Abstract
Understanding the functional consequence of rare cystic fibrosis (CF) mutations is mandatory for the adoption of precision therapeutic approaches for CF. Here we studied the effect of the very rare CF mutation, W361R, on CFTR processing and function. We applied western blot, patch clamp and pharmacological modulators of CFTR to study the maturation and ion transport properties of pEGFP-WT and mutant CFTR constructs, W361R, F508del and L69H-CFTR, expressed in HEK293 cells. Structural analyses were also performed to study the molecular environment of the W361 residue. Western blot showed that W361R-CFTR was not efficiently processed to a mature band C, similar to F508del CFTR, but unlike F508del CFTR, it did exhibit significant transport activity at the cell surface in response to cAMP agonists. Importantly, W361R-CFTR also responded well to CFTR modulators: its maturation defect was efficiently corrected by VX-809 treatment and its channel activity further potentiated by VX-770. Based on these results, we postulate that W361R is a novel class-2 CF mutation that causes abnormal protein maturation which can be corrected by VX-809, and additionally potentiated by VX-770, two FDA-approved small molecules. At the structural level, W361 is located within a class-2 CF mutation hotspot that includes other mutations that induce variable disease severity. Analysis of the 3D structure of CFTR within a lipid environment indicated that W361, together with other mutations located in this hotspot, is at the edge of a groove which stably accommodates lipid acyl chains. We suggest this lipid environment impacts CFTR folding, maturation and response to CFTR modulators.
Introduction
Cystic fibrosis (CF) is one of the most common, lethal, autosomal recessive disease and is caused by mutations in the gene encoding the anion channel cystic fibrosis transmembrane conductance regulator (CFTR). CFTR is a major actor in transepithelial fluid secretion and a defect in its expression, location or function results in severe pulmonary and digestive impairments (). More than 2000 CF mutations have been identified to date, and these have been subdivided into six classes based on the functional defect they cause on CFTR mRNA or protein (). The six classes are: (1) defective protein synthesis, (2) impaired protein maturation leading to protein degradation, (3) defective regulation of CFTR channel activity, (4) altered ionic selectivity and conductance, (5) lowered CFTR mRNA levels, and (6) decreased protein stability.
The most common CF mutation is a deletion of phenylalanine at position 508 (F508del), which is a class-2 mutation exhibiting inefficient maturation and reduced plasma membrane expression of the protein (; ). F508del-CFTR also exhibits a gating defect (), and a reduced stability at the plasma membrane (; ), typical defects of class-3 and class-6 mutations, respectively. This mutation is present in 70% of homozygous patients and 90% of heterozygous patients [CFTR2 database1 ]. Patients carrying class-2 CFTR mutations on both alleles generally show severe disease with strong digestive and pulmonary defects.
Here we studied a very rare CF mutation, W361R (NM_000492.3:c.1081T > A), a variant of CFTR described in only a small number of European patients; Spanish, French, Italian (), Greek (), and Swedish (). This mutation was first detected in a French woman (), who had limited respiratory problems during childhood. She was only diagnosed with CF at the age of 37 years, and later died at the age of 44 because of pulmonary decompensation. She was pancreatic sufficient but developed late-onset severe lung disease. She carried a splicing mutation 297-3C > T in intron 2 on the other allele.
In order to gain a better understanding of the effect of CF mutations on CFTR function, and especially why some patients carrying some rare, or very rare, mutations only develop severe symptoms later in life, we examined the functional and cellular consequences of the rare missense mutation, W361R, and compared it to F508del-CFTR, and another class 2 CF mutation, L69H, which causes a severe CF phenotype with pancreatic insufficiency and congenital bilateral absence of the vas deferens (CBAVD) ().
Materials and Methods
Cell Culture
HEK293 cells were cultured at 37°C in 5% CO2 in Dulbecco’s modified Eagle’s medium + GlutaMAX (Life Technologies, United Kingdom) with 10% fetal calf serum (Lonza, Belgium), 1% penicillin/streptomycin (Sigma-Aldrich).
Construction and Expression of CFTR Mutants
The expression vectors used include pEGFP-CFTR-WT and pEGFP-CFTR-F508 plasmids generously provided by K. H. Karlson (Dartmouth College, Hanover, NH) (). The W361R mutation was generated by site-directed mutagenesis as previously described () using the oligonucleotide primer (T to A) 5′-CCCTGGGCTGTACAAACAAGGTATGACTCTCTTGGAGC-3′. Cells were transiently transfected using cationic lipids (JetPEI DNA Transfection Reagent, Polyplus transfection, Illkirch, France) with 0.5 μg/mL (patch-clamp) or 1 μg/mL (western blot analysis) of plasmid.
