobiology and Behavior, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Zunaira Shuja
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Papiya Choudhury
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | | | - Henry M Colecraft
- Doctoral Program in Neurobiology and Behavior, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA. .,Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA. .,Department of Molecular Pharmacology and Therapeutics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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Forskolin-induced swelling of intestinal organoids correlates with disease severity in adults with cystic fibrosis and homozygous F508del mutations. J Cyst Fibros 2019; 19:614-619. [PMID: 31735562 DOI: 10.1016/j.jcf.2019.10.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 10/01/2019] [Accepted: 10/22/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND CFTR function measurements in intestinal organoids may help to better characterise individual disease expression in F508del homozygous people. Our objective was to study correlations between CFTR function as measured with forskolin-induced swelling in rectal organoids with clinical parameters in adult patients with homozygous F508del mutations. METHODS Multicentre observational study. Thirty-four adults underwent rectal biopsy, pulmonary function tests (FEV1 and FVC), chest X-ray and chest CT. Body-mass index (BMI) was assessed at study visit and exacerbation rate was determined during five years prior to study visit. Organoids were cultured and measured after stimulation with 5 µm forskolin for three hours to quantitate CFTR residual function. FINDINGS FIS was positively correlated with FEV1 (r = 0.36, 95% CI 0.02-0.62, p = 0.04) and BMI (r = 0.42, 95% CI 0.09-0.66, p = 0.015). FIS was negatively correlated with PRAGMA-CF CT score for% of disease (r = -0.37, 95% CI -0.62- -0.03, p = 0.049). We found no significant correlation between FIS and chest radiography score for CF (r = -0.16, 95% CI -0.48-0.20, p = 0.44). We observed a trend between higher FIS and a lower mean number of exacerbations over the last 5 years of observation, but this was not statistically significant (Poisson regression, p = 0.089). INTERPRETATION FIS of intestinal organoids varied between subjects with homozygous F508del and correlated with pulmonary and nutritional parameters. These findings suggest that differences at low CFTR residual function may contribute to clinical heterogeneity in F508del homozygous patients and small changes in CFTR residual function might impact long-term disease expression.
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9
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Kerem E, Oren YS, Kerem B. Take it personally: how personal we reach when we are so different from each other? J Cyst Fibros 2019; 18:6-7. [DOI: 10.1016/j.jcf.2018.12.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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10
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Bergougnoux A, Taulan-Cadars M, Claustres M, Raynal C. Current and future molecular approaches in the diagnosis of cystic fibrosis. Expert Rev Respir Med 2018; 12:415-426. [PMID: 29580110 DOI: 10.1080/17476348.2018.1457438] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Cystic Fibrosis is among the first diseases to have general population genetic screening tests and one of the most common indications of prenatal and preimplantation genetic diagnosis for single gene disorders. During the past twenty years, thanks to the evolution of diagnostic techniques, our knowledge of CFTR genetics and pathophysiological mechanisms involved in cystic fibrosis has significantly improved. Areas covered: Sanger sequencing and quantitative methods greatly contributed to the identification of more than 2,000 sequence variations reported worldwide in the CFTR gene. We are now entering a new technological age with the generalization of high throughput approaches such as Next Generation Sequencing and Droplet Digital PCR technologies in diagnostics laboratories. These powerful technologies open up new perspectives for scanning the entire CFTR locus, exploring modifier factors that possibly influence the clinical evolution of patients, and for preimplantation and prenatal diagnosis. Expert commentary: Such breakthroughs would, however, require powerful bioinformatics tools and relevant functional tests of variants for analysis and interpretation of the resulting data. Ultimately, an optimal use of all those resources may improve patient care and therapeutic decision-making.
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Affiliation(s)
- Anne Bergougnoux
- a Laboratoire de Génétique Moléculaire , Centre Hospitalier Universitaire de Montpellier , Montpellier , France.,b EA 7402 , Université de Montpellier , Montpellier , France
| | | | | | - Caroline Raynal
- a Laboratoire de Génétique Moléculaire , Centre Hospitalier Universitaire de Montpellier , Montpellier , France
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11
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Whelan FJ, Surette MG. Early life nasal microbiota in infants with cystic fibrosis. THE LANCET RESPIRATORY MEDICINE 2016; 4:595-596. [PMID: 27342262 DOI: 10.1016/s2213-2600(16)30153-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 05/31/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Fiona J Whelan
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada; Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Michael G Surette
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada.
