Cystic fibrosis transmembrane conductance regulator

CFTR
Available structures
PDBOrtholog search: PDBe RCSB
Identifiers
AliasesCFTR, ABC35, ABCC7, CF, CFTR/MRP, MRP7, TNR-dJ760C5.1, cystic fibrosis transmembrane conductance regulator, CF transmembrane conductance regulator
External IDsOMIM: 602421 MGI: 88388 HomoloGene: 55465 GeneCards: CFTR
EC number5.6.1.6
Orthologs
SpeciesHumanMouse
Entrez

1080

12638

Ensembl

ENSG00000001626

ENSMUSG00000041301

UniProt

P13569

P26361

RefSeq (mRNA)

NM_000492

NM_021050

RefSeq (protein)

NP_000483

NP_066388

Location (UCSC)Chr 7: 117.29 – 117.72 MbChr 6: 18.17 – 18.32 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

Cystic fibrosis transmembrane conductance regulator (CFTR) is a membrane protein and chloride channel in vertebrates that is encoded by the CFTR gene.[5][6]

The CFTR gene codes for an ABC transporter-class ion channel protein that conducts chloride[7] ions across epithelial cell membranes. Mutations of the CFTR gene affecting chloride ion channel function lead to dysregulation of epithelial fluid transport in the lung, pancreas and other organs, resulting in cystic fibrosis. Complications include thickened mucus in the lungs with frequent respiratory infections, and pancreatic insufficiency giving rise to malnutrition and diabetes. These conditions lead to chronic disability and reduced life expectancy. In male patients, the progressive obstruction and destruction of the developing vas deferens (spermatic cord) and epididymis appear to result from abnormal intraluminal secretions,[8] causing congenital absence of the vas deferens and male infertility.

Gene

The location of the CFTR gene on chromosome 7

The gene that encodes the human CFTR protein is found on chromosome 7, on the long arm at position q31.2.[6] from base pair 116,907,253 to base pair 117,095,955. CFTR orthologs[9] occur in the jawed vertebrates.[10]

The CFTR gene has been used in animals as a nuclear DNA phylogenetic marker.[9] Large genomic sequences of this gene have been used to explore the phylogeny of the major groups of mammals,[11] and confirmed the grouping of placental orders into four major clades: Xenarthra, Afrotheria, Laurasiatheria, and Euarchonta plus Glires.

Mutations

Nearly 1000 cystic fibrosis-causing mutations have been described.[12] The most common mutation, DeltaF508 (ΔF508) results from a deletion (Δ) of three nucleotides which results in a loss of the amino acid phenylalanine (F) at the 508th position on the protein.[13] As a result, the protein does not fold normally and is more quickly degraded. The vast majority of mutations are infrequent. The distribution and frequency of mutations varies among different populations which has implications for genetic screening and counseling.

Drug discovery for therapeutics to address CF in all patients is complicated due to the large number of disease-causing mutations. Ideally, a library of cell lines and cell-based assays corresponding to all mutants is required to screen for broadly-active drug candidates. Cell engineering methods including fluorogenic oligonucleotide signaling probes may be used to detect and isolate clonal cell lines for each mutant.[14]

Mutations consist of replacements, duplications, deletions or shortenings in the CFTR gene. This may result in proteins that may not function, work less effectively, are more quickly degraded, or are present in inadequate numbers.[15]

It has been hypothesized that mutations in the CFTR gene may confer a selective advantage to heterozygous individuals. Cells expressing a mutant form of the CFTR protein are resistant to invasion by the Salmonella typhi bacterium, the agent of typhoid fever, and mice carrying a single copy of mutant CFTR are resistant to diarrhea caused by cholera toxin.[16]

The most common mutations that cause cystic fibrosis and pancreatic insufficiency in humans are:[17]

