Cystic fibrosis: Genetics and pathogenesis

INTRODUCTION — Cystic fibrosis (CF) is a multisystem disease affecting the lungs, digestive system, sweat glands, and reproductive tract. The primary abnormality is in transport of chloride and sodium across secretory epithelia, resulting in thickened, viscous secretions in the bronchi, biliary tract, pancreas, intestines, and reproductive system [1,2]. Although the disease is systemic, progressive lung disease continues to be the major cause of morbidity and mortality for most patients. Over a highly variable time course ranging from months to decades after birth, individuals eventually develop chronic infection of the respiratory tract with a characteristic array of bacterial flora, leading to progressive respiratory insufficiency and eventual respiratory failure [3].

The genetics and pathogenesis of CF are discussed here. CF-associated lung disease is discussed in the following topic reviews:

●(See "Cystic fibrosis: Clinical manifestations of pulmonary disease".)

●(See "Cystic fibrosis: Overview of the treatment of lung disease".)

●(See "Cystic fibrosis: Treatment with CFTR modulators".)

●(See "Cystic fibrosis: Management of pulmonary exacerbations".)

●(See "Cystic fibrosis: Antibiotic therapy for chronic pulmonary infection".)

●(See "Cystic fibrosis: Management of advanced lung disease".)

The diagnosis and pathophysiology of CF and its manifestations in other organ systems are also discussed separately:

●(See "Cystic fibrosis: Clinical manifestations and diagnosis".)

●(See "Cystic fibrosis-related diabetes mellitus".)

●(See "Cystic fibrosis: Overview of gastrointestinal disease".)

●(See "Cystic fibrosis: Assessment and management of pancreatic insufficiency".)

●(See "Cystic fibrosis: Nutritional issues".)

●(See "Cystic fibrosis: Hepatobiliary disease".)

GENETICS — CF is caused by pathogenic mutations in a single large gene on chromosome 7 that encodes the cystic fibrosis transmembrane conductance regulator (CFTR) protein [4-9]. Clinical disease generally requires pathogenic mutations in both copies of the CFTR gene, but individuals with a single pathogenic variant (carrier status) occasionally develop disease limited to one organ system, known as CFTR-related disorder. (See 'CFTR-related disorder' below.)

The normal CFTR gene — CFTR belongs to the ABC (ATP-binding cassette) family of proteins, a large group of related proteins that share transmembrane transport functions. ABC proteins include bacterial transporters for amino acids and other nutrients, surfactant transport proteins, and the mammalian multidrug-resistant (MDR) protein (or P-glycoprotein).

CFTR functions as a regulated chloride channel, which, in turn, may regulate the activity of other chloride and sodium channels at the cell surface [10-13]. The CFTR gene spans 250 kilobases on chromosome 7, encoding 1480 amino acids in the mature protein (figure 1). The protein has two groups of six membrane-spanning regions, two intracellular nucleotide-binding folds (NBFs), and a highly charged "R domain" containing multiple phosphorylation sites. Activation of the chloride channel requires phosphokinase A-mediated phosphorylation of the R domain and the continuous presence of ATP in the NBFs [14,15].

Genetic changes in CFTR — The phenotypic expression of disease varies widely, primarily as a function of the specific mutation (or mutations) present [16-21]. The CFTR2 database lists more than 2000 different mutations in the CFTR gene with potential to cause disease.

The most common pathogenic mutation is F508del (also noted as delta F508, delF508, p.Phe508del, or c.1521_1523delCTT, all of which describe the deletion of three DNA bases coding for the 508^th amino acid residue phenylalanine). At least one copy of this mutation is found in approximately 90 percent of CF patients, and 50 percent are homozygotes [22]. Certain mutations are found at higher frequency in some ethnic groups because of apparent founder effects. As an example, five mutations account for an estimated 97 percent of CF alleles in the Ashkenazi Jewish population [23]. A subset of the most frequent CFTR mutations is used for initial screening since the majority of individual mutations are very rare (table 1) [24]. (See "Cystic fibrosis: Clinical manifestations and diagnosis", section on 'Molecular diagnosis'.)

Mutations of the CFTR gene have been divided into five different classes as depicted in the figures (figure 2 and figure 3) [2,25-27]. In general, mutations in classes I to III cause more severe disease than those in classes IV and V [19,27]. However, the clinical implications of a specific combination of mutations vary, likely because of the influence of gene modifiers and other elements of the protein network that mediates CFTR folding, trafficking, and function; this network is sometimes termed the CFTR "functional landscape" [28]. Genotype-phenotype correlations are weak for pulmonary disease in CF and somewhat stronger for the pancreatic insufficiency phenotype. (See 'Gene modifiers' below.)