Western Blotting
After 48 h of transfection, HEK293 cells were lysed (lysis buffer: 10 mM Tris HCl, 1% Non-idet P-40, 0.5% sodium deoxycholate, 1 mM Pefabloc® SC and the protease inhibitors cocktail cOmpleteTM [Roche, Germany); pH 7.5)]. 50 μg of protein were resolved on a 5–10% gradient SDS-PAGE, transferred to a nitrocellulose membrane, probed using the MAB3480 anti-CFTR antibody (a.a 1370–1380, clone M3A7) and the Na/K ATPase (1:1000; Millipore Corporation, United States), then incubated with a secondary peroxidase-conjugated antibody (1:5000; Amersham, GE Healthcare, United Kingdom) followed by chemiluminescence detection.
Maturation level was quantified by densitometry using ImageJ software (Wayne Rasband, National Institute of Health, United States) and normalized to the loading control, the Na/K ATPase protein.
Patch Clamp Recording
Ionic currents were recorded using the whole-cell and the excised inside out configurations of the patch-clamp method.
Whole cell experiments were conducted as previously described (). The external bath solution contained (in mM) 145 NaCl, 4 CsCl, 1 CaCl2, 1 MgCl2, 10 glucose, and 10 N-tris[Hydroxymethyl]methyl-2-aminoethanesulphonic acid (TES) (titrated with NaOH to pH 7.4). The intrapipette solution contained (in mM) 113 L-aspartic acid, 113 CsOH, 27 CsCl, 1 NaCl, 1 MgCl2, 1 EGTA, 10 TES, and 3 MgATP (titrated with CsOH to pH 7.2). In all experiments, CFTR channels were activated by elevating intracellular cAMP levels using 10 μM of the adenylate cyclase agonist forskolin (Fsk) and currents potentiated using 30 μM genistein (Gst) (). Then, the thiazolidinone blocker CFTRinh-172 was used at 10 μM to selectively inhibit CFTR channels (). All experiments were conducted at room temperature (20–25°C).
Microscopic CFTR currents were recorded from inside-out patches with the pipette potential held at + 50 mV (i.e., membrane potential, –50 mV) and inverted for purposes of illustration. The pipette (extracellular) solution contained (mM): 140 N-methyl-D-glucamine (NMDG), 140 aspartic acid, 5 CaCl2, 2 MgSO4 and 10 TES (titrated with Tris to pH 7.3). The bath (intracellular) solution contained (mM): 140 NMDG, 3 MgCl2, 1 CsEGTA, and 10 TES (titrated with HCl to pH 7.3). Currents were recorded at 500 Hz and filtered at 125 Hz using an Axopatch 200B amplifier and an analog/digital interface (Digidata 1440A) and analyzed with pCLAMP 10 software (all from Axon Instruments, Inc., Burlingame, CA, United States). CFTR channels were activated by adding 1 mM MgATP and 75 nM PKA to the bath solution. Experiments were conducted at room temperature (20–25°C).
Chemicals
Forskolin (Fsk), genistein (Gst), and CFTR-inh172 were purchased from Sigma-Aldrich. VX-770 and VX-809 were purchased from Euromedex (Souffelweyersheim, France). Stock solutions of Fsk (10 mM), Gst (30 mM), CFTRinh172 (10 mM), VX-770 (1 mM), and VX-809 (10 mM) were prepared in dimethyl sulfoxide (DMSO). PKA (final concentration, 75 nM – 30 U) was from Promega (Madison, WI, United States); MgATP (1 mM) was from Sigma-Aldrich.
