CFTR Modulators: The Changing Face of Cystic Fibrosis in the Era of Precision Medicine

Miquéias Lopes-Pacheco, Miquéias Lopes-Pacheco

Abstract

Cystic fibrosis (CF) is a lethal inherited disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene, which result in impairment of CFTR mRNA and protein expression, function, stability or a combination of these. Although CF leads to multifaceted clinical manifestations, the respiratory disorder represents the major cause of morbidity and mortality of these patients. The life expectancy of CF patients has substantially lengthened due to early diagnosis and improvements in symptomatic therapeutic regimens. Quality of life remains nevertheless limited, as these individuals are subjected to considerable clinical, psychosocial and economic burdens. Since the discovery of the CFTR gene in 1989, tremendous efforts have been made to develop therapies acting more upstream on the pathogenesis cascade, thereby overcoming the underlying dysfunctions caused by CFTR mutations. In this line, the advances in cell-based high-throughput screenings have been facilitating the fast-tracking of CFTR modulators. These modulator drugs have the ability to enhance or even restore the functional expression of specific CF-causing mutations, and they have been classified into five main groups depending on their effects on CFTR mutations: potentiators, correctors, stabilizers, read-through agents, and amplifiers. To date, four CFTR modulators have reached the market, and these pharmaceutical therapies are transforming patients' lives with short- and long-term improvements in clinical outcomes. Such breakthroughs have paved the way for the development of novel CFTR modulators, which are currently under experimental and clinical investigations. Furthermore, recent insights into the CFTR structure will be useful for the rational design of next-generation modulator drugs. This review aims to provide a summary of recent developments in CFTR-directed therapeutics. Barriers and future directions are also discussed in order to optimize treatment adherence, identify feasible and sustainable solutions for equitable access to these therapies, and continue to expand the pipeline of novel modulators that may result in effective precision medicine for all individuals with CF.

Keywords: CFTR mutations; cell models; clinical trials; cystic fibrosis; drug development; high-throughput screening; lung; personalized medicine.

Copyright © 2020 Lopes-Pacheco.

