Genetic variation and clinical heterogeneity in cystic fibrosis

Abstract

Cystic fibrosis (CF), a lethal genetic disease, is characterized by substantial clinical heterogeneity. Work over the past decade has established that much of the variation is genetically conferred, and recent studies have begun to identify chromosomal locations that identify specific genes as contributing to this variation. Transcriptomic and proteomic data, sampling hundreds and thousands of genes and their products, point to pathways that are altered in the cells and tissues of CF patients. Genetic studies have examined more than half a million polymorphic sites and have identified regions, and probably genes, that contribute to the clinical heterogeneity. The combination of these approaches has great potential because genetic profiling identifies putative disease-modifying processes, and transcript and protein profiling is shedding light on the biology involved. Such studies are providing new insights into the disease, such as altered apoptotic responses, oxidative stress dysregulation, and neuronal involvement, all of which may open new therapeutic avenues to exploration.

Figure 1

Effect of CFTR gene mutations on the cystic fibrosis transmembrane conductance regulator (CFTR) protein and function. (Top) The CFTR gene with examples of each of the mutation classes and their positions in the gene. The horizontal black arrow represents the transcriptional promoter, and the vertical lines represent exons. The 5′ and 3′ untranslated regions are designated by gray shading, and the mutations are designated by vertical arrows. (Bottom) The effects of the mutations on function; the mutation class (12) is circled. G542X, a class 1 mutation, creates a stop codon and causes no full-length, functional protein to be produced. F508del, a class 2 mutation, misfolds and is mostly degraded. If able to reach the plasma membrane, F508del does not activate as readily as normal CFTR; therefore, this mutation is a class 3 example. G551D, another class 3 example, is completely nonresponsive to activation. R117H, a class 4 mutation, resides in a transmembrane region of the protein and impairs chloride transit (conduction) through the channel pore. The T-tract variants in intron 8 represent class 5 mutations in that they alter splicing efficiency. These variants do not eliminate functional CFTR, which differentiates them from class 1 mutants. Note that the original description of CFTR contained only 24 exons; later, exons 6, 14, and 17 were found to contain small introns. These exons were renumbered 6a and 6b, 14a and 14b, and 17a and 17b. Thus, what is referred to as exon 10, for example, is actually exon 11.

Figure 2

Selection of candidate modifier genes. Cystic fibrosis (CF) pulmonary and airway disease has been modeled as a consequence of insufficient luminal hydration (including mucus), an inability to clear bacteria such as Pseudomonas aeruginosa, and an excessive inflammatory burden, either as a response to infection or inherent to CF epithelia. Candidate modifying genes were chosen for their potential to modulate these processes. Genes encoding epithelial ion channels were examined because they can influence airway luminal hydration. Genes encoding chemotactic signaling molecules, such as interleukin (IL)-1β, IL-8, and tumor necrosis factor (TNF)-α, were examined because they can influence the level of immune cell recruitment, and genes involved in antimicrobial processes or immune cell function were investigated because they may exert modifying effects on airway disease by influencing the ability to clear or suppress infection.

Figure 3

Location of single nucleotide polymorphisms (SNPs) identified by genome-wide association studies as associated with lung function. Clusters of associating SNPs are shown as gray boxes. The height of the box corresponds to the most significant SNP in the cluster. For chromosome 11, the most significant association lies between the genes APIP and EHF; less significant associations overlap both genes. The chromosome 20 association is most significant with SNPs 3′ to CBLN4, but there is also a peak over MC3R.