Variant cDNA name (ordered 5' to 3') Variant protein name Variant legacy name rsID # alleles in CFTR2 Allele frequency in CFTR2 % pancreatic insufficient Variant final determination (July 2020)
c.1521_1523delCTTp.Phe508delF508delrs113993960990610.6974498%CF-causing
c.1624G>Tp.Gly542XG542Xrs11399395936100.0254298%CF-causing
c.1652G>Ap.Gly551AspG551Drs7552720729860.0210296%CF-causing
c.3909C>Gp.Asn1303LysN1303Krs8003448622460.0158198%CF-causing
c.350G>Ap.Arg117HisR117Hrs7865542118540.0130523%Varying clinical consequence
c.3846G>Ap.Trp1282XW1282Xrs7701089817260.0121599%CF-causing
c.489+1G>TNo protein name621+1G->Trs7875694113230.0093199%CF-causing
c.1657C>Tp.Arg553XR553Xrs7459732513230.0093197%CF-causing
c.1585-1G>ANo protein name1717-1G->Ars7671377212160.0085697%CF-causing
c.3718-2477C>TNo protein name3849+10kbC->Trs7503978211580.0081533%CF-causing
c.2657+5G>ANo protein name2789+5G->Ars8022456010270.0072343%CF-causing
c.1519_1521delATCp. Ile507delI507delrs1219087456510.0045898%CF-causing
c.3484C>Tp.Arg1162XR1162Xrs747675306510.0045897%CF-causing
c.254G>Ap.Gly85GluG85Ers759613956160.0043485%CF-causing
c.3454G>Cp.Asp1152HisD1152Hrs755419695710.0040224%Varying clinical consequence
c.2051_2052delAAinsGp. Lys684SerfsX382183AA->Grs1219087995420.0038296%CF-causing
c.3528delCp. Lys1177SerfsX153659delCrs1219087475390.0037999%CF-causing
c.1040G>Cp.Arg347ProR347Prs779321965330.0037568%CF-causing
c.1210−12T[5]No protein name5Trs18051775160.0036328%Varying clinical consequence
c.2988+1G>ANo protein name3120+1G->Ars750965515010.0035398%CF-causing
c.1364C>Ap.Ala455GluA455Ers745511285000.0035234%CF-causing
c.3140-26A>GNo protein name3272-26A->Grs761518044700.0033129%CF-causing
c.1000C>Tp.Arg334TrpR334Wrs1219090114290.0030240%CF-causing
c.1766+1G>ANo protein name1898+1G->Ars1219087484210.0029699%CF-causing
c.54-5940_273+10250del21kbp.Ser18ArgfsX16CFTRdele2,3not found4170.00294100%CF-causing
c.1679G>Cp.Arg560ThrR560Trs800556103430.0024198%CF-causing
c.617T>Gp. Leu206TrpL206Wrs1219087523330.0023420%CF-causing
c.2052dupAp.Gln685ThrfsX42184insArs1219087863290.0023285%CF-causing
c.262_263delTTp. Leu88IlefsX22394delTTrs1219087693070.0021697%CF-causing
c.178G>Tp.Glu60XE60Xrs772848922960.0020899%CF-causing
c.1477C>Tp.Gln493XQ493Xrs771012172920.0020698%CF-causing
c.579+1G>TNo protein name711+1G->Trs771883912740.0019398%CF-causing
c.2052delAp. Lys684AsnfsX382184delArs1219087462550.0018098%CF-causing
c.200C>Tp.Pro67LeuP67Lrs3685057532390.0016834%CF-causing
c.3302T>Ap.Met1101LysM1101Krs362107372380.0016869%CF-causing
c.1408A>Gp.Met470ValM470Vrs2139502350.0016546%Non CF-causing
c.3276C>A or c.3276C>Gp.Tyr1092XY1092Xrs1219087612250.0015898%CF-causing
c.3196C>Tp.Arg1066CysR1066Crs781942162200.0015598%CF-causing
c.1021_1022dupTCp.Phe342HisfsX281154insTCrs3879063602140.0015199%CF-causing
c.3773dupTp. Leu1258PhefsX73905insTrs1219087892100.0014897%CF-causing
c.1646G>Ap.Ser549AsnS549Nrs1219087552030.0014384%CF-causing
c.1040G>Ap.Arg347HisR347Hrs779321961990.0014024%CF-causing
c.948delTp.Phe316LeufsX121078delTrs1219087441840.0013099%CF-causing
c.1210-33_1210-6GT[12]T[4]No protein name5T;TG12not found1820.0012814%Varying clinical consequence
c.3472C>Tp.Arg1158XR1158Xrs798502231790.0012699%CF-causing
c.2834C>Tp.Ser945LeuS945Lrs3975084421670.0011840%CF-causing
c.1558G>Tp. Val520PheV520Frs776469041560.0011098%CF-causing
c.443T>Cp. Ile148ThrI148Trs355162861480.0010488%Non CF-causing
c.349C>Tp.Arg117CysR117Crs778341691460.0010324%CF-causing

DeltaF508

DeltaF508 (ΔF508), full name CFTRΔF508 or F508del-CFTR (rs113993960), is a specific mutation within the CFTR gene involving a deletion of three nucleotides spanning positions 507 and 508 of the CFTR gene on chromosome 7, which ultimately results in the loss of a single codon for the amino acid phenylalanine (F). A person with the CFTRΔF508 mutation will produce an abnormal CFTR protein that lacks this phenylalanine residue and which cannot fold properly. This protein does not escape the endoplasmic reticulum for further processing. Having two copies of this mutation (one inherited from each parent) is by far the most common cause of cystic fibrosis (CF), responsible for nearly two-thirds of mutations worldwide.[18]