Molecular Dynamics Simulations
Equilibrium molecular dynamics (MD) simulations were carried out with the NAMD 2.9 program (), using the CHARMM36 force field () as detailed in a previous article (). Cryo-EM- (pdb:6MSM) or model-derived 3D structures of human CFTR were embedded in a POPC lipid bilayer and immersed in an orthorhombic box filled with TIP3P water using the charmm-gui platform (; ; ). Electrical neutrality was achieved by adding Na+ and Cl– ions to reach a final concentration of 150 mM. After equilibration steps, the production phases were carried out in the NPT ensemble at a temperature of 310 K and a pressure of 1 bar, using periodic boundary conditions and Particle Mesh Ewald treatment () for the electrostatic interactions. For the van der Waals interactions, a switching function was applied between 10 and 12 Å from the solute. The integration time step was 2 fs and coordinates were saved every 1000 steps (2 ps). The duration of the simulations was 125 ns for both the cryo-EM structure and the model of the open form. For both simulations, RMSDs were calculated on all Cα atoms except those belonging to the flexible domains [Lasso (residues 1–65), Regulatory Insertion (residues 404–435), ECL4 (residues 886–909), and Linker Insertion [residues 1169–1200)]. RMSDs reach a plateau after ∼25 ns with averaged values (on the last 100 ns) of 1.8 ± 0.2 and 2.3 ± 0.2 Å, respectively, for the cryo-EM structure and the model of the open MD simulations. Contacts between W361 and other amino-acids or lipids were obtained using VLDM which is based on a Laguerre representation of macromolecules (, ). 3D structure representations were made using Pymol (The PyMOL Molecular Graphics System, Version 3.0 Schrödinger, LCC) or Chimera ().
Statistics
Results are expressed as the means ± Standard Error of the Mean (SEM) of n observations. All statistical tests were performed using GraphPad Prism version 5.0 (GraphPad Software, San Diego, CA, United States). Datasets were compared using Student’s t-tests. Differences were considered statistically significant at p < 0.05. ns, no significant difference; ∗p < 0.05; ∗∗p < 0.01; and ∗∗∗p < 0.001.
Results
Expression and Maturation of W361R-CFTR
To study the maturation of W361R-CFTR, we first performed western blot experiments from HEK293 cells transiently transfected with either WT or mutant forms of CFTR. As expected, the WT-CFTR biochemical profile showed the core glycosylated, B-band, and a fully glycosylated, C-band, on western blots (Figure 1A, lane 1), while the well-known class-2 maturation mutant, F508del-CFTR, showed only the core glycosylated B-band (Figure 1A, lane 2). Interestingly, W361R-CFTR showed a very weak mature C-band (Figure 1A, lane 4). This difference in maturation between the two class-2 mutations was confirmed by densitometry analysis (Figure 1B). A similar biochemical profile was observed when W361R-CFTR proteins were expressed in different cell models (BHK and Hela cells, data not shown). Mock transfected cells (HEK293 cells expressing pEGFP-C1 vector without the CFTR coding sequence) were used as negative control (Figure 1A, lane 3). No band was revealed by the anti-CFTR antibody, confirming the specificity of the antibody.
FIGURE 1
Function of W361R Mutant-CFTR
We then studied the Cl– channel function of W361R-CFTR by whole cell, patch clamp experiments. Figure 2A shows representative whole cell recordings taken from HEK293 cells expressing W361R-CFTR under basal conditions, and in the presence of 10 μM Fsk + 30 μM Gst or 10 μM of CFTRinh172 (left panel) and the corresponding current density/voltage (I/V) relationships (right panel). In the presence of Fsk/Gst, the W361R-CFTR mutant exhibited a significant time-independent chloride current completely abolished by CFTRinh172. For comparison, Figures 2B,C show whole cell Cl– currents recorded for WT-CFTR and two CFTR class-2 mutants, F508del-CFTR and L69H-CFTR. Figure 2B shows the CFTR current traces obtained in the presence of the CFTR activation cocktail (Fsk 10 μM + Gst 30 μM) for the three different CFTR variants. Figure 2C summarizes the current densities recorded under basal conditions, in the presence of Fsk/Gst, and in the presence of CFTRinh172. Although the response to Fsk/Gst cocktail for W361R-CFTR was significantly decreased compared to WT-CFTR (current density at +40 mV: 21.65 ± 6.3 pA/pF, n = 6 and 333.5 ± 53 pA/pF, n = 7, respectively), the W361R-CFTR response was clearly greater than either F508del-CFTR or L69H-CFTR (current density at + 40 mV: 6.33 ± 4.4 pA/pF, n = 4 and 4.71 ± 1.4 pA/pF, n = 6, respectively). For mock transfected cells, Fsk/Gst had no effect, confirming all currents recorded were carried by CFTR channels.
