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Ferreira FC, Amaral MD, Bacalhau M, Lopes-Pacheco M. PTI-801 (posenacaftor) shares a common mechanism with VX-445 (elexacaftor) to rescue p.Phe508del-CFTR. Eur J Pharmacol 2024; 967:176390. [PMID: 38336013 DOI: 10.1016/j.ejphar.2024.176390] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 01/05/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024]
Abstract
The deletion of a phenylalanine at position 508 (p.Phe508del) in the CFTR anion channel is the most prevalent variant in people with Cystic Fibrosis (CF). This variant impairs folding and stability of the CF transmembrane conductance regulator (CFTR) protein, resulting in its defective trafficking and premature degradation. Over the last years, therapeutic accomplishments have been attained in developing small molecules that partially correct p.Phe508del-CFTR defects; however, the mechanism of action (MoA) of these compounds has only started to be uncovered. In this study, we employed biochemical, fluorescence microscopy, and functional assays to examine the efficacy and properties of PTI-801, a newly developed p.Phe508del-CFTR corrector. To exploit its MoA, we assessed PTI-801 effects in combination with low temperature, genetic revertants of p.Phe508del-CFTR (the in cis p.Val510Asp, p.Gly550Glu, p.Arg1070Trp, and 4RK) and other correctors. Our results demonstrated that PTI-801 rescues p.Phe508del-CFTR processing, PM trafficking, and channel function (upon agonist stimulation) with greater correction effects in combination with ABBV-2222, FDL-169, VX-661, or VX-809, but not with VX-445. Although PTI-801 exhibited no potentiator activity on low temperature- and corrector-rescued p.Phe508del-CFTR, this compound displayed similar behavior to that of VX-445 on genetic revertants. Such evidence associated with the lack of additivity when PTI-801 and VX-445 were combined indicates that they share a common binding site to correct p.Phe508del-CFTR defects. Despite the high efficacy of PTI-801 in combination with ABBV-2222, FDL-169, VX-661, or VX-809, these dual corrector combinations only partially restored p.Phe508del-CFTR conformational stability, as shown by the lower half-life of the mutant protein compared to that of WT-CFTR. In summary, PTI-801 likely shares a common MoA with VX-445 in rescuing p.Phe508del-CFTR, thus being a feasible alternative for the development of novel corrector combinations with greater capacity to rescue mutant CFTR folding and stability.
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Affiliation(s)
- Filipa C Ferreira
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016, Lisbon, Portugal
| | - Margarida D Amaral
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016, Lisbon, Portugal
| | - Mafalda Bacalhau
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016, Lisbon, Portugal
| | - Miquéias Lopes-Pacheco
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016, Lisbon, Portugal.
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2
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Pócsi M, Fejes Z, Bene Z, Nagy A, Balogh I, Amaral MD, Macek M, Nagy B. Human epididymis protein 4 (HE4) plasma concentration inversely correlates with the improvement of cystic fibrosis lung disease in p.Phe508del-CFTR homozygous cases treated with the CFTR modulator lumacaftor/ivacaftor combination. J Cyst Fibros 2023; 22:1085-1092. [PMID: 37087300 DOI: 10.1016/j.jcf.2023.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/30/2023] [Accepted: 04/06/2023] [Indexed: 04/24/2023]
Abstract
BACKGROUND We previously documented that elevated HE4 plasma concentration decreased in people with CF (pwCF) bearing the p.Gly551Asp-CFTR variant in response to CFTR modulator (CFTRm) ivacaftor (IVA), and this level was inversely correlated with the FEV1% predicted values (ppFEV1). Although the effectiveness of lumacaftor (LUM)/IVA in pwCF homozygous for the p.Phe508del-CFTR variant has been evaluated, plasma biomarkers were not used to monitor treatment efficacy thus far. METHODS Plasma HE4 concentration was examined in 68 pwCF drawn from the PROSPECT study who were homozygous for the p.Phe508del-CFTR variant before treatment and at 1, 3, 6 and 12 months after administration of LUM/IVA therapy. Plasma HE4 was correlated with ppFEV1 using their absolute and delta values. The discriminatory power of delta HE4 was evaluated for the detection of lung function improvements based on ROC-AUC analysis and multiple regression test. RESULTS HE4 plasma concentration was significantly reduced below baseline following LUM/IVA administration during the entire study period. The mean change of ppFEV1 was 2.6% (95% CI, 0.6 to 4.5) by 6 months of therapy in this sub-cohort. A significant inverse correlation between delta values of HE4 and ppFEV1 was observed especially in children with CF (r=-0.7053; p<0.0001). Delta HE4 predicted a 2.6% mean change in ppFEV1 (AUC: 0.7898 [95% CI 0.6823-0.8972]; P < 0.0001) at a cut-off value of -10.7 pmol/L. Moreover, delta HE4 independently represented the likelihood of being a responder with ≥ 5% delta ppFEV1 at 6 months (OR: 0.89, 95% CI: 0.82-0.95; P = 0.001). CONCLUSIONS Plasma HE4 level negatively correlates with lung function improvement assessed by ppFEV1 in pwCF undergoing LUM/IVA CFTRm treatment.
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Affiliation(s)
- Marianna Pócsi
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; Laki Kálmán Doctoral School, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zsolt Fejes
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zsolt Bene
- Department of Pediatrics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Attila Nagy
- Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen, Hungary
| | - István Balogh
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Margarida D Amaral
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - Milan Macek
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine of Charles University and Motol University Hospital, Prague, Czech Republic
| | - Béla Nagy
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
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Railean V, Rodrigues CS, Ramalho SS, Silva IAL, Bartosch J, Farinha CM, Pankonien I, Amaral MD. Personalized medicine: Function of CFTR variant p.Arg334Trp is rescued by currently available CFTR modulators. Front Mol Biosci 2023; 10:1155705. [PMID: 37006619 PMCID: PMC10063961 DOI: 10.3389/fmolb.2023.1155705] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
Most of the 2,100 CFTR gene variants reported to date are still unknown in terms of their disease liability in Cystic Fibrosis (CF) and their molecular and cellular mechanism that leads to CFTR dysfunction. Since some rare variants may respond to currently approved modulators, characterizing their defect and response to these drugs is essential for effective treatment of people with CF (pwCF) not eligible for the current treatment. Here, we assessed how the rare variant, p.Arg334Trp, impacts on CFTR traffic and function and its response to existing CFTR modulators. To this end, we performed the forskolin-induced swelling (FIS) assay on intestinal organoids from 10 pwCF bearing the p.Arg334Trp variant in one or both alleles of the CFTR gene. In parallel, a novel p.Arg334Trp-CFTR expressing CFBE cell line was generated to characterize the variant individually. Results show that p.Arg334Trp-CFTR does not significantly affect the plasma membrane traffic of CFTR and evidences residual CFTR function. This CFTR variant is rescued by currently available CFTR modulators independently of the variant in the second allele. The study, predicting clinical benefit for CFTR modulators in pwCF with at least one p.Arg334Trp variant, demonstrates the high potential of personalized medicine through theranostics to extend the label of approved drugs for pwCF carrying rare CFTR variants. We recommend that this personalized approach should be considered for drug reimbursement policies by health insurance systems/national health services.
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Santos L, Nascimento R, Duarte A, Railean V, Amaral MD, Harrison PT, Gama-Carvalho M, Farinha CM. Mutation-class dependent signatures outweigh disease-associated processes in cystic fibrosis cells. Cell Biosci 2023; 13:26. [PMID: 36759923 PMCID: PMC9912517 DOI: 10.1186/s13578-023-00975-y] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 01/28/2023] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND The phenotypic heterogeneity observed in Cystic Fibrosis (CF) patients suggests the involvement of other genes, besides CFTR. Here, we combined transcriptome and proteome analysis to understand the global gene expression patterns associated with five prototypical CFTR mutations. RESULTS Evaluation of differentially expressed genes and proteins unveiled common and mutation-specific changes revealing functional signatures that are much more associated with the specific molecular defects associated with each mutation than to the CFTR loss-of-function phenotype. The combination of both datasets revealed that mutation-specific detected translated-transcripts (Dtt) have a high level of consistency. CONCLUSIONS This is the first combined transcriptomic and proteomic study focusing on prototypical CFTR mutations. Analysis of Dtt provides novel insight into the pathophysiology of CF, and the mechanisms through which each mutation class causes disease and will likely contribute to the identification of new therapeutic targets and/or biomarkers for CF.
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Affiliation(s)
- Lúcia Santos
- grid.9983.b0000 0001 2181 4263BioISI – Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal ,grid.7872.a0000000123318773Department of Physiology, University College Cork, Cork, T12 K8AF Ireland
| | - Rui Nascimento
- grid.9983.b0000 0001 2181 4263BioISI – Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Aires Duarte
- grid.9983.b0000 0001 2181 4263BioISI – Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Violeta Railean
- grid.9983.b0000 0001 2181 4263BioISI – Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Margarida D. Amaral
- grid.9983.b0000 0001 2181 4263BioISI – Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Patrick T. Harrison
- grid.7872.a0000000123318773Department of Physiology, University College Cork, Cork, T12 K8AF Ireland
| | - Margarida Gama-Carvalho
- grid.9983.b0000 0001 2181 4263BioISI – Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Carlos M. Farinha
- grid.9983.b0000 0001 2181 4263BioISI – Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
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Clarke LA, Amaral MD. What Can RNA-Based Therapy Do for Monogenic Diseases? Pharmaceutics 2023; 15:pharmaceutics15010260. [PMID: 36678889 PMCID: PMC9863139 DOI: 10.3390/pharmaceutics15010260] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
The use of RNA-based approaches to treat monogenic diseases (i.e., hereditary disorders caused by mutations in single genes) has been developed on different fronts. One approach uses small antisense oligonucleotides (ASOs) to modulate RNA processing at various stages; namely, to enhance correct splicing, to stimulate exon skipping (to exclude premature termination codon variants), to avoid undesired messenger RNA (mRNA) transcript degradation via the nonsense-mediated decay (NMD) pathway, or to induce mRNA degradation where they encode toxic proteins (e.g., in dominant diseases). Another approach consists in administering mRNA, which, like gene therapy, is a mutation-agnostic approach with potential application to any recessive monogenic disease. This is simpler than gene therapy because instead of requiring targeting of the nucleus, the mRNA only needs to be delivered to the cytoplasm. Although very promising (as demonstrated by COVID-19 vaccines), these approaches still have potential for optimisation, namely regarding delivery efficiency, adverse drug reactions and toxicity.
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Bacalhau M, Ferreira FC, Silva IAL, Buarque CD, Amaral MD, Lopes-Pacheco M. Additive Potentiation of R334W-CFTR Function by Novel Small Molecules. J Pers Med 2023; 13:jpm13010102. [PMID: 36675763 PMCID: PMC9862739 DOI: 10.3390/jpm13010102] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 01/04/2023] Open
Abstract
The R334W (c.1000C>T, p.Arg334Trp) is a rare cystic fibrosis (CF)-causing mutation for which no causal therapy is currently approved. This mutation leads to a significant reduction of CF transmembrane conductance regulator (CFTR) channel conductance that still allows for residual function. Potentiators are small molecules that interact with CFTR protein at the plasma membrane to enhance CFTR-dependent chloride secretion, representing thus pharmacotherapies targeting the root cause of the disease. Here, we generated a new CF bronchial epithelial (CFBE) cell line to screen a collection of compounds and identify novel potentiators for R334W-CFTR. The active compounds were then validated by electrophysiological assays and their additive effects in combination with VX-770, genistein, or VX-445 were exploited in this cell line and further confirmed in intestinal organoids. Four compounds (LSO-24, LSO-25, LSO-38, and LSO-77) were active in the functional primary screen and their ability to enhance R334W-CFTR-dependent chloride secretion was confirmed using electrophysiological measurements. In silico ADME analyses demonstrated that these compounds follow Lipinski’s rule of five and are thus suggested to be orally bioavailable. Dose−response relationships revealed nevertheless suboptimal efficacy and weak potency exerted by these compounds. VX-770 and genistein also displayed a small potentiation of R334W-CFTR function, while VX-445 demonstrated no potentiator activity for this mutation. In the R334W-expressing cell line, CFTR function was further enhanced by the combination of LSO-24, LSO-25, LSO-38, or LSO-77 with VX-770, but not with genistein. The efficacy of potentiator VX-770 combined with active LSO compounds was further confirmed in intestinal organoids (R334W/R334W genotype). Taken together, these molecules were demonstrated to potentiate R334W-CFTR function by a different mechanism than that of VX-770. They may provide a feasible starting point for the design of analogs with improved CFTR-potentiator activity.
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Affiliation(s)
- Mafalda Bacalhau
- Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Filipa C. Ferreira
- Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Iris A. L. Silva
- Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Camilla D. Buarque
- Department of Chemistry, Pontifical Catholic University of Rio de Janeiro, Rio de Janeiro 22541-041, Brazil
| | - Margarida D. Amaral
- Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Miquéias Lopes-Pacheco
- Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
- Correspondence:
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Bacalhau M, Ferreira FC, Kmit A, Souza FR, da Silva VD, Pimentel AS, Amaral MD, Buarque CD, Lopes-Pacheco M. Identification of novel F508del-CFTR traffic correctors among triazole derivatives. Eur J Pharmacol 2022; 938:175396. [PMID: 36410419 DOI: 10.1016/j.ejphar.2022.175396] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/21/2022]
Abstract
The most prevalent cystic fibrosis (CF)-causing mutation - F508del - impairs the folding of CFTR protein, resulting in its defective trafficking and premature degradation. Small molecules termed correctors may rescue F508del-CFTR and therefore constitute promising pharmacotherapies acting on the fundamental cause of the disease. Here, we screened a collection of triazole compounds to identify novel F508del-CFTR correctors. The functional primary screen identified four hit compounds (LSO-18, LSO-24, LSO-28, and LSO-39), which were further validated and demonstrated to rescue F508del-CFTR processing, plasma membrane trafficking, and function. To interrogate their mechanism of action (MoA), we examined their additivity to the clinically approved drugs VX-661 and VX-445, low temperature, and genetic revertants of F508del-CFTR. Rescue of F508del-CFTR processing and function by LSO-18, LSO-24, and LSO-28, but not by LSO-39, was additive to VX-661, whereas LSO-28 and LSO-39, but not LSO-18 nor LSO-24, were additive to VX-445. All compounds under investigation demonstrated additive rescue of F508del-CFTR processing and function to low temperature as well as to rescue by genetic revertants G550E and 4RK. Nevertheless, none of these compounds was able to rescue processing nor function of DD/AA-CFTR, and LSO-39 (similarly to VX-661) exhibited no additivity to genetic revertant R1070W. From these findings, we suggest that LSO-39 (like VX-661) has a putative binding site at the NBD1:ICL4 interface, LSO-18 and LSO-24 seem to share the MoA with VX-445, and LSO-28 appears to act by a different MoA. Altogether, these findings represent an encouraging starting point to further exploit this chemical series for the development of novel CFTR correctors.