Effects

The CFTR protein is largely expressed in cells of the pancreas, intestinal and respiratory epithelia, and all exocrine glands. When properly folded, it is shuttled to the cell membrane, where it becomes a transmembrane protein responsible for opening channels which release chloride ions out of cells; it also simultaneously inhibits the uptake of sodium ions by another channel protein. Both of these functions help to maintain an ion gradient that causes osmosis to draw water out of the cells.[19] The ΔF508 mutation leads to the misfolding of CFTR and its eventual degradation in the ER. In organisms with two complements of the mutation, the protein is entirely absent from the cell membrane, and these critical ion transport functions are not performed.[20]

Having a homozygous pair of genes with the ΔF508 mutation prevents the CFTR protein from assuming its normal position in the cell membrane. This causes increased water retention in cells, corresponding dehydration of the extracellular space, and an associated cascade of effects on various parts of the body. These effects include: thicker mucous membranes in the epithelia of afflicted organs; obstruction of narrow respiratory airways as a result of thicker mucous and inhibition of the free movement of mucocilia; congenital absence of the vas deferens due to increased mucus thickness during fetal development; pancreatic insufficiency due to blockage of the pancreatic duct with mucus; and increased risk of respiratory infection due to build-up of thick, nutrient-rich mucus where bacteria thrive. These are the symptoms of cystic fibrosis, a genetic disorder; however, ΔF508 is not the only mutation that causes this disorder.

Being a heterozygous carrier (having a single copy of ΔF508) results in decreased water loss during diarrhea because malfunctioning or absent CFTR proteins cannot maintain stable ion gradients across cell membranes. Typically there is a build-up of both Cl− and Na+ ions inside affected cells, creating a hypotonic solution outside the cells and causing water to diffuse into the cells by osmosis. Several studies indicate that heterozygous carriers are at increased risk for various symptoms. For example, it has been shown that heterozygosity for cystic fibrosis is associated with increased airway reactivity, and heterozygotes may be at risk for poor pulmonary function. Heterozygotes with wheeze have been shown to be at higher risk for poor pulmonary function or development and progression of chronic obstructive lung disease. One gene for cystic fibrosis is sufficient to produce mild lung abnormalities even in the absence of infection.[21]

Mechanism

The CFTR gene is located on the long arm of chromosome 7, at position q31.2, and ultimately codes for a sequence of 1,480 amino acids. Normally, the three DNA base pairs A-T-C (paired with T-A-G on the opposite strand) at the gene's 507th position form the template for the mRNA codon A-U-C for isoleucine, while the three DNA base pairs T-T-T (paired with A-A-A) at the adjacent 508th position form the template for the codon U-U-U for phenylalanine.[22] The ΔF508 mutation is a deletion of the C-G pair from position 507 along with the first two T-A pairs from position 508, leaving the DNA sequence A-T-T (paired with T-A-A) at position 507, which is transcribed into the mRNA codon A-U-U. Since A-U-U also codes for isoleucine, position 507's amino acid does not change, and the mutation's net effect is equivalent to a deletion ("Δ") of the sequence resulting in the codon for phenylalanine at position 508.[23]

Prevalence

ΔF508 is present on at least one copy of chromosome 7 in approximately one in 30 Caucasians. Presence of the mutation on both copies causes the autosomal recessive disease cystic fibrosis. Scientists have estimated that the original mutation occurred over 52,000 years ago in Northern Europe. The young allele age may be a consequence of past selection. One hypothesis as to why the otherwise detrimental mutation has been maintained by natural selection is that a single copy may present a positive effect by reducing water loss during cholera, though the introduction of pathogenic Vibrio cholerae into Europe did not occur until the late 18th century.[24] Another theory posits that CF carriers (heterozygotes for ΔF508) are more resistant to typhoid fever, since CFTR has been shown to act as a receptor for Salmonella typhi bacteria to enter intestinal epithelial cells.[25]

Cystic fibrosis ΔF508 heterozygotes may be overrepresented among individuals with asthma and may have poorer lung function than non-carriers.[26][27] Carriers of a single CF mutation have a higher prevalence of chronic rhinosinusitis than the general population.[28] Approximately 50% of cystic fibrosis cases in Europe are due to homozygous ΔF508 mutations (this varies widely by region),[29] while the allele frequency of ΔF508 is about 70%.[30] The remaining cases are caused by over 1,500 other mutations, including R117H, 1717-1G>A, and 2789+56G>A. These mutations, when combined with each other or even a single copy of ΔF508, may cause CF symptoms. The genotype is not strongly correlated with severity of the CF, though specific symptoms have been linked to certain mutations.