FIGURE 2
To investigate further the functional properties of W361R-CFTR, we performed single channel patch clamp experiments, using excised, inside-out patches from transfected HEK293 cells, exposed to 1 mM Mg-ATP and 75 nM PKA to activate CFTR. Figure 3A shows representative traces of microscopic currents for WT-CFTR (left panel) and W361R-CFTR (right panel). The upper traces represent 4 min of recording whereas the lower traces show an expanded 15 s portion of the 4 min trace, as indicated by the bars. We recorded functional W361R-CFTR at the plasma membrane (Figure 3A) in 75% of patches, while WT-CFTR was recorded in 100% of patches (n = 6) and F508del-CFTR or L69H were never detected in the absence of correction (n = 8). We recorded 1 to 4 channels in excised patches obtained from W361R-CFTR transfected cells, and more than 10 channels for each patch for WT-CFTR, confirming the lower channel density of the W361 mutant. The unitary current (i) of W361R-CFTR was 0.47 ± 0.02 pA at –50 mV which was not significantly different from WT CFTR (i = 0.52 ± 0.03 pA at –50 mV) (Figure 3B). As we did not obtain patches with a single channel for any conditions, we could not investigate the kinetics of the CFTR variants, but these results clearly demonstrate a significant functionality of the W361R-CFTR channels.
FIGURE 3
Sensitivity of W361R Mutant to CFTR Modulators
Because the maturation process of CFTR can be strongly affected by class-2 CF mutations, we studied the effect of the FDA-approved corrector VX-809 () on the W361R-CFTR variant, by western blot and patch clamp (Figure 4). First, we detected an increase of the mature C-band of W361R-CFTR in western blot experiments when cells were incubated for 24 h at 37°C with 10 μM VX-809 (Figure 4A, lane 3). Densitometry analyses confirmed a significant, twofold, correction of the maturation defect.
FIGURE 4
Then whole cell patch clamp current recordings from HEK293 cells expressing corrected W361R-CFTR and corrected F508del-CFTR confirmed the western blot results (Figure 4B). Figure 4B shows the current densities obtained in the presence of Fsk/Gst under non-treated (NT) conditions, or after 24 h incubation with 10 μM VX-809 at 37°C (+ VX-809). In the presence of VX-809, the activator cocktail induced a larger CFTR current for both mutants. Moreover, corrected W361R-CFTR showed a better functionality than the corrected F508del-CFTR (at +40 mV: 89.9 ± 21.4 pA/pF n = 7 and 35.9 ± 5.6 pA/pF n = 6, respectively). Inside-out recordings confirmed there was an increase in W361R channels present at the plasma membrane. We recorded channel activity in 100% of patches from corrected W361R-CFTR transfected cells (n = 6) with an estimated number of channel between 4 and 10. Unitary conductance was not modified after the VX-809 treatment (i = 0.51 ± 0.02 pA at –50 mV).
Finally, we tested the effect of the FDA-approved CFTR modulator VX-770 on non-corrected W361R-CFTR by whole cell patch clamp. Figure 4D shows the I/V relationships under basal conditions and after sequential addition of 10 μM Fsk, 1 μM VX-770, and 10 μM CFTRinh172. VX-770 clearly potentiated the Fsk-activated current and caused a further twofold increase in whole cell current (at +40 mV: 10.2 ± 2 pA/pF for Fsk alone and 22.6 ± 3.7 for Fsk + VX-770, n = 5). This VX-770 dependent current was completely abolished by CFTRinh172. These results clearly show that small molecules correct both the maturation and the function of the W361R-CFTR mutant.
Position of W361 on the CFTR 3D Structures and Possible Involvement in Protein-Lipid Interactions
Cryo-electron microscopy (cryo-EM) of the full-length CFTR protein has given information about both an ATP-free, non-phosphorylated apo conformation [human and zebrafish CFTR (; )] and an ATP-bound, phosphorylated, yet closed conformation [human and zebrafish CFTR (, )]. These ATP-free and ATP-bound conformations, both corresponding to closed channels, are very similar in the W361 area (root mean square standard deviation (RMSD) of 2.95 Å for 204 superimposed Cα). In the close 3D neighborhood of W361 are found E56, P67, R74, G85, H199, P205 and L206, amino acids that are affected by CF-causing mutations [() and CFTR2 database (see text footnote 1), Figure 5A]. This region, including the N- (elbow and TM1) and C-termini (TM6) of membrane spanning domain 1 (MSD1) as well as the N-terminal extension (in the so-called lasso conformation), thus appears sensitive to deleterious mutations. It is worth noting that this region is also found in a model of the open form of the CFTR channel (Supplementary Figure 1A, RMSD 4.7 Å on 204 Cα, ). This model, supported by experimental data () and consistent with the cryo-EM 3D structure at the level of individual blocks of TM helices (), gives insight into an alternative conformation of the CFTR channel, with a different configuration of the TM7-TM8 hairpin as well as of the N-terminal extension (lasso in the cryo-EM 3D structure), free for interaction with cytosolic partners (Supplementary Figure 1A).