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Affiliation(s)
- Mafalda Bacalhau
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Filipa C Ferreira
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Arthur Kmit
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Felipe R Souza
- Department of Chemistry, Pontifical Catholic University of Rio de Janeiro (PUC-Rio), Rio de Janeiro, Brazil
| | - Verônica D da Silva
- Department of Chemistry, Pontifical Catholic University of Rio de Janeiro (PUC-Rio), Rio de Janeiro, Brazil
| | - André S Pimentel
- Department of Chemistry, Pontifical Catholic University of Rio de Janeiro (PUC-Rio), Rio de Janeiro, Brazil
| | - Margarida D Amaral
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Camilla D Buarque
- Department of Chemistry, Pontifical Catholic University of Rio de Janeiro (PUC-Rio), Rio de Janeiro, Brazil
| | - Miquéias Lopes-Pacheco
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, Lisbon, Portugal.
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Jo S, Centeio R, Park J, Ousingsawat J, Jeon DK, Talbi K, Schreiber R, Ryu K, Kahlenberg K, Somoza V, Delpiano L, Gray MA, Amaral MD, Railean V, Beekman JM, Rodenburg LW, Namkung W, Kunzelmann K. The SLC26A9 inhibitor S9-A13 provides no evidence for a role of SLC26A9 in airway chloride secretion but suggests a contribution to regulation of ASL pH and gastric proton secretion. FASEB J 2022; 36:e22534. [PMID: 36183361 DOI: 10.1096/fj.202200313rr] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 08/11/2022] [Accepted: 08/24/2022] [Indexed: 11/11/2022]
Abstract
The solute carrier 26 family member A9 (SLC26A9) is an epithelial anion transporter that is assumed to contribute to airway chloride secretion and surface hydration. Whether SLC26A9 or CFTR is responsible for airway Cl- transport under basal conditions is still unclear, due to the lack of a specific inhibitor for SLC26A9. In the present study, we report a novel potent and specific inhibitor for SLC26A9, identified by screening of a drug-like molecule library and subsequent chemical modifications. The most potent compound S9-A13 inhibited SLC26A9 with an IC50 of 90.9 ± 13.4 nM. S9-A13 did not inhibit other members of the SLC26 family and had no effects on Cl- channels such as CFTR, TMEM16A, or VRAC. S9-A13 inhibited SLC26A9 Cl- currents in cells that lack expression of CFTR. It also inhibited proton secretion by HGT-1 human gastric cells. In contrast, S9-A13 had minimal effects on ion transport in human airway epithelia and mouse trachea, despite clear expression of SLC26A9 in the apical membrane of ciliated cells. In both tissues, basal and stimulated Cl- secretion was due to CFTR, while acidification of airway surface liquid by S9-A13 suggests a role of SLC26A9 for airway bicarbonate secretion.
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Affiliation(s)
- Sungwoo Jo
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, South Korea
| | - Raquel Centeio
- Physiological Institute, University of Regensburg, Regensburg, Germany
| | - Jinhong Park
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, South Korea
| | | | - Dong-Kyu Jeon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, South Korea
| | - Khaoula Talbi
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Rainer Schreiber
- Physiological Institute, University of Regensburg, Regensburg, Germany
| | - Kunhi Ryu
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, South Korea
| | - Kristin Kahlenberg
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Veronika Somoza
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Livia Delpiano
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Michael A Gray
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Margarida D Amaral
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisbon, Portugal
| | - Violeta Railean
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisbon, Portugal
| | - Jeffrey M Beekman
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, Netherlands
| | - Lisa W Rodenburg
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, Netherlands
| | - Wan Namkung
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, South Korea
| | - Karl Kunzelmann
- Physiological Institute, University of Regensburg, Regensburg, Germany
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9
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Amaral MD. Using the genome to correct the ion transport defect in cystic fibrosis. J Physiol 2022; 601:1573-1582. [PMID: 36068724 DOI: 10.1113/jp282308] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/31/2022] [Indexed: 11/08/2022] Open
Abstract
KEY POINTS Human genome information can help finding drugs for human diseases. 'Omics' allow unbiased identification of novel drug targets. High-throughput (HT) approaches provide a global view on disease mechanisms. As a monogenic disease CF has led the way in multiple 'Omic' studies. 'Multi-omics' integration will generate maximal biological significance. ABSTRACT Today Biomedicine faces one of its greatest challenges, i.e. treating diseases through their causative dysfunctional processes and not just their symptoms. However, we still miss a global view of mechanisms and pathways involved in pathophysiology of most diseases. In fact, disease mechanisms and pathways can be achieved by holistic studies provided by 'Omic' approaches. Cystic Fibrosis (CF), caused by mutations in the CF transmembrane conductance regulator (CFTR) gene which encodes an anion channel, is paradigmatic for monogenic disorders, namely channelopathies. A high number of 'omics studies' have focussed on CF, namely several cell-based high-throughput (HT) approaches were developed and applied towards a global mechanistic characterization of CF pathophysiology and the identification of novel and 'unbiased' drug targets. Notwithstanding, it is likely that, through the integration of all these 'layers' of large datasets into comprehensive disease maps that biological significance can be extracted so that the enormous potential of these approaches to identifying dysfunctional mechanisms and novel drugs may become a reality. Abstract figure legend Schematic overview of the 3 main approaches to discovery of new drugs/drug targets. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Margarida D Amaral
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande-C8 bdg, Lisboa, 1749-016, Portugal
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10
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Quaresma MC, Botelho HM, Pankonien I, Rodrigues CS, Pinto MC, Costa PR, Duarte A, Amaral MD. Exploring YAP1-centered networks linking dysfunctional CFTR to epithelial-mesenchymal transition. Life Sci Alliance 2022; 5:5/9/e202101326. [PMID: 35500936 PMCID: PMC9060002 DOI: 10.26508/lsa.202101326] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 04/20/2022] [Accepted: 04/20/2022] [Indexed: 12/21/2022] Open
Abstract
In this work, a systems biology approach identifies potentially dysregulated EMT signaling in CF (including the Hippo, Wnt, TGF-β, p53, and MYC pathways), integrated by YAP1 and TEAD4. Mutations in the CFTR anion channel cause cystic fibrosis (CF) and have also been related to higher cancer incidence. Previously we proposed that this is linked to an emerging role of functional CFTR in protecting against epithelial–mesenchymal transition (EMT). However, the pathways bridging dysfunctional CFTR to EMT remain elusive. Here, we applied systems biology to address this question. Our data show that YAP1 is aberrantly active in the presence of mutant CFTR, interacting with F508del, but not with wt-CFTR, and that YAP1 knockdown rescues F508del-CFTR processing and function. Subsequent analysis of YAP1 interactors and roles in cells expressing either wt- or F508del-CFTR reveal that YAP1 is an important mediator of the fibrotic/EMT processes in CF. Alongside, five main pathways emerge here as key in linking mutant CFTR to EMT, namely, (1) the Hippo pathway; (2) the Wnt pathway; (3) the TGFβ pathway; (4) the p53 pathway; and (5) MYC signaling. Several potential hub proteins which mediate the crosstalk among these pathways were also identified, appearing as potential therapeutic targets for both CF and cancer.
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Affiliation(s)
- Margarida C Quaresma
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - Hugo M Botelho
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - Ines Pankonien
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - Cláudia S Rodrigues
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - Madalena C Pinto
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - Pau R Costa
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - Aires Duarte
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - Margarida D Amaral
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisboa, Portugal
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11
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Amaral MD. Precision medicine for rare diseases: The times they are A-Changin'. Curr Opin Pharmacol 2022; 63:102201. [DOI: 10.1016/j.coph.2022.102201] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/26/2022] [Accepted: 01/31/2022] [Indexed: 12/30/2022]
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12
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Roda J, Teixeira T, Ai Silva I, Silva TR, Ferreira R, Amaral MD, Oliveira G. Pediatric population with cystic fibrosis in the centre of Portugal: candidates for new therapies. J Pediatr (Rio J) 2022; 98:212-217. [PMID: 34252371 PMCID: PMC9432345 DOI: 10.1016/j.jped.2021.05.010] [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] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVES Cystic fibrosis (CF) is a severe autosomal recessive disease that results from mutations in a gene encoding the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein, a chloride channel. This study aims to characterize the clinical and genetic features of a cohort of pediatric people with CF (PwCF) in the center of Portugal and to determine which ones are candidates for the new drugs modulating the CFTR channel. METHODS A review of the demographic, genetic and clinical characteristics of PwCF undergoing follow-up at a CF reference center was carried out. RESULTS Twenty-three PwCF (12 male), with a median age of 12 years, were followed up. All patients carry the F508del mutation in at least one allele. Fifteen PwCF were F508del-homozygous, median BMI z-score was -0.13, all are pancreatic insufficient and median FEV1 value was 78.1%. These PwCF are eligible for dual therapy (lumacaftor/tezacaftor+ivacaftor) and for triple therapy (tezacaftor+ivacaftor+elexacaftor). PwCF with 711 +1G->T (n = 2), 2184insA (n = 1) mutations and a novel mutation c.3321dup (n = 1) have minimal function mutation and patients with a residual function mutation: R334W (n = 3) and P5L (n = 1) have a less severe phenotype. All these patients, because they also carry F508del mutation, are elegible to triple therapy. CONCLUSIONS Genetic and molecular characterization of PwCF poses an important step not just for CF diagnosis and prognosis which is tightly correlated with the clinical phenotype, but also for the eligibility of CFTR modulator drugs.
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Affiliation(s)
- Juliana Roda
- Centro Hospitalar e Universitário de Coimbra, Hospital Pediátrico, Unidade de Gastroenterologia e Nutrição Pediátrica, Coimbra, Portugal; Faculdade de Medicina da Universidade de Coimbra, Clínica Universitária de Pediatria, Coimbra, Portugal.
| | - Teresa Teixeira
- Faculdade de Medicina da Universidade de Coimbra, Clínica Universitária de Pediatria, Coimbra, Portugal
| | - Iris Ai Silva
- Universidade de Lisboa, Faculdade de Ciências, Instituto de Biossistemas e Ciências Integrativas (BioISI), Lisbon, Portugal
| | - Teresa Reis Silva
- Centro Hospitalar e Universitário de Coimbra, Centro de Referência em Fibrose Cística, Unidade Pediátrica, Coimbra, Portugal
| | - Ricardo Ferreira
- Centro Hospitalar e Universitário de Coimbra, Hospital Pediátrico, Unidade de Gastroenterologia e Nutrição Pediátrica, Coimbra, Portugal
| | - Margarida D Amaral
- Universidade de Lisboa, Faculdade de Ciências, Instituto de Biossistemas e Ciências Integrativas (BioISI), Lisbon, Portugal
| | - Guiomar Oliveira
- Faculdade de Medicina da Universidade de Coimbra, Clínica Universitária de Pediatria, Coimbra, Portugal; Centro Hospitalar e Universitário de Coimbra, Centro de Desenvolvimento da Criança e Centro de Investigação e Formação Clínica, Hospital Pediátrico, Coimbra, Portugal
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13
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Pankonien I, Quaresma MC, Rodrigues CS, Amaral MD. CFTR, Cell Junctions and the Cytoskeleton. Int J Mol Sci 2022; 23:ijms23052688. [PMID: 35269829 PMCID: PMC8910340 DOI: 10.3390/ijms23052688] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 02/25/2022] [Accepted: 02/27/2022] [Indexed: 02/05/2023] Open
Abstract
The multi-organ disease cystic fibrosis (CF) is caused by mutations in the gene encoding the CF transmembrane conductance regulator (CFTR) protein, a cAMP regulated chloride (Cl−) and bicarbonate (HCO3−) ion channel expressed at the apical plasma membrane (PM) of epithelial cells. Reduced CFTR protein results in decreased Cl− secretion and excessive sodium reabsorption in epithelial cells, which consequently leads to epithelial dehydration and the accumulation of thick mucus within the affected organs, such as the lungs, pancreas, gastrointestinal (GI) tract, reproductive system and sweat glands. However, CFTR has been implicated in other functions besides transporting ions across epithelia. The rising number of references concerning its association to actin cytoskeleton organization, epithelial cell junctions and extracellular matrix (ECM) proteins suggests a role in the formation and maintenance of epithelial apical basolateral polarity. This review will focus on recent literature (the last 10 years) substantiating the role of CFTR in cell junction formation and actin cytoskeleton organization with its connection to the ECM.
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14
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Lim SH, Snider J, Birimberg‐Schwartz L, Ip W, Serralha JC, Botelho HM, Lopes‐Pacheco M, Pinto MC, Moutaoufik MT, Zilocchi M, Laselva O, Esmaeili M, Kotlyar M, Lyakisheva A, Tang P, López Vázquez L, Akula I, Aboualizadeh F, Wong V, Grozavu I, Opacak‐Bernardi T, Yao Z, Mendoza M, Babu M, Jurisica I, Gonska T, Bear CE, Amaral MD, Stagljar I. CFTR interactome mapping using the mammalian membrane two‐hybrid high‐throughput screening system. Mol Syst Biol 2022; 18:e10629. [PMID: 35156780 PMCID: PMC8842165 DOI: 10.15252/msb.202110629] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/16/2022] [Accepted: 01/19/2022] [Indexed: 12/19/2022] Open
Abstract
Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) is a chloride and bicarbonate channel in secretory epithelia with a critical role in maintaining fluid homeostasis. Mutations in CFTR are associated with Cystic Fibrosis (CF), the most common lethal autosomal recessive disorder in Caucasians. While remarkable treatment advances have been made recently in the form of modulator drugs directly rescuing CFTR dysfunction, there is still considerable scope for improvement of therapeutic effectiveness. Here, we report the application of a high‐throughput screening variant of the Mammalian Membrane Two‐Hybrid (MaMTH‐HTS) to map the protein–protein interactions of wild‐type (wt) and mutant CFTR (F508del), in an effort to better understand CF cellular effects and identify new drug targets for patient‐specific treatments. Combined with functional validation in multiple disease models, we have uncovered candidate proteins with potential roles in CFTR function/CF pathophysiology, including Fibrinogen Like 2 (FGL2), which we demonstrate in patient‐derived intestinal organoids has a significant effect on CFTR functional expression.