Structure

The Overall Structure of Human CFTR in the Dephosphorylated, ATP-Free Conformation. Domains are labeled. Made from PDB 5UAK

The CFTR gene is approximately 189 kb in length, with 27 exons and 26 introns.[31] CFTR is a glycoprotein with 1480 amino acids. The protein consists of 7 domains. There are 2 transmembrane domains, each with 6 spans of alpha helices. These are each connected to a nucleotide binding domain (NBD) in the cytoplasm. The first NBD is connected to the second transmembrane domain by a regulatory "R" domain that is a unique feature of CFTR, not present in other ABC transporters. The ion channel only opens when its R-domain has been phosphorylated by PKA and ATP is bound at the NBDs.[32] The amino-terminus is part of the lasso motif which anchors into the cell membrane.[33] The carboxyl terminal of the protein is anchored to the cytoskeleton by a PDZ-interacting domain.[34] The structure shown (PDB# 1XMI) shows a homopentameric assembly of mutated NBD1, the first nucleotide binding domain (NBD1) of the transporter.

Location and function

The CFTR protein is a channel protein that controls the flow of H2O and Cl− ions in and out of cells inside the lungs. When the CFTR protein is working correctly, as shown in Panel 1, ions freely flow in and out of the cells. However, when the CFTR protein is malfunctioning as in Panel 2, these ions cannot flow out of the cell due to blocked CFTR channels. This occurs in cystic fibrosis, characterized by the buildup of thick mucus in the lungs.

CFTR functions as a phosphorylation and ATP-gated anion channel, increasing the conductance for certain anions (e.g. Cl−) to flow down their electrochemical gradient. ATP-driven conformational changes in CFTR open and close a gate to allow transmembrane flow of anions down their electrochemical gradient.[5] This in contrast to other ABC proteins, in which ATP-driven conformational changes fuel uphill substrate transport across cellular membranes. Essentially, CFTR is an ion channel that evolved as a 'broken' ABC transporter that leaks when in open conformation.

CFTRs have two transmembrane domains, each linked to a nucleotide-binding domain. CFTR also contains another domain called the regulatory domain. Other members of the ABC transporter superfamily are involved in the uptake of nutrients in prokaryotes, or in the export of a variety of substrates in eukaryotes. ABC transporters have evolved to transduce the free energy of ATP hydrolysis to the uphill movement of substrates across the cell membrane. They have two main conformations, one where the cargo binding site is facing the cytosol or inward facing (ATP free), and one where it is outward facing (ATP bound). ATP binds to each nucleotide binding domain, which results in the subsequent NBD dimerization, leading to the rearrangement of the transmembrane helices. This changes the accessibility of the cargo binding site from an inward facing position to an outward facing one. ATP binding, and the hydrolysis that follows, drives the alternative exposure of the cargo binding site, ensuring a unidirectional transport of cargo against an electrochemical gradient. In CFTR, alternating between an inward-facing conformation to an outward-facing one results in channel gating. In particular, NBD dimerization (favoured by ATP binding) is coupled to transition to an outward-facing conformation in which an open transmembrane pathway for anions is formed. Subsequent hydrolysis (at the canonical active site, site 2, including Walker motifs of NBD2) destabilizes the NBD dimer and favours return to the inward-facing conformation, in which the anion permeation pathway is closed off.[5]

The CFTR is found in the epithelial cells of many organs including the lung, liver, pancreas, digestive tract, and the female[35] and male reproductive tracts.[36][37]

In the airways of the lung, CFTR is most highly expressed by rare specialized cells called pulmonary ionocytes.[38][39][40] In the skin CFTR is strongly expressed in the sebaceous and eccrine sweat glands.[41] In the eccrine glands, CFTR is located on the apical membrane of the epithelial cells that make up the duct of these sweat glands.[41]

Normally, the protein allows movement of chloride and thiocyanate[42] ions (with a negative charge) out of an epithelial cell into the Airway Surface Liquid and mucus. Positively charged sodium ions follow passively, increasing the total electrolyte concentration in the mucus, resulting in the movement of water out of the cell via osmosis.