In most cases, specific mutations should not be used to make assumptions about the severity of disease in an individual patient. Knowledge of the mutations may be useful to guide initial therapy, but clinical decisions should be guided by observable parameters of growth, lung function, and nutritional status. Some new therapies are directed at specific classes of CFTR mutation.

Class I mutations: Defective protein production — This type of defect is usually caused by nonsense, frameshift, or splice-site mutations, leading to premature termination of the messenger RNA (mRNA) and complete absence of CFTR protein. Examples include G542X, W1282X, R553X, 621+G>T, and 1717-1G>A [27,29]. This type of mutation is present in approximately 20 percent of patients with CF (figure 3). In some genetically homogenous populations, the percentage may be much higher [30].

Class II mutations: Defective protein processing — Class II mutations in the CFTR sequence cause abnormal post-translational processing of the CFTR protein, which prevents the protein from trafficking to the correct cellular location (figure 3). This category includes the F508del (c.1521_1523delCTT) mutation. Approximately 50 percent of CF patients are homozygous for this mutation, and 90 percent will carry at least one copy [27]. N1303Lys (N1303K) and A455E are also class II mutations; the latter is associated with relatively mild lung disease and pancreatic sufficiency. Newly developed modulators of CFTR (eg, the triple drug combination elexacaftor-tezacaftor-ivacaftor) function in part by causing the cell to send the defective CFTR protein to the cell surface, where it may have some degree of function. (See "Cystic fibrosis: Treatment with CFTR modulators".)

Class III mutations: Defective regulation — Class III mutations, also known as gating mutations, lead to diminished channel activity in response to ATP. Many involve alterations of the NBF regions, NBO1 and NBO2, which may retain varying degrees of sensitivity to nucleotide binding (figure 2). Other CFTR mutations, mapped to the R domain, may also fall into this category. G551D is the most common class III mutation in White populations [27]. Ivacaftor, a modulator of CFTR function, improves CFTR function in patients with gating defects by allowing constitutive (ie, unmodulated) opening of the CFTR channel; these and other mutations that are responsive to ivacaftor are included in the table (table 2). (See "Cystic fibrosis: Treatment with CFTR modulators", section on 'Ivacaftor monotherapy'.)

Class IV mutations: Defective conduction — With class IV mutations, the protein is produced and correctly localized to the cell surface. However, although chloride currents are generated in response to cAMP stimulation, the rate of ion flow and the duration of channel opening are reduced when compared with normal CFTR function. R117H is the most common class IV mutation in White populations [27].

Class V mutations: Reduced amounts of functional CFTR protein — This class of mutation is not included in some schemes. It includes mutations that alter the stability of mRNA and others that alter the stability of the mature CFTR protein (the latter is sometimes classified separately into a class VI) [31,32]. The mutation A455E has been classified as class II [29] or class V [19,33,34].

GENE MODIFIERS — The inconsistent association between CF genotypes and phenotypes points to a role for gene modifiers. These genetic variations are not directly related to the CFTR gene (cystic fibrosis transmembrane conductance regulator) but affect the severity or clinical manifestations of disease. Research into a variety of candidate genes is ongoing. There is good evidence that the following genes act as modifiers in CF and that approximately 20 percent of patients with classic CF carry mutations in one or both of these genes that exacerbates the pulmonary disease [35].

●Transforming growth factor-beta 1 (TGF-beta 1) – TGF-beta is a potent suppressor of T cell activation and can decrease T cell proliferation and cytokine production. In a study of 808 patients who were homozygous for the F508del mutation, polymorphisms in the TGF-beta 1 gene were associated with more severe CF lung disease [36]. (See "The adaptive cellular immune response: T cells and cytokines", section on 'Role of cytokines in negative feedback' and "The adaptive cellular immune response: T cells and cytokines", section on 'Treg'.)

●Mannose-binding lectin (MBL) – MBL is an important component of the complement system, and deficiencies in this protein increase the risk for pyogenic infections. In individuals with CF, variant MBL alleles are associated with reduced lung function, increased risk for chronic Pseudomonas aeruginosa and Burkholderia cepacia complex infections, and early death [37]. In young patients with CF and pancreatic insufficiency, lower MBL-2 protein levels were associated with a steeper rate of decline in lung function and earlier age at first infection with P. aeruginosa [35]. These effects were exaggerated in individuals who also carried the TGF-beta 1 variant described above. (See "Inherited disorders of the complement system".)