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Affiliation(s)
- Sang Hyun Lim
- Donnelly Centre University of Toronto Toronto ON Canada
- Department of Biochemistry University of Toronto Toronto ON Canada
| | - Jamie Snider
- Donnelly Centre University of Toronto Toronto ON Canada
| | - Liron Birimberg‐Schwartz
- Programme in Translational Medicine The Hospital for Sick Children Toronto ON Canada
- Division of Gastroenterology, Hepatology and Nutrition Department of Pediatrics University of Toronto Toronto ON Canada
| | - Wan Ip
- Programme in Translational Medicine The Hospital for Sick Children Toronto ON Canada
| | - Joana C Serralha
- Faculty of Sciences BioISI‐Biosystems and Integrative Sciences Institute University of Lisboa Lisboa Portugal
- Faculty of Life Sciences and Medicine School of Bioscience Education King’s College London London UK
| | - Hugo M Botelho
- Faculty of Sciences BioISI‐Biosystems and Integrative Sciences Institute University of Lisboa Lisboa Portugal
| | - Miquéias Lopes‐Pacheco
- Faculty of Sciences BioISI‐Biosystems and Integrative Sciences Institute University of Lisboa Lisboa Portugal
| | - Madalena C Pinto
- Faculty of Sciences BioISI‐Biosystems and Integrative Sciences Institute University of Lisboa Lisboa Portugal
| | - Mohamed Taha Moutaoufik
- Department of Biochemistry, Research and Innovation Centre University of Regina Regina SK Canada
| | - Mara Zilocchi
- Department of Biochemistry, Research and Innovation Centre University of Regina Regina SK Canada
| | - Onofrio Laselva
- Department of Physiology University of Toronto Toronto ON Canada
| | - Mohsen Esmaeili
- Program in Genetics and Genome Biology The Hospital for Sick Children Toronto ON Canada
| | - Max Kotlyar
- Osteoarthritis Research Program Division of Orthopedic Surgery Schroeder Arthritis Institute University Health Network Toronto ON Canada
- Data Science Discovery Centre for Chronic Diseases Krembil Research Institute University Health Network Toronto ON Canada
| | | | | | | | - Indira Akula
- Donnelly Centre University of Toronto Toronto ON Canada
| | | | - Victoria Wong
- Donnelly Centre University of Toronto Toronto ON Canada
| | - Ingrid Grozavu
- Donnelly Centre University of Toronto Toronto ON Canada
- Department of Biochemistry University of Toronto Toronto ON Canada
| | | | - Zhong Yao
- Donnelly Centre University of Toronto Toronto ON Canada
| | - Meg Mendoza
- Department of Molecular Genetics University of Toronto Toronto ON Canada
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Centre University of Regina Regina SK Canada
| | - Igor Jurisica
- Osteoarthritis Research Program Division of Orthopedic Surgery Schroeder Arthritis Institute University Health Network Toronto ON Canada
- Data Science Discovery Centre for Chronic Diseases Krembil Research Institute University Health Network Toronto ON Canada
- Departments of Medical Biophysics and Computer Science University of Toronto Toronto ON Canada
- Institute of Neuroimmunology Slovak Academy of Sciences Bratislava Slovakia
| | - Tanja Gonska
- Programme in Translational Medicine The Hospital for Sick Children Toronto ON Canada
- Division of Gastroenterology, Hepatology and Nutrition Department of Pediatrics University of Toronto Toronto ON Canada
| | - Christine E Bear
- Department of Biochemistry University of Toronto Toronto ON Canada
- Department of Physiology University of Toronto Toronto ON Canada
| | - Margarida D Amaral
- Faculty of Sciences BioISI‐Biosystems and Integrative Sciences Institute University of Lisboa Lisboa Portugal
| | - Igor Stagljar
- Donnelly Centre University of Toronto Toronto ON Canada
- Department of Biochemistry University of Toronto Toronto ON Canada
- Department of Molecular Genetics University of Toronto Toronto ON Canada
- Mediterranean Institute for Life Sciences Split Croatia
- School of Medicine University of Split Split Croatia
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15
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Pinto MC, Botelho HM, Silva IAL, Railean V, Neumann B, Pepperkok R, Schreiber R, Kunzelmann K, Amaral MD. Systems Approaches to Unravel Molecular Function: High-content siRNA Screen Identifies TMEM16A Traffic Regulators as Potential Drug Targets for Cystic Fibrosis. J Mol Biol 2022; 434:167436. [PMID: 34990652 DOI: 10.1016/j.jmb.2021.167436] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/28/2021] [Accepted: 12/28/2021] [Indexed: 11/25/2022]
Abstract
An attractive approach to treat people with Cystic Fibrosis (CF), a life-shortening disease caused by mutant CFTR, is to compensate for the absence of this chloride/bicarbonate channel by activating alternative (non-CFTR) chloride channels. One obvious target for such "mutation-agnostic" therapeutic approach is TMEM16A (anoctamin-1/ANO1), a calcium-activated chloride channel (CaCC) which is also expressed in the airways of people with CF, albeit at low levels. To find novel TMEM16A regulators of both traffic and function, with the main goal of identifying candidate CF drug targets, we performed a fluorescence cell-based high-throughput siRNA microscopy screen for TMEM16A trafficking using a double-tagged construct expressed in human airway cells. About 700 genes were screened (2 siRNAs per gene) of which 262 were identified as candidate TMEM16A modulators (179 siRNAs enhanced and 83 decreased TMEM16A traffic), being G-protein coupled receptors (GPCRs) enriched on the primary hit list. Among the 179 TMEM16A traffic enhancer siRNAs subjected to secondary screening 20 were functionally validated. Further hit validation revealed that siRNAs targeting two GPCRs - ADRA2C and CXCR3 - increased TMEM16A-mediated chloride secretion in human airway cells, while their overexpression strongly diminished calcium-activated chloride currents in the same cell model. The knockdown, and likely also the inhibition, of these two TMEM16A modulators is therefore an attractive potential therapeutic strategy to increase chloride secretion in CF.
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Affiliation(s)
- Madalena C Pinto
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal. https://twitter.com/madalenacfpinto
| | - Hugo M Botelho
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Iris A L Silva
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Violeta Railean
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Beate Neumann
- Cell Biology/Biophysics Unit, and ALMF, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Rainer Pepperkok
- Cell Biology/Biophysics Unit, and ALMF, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Rainer Schreiber
- Institut für Physiologie, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Karl Kunzelmann
- Institut für Physiologie, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Margarida D Amaral
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal.
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16
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Simões FB, Kmit A, Amaral MD. Cross-talk of inflammatory mediators and airway epithelium reveals the cystic fibrosis transmembrane conductance regulator as a major target. ERJ Open Res 2021; 7:00247-2021. [PMID: 34912883 PMCID: PMC8666577 DOI: 10.1183/23120541.00247-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/13/2021] [Indexed: 11/05/2022] Open
Abstract
Airway inflammation, mucus hyperproduction and epithelial remodelling are hallmarks of many chronic airway diseases, including asthma, COPD and cystic fibrosis. While several cytokines are dysregulated in these diseases, most studies focus on the response of airways to interleukin (IL)-4 and IL-13, which have been shown to induce mucus hyperproduction and shift the airway epithelium towards a hypersecretory phenotype. We hypothesised that other cytokines might induce the expression of chloride (Cl-) channels/transporters, and regulate epithelial differentiation and mucus production. To this end, fully differentiated human airway basal cells (BCi-NS1.1) were treated with cytokines identified as dysregulated in those diseases, namely IL-8, IL-1β, IL-4, IL-17A, IL-10 and IL-22, and tumour necrosis factor-α. Our results show that the cystic fibrosis transmembrane conductance regulator (CFTR) is the main Cl- channel modulated by inflammation, in contrast to transmembrane protein 16A (TMEM16A), whose levels only changed with IL-4. Furthermore, we identified novel roles for IL-10 and IL-22 by influencing epithelial differentiation towards ciliated cells and away from pulmonary ionocytes. In contrast, IL-1β and IL-4 reduced the number of ciliated cells while increasing club cells. Interestingly, while IL-1β, IL-4 and IL-10 upregulated CFTR expression, IL-4 was the only cytokine that increased both its function and the number of CFTR-expressing club cells, suggesting that this cell type may be the main contributor for CFTR function. Additionally, all cytokines assessed increased mucus production through a differential upregulation of MUC5AC and MUC5B transcript levels. This study reveals a novel insight into differentiation resulting from the cross-talk of inflammatory mediators and airway epithelial cells, which is particularly relevant for chronic airway diseases.
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Affiliation(s)
- Filipa B Simões
- Faculty of Sciences, University of Lisbon, BioISI - Biosystems and Integrative Sciences Institute, Lisbon, Portugal
| | - Arthur Kmit
- Faculty of Sciences, University of Lisbon, BioISI - Biosystems and Integrative Sciences Institute, Lisbon, Portugal
| | - Margarida D Amaral
- Faculty of Sciences, University of Lisbon, BioISI - Biosystems and Integrative Sciences Institute, Lisbon, Portugal
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17
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Pereira C, Mazein A, Farinha CM, Gray MA, Kunzelmann K, Ostaszewski M, Balaur I, Amaral MD, Falcao AO. CyFi-MAP: an interactive pathway-based resource for cystic fibrosis. Sci Rep 2021; 11:22223. [PMID: 34782688 PMCID: PMC8592983 DOI: 10.1038/s41598-021-01618-3] [Citation(s) in RCA: 3] [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: 07/28/2021] [Accepted: 10/27/2021] [Indexed: 12/11/2022] Open
Abstract
Cystic fibrosis (CF) is a life-threatening autosomal recessive disease caused by more than 2100 mutations in the CF transmembrane conductance regulator (CFTR) gene, generating variability in disease severity among individuals with CF sharing the same CFTR genotype. Systems biology can assist in the collection and visualization of CF data to extract additional biological significance and find novel therapeutic targets. Here, we present the CyFi-MAP-a disease map repository of CFTR molecular mechanisms and pathways involved in CF. Specifically, we represented the wild-type (wt-CFTR) and the F508del associated processes (F508del-CFTR) in separate submaps, with pathways related to protein biosynthesis, endoplasmic reticulum retention, export, activation/inactivation of channel function, and recycling/degradation after endocytosis. CyFi-MAP is an open-access resource with specific, curated and continuously updated information on CFTR-related pathways available online at https://cysticfibrosismap.github.io/ . This tool was developed as a reference CF pathway data repository to be continuously updated and used worldwide in CF research.
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Affiliation(s)
- Catarina Pereira
- Faculty of Sciences, BioISI-Biosystems Integrative Sciences Institute, University of Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
- LASIGE, Faculty of Sciences, University of Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Alexander Mazein
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, 4367, Belvaux, Luxembourg
- CIRI UMR5308, CNRS-ENS-UCBL-INSERM, European Institute for Systems Biology and Medicine, Université de Lyon, 50 Avenue Tony Garnier, 69007, Lyon, France
| | - Carlos M Farinha
- Faculty of Sciences, BioISI-Biosystems Integrative Sciences Institute, University of Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Michael A Gray
- Biosciences Institute, University Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | | | - Marek Ostaszewski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, 4367, Belvaux, Luxembourg
| | - Irina Balaur
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, 4367, Belvaux, Luxembourg
- CIRI UMR5308, CNRS-ENS-UCBL-INSERM, European Institute for Systems Biology and Medicine, Université de Lyon, 50 Avenue Tony Garnier, 69007, Lyon, France
| | - Margarida D Amaral
- Faculty of Sciences, BioISI-Biosystems Integrative Sciences Institute, University of Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Andre O Falcao
- Faculty of Sciences, BioISI-Biosystems Integrative Sciences Institute, University of Lisboa, Campo Grande, 1749-016, Lisbon, Portugal.
- LASIGE, Faculty of Sciences, University of Lisboa, Campo Grande, 1749-016, Lisbon, Portugal.
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18
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Pinto MC, Silva IAL, Figueira MF, Amaral MD, Lopes-Pacheco M. Pharmacological Modulation of Ion Channels for the Treatment of Cystic Fibrosis. J Exp Pharmacol 2021; 13:693-723. [PMID: 34326672 PMCID: PMC8316759 DOI: 10.2147/jep.s255377] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/30/2021] [Indexed: 12/12/2022] Open
Abstract
Cystic fibrosis (CF) is a life-shortening monogenic disease caused by mutations in the gene encoding the CF transmembrane conductance regulator (CFTR) protein, an anion channel that transports chloride and bicarbonate across epithelia. Despite clinical progress in delaying disease progression with symptomatic therapies, these individuals still develop various chronic complications in lungs and other organs, which significantly restricts their life expectancy and quality of life. The development of high-throughput assays to screen drug-like compound libraries have enabled the discovery of highly effective CFTR modulator therapies. These novel therapies target the primary defect underlying CF and are now approved for clinical use for individuals with specific CF genotypes. However, the clinically approved modulators only partially reverse CFTR dysfunction and there is still a considerable number of individuals with CF carrying rare CFTR mutations who remain without any effective CFTR modulator therapy. Accordingly, additional efforts have been pursued to identify novel and more potent CFTR modulators that may benefit a larger CF population. The use of ex vivo individual-derived specimens has also become a powerful tool to evaluate novel drugs and predict their effectiveness in a personalized medicine approach. In addition to CFTR modulators, pro-drugs aiming at modulating alternative ion channels/transporters are under development to compensate for the lack of CFTR function. These therapies may restore normal mucociliary clearance through a mutation-agnostic approach (ie, independent of CFTR mutation) and include inhibitors of the epithelial sodium channel (ENaC), modulators of the calcium-activated channel transmembrane 16A (TMEM16, or anoctamin 1) or of the solute carrier family 26A member 9 (SLC26A9), and anionophores. The present review focuses on recent progress and challenges for the development of ion channel/transporter-modulating drugs for the treatment of CF.