FIGURE 5
We performed all-atom MD simulations of wild-type CFTR embedded in a lipid environment, starting with both the experimental (closed channel) and theoretical (open channel) 3D structures. Cryo-EM 3D structures were very similar before and after MD simulations (Figure 5B), with a rotation of the W361 side chain, while lipid (POPC) acyl chains filled the groove formed by TM1, TM3 and TM6, as well as the elbow helix, establishing stable contacts in particular with aromatic (W361, W202) and basic residues (R74, R202) (Figures 5B,C and Supplementary Figure 2A). These global features were also observed in another MD simulation performed in similar conditions using cryo-EM 3D structures, irrespective of the natural variability of side chain positions between the simulations or within the same simulation (Supplementary Figure 3). A similar situation is observed after MD simulation of the WT CFTR model of the open channel (Supplementary Figures 1B,C, 2B).
From these data, we suggest that the introduction of an arginine residue instead of tryptophan at position 361, near to the beginning (N66 in transmembrane helix TM1) and the end (Q376 in TM6) of MSD1, which are in close proximity to a groove likely occupied by lipids, may disturb the proper folding and stability of the mutated protein. This suggestion is consistent with the biochemical and electrophysiological profiles we have obtained experimentally. This hypothesis is supported by the fact that F374 and L375, at the end of TM6, also play critical role for MSD1 folding (
Discussion
In the present work, we have investigated the effects of the rare CFTR mutation W361R. We found a strong decrease in the levels of the fully glycosylated mature form compared to WT-CFTR, a hallmark of class-2 CF mutations (
W361 is located in the TM6 helix, within a region bringing together the MSD1 elbow helix, TM1, TM3 and TM6, and forming a groove at the protein/membrane interface that can be stably occupied by lipid acyl chains (Figure 5). This region appears vulnerable to mutations, as several CF class-2 mutations are found there, forming a mutation hotspot, which are associated with both mild and severe maturation defects (
VX-809 has been shown to partially correct F508del-CFTR folding by positively affecting the MSD1 conformation, thereby improving the efficiency of interactions with other domains (
To conclude, these results on W361R support the revision of the mutation classification that we (
Statements
Data availability statement
All datasets generated for this study are included in the article/Supplementary Material.
Author contributions
AB, AE, MJ-S, BH, J-PM, IC, and FB designed the experiments. AB and MJ-S performed and analyzed the biochemical experiments. AB performed and analyzed the patch clamp experiments. AE performed the molecular dynamics simulations. AE, BH, J-PM, and IC analyzed the structural data. AB, AE, IC, and FB wrote the manuscript.
Funding
This research was supported by the French associations “Amandine Contre La Mucoviscidose,” “Vaincre La Mucoviscidose” and UK CF trust (SRC005). The authors wish to thank Amandine and her family and friends for the valuable support for this study. This work was performed using HPC resources from GENCI-[CINES] (2019-A0060707206).
Acknowledgments
We thank Dr. MA Gray for his critical comments on the manuscript.
Conflict of interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Supplementary material
The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fphar.2020.00295/full#supplementary-material
Abbreviations
- CF
cystic fibrosis
- CFTR
cystic fibrosis transmembrane conductance regulator
- GFP
green fluorescent protein
- WT-CFTR
wild-type CFTR.
Footnotes
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Summary
Keywords
W361R-CFTR, missense CF mutations, class-2 CF mutations, small molecules modulators, cystic fibrosis transmembrane conductance regulator
Citation
Billet A, Elbahnsi A, Jollivet-Souchet M, Hoffmann B, Mornon J-P, Callebaut I and Becq F (2020) Functional and Pharmacological Characterization of the Rare CFTR Mutation W361R. Front. Pharmacol. 11:295. doi: 10.3389/fphar.2020.00295
Received
04 November 2019
Accepted
27 February 2020
Published
17 March 2020
Volume
11 - 2020
Edited by
Gildas Loussouarn, Université de Nantes, France
Reviewed by
Tzyh-Chang Hwang, University of Missouri, United States; Nael McCarty, Emory University, United States
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Copyright
© 2020 Billet, Elbahnsi, Jollivet-Souchet, Hoffmann, Mornon, Callebaut and Becq.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Arnaud Billet, arnaud.billet@univ-poitiers.fr
†Present address: Brice Hoffmann, Iktos, Paris, France
This article was submitted to Pharmacology of Ion Channels and Channelopathies, a section of the journal Frontiers in Pharmacology
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