In epithelial cells with motile cilia lining the bronchus and the oviduct, CFTR is located on the apical cell membrane but not on cilia.[35] In contrast, ENaC (Epithelial sodium channel) is located along the entire length of the cilia.[35]

In sweat glands, defective CFTR results in reduced transport of sodium chloride and sodium thiocyanate[43] in the reabsorptive duct and therefore saltier sweat. This is the basis of a clinically important sweat test for cystic fibrosis often used diagnostically with genetic screening.[44]

Interactions

Cystic fibrosis transmembrane conductance regulator has been shown to interact with:

It is inhibited by the anti-diarrhoea drug crofelemer.

  • Congenital bilateral absence of vas deferens: Males with congenital bilateral absence of the vas deferens most often have a mild mutation (a change that allows partial function of the gene) in one copy of the CFTR gene and a cystic fibrosis-causing mutation in the other copy of CFTR.
  • Cystic fibrosis: More than 1,800 mutations in the CFTR gene have been found[58] but the majority of these have not been associated with cystic fibrosis.[59] Most of these mutations either substitute one amino acid (a building block of proteins) for another amino acid in the CFTR protein or delete a small amount of DNA in the CFTR gene. The most common mutation, called ΔF508, is a deletion (Δ) of one amino acid (phenylalanine) at position 508 in the CFTR protein. This altered protein never reaches the cell membrane because it is degraded shortly after it is made. All disease-causing mutations in the CFTR gene prevent the channel from functioning properly, leading to a blockage of the movement of salt and water into and out of cells. As a result of this blockage, cells that line the passageways of the lungs, pancreas, and other organs produce abnormally thick, sticky mucus. This mucus obstructs the airways and glands, causing the characteristic signs and symptoms of cystic fibrosis. In addition, only thin mucus can be removed by cilia; thick mucus cannot, so it traps bacteria that give rise to chronic infections.
  • Cholera: ADP-ribosylation caused by cholera toxin results in increased production of cyclic AMP which in turn opens the CFTR channel which leads to oversecretion of Cl−. Na+ and H2O follow Cl− into the small intestine, resulting in dehydration and loss of electrolytes.[60]

Drug target

CFTR has been a drug target in efforts to find treatments for related conditions. Ivacaftor (trade name Kalydeco, developed as VX-770) is a drug approved by the FDA in 2012 for people with cystic fibrosis who have specific CFTR mutations.[61][62] Ivacaftor was developed by Vertex Pharmaceuticals in conjunction with the Cystic Fibrosis Foundation and is the first drug that treats the underlying cause rather than the symptoms of the disease.[63] Called "the most important new drug of 2012",[64] and "a wonder drug"[65] it is one of the most expensive drugs, costing over US$300,000 per year, which has led to criticism of Vertex for the high cost.

References

  1. 1 2 3 GRCh38: Ensembl release 89: ENSG00000001626 - Ensembl, May 2017
  2. 1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000041301 - Ensembl, May 2017
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  4. ↑ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. 1 2 3 Csanády L, Vergani P, Gadsby DC (January 2019). "Structure, Gating, and Regulation of the CFTR Anion Channel" (PDF). Physiological Reviews. 99 (1): 707–738. doi:10.1152/physrev.00007.2018. PMID 30516439.
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  22. ↑ CCDS Report for Consensus CDS: Report for CCDS5773.1 (current version) NCBI
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  28. ↑ Wang X, Kim J, McWilliams R, Cutting GR (March 2005). "Increased prevalence of chronic rhinosinusitis in carriers of a cystic fibrosis mutation". Archives of Otolaryngology–Head & Neck Surgery. 131 (3): 237–40. doi:10.1001/archotol.131.3.237. PMID 15781764.
  29. ↑ ECFS Annual Report: What It Means to the UK Cystic Fibrosis Trust
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  31. ↑ Cystic Fibrosis Mutation Database. "Genomic DNA sequence". Archived from the original on 2016-08-22. Retrieved 2013-04-06.
  32. ↑ Sheppard DN, Welsh MJ (January 1999). "Structure and function of the CFTR chloride channel". Physiological Reviews. 79 (1 Suppl): S23-45. doi:10.1152/physrev.1999.79.1.S23. PMID 9922375.
  33. ↑ Zhang Z, Liu F, Chen J (December 2018). "Molecular structure of the ATP-bound, phosphorylated human CFTR". Proceedings of the National Academy of Sciences of the United States of America. 115 (50): 12757–12762. doi:10.1073/pnas.1815287115. PMC 6294961. PMID 30459277.
  34. 1 2 Short DB, Trotter KW, Reczek D, Kreda SM, Bretscher A, Boucher RC, et al. (July 1998). "An apical PDZ protein anchors the cystic fibrosis transmembrane conductance regulator to the cytoskeleton". The Journal of Biological Chemistry. 273 (31): 19797–801. doi:10.1074/jbc.273.31.19797. PMID 9677412.
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