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Affiliation(s)
- Madalena C Pinto
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - Iris A L Silva
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - Miriam F Figueira
- Marsico Lung Institute/Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Margarida D Amaral
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - Miquéias Lopes-Pacheco
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
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Silva IAL, Railean V, Duarte A, Amaral MD. Personalized Medicine Based on Nasal Epithelial Cells: Comparative Studies with Rectal Biopsies and Intestinal Organoids. J Pers Med 2021; 11:421. [PMID: 34065744 PMCID: PMC8156700 DOI: 10.3390/jpm11050421] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/09/2021] [Accepted: 05/12/2021] [Indexed: 12/20/2022] Open
Abstract
As highly effective CFTR modulator therapies (HEMT) emerge, there is an unmet need to find effective drugs for people with CF (PwCF) with ultra-rare mutations who are too few for classical clinical trials and for whom there are no drug discovery programs. Therefore, biomarkers reliably predicting the benefit from CFTR modulator therapies are essential to find effective drugs for PwCF through personalized approaches termed theranostics. Here, we assess CFTR basal function and the individual responses to CFTR modulators in primary human nasal epithelial (pHNE) cells from PwCF carrying rare mutations and compare these measurements with those in native rectal biopsies and intestinal organoids, respectively, in the same individual. The basal function in pHNEs shows good correlation with CFTR basal function in rectal biopsies. In parallel, CFTR rescue in pHNEs by CFTR modulators correlates to that in intestinal organoids. Altogether, results show that pHNEs are a bona fide theranostic model to assess CFTR rescue by CFTR modulator drugs, in particular for PwCF and rare mutations.
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Affiliation(s)
| | | | | | - Margarida D. Amaral
- BioISI—Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal; (I.A.L.S.); (V.R.); (A.D.)
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20
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Bene Z, Fejes Z, Szanto TG, Fenyvesi F, Váradi J, Clarke LA, Panyi G, Macek M, Amaral MD, Balogh I, Nagy B. Enhanced Expression of Human Epididymis Protein 4 (HE4) Reflecting Pro-Inflammatory Status Is Regulated by CFTR in Cystic Fibrosis Bronchial Epithelial Cells. Front Pharmacol 2021; 12:592184. [PMID: 34054511 PMCID: PMC8160512 DOI: 10.3389/fphar.2021.592184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 04/16/2021] [Indexed: 12/18/2022] Open
Abstract
Decreased human epididymis protein 4 (HE4) plasma levels were reported in cystic fibrosis (CF) patients under CFTR potentiator ivacaftor therapy, which inversely correlated with lung function improvement. In this study, we investigated whether HE4 expression was affected via modulation of CFTR function in CF bronchial epithelial (CFBE) cells in vitro. HE4 protein levels were measured in the supernatants of CFBE 41o− cells expressing F508del-CFTR or wild-type CFTR (wt-CFTR) after administration of lumacaftor/ivacaftor or tezacaftor/ivacaftor, while HE4 expression in CFBE 41o− cells were also analyzed following application of adenylate cyclase activators Forskolin/IBMX or CFTRinh172. The effect of all of these compounds on CFTR function was monitored by the whole-cell patch-clamp technique. Induced HE4 expression was studied with interleukin-6 (IL-6) in F508del-CFTR CFBE 41o− cells under TNF-α stimulation for 1 h up to 1 week in duration. In parallel, plasma HE4 was determined in CF subjects homozygous for p.Phe508del-CFTR mutation receiving lumacaftor/ivacaftor (Orkambi®) therapy. NF-κB-mediated signaling was observed via the nuclear translocation of p65 subunit by fluorescence microscopy together with the analysis of IL-6 expression by an immunoassay. In addition, HE4 expression was examined after NF-κB pathway inhibitor BAY 11-7082 treatment with or without CFTR modulators. CFTR modulators partially restored the activity of F508del-CFTR and reduced HE4 concentration was found in F508del-CFTR CFBE 41o− cells that was close to what we observed in CFBE 41o− cells with wt-CFTR. These data were in agreement with decreased plasma HE4 concentrations in CF patients treated with Orkambi®. Furthermore, CFTR inhibitor induced elevated HE4 levels, while CFTR activator Forskolin/IBMX downregulated HE4 in the cell cultures and these effects were more pronounced in the presence of CFTR modulators. Higher activation level of baseline and TNF-α stimulated NF-κB pathway was detected in F508del-CFTR vs. wt-CFTR CFBE 41o− cells that was substantially reduced by CFTR modulators based on lower p65 nuclear positivity and IL-6 levels. Finally, HE4 expression was upregulated by TNF-α with elevated IL-6, and both protein levels were suppressed by combined administration of NF-κB pathway inhibitor and CFTR modulators in CFBE 41o− cells. In conclusion, CFTR dysfunction contributes to abnormal HE4 expression via NF-κB in CF.
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Affiliation(s)
- Zsolt Bene
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Department of Pediatrics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Kálmán Laki Doctoral School of Biomedical and Clinical Sciences, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zsolt Fejes
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Kálmán Laki Doctoral School of Biomedical and Clinical Sciences, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Tibor Gabor Szanto
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Ferenc Fenyvesi
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Debrecen, Debrecen, Hungary
| | - Judit Váradi
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Debrecen, Debrecen, Hungary
| | - Luka A Clarke
- Faculty of Sciences, BioISI-Biosystems and Integrative Sciences Institute, University of Lisboa, Lisboa, Portugal
| | - Gyorgy Panyi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Milan Macek
- Department of Biology and Medical Genetics, Charles University-2nd Faculty of Medicine and Motol University Hospital, Prague, Czech
| | - Margarida D Amaral
- Faculty of Sciences, BioISI-Biosystems and Integrative Sciences Institute, University of Lisboa, Lisboa, Portugal
| | - István Balogh
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Béla Nagy
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Kálmán Laki Doctoral School of Biomedical and Clinical Sciences, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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21
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Hagemeijer MC, Vonk AM, Awatade NT, Silva IAL, Tischer C, Hilsenstein V, Beekman JM, Amaral MD, Botelho HM. An open-source high-content analysis workflow for CFTR function measurements using the forskolin-induced swelling assay. Bioinformatics 2020; 36:5686-5694. [PMID: 33367496 DOI: 10.1093/bioinformatics/btaa1073] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 11/13/2020] [Accepted: 12/14/2020] [Indexed: 01/20/2023] Open
Abstract
MOTIVATION The forskolin-induced swelling (FIS) assay has become the preferential assay to predict the efficacy of approved and investigational CFTR-modulating drugs for individuals with cystic fibrosis (CF). Currently, no standardized quantification method of FIS data exists thereby hampering inter-laboratory reproducibility. RESULTS We developed a complete open-source workflow for standardized high-content analysis of CFTR function measurements in intestinal organoids using raw microscopy images as input. The workflow includes tools for (i) file and metadata handling; (ii) image quantification and (iii) statistical analysis. Our workflow reproduced results generated by published proprietary analysis protocols and enables standardized CFTR function measurements in CF organoids. AVAILABILITY All workflow components are open-source and freely available: the htmrenamer R package for file handling https://github.com/hmbotelho/htmrenamer; CellProfiler and ImageJ analysis scripts/pipelines https://github.com/hmbotelho/FIS_image_analysis; the Organoid Analyst application for statistical analysis https://github.com/hmbotelho/organoid_analyst; detailed usage instructions and a demonstration dataset https://github.com/hmbotelho/FIS_analysis. Distributed under GPL v3.0. SUPPLEMENTARY INFORMATION Supplementary information and a stepwise guide for software installation and data analysis for training purposes are available at Bioinformatics online.
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Affiliation(s)
- Marne C Hagemeijer
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands; Regenerative Medicine Center Utrecht, University Medical Centre Utrecht, 3584 EA, Utrecht, The Netherlands.,Department of Clinical Genetics, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Annelotte M Vonk
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands; Regenerative Medicine Center Utrecht, University Medical Centre Utrecht, 3584 EA, Utrecht, The Netherlands
| | - Nikhil T Awatade
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal.,>School of Women's & Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Iris A L Silva
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
| | - Christian Tischer
- European Molecular Biology Laboratory (EMBL), Centre for Bioimage Analysis (CBA), 69117, Heidelberg, Germany
| | - Volker Hilsenstein
- European Molecular Biology Laboratory (EMBL), Advanced Light Microscopy Facility (ALMF), 69117, Heidelberg, Germany.,Monash Micro Imaging, Monash University, Melbourne, Australia
| | - Jeffrey M Beekman
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands; Regenerative Medicine Center Utrecht, University Medical Centre Utrecht, 3584 EA, Utrecht, The Netherlands
| | - Margarida D Amaral
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
| | - Hugo M Botelho
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
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22
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Silva IAL, Duarte A, Marson FAL, Centeio R, Doušová T, Kunzelmann K, Amaral MD. Assessment of Distinct Electrophysiological Parameters in Rectal Biopsies for the Choice of the Best Diagnosis/Prognosis Biomarkers for Cystic Fibrosis. Front Physiol 2020; 11:604580. [PMID: 33424627 PMCID: PMC7786280 DOI: 10.3389/fphys.2020.604580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/07/2020] [Indexed: 12/11/2022] Open
Abstract
Most cases of Cystic Fibrosis (CF) are diagnosed early in life. However, people with atypical CF forms pose diagnosis dilemmas, requiring laboratory support for diagnosis confirmation/exclusion. Ex vivo analysis of fresh rectal biopsies by Ussing chamber has been the best discriminant biomarker for CF diagnosis/prognosis so far. Here we aimed to evaluate different electrophysiological parameters from Ussing chamber analysis of rectal biopsies from people with CF (PwCF) to establish the one with highest correlations with clinical features as the best CF diagnosis/prognosis biomarker. We analyzed measurements of CFTR-mediated Cl- secretion in rectal biopsies from 143 individuals (∼592 biopsies), the largest cohort so far analyzed by this approach. New parameters were analyzed and compared with the previous biomarker, i.e., the IBMX (I)/Forskolin (F)/Carbachol (C)-stimulated short-circuit current (I'sc-I/F/C). Correlations with clinical features showed that the best parameter corresponded to voltage measurements of the I/F + (I/F/CCH) response (VI/F+I/F/C), with higher correlations vs. I'sc-I/F/C for: sweat chloride (59 vs. 52%), fecal elastase (69 vs. 55%) and lung function, measured by FEV1 (27 vs. 20%). Altogether data show that VI/F+I/F/C is the most sensitive, reproducible, and robust predictive biomarker for CF diagnosis/prognosis effectively discriminating classical, atypical CF and non-CF groups.
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Affiliation(s)
- Iris A. L. Silva
- BioISI – Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Aires Duarte
- BioISI – Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Fernando A. L. Marson
- BioISI – Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
- Laboratory of Cell and Molecular Tumor Biology and Bioactive Compounds, São Francisco University, Bragança Paulista, Brazil
- Laboratory of Human and Medical Genetics, São Francisco University, Bragança Paulista, Brazil
| | - Raquel Centeio
- BioISI – Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
- Institut für Physiologie, Universität Regensburg, Regensburg, Germany
| | - Tereza Doušová
- BioISI – Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
- Department of Paediatrics, 2nd Faculty of Medicine, Motol University Hospital, Charles University, Prague, Czechia
| | - Karl Kunzelmann
- Institut für Physiologie, Universität Regensburg, Regensburg, Germany
| | - Margarida D. Amaral
- BioISI – Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
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23
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Amaral MD. How to determine the mechanism of action of CFTR modulator compounds: A gateway to theranostics. Eur J Med Chem 2020; 210:112989. [PMID: 33190956 DOI: 10.1016/j.ejmech.2020.112989] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/02/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022]
Abstract
The greatest challenge of 21st century biology is to fully understand mechanisms of disease to drive new approaches and medical innovation. Parallel to this is the huge biomedical endeavour of treating people through personalized medicine. Until now all CFTR modulator drugs that have entered clinical trials have been genotype-dependent. An emerging alternative is personalized/precision medicine in CF, i.e., to determine whether rare CFTR mutations respond to existing (or novel) CFTR modulator drugs by pre-assessing them directly on patient's tissues ex vivo, an approach also now termed theranostics. To administer the right drug to the right person it is essential to understand how drugs work, i.e., to know their mechanism of action (MoA), so as to predict their applicability, not just in certain mutations but also possibly in other diseases that share the same defect/defective pathway. Moreover, an understanding the MoA of a drug before it is tested in clinical trials is the logical path to drug discovery and can increase its chance for success and hence also approval. In conclusion, the most powerful approach to determine the MoA of a compound is to understand the underlying biology. Novel large datasets of intervenients in most biological processes, namely those emerging from the post-genomic era tools, are available and should be used to help in this task.
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Affiliation(s)
- Margarida D Amaral
- BioISI - Biosystems & Integrative Sciences Institute, Lisboa, Faculty of Sciences, University of Lisboa, Portugal.
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24
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Silva IAL, Doušová T, Ramalho S, Centeio R, Clarke LA, Railean V, Botelho HM, Holubová A, Valášková I, Yeh JT, Hwang TC, Farinha CM, Kunzelmann K, Amaral MD. Organoids as a personalized medicine tool for ultra-rare mutations in cystic fibrosis: The case of S955P and 1717-2A>G. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165905. [PMID: 32730979 PMCID: PMC7484254 DOI: 10.1016/j.bbadis.2020.165905] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 01/14/2020] [Revised: 07/07/2020] [Accepted: 07/22/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND For most of the >2000 CFTR gene variants reported, neither the associated disease liability nor the underlying basic defect are known, and yet these are essential for disease prognosis and CFTR-based therapeutics. Here we aimed to characterize two ultra-rare mutations - 1717-2A > G (c.1585-2A > G) and S955P (p.Ser955Pro) - as case studies for personalized medicine. METHODS Patient-derived rectal biopsies and intestinal organoids from two individuals with each of these mutations and F508del (p.Phe508del) in the other allele were used to assess CFTR function, response to modulators and RNA splicing pattern. In parallel, we used cellular models to further characterize S955P independently of F508del and to assess its response to CFTR modulators. RESULTS Results in both rectal biopsies and intestinal organoids from both patients evidence residual CFTR function. Further characterization shows that 1717-2A > G leads to alternative splicing generating <1% normal CFTR mRNA and that S955P affects CFTR gating. Finally, studies in organoids predict that both patients are responders to VX-770 alone and even more to VX-770 combined with VX-809 or VX-661, although to different levels. CONCLUSION This study demonstrates the high potential of personalized medicine through theranostics to extend the label of approved drugs to patients with rare mutations.