INCOMPLETE PHENOTYPE

CFTR-related disorder — A cystic fibrosis transmembrane conductance regulator (CFTR)-related disorder is defined as clinical disease limited to only one organ system associated with some evidence of CFTR dysfunction that does not meet full genetic or functional criteria for a CF diagnosis. Clinical manifestations may include isolated obstructive azoospermia, chronic rhinosinusitis, chronic pancreatitis, or pulmonary disease in adulthood [38,39]. The pathogenetic mechanism responsible for clinical disease without two CFTR gene mutations is unclear, but other genetic or environmental factors likely contribute to the risk in some cases. (See "Cystic fibrosis: Clinical manifestations and diagnosis", section on 'CFTR-related disorder'.)

CFTR-related metabolic syndrome — CFTR-related metabolic syndrome (CRMS) is a term that describes infants and children with an equivocal diagnosis following newborn screening for CF and is found in 3 to 4 percent of infants with a positive newborn screen (table 3). The term "CF screen positive, inconclusive diagnosis" (CFSPID) is equivalent and is used in Europe. (See "Cystic fibrosis: Clinical manifestations and diagnosis", section on 'CRMS/CFSPID'.)

DISEASE PATHOGENESIS — The pathogenesis of the organ dysfunction seen in CF has been studied in humans and cystic fibrosis transmembrane conductance regulator (CFTR)-knockout mice but remains incompletely understood [40,41]. It appears that the physical and chemical abnormalities of CF airway secretions result in chronic infection with phenotypically unique bacteria, particularly Pseudomonas species. Other genetic factors, including polymorphisms of the tumor necrosis factor alpha (TNF-alpha) gene, may increase susceptibility to P. aeruginosa infection and contribute to the clinical manifestations of CF [42].

Primary abnormalities in fatty acid metabolism have been noted in biopsies of CFTR-expressing tissue from patients with CF [43]. These changes, which result in increased tissue levels of arachidonic acid, also are present in the mouse model of CF but are not seen in tissue from patients with inflammatory bowel disease. Thus, increased tissue expression of arachidonic acid and its metabolites may contribute to the abnormal inflammation characteristic of CF.

Abnormal secretions — CFTR malfunction in the respiratory epithelium is associated with a variety of changes in electrolyte and water transport. The mechanisms involved and ultimate electrolyte composition of airway surface fluid in CF airways is a subject of ongoing research [11-13,44-47]. The net result of these changes is an alteration in the rheology of airway secretions, which become thick and difficult to clear [48]. An associated finding is an increased concentration of chloride in sweat secretions, which constitutes one of the methods of diagnosis of CF. (See "Cystic fibrosis: Clinical manifestations and diagnosis".)

Gastrointestinal effects — Thickened secretions caused by CFTR malfunction cause the gastrointestinal complications of CF. Impaired flow of bile and pancreatic secretions cause maldigestion and malabsorption, as well as progressive liver and pancreatic disease, leading to CF-related diabetes. Because of thickened intestinal secretions and maldigestion, CF patients are prone to intestinal obstruction (distal intestinal obstruction syndrome or intussusception) and to rectal prolapse. (See "Cystic fibrosis: Overview of gastrointestinal disease".)

Chronic lung infection — The chronic airway obstruction caused by viscous secretions is followed by progressive pulmonary colonization with pathogenic bacteria, including Haemophilus influenzae, Staphylococcus aureus, and eventually P. aeruginosa and/or B. cepacia complex bacteria. (See "Cystic fibrosis: Clinical manifestations of pulmonary disease", section on 'Progression of pulmonary disease'.)

Once infection is established, neutrophils are unable to control the bacteria, even though there is massive infiltration of these inflammatory cells into the lung tissue [49]. Recruited neutrophils subsequently release elastase, which overwhelms the antiproteases of the lung and contributes to tissue destruction in a process known as "prolonged endobronchial protease activity" [50]. In addition, large amounts of DNA and cytosol matrix proteins are released by degranulating neutrophils, contributing to the increased viscosity of the airway mucus [51].

Inflammation has been noted prior to the development of bacterial colonization and may be triggered by viral infections [52]. In turn, chronic infection appears to be the major stimulus for an exuberant but ultimately ineffective inflammatory response that subsequently results in bronchiectasis [53,54]. The inflammatory response itself appears to contribute to the progression of pulmonary dysfunction; this mechanism is the basis for the use of some antiinflammatory agents in treating CF lung disease [55,56].