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12
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Bergougnoux A, Claustres M, De Sario A. Nasal epithelial cells: a tool to study DNA methylation in airway diseases. Epigenomics 2015; 7:119-26. [PMID: 25687471 DOI: 10.2217/epi.14.65] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
A number of chronic airway diseases are characterized by high inflammation and unbalanced activation of the immune response, which lead to tissue damage and progressive reduction of the pulmonary function. Because they are exposed to various environmental stimuli, lung cells are prone to epigenomic changes. Many genes responsible for the immune response and inflammation are tightly regulated by DNA methylation, which suggests that alteration of the epigenome in lung cells may have a considerable impact on the penetrance and/or the severity of airway diseases. A major hurdle in clinical epigenomic studies is to gather appropriate biospecimens. Herein, we show that nasal epithelial cells are suitable to analyze DNA methylation in human diseases primarily affecting the lower airway tract.
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Affiliation(s)
- Anne Bergougnoux
- Laboratory Genetics of Rare Diseases, INSERM U827, Montpellier, France
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The Contribution of the Airway Epithelial Cell to Host Defense. Mediators Inflamm 2015; 2015:463016. [PMID: 26185361 PMCID: PMC4491388 DOI: 10.1155/2015/463016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Accepted: 12/11/2014] [Indexed: 12/19/2022] Open
Abstract
In the context of cystic fibrosis, the epithelial cell has been characterized in terms of its ion transport capabilities. The ability of an epithelial cell to initiate CFTR-mediated chloride and bicarbonate transport has been recognized early as a means to regulate the thickness of the epithelial lining fluid and recently as a means to regulate the pH, thereby determining critically whether or not host defense proteins such as mucins are able to fold appropriately. This review describes how the epithelial cell senses the presence of pathogens and inflammatory conditions, which, in turn, facilitates the activation of CFTR and thus directly promotes pathogens clearance and innate immune defense on the surface of the epithelial cell. This paper summarizes functional data that describes the effect of cytokines, chemokines, infectious agents, and inflammatory conditions on the ion transport properties of the epithelial cell and relates these key properties to the molecular pathology of cystic fibrosis. Recent findings on the role of cystic fibrosis modifier genes that underscore the role of the epithelial ion transport in host defense and inflammation are discussed.
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Du K, Karp PH, Ackerley C, Zabner J, Keshavjee S, Cutz E, Yeger H. Aggregates of mutant CFTR fragments in airway epithelial cells of CF lungs: new pathologic observations. J Cyst Fibros 2014; 14:182-93. [PMID: 25453871 DOI: 10.1016/j.jcf.2014.09.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/24/2014] [Accepted: 09/25/2014] [Indexed: 01/12/2023]
Abstract
Cystic fibrosis (CF) is caused by a mutation in the CF transmembrane conductance regulator (CFTR) gene resulting in a loss of Cl(-) channel function, disrupting ion and fluid homeostasis, leading to severe lung disease with airway obstruction due to mucus plugging and inflammation. The most common CFTR mutation, F508del, occurs in 90% of patients causing the mutant CFTR protein to misfold and trigger an endoplasmic reticulum based recycling response. Despite extensive research into the pathobiology of CF lung disease, little attention has been paid to the cellular changes accounting for the pathogenesis of CF lung disease. Here we report a novel finding of intracellular retention and accumulation of a cleaved fragment of F508del CFTR in concert with autophagic like phagolysosomes in the airway epithelium of patients with F508del CFTR. Aggregates consisting of poly-ubiquitinylated fragments of only the N-terminal domain of F508del CFTR but not the full-length molecule accumulate to appreciable levels. Importantly, these undegraded intracytoplasmic aggregates representing the NT-NBD1 domain of F508del CFTR were found in ciliated, in basal, and in pulmonary neuroendocrine cells. Aggregates were found in both native lung tissues and ex-vivo primary cultures of bronchial epithelial cells from CF donors, but not in normal control lungs. Our findings present a new, heretofore, unrecognized innate CF gene related cell defect and a potential contributing factor to the pathogenesis of CF lung disease. Mutant CFTR intracytoplasmic aggregates could be analogous to the accumulation of misfolded proteins in other degenerative disorders and in pulmonary "conformational protein-associated" diseases. Consequently, potential alterations to the functional integrity of airway epithelium and regenerative capacity may represent a critical new element in the pathogenesis of CF lung disease.
