Exomes to the extreme to identify modifier gene in cystic fibrosis

Monogenic modifiers. Exome sequencing is a well established method to find causative genes in monogenic disorders, with probably more than 100 genes identified through this method in the last two years. In contrast to the ever-expanding list of monogenic diseases solved through massive parallel sequencing, there is widespread skepticism regarding its usefulness in complex genetic disorders. Now, a recent study in Nature Genetics suggests another application for exome sequencing, the identification of modifier genes in monogenic disorders.

Cystic fibrosis and Pseudomonas aeruginosa. Cystic fibrosis (CF or mucoviscidosisis) is a multisystem disease due to recessive mutations in CFTR, the gene coding for cystic fibrosis transmembrane conductance regulator. Defects in this protein lead to an abnormal transport of sodium and chloride across epithelial cells, resulting in thickened mucous. This viscerous mucous leads to impaired organ function in lungs and sinuses, the gastrointestinal tract and endocrine organs. Patients with CF are prone to infections with atypical pathogens. Particularly P. aeruginosa infections represent a common problem as this bacteria is resistant to many antibiotic drugs. Early P. aeruginosa acquisition is associated with a poor outcome in CF patients. The reason why some patients acquire P. aeruginosa at different stages of their disease is unknown and some patients are colonized quite early. Via exome sequencing, a recent study by Emond et al. now identifies mutations in DCTN4 to be associated with early P. aeruginosa colonization in CF patients, a novel, interesting strategy to identify modifying genetic factors.

DCTN4 in CF patients. Emond and collaborators used a so-called extreme design for 91 patients, chosing the patients with the youngest and oldest age for P. aeruginosa colonization. Using logistic regression, they identified mutations in the DCTN4, coding for a dynactin protein involved intracellular transport. Looking back at the original data after the initial analysis, 12/43 early colonizers and 0/48 later colonizers carried mutations in DCTN4.  Subsequently, the authors followed their findings up in a cohort of ~700 CF patients and found that the presence of at least one missense mutation in DCTN4 is associated with age of P. aeruginosacolonization, basically validating their finding from the screening cohort. In summary, mutations in DCTN4 predispose to P. aeruginosa colonization in CF patients and represent and important modifier for a relatively common autosomal recessive disorder.

Study design used by Emond et al. to identify DCTN4 as a genetic modifier for Cystic Fibrosis. In the first stage, the authors used an extreme design, followed by confirmation in a large second cohort of CF patients.

A taste of complexity. Genetic research in monogenic disorders does not stop with the identification of the causative gene. Many monogenic disorders have variable expressivity, and genetic and non-genetic modifiers are thought to be involved. In fact, these modifiers might have a particular medical relevance as they can provide a glimpse into possible mechanism for treatment. The study by Emond et al. is also interesting from a technical standpoint. There is little you can do with 100 exomes in complex genetic disorders, as risk factors are either strong but rare or common but weak, resulting in insufficient statistical power for this analysis with moderate sample sizes. However, modifiers may well be identified within a smaller cohort. Historically, the extreme design is particularly successful in human genetics. The first common variants through genome-wide association studies were also identified in a similar design in age-related macular degeneration (AMD).

Application to epilepsy. CF has little to do with epilepsy, but a similar approach might be feasible to identify modifying genetic risk factors in genetic epilepsies. Particularly some genetic epilepsies are known for the variable expressivity including Genetic Epilepsy with Febrile Seizures Plus (GEFS+). Also, there is already some indication that variants in SCN9A may modify the phenotypic expression of Dravet Syndrome, but the initial study has not yet been successfully validated. However, why look for candidate genes when exome sequencing is widely available? A similar study design to the Emond study may in fact be possible for Dravet Syndrome comparing good and poor outcome. Likewise, genetic modifiers for pharmacological responses in epilepsy as studied in the EpiPGX project could be identified through such an approach.

 

4 thoughts on “Exomes to the extreme to identify modifier gene in cystic fibrosis

  1. Pingback: From unaffected to Dravet Syndrome – extreme SCN1A phenotypes in a large GEFS+ family | Beyond the Ion Channel

  2. Pingback: 2013 in review: top three lists and the gene finding of the year | Beyond the Ion Channel

  3. Pingback: Modifier genes in Dravet Syndrome: where to look and how to find them | Beyond the Ion Channel

  4. Pingback: SCN1A – This is what you need to know in 2014 | Beyond the Ion Channel

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