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Affiliation(s)
- Iris A L Silva
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Tereza Doušová
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University and University Hospital Motol, V Uvalu 84,Prague 5, 150 06 Prague, Czech Republic
| | - Sofia Ramalho
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Raquel Centeio
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Luka A Clarke
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Violeta Railean
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Hugo M Botelho
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Andrea Holubová
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University and University Hospital Motol, V Uvalu 84,Prague 5, 150 06 Prague, Czech Republic
| | - Iveta Valášková
- Department of Medical Genetics, Masaryk University Brno and University Hospital Brno, Jihlavská 20, Brno 625 00, Czech Republic
| | - Jiunn-Tyng Yeh
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, United States of America
| | - Tzyh-Chang Hwang
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, United States of America
| | - Carlos M Farinha
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Karl Kunzelmann
- Institut für Physiologie, Universität Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Margarida D Amaral
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal.
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25
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Quaresma MC, Pankonien I, Clarke LA, Sousa LS, Silva IAL, Railean V, Doušová T, Fuxe J, Amaral MD. Mutant CFTR Drives TWIST1 mediated epithelial-mesenchymal transition. Cell Death Dis 2020; 11:920. [PMID: 33106471 PMCID: PMC7588414 DOI: 10.1038/s41419-020-03119-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 12/12/2022]
Abstract
Cystic fibrosis (CF) is a monogenetic disease resulting from mutations in the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) gene encoding an anion channel. Recent evidence indicates that CFTR plays a role in other cellular processes, namely in development, cellular differentiation and wound healing. Accordingly, CFTR has been proposed to function as a tumour suppressor in a wide range of cancers. Along these lines, CF was recently suggested to be associated with epithelial–mesenchymal transition (EMT), a latent developmental process, which can be re-activated in fibrosis and cancer. However, it is unknown whether EMT is indeed active in CF and if EMT is triggered by dysfunctional CFTR itself or a consequence of secondary complications of CF. In this study, we investigated the occurrence of EMT in airways native tissue, primary cells and cell lines expressing mutant CFTR through the expression of epithelial and mesenchymal markers as well as EMT-associated transcription factors. Transepithelial electrical resistance, proliferation and regeneration rates, and cell resistance to TGF-β1induced EMT were also measured. CF tissues/cells expressing mutant CFTR displayed several signs of active EMT, namely: destructured epithelial proteins, defective cell junctions, increased levels of mesenchymal markers and EMT-associated transcription factors, hyper-proliferation and impaired wound healing. Importantly, we found evidence that the mutant CFTR triggered EMT was mediated by EMT-associated transcription factor TWIST1. Further, our data show that CF cells are over-sensitive to EMT but the CF EMT phenotype can be reversed by CFTR modulator drugs. Altogether, these results identify for the first time that EMT is intrinsically triggered by the absence of functional CFTR through a TWIST1 dependent mechanism and indicate that CFTR plays a direct role in EMT protection. This mechanistic link is a plausible explanation for the high incidence of fibrosis and cancer in CF, as well as for the role of CFTR as tumour suppressor protein.
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Affiliation(s)
- Margarida C Quaresma
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, C8 bdg, 1749-016, Campo Grande, Lisboa, Portugal
| | - Ines Pankonien
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, C8 bdg, 1749-016, Campo Grande, Lisboa, Portugal
| | - Luka A Clarke
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, C8 bdg, 1749-016, Campo Grande, Lisboa, Portugal
| | - Luís S Sousa
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, C8 bdg, 1749-016, Campo Grande, Lisboa, Portugal
| | - Iris A L Silva
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, C8 bdg, 1749-016, Campo Grande, Lisboa, Portugal
| | - Violeta Railean
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, C8 bdg, 1749-016, Campo Grande, Lisboa, Portugal
| | - Tereza Doušová
- Department of Paediatrics, 2nd Faculty of Medicine, Charles University and University Hospital Motol, V Uvalu 84, 15006, Prague, Czech Republic
| | - Jonas Fuxe
- Division of Pathology, Department of Laboratory Medicine (LABMED), Karolinska Institutet and Karolinska University hospital, Huddinge, Stockholm, Sweden
| | - Margarida D Amaral
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, C8 bdg, 1749-016, Campo Grande, Lisboa, Portugal.
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26
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da Silva Filho LVRF, Maróstica PJC, Athanazio RA, Reis FJC, Damaceno N, Paes AT, Hira AY, Schlesinger D, Kok F, Amaral MD. Extensive CFTR sequencing through NGS in Brazilian individuals with cystic fibrosis: unravelling regional discrepancies in the country. J Cyst Fibros 2020; 20:473-484. [PMID: 32819855 DOI: 10.1016/j.jcf.2020.08.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/14/2020] [Accepted: 08/10/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND The Brazilian population has a tri-hybrid composition with a high degree of ethnic admixture. We hypothesized that Brazilian individuals with CF from different Brazilian regions have a specific distribution of CFTR variants. METHODS Individuals with CF with data available in the Patient Registry and without an established genotype were submitted to CFTR sequencing by Next Generation Sequencing (NGS) methodology, and results were anonymously incorporated to the Registry Database. Genotyping results were expressed as 'positive', 'inconclusive' or 'negative'. Logistic regression models were performed to investigate the association between demographic/clinical variables and genotyping results. Mediation analysis was conducted to estimate direct and indirect effects of Brazilian region on a binary positive genotyping response. RESULTS In October 2017, data from 4,654 individuals with CF were available, and 3,104(66.7%) of them had a genotyping result. A total of 236 variants (114 new variants) were identified, with F508del identified in 46% of the alleles tested. Genotyping revealed 2,002(64.5%) individuals positive, 757(24.4%) inconclusive and 345(11.1%) negative. Distribution of genotype categories was markedly different across Brazilian Regions, with greater proportions of negative individuals in the North (45%) and Northeast (26%) regions. Newborn screening (CF-NBS) and age at diagnosis were identified as mediators of the effect of Brazilian region on a positive genotyping result. CONCLUSIONS This large initiative of CFTR genotyping showed significant regional discrepancies in Brazil, probably related to socio-economic conditions, lack of adequate CF-NBS and poor access to reliable sweat testing. These results may be useful to indicate Regions where CF care demands more attention.
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Affiliation(s)
- Luiz Vicente Ribeiro Ferreira da Silva Filho
- Pediatric Pulmonology Unit, Instituto da Criança do Hospital das Clínicas da FMUSP, São Paulo, São Paulo, Brazil; Instituto de Ensino e Pesquisa, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil.
| | - Paulo José Cauduro Maróstica
- Pediatric Pulmonology Department, Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Rodrigo Abensur Athanazio
- Pulmonary Division - Heart Institute (InCor) - Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Francisco José Caldeira Reis
- Pediatric Pulmonology Department, Hospital Infantil João Paulo II - Rede FHEMIG, Belo Horizonte, Minas Gerais, Brazil
| | - Neiva Damaceno
- Pediatric Pumonology Department, Santa Casa de São Paulo, São Paulo, São Paulo, Brazil
| | - Angela Tavares Paes
- Faculdade Israelita de Ciências da Saúde Albert Einstein (FICSAE), São Paulo, São Paulo, Brazil
| | - Adilson Yuuji Hira
- Laboratório de Sistemas Integráveis (LSI), Escola Politécnica da USP, São Paulo, São Paulo, Brazil
| | | | | | - Margarida D Amaral
- BioISI - Biosystems & Integrative Sciences Institute, Lisboa, Faculty of Sciences, University of Lisboa, Portugal
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Sousa L, Pankonien I, Clarke LA, Silva I, Kunzelmann K, Amaral MD. KLF4 Acts as a wt-CFTR Suppressor through an AKT-Mediated Pathway. Cells 2020; 9:cells9071607. [PMID: 32630830 PMCID: PMC7408019 DOI: 10.3390/cells9071607] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 06/24/2020] [Accepted: 06/30/2020] [Indexed: 02/06/2023] Open
Abstract
Cystic Fibrosis (CF) is caused by >2000 mutations in the CF transmembrane conductance regulator (CFTR) gene, but one mutation-F508del-occurs in ~80% of patients worldwide. Besides its main function as an anion channel, the CFTR protein has been implicated in epithelial differentiation, tissue regeneration, and, when dysfunctional, cancer. However, the mechanisms that regulate such relationships are not fully elucidated. Krüppel-like factors (KLFs) are a family of transcription factors (TFs) playing central roles in development, stem cell differentiation, and proliferation. Herein, we hypothesized that these TFs might have an impact on CFTR expression and function, being its missing link to differentiation. Our results indicate that KLF4 (but not KLF2 nor KLF5) is upregulated in CF vs. non-CF cells and that it negatively regulates wt-CFTR expression and function. Of note, F508del-CFTR expressing cells are insensitive to KLF4 modulation. Next, we investigated which KLF4-related pathways have an effect on CFTR. Our data also show that KLF4 modulates wt-CFTR (but not F508del-CFTR) via both the serine/threonine kinase AKT1 (AKT) and glycogen synthase kinase 3 beta (GSK3β) signaling. While AKT acts positively, GSK3β is a negative regulator of CFTR. This crosstalk between wt-CFTR and KLF4 via AKT/ GSK3β signaling, which is disrupted in CF, constitutes a novel mechanism linking CFTR to the epithelial differentiation.
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Affiliation(s)
- Luis Sousa
- BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal; (L.S.); (I.P.); (L.A.C.); (I.S.)
| | - Ines Pankonien
- BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal; (L.S.); (I.P.); (L.A.C.); (I.S.)
| | - Luka A Clarke
- BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal; (L.S.); (I.P.); (L.A.C.); (I.S.)
| | - Iris Silva
- BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal; (L.S.); (I.P.); (L.A.C.); (I.S.)
| | - Karl Kunzelmann
- Department of Physiology, University of Regensburg, 93053 Regensburg, Germany;
| | - Margarida D Amaral
- BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal; (L.S.); (I.P.); (L.A.C.); (I.S.)
- Correspondence: ; Tel.: +351-21-750-08-61; Fax: +351-21-750-00-88
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Uliyakina I, Botelho HM, da Paula AC, Afonso S, Lobo MJ, Felício V, Farinha CM, Amaral MD. Full Rescue of F508del-CFTR Processing and Function by CFTR Modulators Can Be Achieved by Removal of Two Regulatory Regions. Int J Mol Sci 2020; 21:ijms21124524. [PMID: 32630527 PMCID: PMC7350234 DOI: 10.3390/ijms21124524] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/20/2020] [Accepted: 06/22/2020] [Indexed: 01/07/2023] Open
Abstract
Cystic Fibrosis (CF) is caused by mutations in the CF Transmembrane conductance Regulator (CFTR), the only ATP-binding cassette (ABC) transporter functioning as a channel. Unique to CFTR is a regulatory domain which includes a highly conformationally dynamic region—the regulatory extension (RE). The first nucleotide-binding domain of CFTR contains another dynamic region—regulatory insertion (RI). Removal of RI rescues the trafficking defect of CFTR with F508del, the most common CF-causing mutation. Here we aimed to assess the impact of RE removal (with/without RI or genetic revertants) on F508del-CFTR trafficking and how CFTR modulator drugs VX-809/lumacaftor and VX-770/ivacaftor rescue these variants. We generated cell lines expressing ΔRE and ΔRI CFTR (with/without genetic revertants) and assessed CFTR expression, stability, plasma membrane levels, and channel activity. Our data demonstrated that ΔRI significantly enhanced rescue of F508del-CFTR by VX-809. While the presence of the RI seems to be precluding full rescue of F508del-CFTR processing by VX-809, this region appears essential to rescue its function by VX-770, suggesting some contradictory role in rescue of F508del-CFTR by these two modulators. This negative impact of RI removal on VX-770-stimulated currents on F508del-CFTR can be compensated by deletion of the RE which also leads to the stabilization of this mutant. Despite both regions being conformationally dynamic, RI precludes F508del-CFTR processing while RE affects mostly its stability and channel opening.
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Vonk AM, van Mourik P, Ramalho AS, Silva IAL, Statia M, Kruisselbrink E, Suen SWF, Dekkers JF, Vleggaar FP, Houwen RHJ, Mullenders J, Boj SF, Vries R, Amaral MD, de Boeck K, van der Ent CK, Beekman JM. Protocol for Application, Standardization and Validation of the Forskolin-Induced Swelling Assay in Cystic Fibrosis Human Colon Organoids. STAR Protoc 2020; 1:100019. [PMID: 33111074 PMCID: PMC7580120 DOI: 10.1016/j.xpro.2020.100019] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
This protocol describes the isolation, handling, culture of, and experiments with human colon stem cell organoids in the context of cystic fibrosis (CF). In human colon organoids, the function of cystic fibrosis transmembrane conductance regulator (CFTR) protein and its rescue by CFTR modulators can be quantified using the forskolin-induced swelling assay. Implementation procedures and validation experiments are described for six CF human colon organoid lines, and representative CFTR genotypes are tested for basal CFTR function and response to CFTR-modulating drugs. For complete details on the use and execution of this protocol, please refer to Dekkers et al (2016) and Berkers and van Mourik (2019). Rectal biopsies are used to efficiently establish human colon organoid cultures Human colon organoids can be cultured and biobanked for prolonged periods Human colon organoids can be used to measure function of the CFTR protein using FIS Reference CF organoid lines are available for validation of the FIS assay
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Affiliation(s)
- Annelotte M Vonk
- Dept. of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.,Regenerative Medicine Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Peter van Mourik
- Dept. of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.,Regenerative Medicine Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Anabela S Ramalho
- Katholieke Universiteit Leuven, Dept. of Development and Regeneration, Leuven, Belgium
| | - Iris A L Silva
- University of Lisboa, Faculty of Sciences, BioISI- Biosystems & Integrative Sciences Institute, Lisboa, Portugal
| | - Marvin Statia
- Hubrecht Organoid Technology (HUB), Utrecht, the Netherlands
| | - Evelien Kruisselbrink
- Dept. of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.,Regenerative Medicine Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Sylvia W F Suen
- Dept. of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.,Regenerative Medicine Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | | | - Frank P Vleggaar
- Gastroenterology and Hepatology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Roderick H J Houwen
- Dept. of Pediatric Gastroenterology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Sylvia F Boj
- Hubrecht Organoid Technology (HUB), Utrecht, the Netherlands
| | - Robert Vries
- Hubrecht Organoid Technology (HUB), Utrecht, the Netherlands
| | - Margarida D Amaral
- University of Lisboa, Faculty of Sciences, BioISI- Biosystems & Integrative Sciences Institute, Lisboa, Portugal
| | - Kris de Boeck
- Katholieke Universiteit Leuven, Dept. of Development and Regeneration, Leuven, Belgium
| | - Cornelis K van der Ent
- Dept. of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Jeffrey M Beekman
- Dept. of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.,Regenerative Medicine Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
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Bene Z, Fejes Z, Macek M, Amaral MD, Balogh I, Nagy B. Laboratory biomarkers for lung disease severity and progression in cystic fibrosis. Clin Chim Acta 2020; 508:277-286. [PMID: 32428503 DOI: 10.1016/j.cca.2020.05.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 04/20/2020] [Accepted: 05/07/2020] [Indexed: 12/22/2022]
Abstract
Although the clinical outcomes of cystic fibrosis (CF) have been markedly improved through the recent implementation of novel CF transmembrane conductance regulator (CFTR) modulator drugs, robust and reliable biomarkers are still demanded for the early detection of CF lung disease progression, monitoring treatment efficacy and predicting life-threatening clinical complications. Thus, there is an unmet need to identify and validate novel, ideally blood based biomarkers with strong correlations to the severity of CF lung disease, which represents a major contribution to overall CF morbidity and mortality. In this review, we aim to summarize the utility of thus far studied blood-, sputum- and bronchoalveolar lavage (BAL)-based biomarkers to evaluate inflammatory conditions in the lung and to follow treatment efficacy in CF. Measurements of sweat chloride concentrations and the spirometric parameter FEV1 are currently utilized to monitor CFTR function and the effect of various CF therapies. Nonetheless, both have inherent pitfalls and limitations, thus routinely analyzed biomarkers in blood, sputum or BAL samples are required as surrogates for lung disorders. Recent discovery of new protein (e.g. HE4) and RNA-based biomarkers, such as microRNAs may offer a higher efficacy, which in aggregate may be valuable to evaluate disease prognosis and to substantiate CF drug efficacy.