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Affiliation(s)
- Kai Du
- Program in Developmental & Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada.
| | - Philip H Karp
- Department of Medicine, The Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA; Department of Molecular Physiology and Biophysics, Howard Hughes Medical Institute, The Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Cameron Ackerley
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Joseph Zabner
- Department of Medicine, The Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Shaf Keshavjee
- Division of Experimental Therapeutics - Respiratory & Critical Care, Toronto General Research Institute (TGRI), Toronto, Ontario M5G 2C4, Canada; University of Toronto, Toronto, Ontario M5S 3G3, Canada
| | - Ernest Cutz
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada; University of Toronto, Toronto, Ontario M5S 3G3, Canada
| | - Herman Yeger
- Program in Developmental & Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada; Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada; University of Toronto, Toronto, Ontario M5S 3G3, Canada.
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Keenan K, Avolio J, Rueckes-Nilges C, Tullis E, Gonska T, Naehrlich L. Nasal potential difference: Best or average result for CFTR function as diagnostic criteria for cystic fibrosis? J Cyst Fibros 2014; 14:310-6. [PMID: 25300456 DOI: 10.1016/j.jcf.2014.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 09/11/2014] [Accepted: 09/12/2014] [Indexed: 12/23/2022]
Abstract
BACKGROUND The current practice of averaging the nasal potential difference (NPD) results of right and left nostril measurements reduce inter-individual variability but may underestimate individual CFTR function. METHODS Best NPD response to Cl(-)-free and isoproterenol perfusion (=largest ΔPD(0Cl/Iso)) from the right and left nostril was compared to the average result in 13 cystic fibrosis (CF), 78 query-CF patients and 22 healthy controls from 2 cohorts. RESULTS Despite moderate to good correlation (p<0.001) between right and left measured ΔPD(0Cl/Iso), we observed large differences in some individuals. A comparison of average versus best ΔPD(0Cl/Iso) showed only moderate agreement (Giessen κ=0.538; Toronto κ=0.607). Averaging ΔPD(0Cl/Iso) showed a lower composite chloride response compared to best ΔPD(0Cl/Iso) and altered diagnostic NPD interpretation in 30 of 113 (27%) subjects. CONCLUSIONS The current practice of averaging the NPD results of right and left nostril measurements leads to an underestimation of the individual CFTR function and should be reconsidered.
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Affiliation(s)
- Katherine Keenan
- Division of Paediatric Gastroenterology, Hepatology and Nutrition, University of Toronto and Physiology and Experimental Medicine, Research Institute, the Hospital for Sick Children, Toronto, Ontario, Canada.
| | - Julie Avolio
- Division of Paediatric Gastroenterology, Hepatology and Nutrition, University of Toronto and Physiology and Experimental Medicine, Research Institute, the Hospital for Sick Children, Toronto, Ontario, Canada.
| | | | - Elizabeth Tullis
- Department of Medicine, University of Toronto and Division of Respirology and Keenan Research Centre of Li Ka Shing Knowledge Institute St. Michael's Hospital, Toronto, Ontario, Canada.
| | - Tanja Gonska
- Division of Paediatric Gastroenterology, Hepatology and Nutrition, University of Toronto and Physiology and Experimental Medicine, Research Institute, the Hospital for Sick Children, Toronto, Ontario, Canada.
| | - Lutz Naehrlich
- Department of Pediatrics, Justus-Liebig-University Giessen, Giessen, Germany.