Individuals with CF are particularly prone to chronic infection with P. aeruginosa, due in part to increased oxygen utilization by epithelial cells, which results in an abnormally decreased oxygen tension within the hyperviscous mucous layer (figure 4) [57]. This local hypoxia induces the characteristic phenotypic changes in P. aeruginosa (and some other gram-negative bacteria), including alginate production and loss of motility. This phenotype is consistent with the development of bacterial macrocolonies (or "biofilms") within the hypoxic regions of the airway mucus layer. Once this occurs, eradication of the organism is almost impossible. (See "Epidemiology, microbiology, and pathogenesis of Pseudomonas aeruginosa infection", section on 'Persistence of the organism in the airways'.)

The frequent colonization and persistent infection caused by P. aeruginosa in CF patients is also related to the defective CFTR protein itself [49]. Normal CFTR protein serves as the receptor for binding of P. aeruginosa lipopolysaccharide in vitro and extracts lipopolysaccharide from the surface of the organism for endocytosis into epithelial cells [45,58,59]. This results in increased intranuclear translocation of the nuclear transcription factor NF kappa B and subsequent immunoactivation [58-60]. This process does not occur in the presence of abnormal CFTR or in CFTR-knockout mice [60], which may partially explain the inability of CF patients to control these infections. Disease-modifier genes appear to further affect the predisposition to P. aeruginosa infection, as described above. (See 'Gene modifiers' above and "Epidemiology, microbiology, and pathogenesis of Pseudomonas aeruginosa infection".)

SOCIETY GUIDELINE LINKS — Links to society and government-sponsored guidelines from selected countries and regions around the world are provided separately. (See "Society guideline links: Cystic fibrosis".)

SUMMARY

●Genetic basis of cystic fibrosis

•Cystic fibrosis (CF) is caused by mutations in a single large gene on chromosome 7 that encodes the cystic fibrosis transmembrane conductance regulator (CFTR) protein. (See 'Genetics' above.)

•Clinical disease requires disease-causing mutations in both copies of the CFTR gene. The phenotypic expression of disease varies widely, as a function of the specific mutations present and the presence of gene modifiers. (See 'Genetic changes in CFTR' above.)

●CFTR mutation classes – Mutations of the CFTR gene have been divided into five different classes, depicted in the figures (figure 2 and figure 3). In general, mutations in classes I to III cause more severe disease than those in classes IV and V. However, the clinical implications of a specific combination of mutations are often unclear and specific mutations should not be used to make assumptions about the severity of disease in an individual patient. (See 'Genetic changes in CFTR' above.)

●Common CFTR mutations

•A subset of the most frequent CFTR mutations is recommended for initial testing since the majority of individual mutations are very rare (table 1). (See 'Genetic changes in CFTR' above.)

•The most common mutation is F508del (also noted as delta F508 or c.1521_1523delCTT, referring to deletion of three DNA bases coding for the 508^th amino acid residue phenylalanine), which is found in approximately 70 percent of White patients with CF in the United States. (See 'Class II mutations: Defective protein processing' above.)

●Gene modifiers – Gene modifiers are genetic variations that are not directly related to the CFTR gene but which nonetheless affect the severity or clinical manifestations of disease. Transforming growth factor-beta (TGF-beta) and mannose-binding lectin (MBL) are important gene modifiers in CF, and approximately 20 percent of CF patients carry variants in one or both of these genes that may exacerbate the pulmonary disease. (See 'Gene modifiers' above.)

●Disease pathogenesis

•CFTR malfunction is associated with low water content in secretions from the respiratory, pancreatic, and biliary epithelium, which causes the secretions to be viscous and difficult to clear. (See 'Abnormal secretions' above.)

•In the gastrointestinal tract, the abnormal bile and pancreatic secretions cause maldigestion and malabsorption, progressive liver and pancreatic disease, rectal prolapse, and intestinal obstruction (distal intestinal obstruction syndrome or intussusception). (See 'Gastrointestinal effects' above.)

•In the lung, the abnormal secretions cause chronic airway obstruction and reduce bactericidal killing, leading to progressive pulmonary colonization with pathogenic bacteria and to the formation of bacterial biofilms. Chronic infection causes an inflammatory response and tissue destruction, causing bronchiectasis. Infection with Pseudomonas aeruginosa is particularly favored in patients with CF due to abnormally decreased oxygen tension within the hyperviscous mucous layer. (See 'Chronic lung infection' above.)