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Affiliation(s)
- Zsolt Bene
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; Department of Pediatrics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zsolt Fejes
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Milan Macek
- Department of Biology and Medical Genetics, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Margarida D Amaral
- University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Lisboa, Portugal
| | - István Balogh
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Béla Nagy
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
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Amaral MD. Letter to the editor of JCF. J Cyst Fibros 2020; 19:503. [DOI: 10.1016/j.jcf.2020.02.011] [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: 11/25/2022]
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Amaral MD, Beekman JM. Activating alternative chloride channels to treat CF: Friends or Foes? J Cyst Fibros 2020; 19:11-15. [DOI: 10.1016/j.jcf.2019.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/05/2019] [Accepted: 10/07/2019] [Indexed: 01/15/2023]
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Simões FB, Quaresma MC, Clarke LA, Silva IA, Pankonien I, Railean V, Kmit A, Amaral MD. TMEM16A chloride channel does not drive mucus production. Life Sci Alliance 2019; 2:2/6/e201900462. [PMID: 31732694 PMCID: PMC6859295 DOI: 10.26508/lsa.201900462] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/29/2019] [Accepted: 11/06/2019] [Indexed: 01/07/2023] Open
Abstract
Despite being essential for airway hydration, TMEM16A is not required for mucus (MUC5AC) production. Cell proliferation is the main driver for TMEM16A up-regulation during inflammation. Airway mucus obstruction is the main cause of morbidity in cystic fibrosis, a disease caused by mutations in the CFTR Cl− channel. Activation of non-CFTR Cl− channels such as TMEM16A can likely compensate for defective CFTR. However, TMEM16A was recently described as a key driver in mucus production/secretion. Here, we have examined whether indeed there is a causal relationship between TMEM16A and MUC5AC production, the main component of respiratory mucus. Our data show that TMEM16A and MUC5AC are inversely correlated during differentiation of human airway cells. Furthermore, we show for the first time that the IL-4–induced TMEM16A up-regulation is proliferation-dependent, which is supported by the correlation found between TMEM16A and Ki-67 proliferation marker during wound healing. Consistently, the notch signaling activator DLL4 increases MUC5AC levels without inducing changes neither in TMEM16A nor in Ki-67 expression. Moreover, TMEM16A inhibition decreased airway surface liquid height. Altogether, our findings demonstrate that up-regulation of TMEM16A and MUC5AC is only circumstantial under cell proliferation, but with no causal relationship between them. Thus, although essential for airway hydration, TMEM16A is not required for MUC5AC production.
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Affiliation(s)
- Filipa B Simões
- University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Lisboa, Portugal
| | - Margarida C Quaresma
- University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Lisboa, Portugal
| | - Luka A Clarke
- University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Lisboa, Portugal
| | - Iris Al Silva
- University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Lisboa, Portugal
| | - Ines Pankonien
- University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Lisboa, Portugal
| | - Violeta Railean
- University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Lisboa, Portugal
| | - Arthur Kmit
- University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Lisboa, Portugal
| | - Margarida D Amaral
- University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Lisboa, Portugal
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Amaral MD, Hutt DM, Tomati V, Botelho HM, Pedemonte N. CFTR processing, trafficking and interactions. J Cyst Fibros 2019; 19 Suppl 1:S33-S36. [PMID: 31680043 DOI: 10.1016/j.jcf.2019.10.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/09/2019] [Accepted: 10/15/2019] [Indexed: 01/04/2023]
Abstract
Mutations associated with cystic fibrosis (CF) have complex effects on the cystic fibrosis transmembrane conductance regulator (CFTR) protein. The most common CF mutation, F508del, disrupts the processing to and stability at the plasma membrane and function as a Cl- channel. CFTR is surrounded by a dynamic network of interacting components, referred to as the CFTR Functional Landscape, that impact its synthesis, folding, stability, trafficking and function. CFTR interacting proteins can be manipulated by functional genomic approaches to rescue the trafficking and functional defects characteristic of CF. Here we review recent efforts to elucidate the impact of genetic variation on the ability of the nascent CFTR polypeptide to interact with the proteostatic environment. We also provide an overview of how specific components of this protein network can be modulated to rescue the trafficking and functional defects associated with the F508del variant of CFTR. The identification of novel proteins playing key roles in the processing of CFTR could pave the way for their use as novel therapeutic targets to provide synergistic correction of mutant CFTR for the greater benefit of individuals with CF.
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Affiliation(s)
- Margarida D Amaral
- University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Portugal
| | - Darren M Hutt
- Department of Molecular Medicine, Scripps Research, La Jolla CA, USA
| | - Valeria Tomati
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, Genova 16147, Italy
| | - Hugo M Botelho
- University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Portugal
| | - Nicoletta Pedemonte
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, Genova 16147, Italy.
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Matos AM, Pinto FR, Barros P, Amaral MD, Pepperkok R, Matos P. Inhibition of calpain 1 restores plasma membrane stability to pharmacologically rescued Phe508del-CFTR variant. J Biol Chem 2019; 294:13396-13410. [PMID: 31324722 PMCID: PMC6737230 DOI: 10.1074/jbc.ra119.008738] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 04/04/2019] [Revised: 07/01/2019] [Indexed: 07/30/2023] Open
Abstract
Cystic fibrosis (CF) is a genetic disease caused by mutations in the gene encoding CF transmembrane conductance regulator (CFTR), a chloride channel normally expressed at the surface of epithelial cells. The most frequent mutation, resulting in Phe-508 deletion, causes CFTR misfolding and its premature degradation. Low temperature or pharmacological correctors can partly rescue the Phe508del-CFTR processing defect and enhance trafficking of this channel variant to the plasma membrane (PM). Nevertheless, the rescued channels have an increased endocytosis rate, being quickly removed from the PM by the peripheral protein quality-control pathway. We previously reported that rescued Phe508del-CFTR (rPhe508del) can be retained at the cell surface by stimulating signaling pathways that coax the adaptor molecule ezrin (EZR) to tether rPhe508del-Na+/H+-exchange regulatory factor-1 complexes to the actin cytoskeleton, thereby averting the rapid internalization of this channel variant. However, the molecular basis for why rPhe508del fails to recruit active EZR to the PM remains elusive. Here, using a proteomics approach, we characterized and compared the core components of wt-CFTR- or rPhe508del-containing macromolecular complexes at the surface of human bronchial epithelial cells. We identified calpain 1 (CAPN1) as an exclusive rPhe508del interactor that prevents active EZR recruitment, impairs rPhe508del anchoring to actin, and reduces its stability in the PM. We show that either CAPN1 down-regulation or its chemical inhibition dramatically improves the functional rescue of Phe508del-CFTR in airway cells. These observations suggest that CAPN1 constitutes an appealing target for pharmacological intervention, as part of CF combination therapies restoring Phe508del-CFTR function.
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Affiliation(s)
- Ana M Matos
- Department of Human Genetics, National Health Institute Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, 1749-016 Lisboa, Portugal
| | - Francisco R Pinto
- University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, 1749-016 Lisboa, Portugal
| | - Patrícia Barros
- Department of Human Genetics, National Health Institute Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, 1749-016 Lisboa, Portugal
| | - Margarida D Amaral
- University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, 1749-016 Lisboa, Portugal
| | - Rainer Pepperkok
- Cell Biology and Biophysics Unit and Advanced Light Microscopy Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Paulo Matos
- Department of Human Genetics, National Health Institute Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, 1749-016 Lisboa, Portugal.
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Amaral MD, de Boeck K. Theranostics by testing CFTR modulators in patient-derived materials: The current status and a proposal for subjects with rare CFTR mutations. J Cyst Fibros 2019; 18:685-692. [PMID: 31326274 DOI: 10.1016/j.jcf.2019.06.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/03/2019] [Accepted: 06/18/2019] [Indexed: 12/30/2022]
Abstract
The last decade has witnessed developments in the CF drug pipeline which are both exciting and unprecedented, bringing with them previously unconsidered challenges. The Task Force group came together to consider these challenges and possible strategies to address them. Over the last 18 months, we have discussed internally and gathered views from a broad range of individuals representing patient organizations, clinical and research teams, the pharmaceutical industry and regulatory agencies. In this and the accompanying article, we discuss two main areas of focus: i) optimising trial design and delivery for speed/efficiency; ii) drug development for patients with rare CFTR mutations. We propose some strategies to tackle the challenges ahead and highlight areas where further thought is needed. We see this as the start of a process rather than the end and hope herewith to engage the wider community in seeking solutions to improved treatments for all patients with CF.
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Nagy B, Bene Z, Fejes Z, Heltshe SL, Reid D, Ronan NJ, McCarthy Y, Smith D, Nagy A, Joseloff E, Balla G, Kappelmayer J, Macek M, Bell SC, Plant BJ, Amaral MD, Balogh I. Human epididymis protein 4 (HE4) levels inversely correlate with lung function improvement (delta FEV 1) in cystic fibrosis patients receiving ivacaftor treatment. J Cyst Fibros 2019; 18:271-277. [PMID: 30268371 DOI: 10.1016/j.jcf.2018.08.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/28/2018] [Accepted: 08/28/2018] [Indexed: 12/26/2022]
Abstract
BACKGROUND We have recently shown that human epididymis protein 4 (HE4) levels correlate with the severity of cystic fibrosis (CF) lung disease. However, there are no data on how HE4 levels alter in patients receiving CFTR modulating therapy. METHODS In this retrospective clinical study, 3 independent CF patient cohorts (US-American: 29, Australian: 12 and Irish: 19 cases) were enrolled carrying at least one Class III CFTR CF-causing mutation (p.Gly551Asp) and being treated with CFTR potentiator ivacaftor. Plasma HE4 was measured by immunoassay before treatment (baseline) and 1-6 months after commencement of ivacaftor, and were correlated with FEV1 (% predicted), sweat chloride, C-reactive protein (CRP) and body mass index (BMI). RESULTS After 1 month of therapy, HE4 levels were significantly lower than at baseline and remained decreased up to 6 months. A significant inverse correlation between absolute and delta values of HE4 and FEV1 (r = -0.5376; P < .001 and r = -0.3285; P < .001), was retrospectively observed in pooled groups, including an independent association of HE4 with FEV1 by multiple regression analysis (β = -0.57, P = .019). Substantial area under the receiver operating characteristic curve (ROC-AUC) value was determined for HE4 when 7% mean change of FEV1 (0.722 [95% CI 0.581-0.863]; P = .029) were used as classifier, especially in the first 2 months of treatment (0.806 [95% CI 0.665-0.947]; P < .001). CONCLUSIONS This study shows that plasma HE4 levels inversely correlate with lung function improvement in CF patients receiving ivacaftor. Overall, this potential biomarker may be of value for routine clinical and laboratory follow-up of CFTR modulating therapy.
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Affiliation(s)
- Béla Nagy
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
| | - Zsolt Bene
- Department of Pediatrics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zsolt Fejes
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Sonya L Heltshe
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - David Reid
- QIMR Berghofer Medical Research Institute and The Prince Charles Hospital, Brisbane, Australia
| | - Nicola J Ronan
- Cork Adult Cystic Fibrosis Centre, Cork University Hospital, Cork, Ireland
| | - Yvonne McCarthy
- Cork Adult Cystic Fibrosis Centre, Cork University Hospital, Cork, Ireland
| | - Daniel Smith
- QIMR Berghofer Medical Research Institute and The Prince Charles Hospital, Brisbane, Australia
| | - Attila Nagy
- Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen, Hungary
| | | | - György Balla
- Department of Pediatrics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; MTA-DE Vascular Biology, Thrombosis and Hemostasis Research Group, Hungarian Academy of Sciences, Debrecen, Hungary
| | - János Kappelmayer
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Milan Macek
- Department of Biology and Medical Genetics, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Scott C Bell
- QIMR Berghofer Medical Research Institute and The Prince Charles Hospital, Brisbane, Australia
| | - Barry J Plant
- Cork Adult Cystic Fibrosis Centre, Cork University Hospital, Cork, Ireland
| | - Margarida D Amaral
- University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Lisboa, Portugal
| | - István Balogh
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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Patel W, Moore PJ, Sassano MF, Lopes-Pacheco M, Aleksandrov AA, Amaral MD, Tarran R, Gray MA. Increases in cytosolic Ca 2+ induce dynamin- and calcineurin-dependent internalisation of CFTR. Cell Mol Life Sci 2018; 76:977-994. [PMID: 30547226 PMCID: PMC6394554 DOI: 10.1007/s00018-018-2989-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 11/28/2018] [Accepted: 12/04/2018] [Indexed: 12/12/2022]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) is a cAMP-regulated, apical anion channel that regulates ion and fluid transport in many epithelia including the airways. We have previously shown that cigarette smoke (CS) exposure to airway epithelia causes a reduction in plasma membrane CFTR expression which correlated with a decrease in airway surface hydration. The effect of CS on CFTR was dependent on an increase in cytosolic Ca2+. However, the underlying mechanism for this Ca2+-dependent, internalisation of CFTR is unknown. To gain a better understanding of the effect of Ca2+ on CFTR, we performed whole cell current recordings to study the temporal effect of raising cytosolic Ca2+ on CFTR function. We show that an increase in cytosolic Ca2+ induced a time-dependent reduction in whole cell CFTR conductance, which was paralleled by a loss of cell surface CFTR expression, as measured by confocal and widefield fluorescence microscopy. The decrease in CFTR conductance and cell surface expression were both dynamin-dependent. Single channel reconstitution studies showed that raising cytosolic Ca2+ per se had no direct effect on CFTR. In fact, the loss of CFTR plasma membrane activity correlated with activation of calcineurin, a Ca2+-dependent phosphatase, suggesting that dephosphorylation of CFTR was linked to the loss of surface expression. In support of this, the calcineurin inhibitor, cyclosporin A, prevented the Ca2+-induced decrease in cell surface CFTR. These results provide a hitherto unrecognised role for cytosolic Ca2+ in modulating the residency of CFTR at the plasma membrane through a dynamin- and calcineurin-dependent mechanism.