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Bagheri-Hanson A, Nedwed S, Rueckes-Nilges C, Naehrlich L. Intestinal current measurement versus nasal potential difference measurements for diagnosis of cystic fibrosis: a case-control study. BMC Pulm Med 2014; 14:156. [PMID: 25280757 PMCID: PMC4199064 DOI: 10.1186/1471-2466-14-156] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 09/29/2014] [Indexed: 12/16/2022] Open
Abstract
Background Nasal potential difference (NPD) and intestinal current measurement (ICM) are functional CFTR tests that are used as adjunctive diagnostic tools for cystic fibrosis (CF). Smoking has a systemic negative impact on CFTR function. A diagnostic comparison between NPD and ICM and the impact of smoking on both CFTR tests has not been done. Methods The sweat chloride test, NPD, and ICM were performed in 18 patients with CF (sweat chloride >60 mmol/l), including 6 pancreatic sufficient (PS) patients, and 13 healthy controls, including 8 smokers. The NPD CFTR response to Cl-free and isoproterenol perfusion (Δ0Cl- + Iso) was compared to the ICM CFTR response to forskolin/IBMX, carbachol, and histamine (ΔIsc, forskolin/IBMX+ carbachol+histamine). Results The mean NPD CFTR response and ICM CFTR response between patients with CF and healthy controls was significantly different (p <0.001), but not between patients with CF who were PS and those who were pancreatic insufficient (PI). Smokers have a decreased CFTR response measured by NPD (p = 0.049). For ICM there is a trend towards decreased CFTR response (NS). Three healthy control smokers had NPD responses within the CF-range. In contrast to NPD, there was no overlap of the ICM response between patients with CF and controls. Conclusions ICM is superior to NPD in distinguishing between patients with CF who have a sweat chloride > 60 mmol/l and healthy controls, including smokers. Neither NPD nor ICM differentiated between patients with CF who were PS from those who were PI. Smoking has a negative impact on CFTR function in healthy controls measured by NPD and challenges the diagnostic interpretation of NPD, but not ICM. Electronic supplementary material The online version of this article (doi:10.1186/1471-2466-14-156) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Lutz Naehrlich
- Department of Pediatrics, Justus-Liebig-University Giessen, Feulgenstrasse 12, 35385 Giessen, Germany.
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Dekkers JF, van der Ent CK, Beekman JM. Novel opportunities for CFTR-targeting drug development using organoids. Rare Dis 2013; 1:e27112. [PMID: 25003014 PMCID: PMC3915567 DOI: 10.4161/rdis.27112] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 10/09/2013] [Accepted: 11/06/2013] [Indexed: 01/21/2023] Open
Abstract
Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. CFTR mutations lead to production of non-functional CFTR, reduced amounts of normal functioning CFTR or misfolded CFTR with defects in trafficking or function. For decades, CF treatment has been focused on the symptoms of CF, but pharmacotherapy using small molecules that target the basic defect of CF, the mutant CFTR protein, is now possible for a limited amount of subjects with CF. This raises the exciting possibility that the majority of people with CF may receive effective treatment targeting the different CFTR mutants in the future. We recently described a functional CFTR assay using rectal biopsies from subjects with CF that were cultured in vitro into self-organizing mini-guts or organoids. We here describe how this model may assist in the discovery of new CFTR-targeting drugs, the subjects that may benefit from these drugs, and the mechanisms underlying variability in CFTR genotype-phenotype relations.
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Affiliation(s)
- Johanna F Dekkers
- Department of Pediatric Pulmonology; University Medical Center Utrecht; Children's Hospital; Utrecht, the Netherlands ; Department of Immunology; University Medical Center Utrecht; Children's Hospital; Utrecht, the Netherlands
| | - Cornelis K van der Ent
- Department of Pediatric Pulmonology; University Medical Center Utrecht; Children's Hospital; Utrecht, the Netherlands
| | - Jeffrey M Beekman
- Department of Pediatric Pulmonology; University Medical Center Utrecht; Children's Hospital; Utrecht, the Netherlands ; Department of Immunology; University Medical Center Utrecht; Children's Hospital; Utrecht, the Netherlands
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