Figures

Figure 1
Figure 1
From gene to protein structure. (A) CF transmembrane conductance regulator (CFTR) gene is located on the long arm of chromosome (Chr) 7. (B) The gene contains 27 exons and spans approximately 190 kb of human genomic DNA. (C) The mRNA is 6.2 kb long including the untranslated regions (adapted from Collins, 1992). (D) The protein forms a chloride/bicarbonate channel composed of five domains: two transmembrane domains (TMD1 and TMD2), two nucleotide-binding domains (NBD1 and NBD2) and a regulatory domain (RD) (adapted from Lopes-Pacheco, 2016). (E) The overall structure of human CFTR in the dephosphorylated, ATP-free conformation (adapted from Liu et al., 2017 with permission from Prof. J. Chen). (F) The 2,075 CFTR gene variants that have so far been reported consist of missense (38.9%), frameshift (16.1%), splicing (11.1%), and nonsense (8.4%) mutations; in-frame (2.1%) and large (2.8%) deletions or insertions; promoter mutations (0.9%); and possibly non-pathogenic variants (13.0%) (adapted from CFTR1 Database).
Figure 2
Figure 2
Demography of cystic fibrosis patients in different countries. (A) Distribution according to the total number of patients registered. (B) Top 10 countries with the highest number of patients registered. (C) Distribution according to the estimated prevalence of patients per 100,000 habitants. (D) Top 10 countries with the highest number of patients per 100,000 habitants. Global distribution by gender (E) and by age (F). [Data compiled from the last Patient Registry Report in Argentina (Pereyro et al., 2018), Australia (Cystic Fibrosis Australia, 2018), Brazil (Brazilian Cystic Fibrosis Study Group, 2019), Canada (Cystic Fibrosis Canada, 2019), Europe (European Cystic Fibrosis Society, 2019), New Zealand (Cystic Fibrosis New Zealand, 2019), South Africa (Zampoli et al., 2019), UK (Cystic Fibrosis Trust, 2019), and the USA (Cystic Fibrosis Foundation, 2019)].
Figure 3
Figure 3
Demography of CF transmembrane conductance regulator (CFTR) mutations in different countries. (A) Distribution according to the percentage of patients carrying the F508del mutation in at least one allele. (B) Global distribution by CF genotype: F508del-homozygous, F508del-heterozygous and carrying non-F508del mutations in both alleles. (C) Top 25 most prevalent non-F508del CFTR mutations considering the whole CF population. [Data compiled from the last Patient Registry Report in Argentina (Pereyro et al., 2018), Australia (Cystic Fibrosis Australia, 2018), Brazil (Brazilian Cystic Fibrosis Study Group, 2019), Canada (Cystic Fibrosis Canada, 2019), Europe (European Cystic Fibrosis Society, 2019), New Zealand (Cystic Fibrosis New Zealand, 2019), UK (Cystic Fibrosis Trust, 2019), and the USA (Cystic Fibrosis Foundation, 2019), and CFTR2 Database].
Figure 4
Figure 4
Classes of CF transmembrane conductance regulator (CFTR) mutations. Class I mutations lead to no protein synthesis or translation of shortened, truncated forms. They result from splice site abnormalities, frameshifts due to deletions or insertions, or nonsense mutations, which generate premature termination codons (PTCs). Class II mutations lead to a misfolding protein that fails to achieve conformational stability in the endoplasmic reticulum and then does not traffic to the plasma membrane (PM), being instead prematurely degraded by proteasomes. Class III mutations lead to a gating channel defect due to impaired response to agonists, although the protein is present at the PM. Class IV mutations lead to a channel conductance defect with a significant reduction in CFTR-dependent chloride transport. Class V mutations lead to a reduction in protein abundance of functional CFTR due to reduced synthesis or inefficient protein maturation. They result from alternative splicing, promoter or missense mutations. Class VI mutations lead to reduced protein stability at the PM, which results in increased endocytosis and degradation by lysosomes, and reduced recycling to the PM. Mutations in classes I and II are also known as minimal function mutations since they demonstrate no to very little CFTR function, while those in classes IV, V, and VI are known as residual function mutations since they demonstrate some CFTR function, although it is lower compared to the wild type (WT)-CFTR. (adapted from Lopes-Pacheco, 2016).
Figure 5
Figure 5
Cellular and molecular defects and potential CF transmembrane conductance regulator (CFTR) modulator approaches. Flowchart demonstrating the steps to identify each cellular and molecular defect of a CFTR gene variant and potential therapeutic approaches to correct each of these defects. Abbreviations: A, abrogated; I, impaired; N, normal; R, rescued.
Figure 6
Figure 6
Chemical structure of several CF transmembrane conductance regulator (CFTR) modulators tested in clinical trials or currently in the market. Advances in high-throughput screening technologies have been enabling the identification of small-molecules from different chemical series. In addition to the compounds displayed in this figure, the compounds VX-121, ABBV-2737, ABBV-3067, FDL176, and PTI-808 are also under investigation in clinical trials, but the chemical structures are still not available on the PubChem or DrugBank. *Clinical development has been discontinued.
Figure 7
Figure 7
A common binding site for ABBV-974 and ivacaftor. Ribbon diagram of the phosphorylated, ATP-bound CFTR in complex with (A) ABBV-974 and (B) ivacaftor. These structures have been deposited on the Protein Data Bank under accession codes 6O1V (CFTR-ABBV-974) and 6O2P (CFTR-ivacaftor). (adapted from Liu F. et al., 2019 with permission from Prof. J. Chen).
Figure 8
Figure 8
Timeline with several milestones in experimental and clinical research for cystic fibrosis since the discovery of CF transmembrane conductance regulator (CFTR) gene in 1989. The knowledge accumulated over these 30 years has been ensuring a better understanding of the molecular biology and protein structure of CFTR, and the pathophysiology of CF in order to translate the basic sciences into clinical practice. More than 10 novel CF therapies have been approved by the U.S. Food and Drug Administration (FDA) during this period with four of these being CFTR modulator drugs.

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