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Affiliation(s)
- Waseema Patel
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.,Marsico Lung Institute, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Patrick J Moore
- Marsico Lung Institute, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - M Flori Sassano
- Marsico Lung Institute, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Miquéias Lopes-Pacheco
- Faculty of Sciences, BioISI-Biosystems and Integrative Sciences Institute, University of Lisboa, Lisbon, Portugal
| | - Andrei A Aleksandrov
- Department of Biochemistry and Biophysics, Cystic Fibrosis Research and Treatment Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Margarida D Amaral
- Faculty of Sciences, BioISI-Biosystems and Integrative Sciences Institute, University of Lisboa, Lisbon, Portugal
| | - Robert Tarran
- Marsico Lung Institute, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Cell Biology and Physiology, Cystic Fibrosis Research and Treatment Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael A Gray
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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Clarke LA, Awatade NT, Felício VM, Silva IA, Calucho M, Pereira L, Azevedo P, Cavaco J, Barreto C, Bertuzzo C, Gartner S, Beekman J, Amaral MD. The effect of premature termination codon mutations on CFTR mRNA abundance in human nasal epithelium and intestinal organoids: a basis for read-through therapies in cystic fibrosis. Hum Mutat 2018; 40:326-334. [PMID: 30488522 DOI: 10.1002/humu.23692] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 11/08/2018] [Accepted: 11/27/2018] [Indexed: 02/06/2023]
Abstract
A major challenge in cystic fibrosis (CF) research is applying mutation-specific therapy to individual patients with diverse and rare CF transmembrane conductance regulator (CFTR) genotypes. Read-through agents are currently the most promising approach for Class I mutations that introduce premature termination codons (PTCs) into CFTR mRNA. However, variations in degradation of PTC containing transcripts by nonsense mediated decay (NMD) might lower read-through efficacy. Allele specific quantitative real time (qRT)-PCR was used to measure variations in CFTR mRNA abundance for several PTC mutations in respiratory cells and intestinal organoids. The majority of PTC mutations were associated with reduced levels of relative mRNA transcript abundance (∼33% and 26% of total CFTR mRNA in respiratory cells and intestinal organoids, respectively, compared to >50% for non-PTC causing mutations). These levels were generally not affected by PTC mutation type or position, but there could be twofold variations between individuals bearing the same genotype. Most PTC mutations in CFTR are subject to similar levels of NMD, which reduce but do not abolish PTC bearing mRNAs. Measurement of individual NMD levels in intestinal organoids and HNE cells might, therefore, be useful in predicting efficacy of PTC read-through in the context of personalized CFTR modulator therapy.
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Affiliation(s)
- Luka A Clarke
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, Portugal
| | - Nikhil T Awatade
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, Portugal
| | - Veronica M Felício
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, Portugal
| | - Iris A Silva
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, Portugal
| | - Maite Calucho
- Pediatric Pulmonology & CF Unit. Hospital Universitari, Vall d'Hebron, Spain
| | - Luisa Pereira
- Department of Pediatrics, Hospital de Santa Maria, Lisboa, Portugal
| | - Pilar Azevedo
- Department of Pediatrics, Hospital de Santa Maria, Lisboa, Portugal
| | - José Cavaco
- Centro de Referência de Fibrose Quística, Hospital de Dona Estefânia, Centro Hospitalar de Lisboa Central, Lisboa, Portugal
| | - Celeste Barreto
- Department of Pediatrics, Hospital de Santa Maria, Lisboa, Portugal
| | - Carmen Bertuzzo
- Human Genetics Department, Faculty of Medical Sciences, University of Campinas, Campinas, Brazil
| | - Silvia Gartner
- Pediatric Pulmonology & CF Unit. Hospital Universitari, Vall d'Hebron, Spain
| | - Jeffrey Beekman
- Department of Pediatric Pulmonology, UMCU, Utrecht, Netherlands
| | - Margarida D Amaral
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, Portugal
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40
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Matos AM, Gomes-Duarte A, Faria M, Barros P, Jordan P, Amaral MD, Matos P. Prolonged co-treatment with HGF sustains epithelial integrity and improves pharmacological rescue of Phe508del-CFTR. Sci Rep 2018; 8:13026. [PMID: 30158635 PMCID: PMC6115363 DOI: 10.1038/s41598-018-31514-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/20/2018] [Indexed: 02/06/2023] Open
Abstract
Cystic fibrosis (CF), the most common inherited disease in Caucasians, is caused by mutations in the CFTR chloride channel, the most frequent of which is Phe508del. Phe508del causes not only intracellular retention and premature degradation of the mutant CFTR protein, but also defective channel gating and decreased half-life when experimentally rescued to the plasma membrane (PM). Despite recent successes in the functional rescue of several CFTR mutations with small-molecule drugs, the folding-corrector/gating-potentiator drug combinations approved for Phe508del-CFTR homozygous patients have shown only modest benefit. Several factors have been shown to contribute to this outcome, including an unexpected intensification of corrector-rescued Phe508del-CFTR PM instability after persistent co-treatment with potentiator drugs. We have previously shown that acute co-treatment with hepatocyte growth factor (HGF) can significantly enhance the chemical correction of Phe508del-CFTR. HGF coaxes the anchoring of rescued channels to the actin cytoskeleton via induction of RAC1 GTPase signalling. Here, we demonstrate that a prolonged, 15-day HGF treatment also significantly improves the functional rescue of Phe508del-CFTR by the VX-809 corrector/VX-770 potentiator combination, in polarized bronchial epithelial monolayers. Importantly, we found that HGF treatment also prevented VX-770-mediated destabilization of rescued Phe508del-CFTR and enabled further potentiation of the rescued channels. Most strikingly, prolonged HGF treatment prevented previously unrecognized epithelial dedifferentiation effects of sustained exposure to VX-809. This was observed in epithelium-like monolayers from both lung and intestinal origin, representing the two systems most affected by adverse symptoms in patients treated with VX-809 or the VX-809/VX-770 combination. Taken together, our findings strongly suggest that co-administration of HGF with corrector/potentiator drugs could be beneficial for CF patients.
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Affiliation(s)
- Ana M Matos
- Department of Human Genetics, National Health Institute 'Dr. Ricardo Jorge', Av. Padre Cruz, 1649-016, Lisboa, Portugal.,University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande - C8, 1749-016, Lisboa, Portugal
| | - Andreia Gomes-Duarte
- Department of Human Genetics, National Health Institute 'Dr. Ricardo Jorge', Av. Padre Cruz, 1649-016, Lisboa, Portugal.,University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande - C8, 1749-016, Lisboa, Portugal
| | - Márcia Faria
- Department of Human Genetics, National Health Institute 'Dr. Ricardo Jorge', Av. Padre Cruz, 1649-016, Lisboa, Portugal.,University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande - C8, 1749-016, Lisboa, Portugal.,Serviço de Endocrinologia, Diabetes e Metabolismo, do CHLN - Hospital Santa Maria, Lisboa, Portugal
| | - Patrícia Barros
- Department of Human Genetics, National Health Institute 'Dr. Ricardo Jorge', Av. Padre Cruz, 1649-016, Lisboa, Portugal.,University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande - C8, 1749-016, Lisboa, Portugal
| | - Peter Jordan
- Department of Human Genetics, National Health Institute 'Dr. Ricardo Jorge', Av. Padre Cruz, 1649-016, Lisboa, Portugal.,University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande - C8, 1749-016, Lisboa, Portugal
| | - Margarida D Amaral
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande - C8, 1749-016, Lisboa, Portugal
| | - Paulo Matos
- Department of Human Genetics, National Health Institute 'Dr. Ricardo Jorge', Av. Padre Cruz, 1649-016, Lisboa, Portugal. .,University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande - C8, 1749-016, Lisboa, Portugal.
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41
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Canato S, Santos JD, Carvalho AS, Aloria K, Amaral MD, Matthiesen R, Falcao AO, Farinha CM. Proteomic interaction profiling reveals KIFC1 as a factor involved in early targeting of F508del-CFTR to degradation. Cell Mol Life Sci 2018; 75:4495-4509. [DOI: 10.1007/s00018-018-2896-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 07/26/2018] [Accepted: 07/27/2018] [Indexed: 11/28/2022]
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42
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Awatade NT, Ramalho S, Silva IAL, Felício V, Botelho HM, de Poel E, Vonk A, Beekman JM, Farinha CM, Amaral MD. R560S: A class II CFTR mutation that is not rescued by current modulators. J Cyst Fibros 2018; 18:182-189. [PMID: 30030066 DOI: 10.1016/j.jcf.2018.07.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 06/22/2018] [Accepted: 07/01/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND New therapies modulating defective CFTR have started to hit the clinic and others are in trial or under development. The endeavour of drug discovery for CFTR protein rescue is however difficult one since over 2000 mutations have been reported. For most of these, especially the rare ones, the associated defects, the respective functional class and their responsiveness to available modulators are still unknown. Our aim here was to characterize the rare R560S mutation using patient-derived materials (rectal biopsies and intestinal organoids) from one CF individual homozygous for this mutation, in parallel with cellular models expressing R560S-CFTR and to assess the functional and biochemical responses to CFTR modulators. METHODS Intestinal organoids were prepared from rectal biopsies and analysed by RT-PCR (to assess CFTR mRNA), by Western blot (to assess CFTR protein) and by forskolin-induced swelling (FIS) assay. A novel cell line expressing R560S-CFTR was generated by stably transducing the CFBE parental cell line and used to assess R560S-CFTR processing and function. Both intestinal organoids and the cellular model were used to assess efficacy of CFTR modulators in rescuing this mutation. RESULTS Our results show that: R560S does not affect CFTR mRNA splicing; R560S affects CFTR protein processing, totally abrogating the production of its mature form; R560S-CFTR evidences no function as a Cl- channel; and none of the modulators tested rescued R560S-CFTR processing or function. CONCLUSION Altogether, these results indicate that R560S is a class II mutation. However, unlike F508del, it cannot be rescued by any of the CFTR modulators tested.
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Affiliation(s)
- Nikhil T Awatade
- University of Lisboa, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Sofia Ramalho
- University of Lisboa, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Iris A L Silva
- University of Lisboa, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Verónica Felício
- University of Lisboa, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Hugo M Botelho
- University of Lisboa, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Eyleen de Poel
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, Regenerative Medicine Center Utrecht, University Medical Center Utrecht, the Netherlands
| | - Annelotte Vonk
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, Regenerative Medicine Center Utrecht, University Medical Center Utrecht, the Netherlands
| | - Jeffrey M Beekman
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, Regenerative Medicine Center Utrecht, University Medical Center Utrecht, the Netherlands
| | - Carlos M Farinha
- University of Lisboa, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Margarida D Amaral
- University of Lisboa, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal.
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43
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Clancy JP, Cotton CU, Donaldson SH, Solomon GM, VanDevanter DR, Boyle MP, Gentzsch M, Nick JA, Illek B, Wallenburg JC, Sorscher EJ, Amaral MD, Beekman JM, Naren AP, Bridges RJ, Thomas PJ, Cutting G, Rowe S, Durmowicz AG, Mense M, Boeck KD, Skach W, Penland C, Joseloff E, Bihler H, Mahoney J, Borowitz D, Tuggle KL. CFTR modulator theratyping: Current status, gaps and future directions. J Cyst Fibros 2018; 18:22-34. [PMID: 29934203 DOI: 10.1016/j.jcf.2018.05.004] [Citation(s) in RCA: 165] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/07/2018] [Accepted: 05/08/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND New drugs that improve the function of the cystic fibrosis transmembrane conductance regulator (CFTR) protein with discreet disease-causing variants have been successfully developed for cystic fibrosis (CF) patients. Preclinical model systems have played a critical role in this process, and have the potential to inform researchers and CF healthcare providers regarding the nature of defects in rare CFTR variants, and to potentially support use of modulator therapies in new populations. METHODS The Cystic Fibrosis Foundation (CFF) assembled a workshop of international experts to discuss the use of preclinical model systems to examine the nature of CF-causing variants in CFTR and the role of in vitro CFTR modulator testing to inform in vivo modulator use. The theme of the workshop was centered on CFTR theratyping, a term that encompasses the use of CFTR modulators to define defects in CFTR in vitro, with application to both common and rare CFTR variants. RESULTS Several preclinical model systems were identified in various stages of maturity, ranging from the expression of CFTR variant cDNA in stable cell lines to examination of cells derived from CF patients, including the gastrointestinal tract, the respiratory tree, and the blood. Common themes included the ongoing need for standardization, validation, and defining the predictive capacity of data derived from model systems to estimate clinical outcomes from modulator-treated CF patients. CONCLUSIONS CFTR modulator theratyping is a novel and rapidly evolving field that has the potential to identify rare CFTR variants that are responsive to approved drugs or drugs in development.
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Affiliation(s)
- John Paul Clancy
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.
| | | | - Scott H Donaldson
- University of North Carolina at Chapel Hill - Marsico Lung Institute, United States
| | - George M Solomon
- University of Alabama at Birmingham, University of Alabama at Birmingham
| | - Donald R VanDevanter
- Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Michael P Boyle
- Cystic Fibrosis Foundation, Johns Hopkins University, United States
| | - Martina Gentzsch
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina, Chapel Hill, United States; Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, United States
| | - Jerry A Nick
- National Jewish Health, Denver, CO, United States
| | - Beate Illek
- UCSF Benioff Children's Hospital Oakland, United States
| | - John C Wallenburg
- Cystic Firbosis Canada, Directeur en chef des activites scientifiques, fibrose kystique, Canada
| | | | | | | | | | | | | | - Garry Cutting
- Johns Hopkins University School of Medicine, United States
| | - Steven Rowe
- University of Alabama at Birmingham, University of Alabama at Birmingham
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Amaral MD, Boj SF, Shaw J, Leipziger J, Beekman JM. Cystic fibrosis: Beyond the airways. Report on the meeting of the basic science working group in Loutraki, Greece. J Cyst Fibros 2018; 17:441-443. [PMID: 29866530 DOI: 10.1016/j.jcf.2018.05.008] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 05/15/2018] [Accepted: 05/15/2018] [Indexed: 11/16/2022]
Abstract
The European Cystic Fibrosis Society (ECFS) Basic Science Working Group (BSWG) organized a session on the topic "Cystic Fibrosis: Beyond the Airways", within the 15th ECFS Basic Science Conference which gathered around 200 researchers working in the basic science of CF. The session was organized and chaired by Margarida Amaral (BioISI, University of Lisboa, Portugal) and Jeffrey Beekman (University Medical Centre Utrecht, Netherlands) as Chair and Vice-Chair of the BSWG and its purpose was to bring attention of participants of the ECFS Basic Science Conference to "more forgotten" organs in CF disease. In this report we attempt to review and integrate the ideas that emerged at the session.
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Affiliation(s)
- Margarida D Amaral
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal.
| | - Sylvia F Boj
- Hubrecht Organoid Technology, Yalelaan 62, 3584 CM Utrecht, The Netherlands
| | - James Shaw
- Institute of Cellular Medicine, Newcastle University Institute, The Medical School, 4(th) Floor William Leech Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Jens Leipziger
- Department of Biomedicine, Physiology and Biophysics, University of Aahrus, Ole Worms Alle 3, build 1170, 8000 Aarhus, Denmark
| | - Jeffrey M Beekman
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, Regenerative Medicine Center Utrecht, University Medical Center Utrecht, The Netherlands.
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45
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Hiatt SM, Amaral MD, Bowling KM, Finnila CR, Thompson ML, Gray DE, Lawlor JMJ, Cochran JN, Bebin EM, Brothers KB, East KM, Kelley WV, Lamb NE, Levy SE, Lose EJ, Neu MB, Rich CA, Simmons S, Myers RM, Barsh GS, Cooper GM. Systematic reanalysis of genomic data improves quality of variant interpretation. Clin Genet 2018; 94:174-178. [PMID: 29652076 DOI: 10.1111/cge.13259] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/22/2018] [Accepted: 03/28/2018] [Indexed: 12/30/2022]
Abstract
As genomic sequencing expands, so does our knowledge of the link between genetic variation and disease. Deeper catalogs of variant frequencies improve identification of benign variants, while sequencing affected individuals reveals disease-associated variation. Accumulation of human genetic data thus makes reanalysis a means to maximize the benefits of clinical sequencing. We implemented pipelines to systematically reassess sequencing data from 494 individuals with developmental disability. Reanalysis yielded pathogenic or likely pathogenic (P/LP) variants that were not initially reported in 23 individuals, 6 described here, comprising a 16% increase in P/LP yield. We also downgraded 3 LP and 6 variants of uncertain significance (VUS) due to updated population frequency data. The likelihood of identifying a new P/LP variant increased over time, as ~22% of individuals who did not receive a P/LP variant at their original analysis subsequently did after 3 years. We show here that reanalysis and data sharing increase the diagnostic yield and accuracy of clinical sequencing.
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Affiliation(s)
- S M Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - M D Amaral
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - K M Bowling
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - C R Finnila
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - M L Thompson
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - D E Gray
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - J M J Lawlor
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - J N Cochran
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - E M Bebin
- University of Alabama at Birmingham, Birmingham, Alabama
| | | | - K M East
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - W V Kelley
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - N E Lamb
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - S E Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - E J Lose
- University of Alabama at Birmingham, Birmingham, Alabama
| | - M B Neu
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - C A Rich
- University of Louisville, Louisville, Kentucky
| | - S Simmons
- University of Alabama at Birmingham, Birmingham, Alabama
| | - R M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - G S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - G M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
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Olivença DV, Uliyakina I, Fonseca LL, Amaral MD, Voit EO, Pinto FR. A Mathematical Model of the Phosphoinositide Pathway. Sci Rep 2018; 8:3904. [PMID: 29500467 PMCID: PMC5834545 DOI: 10.1038/s41598-018-22226-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 02/19/2018] [Indexed: 01/10/2023] Open
Abstract
Phosphoinositides are signalling lipids that constitute a complex network regulating many cellular processes. We propose a computational model that accounts for all species of phosphoinositides in the plasma membrane of mammalian cells. The model replicates the steady-state of the pathway and most known dynamic phenomena. Sensitivity analysis demonstrates model robustness to alterations in the parameters. Model analysis suggest that the greatest contributor to phosphatidylinositol 4,5-biphosphate (PI(4,5)P2) production is a flux representing the direct transformation of PI into PI(4,5)P2, also responsible for the maintenance of this pool when phosphatidylinositol 4-phosphate (PI(4)P) is decreased. PI(5)P is also shown to be a significant source for PI(4,5)P2 production. The model was validated with siRNA screens that knocked down the expression of enzymes in the pathway. The screen monitored the activity of the epithelium sodium channel (ENaC), which is activated by PI(4,5)P2. While the model may deepen our understanding of other physiological processes involving phosphoinositides, we highlight therapeutic effects of ENaC modulation in Cystic Fibrosis (CF). The model suggests control strategies where the activities of the enzyme phosphoinositide 4-phosphate 5-kinase I (PIP5KI) or the PI4K + PIP5KI + DVL protein complex are decreased and cause an efficacious reduction in PI(4,5)P2 levels while avoiding undesirable alterations in other phosphoinositide pools.
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Affiliation(s)
- Daniel V Olivença
- University of Lisbon, Faculty of Sciences, BIOISI: Biosystems and Integrative Sciences Institute. Campo Grande, 1749-016, Lisbon, Portugal.
| | - Inna Uliyakina
- University of Lisbon, Faculty of Sciences, BIOISI: Biosystems and Integrative Sciences Institute. Campo Grande, 1749-016, Lisbon, Portugal
| | - Luis L Fonseca
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 950 Atlantic Drive, Atlanta, Georgia, 30332-2000, USA
| | - Margarida D Amaral
- University of Lisbon, Faculty of Sciences, BIOISI: Biosystems and Integrative Sciences Institute. Campo Grande, 1749-016, Lisbon, Portugal
| | - Eberhard O Voit
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 950 Atlantic Drive, Atlanta, Georgia, 30332-2000, USA
| | - Francisco R Pinto
- University of Lisbon, Faculty of Sciences, BIOISI: Biosystems and Integrative Sciences Institute. Campo Grande, 1749-016, Lisbon, Portugal
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47
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Liu J, Bihler H, Farinha CM, Awatade NT, Romão AM, Mercadante D, Cheng Y, Musisi I, Jantarajit W, Wang Y, Cai Z, Amaral MD, Mense M, Sheppard DN. Partial rescue of F508del-cystic fibrosis transmembrane conductance regulator channel gating with modest improvement of protein processing, but not stability, by a dual-acting small molecule. Br J Pharmacol 2018; 175:1017-1038. [PMID: 29318594 DOI: 10.1111/bph.14141] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 12/08/2017] [Accepted: 12/10/2017] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND AND PURPOSE Rescue of F508del-cystic fibrosis (CF) transmembrane conductance regulator (CFTR), the most common CF mutation, requires small molecules that overcome protein processing, stability and channel gating defects. Here, we investigate F508del-CFTR rescue by CFFT-004, a small molecule designed to independently correct protein processing and channel gating defects. EXPERIMENTAL APPROACH Using CFTR-expressing recombinant cells and CF patient-derived bronchial epithelial cells, we studied CFTR expression by Western blotting and channel gating and stability with the patch-clamp and Ussing chamber techniques. KEY RESULTS Chronic treatment with CFFT-004 improved modestly F508del-CFTR processing, but not its plasma membrane stability. By contrast, CFFT-004 rescued F508del-CFTR channel gating better than C18, an analogue of the clinically used CFTR corrector lumacaftor. Subsequent acute addition of CFFT-004, but not C18, potentiated F508del-CFTR channel gating. However, CFFT-004 was without effect on A561E-CFTR, a CF mutation with a comparable mechanism of CFTR dysfunction as F508del-CFTR. To investigate the mechanism of action of CFFT-004, we used F508del-CFTR revertant mutations. Potentiation by CFFT-004 was unaffected by revertant mutations, but correction was abolished by the revertant mutation G550E. These data suggest that correction, but not potentiation, by CFFT-004 might involve nucleotide-binding domain 1 of CFTR. CONCLUSIONS AND IMPLICATIONS CFFT-004 is a dual-acting small molecule with independent corrector and potentiator activities that partially rescues F508del-CFTR in recombinant cells and native airway epithelia. The limited efficacy and potency of CFFT-004 suggests that combinations of small molecules targeting different defects in F508del-CFTR might be a more effective therapeutic strategy than a single agent.
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Affiliation(s)
- Jia Liu
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
| | - Hermann Bihler
- Cystic Fibrosis Foundation Therapeutics, Lexington, MA, USA
| | - Carlos M Farinha
- Faculty of Sciences, BioISI - Biosystems and Integrative Sciences Institute, University of Lisboa, Lisboa, Portugal
| | - Nikhil T Awatade
- Faculty of Sciences, BioISI - Biosystems and Integrative Sciences Institute, University of Lisboa, Lisboa, Portugal
| | - Ana M Romão
- Faculty of Sciences, BioISI - Biosystems and Integrative Sciences Institute, University of Lisboa, Lisboa, Portugal
| | | | - Yi Cheng
- Cystic Fibrosis Foundation Therapeutics, Lexington, MA, USA
| | - Isaac Musisi
- Cystic Fibrosis Foundation Therapeutics, Lexington, MA, USA
| | - Walailak Jantarajit
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK.,Center of Calcium and Bone Research and Department of Physiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Yiting Wang
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
| | - Zhiwei Cai
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
| | - Margarida D Amaral
- Faculty of Sciences, BioISI - Biosystems and Integrative Sciences Institute, University of Lisboa, Lisboa, Portugal
| | - Martin Mense
- Cystic Fibrosis Foundation Therapeutics, Lexington, MA, USA
| | - David N Sheppard
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
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Lérias JR, Pinto MC, Botelho HM, Awatade NT, Quaresma MC, Silva IAL, Wanitchakool P, Schreiber R, Pepperkok R, Kunzelmann K, Amaral MD. A novel microscopy-based assay identifies extended synaptotagmin-1 (ESYT1) as a positive regulator of anoctamin 1 traffic. Biochim Biophys Acta Mol Cell Res 2017; 1865:421-431. [PMID: 29154949 DOI: 10.1016/j.bbamcr.2017.11.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 11/02/2017] [Accepted: 11/14/2017] [Indexed: 01/14/2023]
Abstract
An attractive possibility to treat Cystic Fibrosis (CF), a severe condition caused by dysfunctional CFTR, an epithelial anion channel, is through the activation of alternative (non-CFTR) anion channels. Anoctamin 1 (ANO1) was demonstrated to be a Ca2+-activated chloride channel (CaCC) and thus of high potential to replace CFTR. Despite that ANO1 is expressed in human lung CF tissue, it is present at the cell surface at very low levels. In addition, little is known about regulation of ANO1 traffic, namely which factors promote its plasma membrane (PM) localization. Here, we generated a novel cellular model, expressing an inducible 3HA-ANO1-eGFP construct, and validated its usage as a microscopy tool to monitor for ANO1 traffic. We demonstrate the robustness and specificity of this cell-based assay, by the identification of siRNAs acting both as ANO1 traffic enhancer and inhibitor, targeting respectively COPB1 and ESYT1 (extended synaptotagmin-1), the latter involved in coupling of the endoplasmic reticulum to the PM at specific microdomains. We further show that knockdown of ESYT1 (and family members ESYT2 and ESYT3) significantly decreased ANO1 current density. This ANO1 cell-based assay constitutes an important tool to be further used in high-throughput screens and drug discovery of high relevance for CF and cancer.
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Affiliation(s)
- Joana R Lérias
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal; Department of Physiology, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Madalena C Pinto
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal; Department of Physiology, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany; Cell Biology and Biophysics Unit and Advanced Light Microscopy Facility, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Hugo M Botelho
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Nikhil T Awatade
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Margarida C Quaresma
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Iris A L Silva
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Podchanart Wanitchakool
- Department of Physiology, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Rainer Schreiber
- Department of Physiology, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Rainer Pepperkok
- Cell Biology and Biophysics Unit and Advanced Light Microscopy Facility, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Karl Kunzelmann
- Department of Physiology, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Margarida D Amaral
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal; Cell Biology and Biophysics Unit and Advanced Light Microscopy Facility, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany.
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De Boeck K, Amaral MD. Progress in therapies for cystic fibrosis. The Lancet Respiratory Medicine 2016; 4:662-674. [DOI: 10.1016/s2213-2600(16)00023-0] [Citation(s) in RCA: 254] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 01/13/2016] [Accepted: 01/14/2016] [Indexed: 12/19/2022]
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De Boeck K, Amaral MD. Classification of CFTR mutation classes - Authors' reply. Lancet Respir Med 2016; 4:e39. [PMID: 27377413 DOI: 10.1016/s2213-2600(16)30189-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 06/15/2016] [Accepted: 06/15/2016] [Indexed: 11/17/2022]
Affiliation(s)
- Kris De Boeck
- Pediatric Pulmonology, Department of Pediatrics, University of Leuven, Leuven 3000, Belgium.
| | - Margarida D Amaral
- Faculty of Sciences, Biosystems and Integrative Sciences Institute (BioISI), University of Lisbon, Lisbon, Portugal
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