The Genetic Landscape of Dystrophin Mutations in Italy: A Nationwide Study

Abstract

Dystrophinopathies are inherited diseases caused by mutations in the dystrophin (DMD) gene for which testing is mandatory for genetic diagnosis, reproductive choices and eligibility for personalized trials. We genotyped the DMD gene in our Italian cohort of 1902 patients (BMD n = 740, 39%; DMD n =1162, 61%) within a nationwide study involving 11 diagnostic centers in a 10-year window (2008-2017). In DMD patients, we found deletions in 57%, duplications in 11% and small mutations in 32%. In BMD, we found deletions in 78%, duplications in 9% and small mutations in 13%. In BMD, there are a higher number of deletions, and small mutations are more frequent than duplications. Among small mutations that are generally frequent in both phenotypes, 44% of DMD and 36% of BMD are nonsense, thus, eligible for stop codon read-through therapy; 63% of all out-of-frame deletions are eligible for single exon skipping. Patients were also assigned to Italian regions and showed interesting regional differences in mutation distribution. The full genetic characterization in this large, nationwide cohort has allowed us to draw several correlations between DMD/BMD genotype landscapes and mutation frequency, mutation types, mutation locations along the gene, exon/intron architecture, and relevant protein domain, with effects on population genetic characteristics and new personalized therapies.

Keywords: dystrophin; exon skipping therapy; muscular dystrophy; nationwide study; read-through therapy.

Figure 1

Overview of mutations distribution in DMD and BMD patients from Italy. Deletions were the most frequent occurring mutations, accounting for 57% of mutation types in the DMD patients (A) and in 78% in the BMD patients (B), duplications occurred at a similar rate in both DMD (11%) and BMD patients (9%), small mutations occurred in 32% of DMD and 13% of BMD patients. Among all mutation types, nonsense are the most frequently occurring small changes both in DMD (14%) and in BMD (5%), followed by frameshifting (DMD 11%, BMD 2%), and splicing canonical sites (DMD 5%, BMD 2 %), missense (DMD 1%, BMD 3%). Mutations occurring in splicing consensus sequences are 1% both in DMD and in BMD.

Figure 2

Small mutations distribution in in-frame or out-of-frame exons in DMD and BMD patients. The majority of small changes in DMD (68.5%, n=211) locates in out-of-frame exons, while only 31.4% (n=97) locates in in-frame exons. Nonsense mutations occur in 62% in-frame exons compared to 51% in out-of-frame exons, frameshifting changes are more frequent in out-of-frame exons and the missense are 2% in in-frame vs 6% out-of-frame. In BMDs, small changes are prevalent in in-frame exons (58.3%, n= 42) compared to out-of-frame (41.6%, n=30) exons. Nonsense mutations occur much more frequently, almost double, in in-frame exons (57% vs 30%), frameshifting changes are equally distributed (17%) and missense mutations are more represented in out-of-frame exons (53% vs 19%).

Figure 3

Geographical distribution of mutations based on the place of birth of DMD and BMD patients. Nonsense mutations account for only 6% in the South compared to 20% in the North, with the counterpart of frameshifting changes being 8% in the North and 16% in the South. Sardinian patients show a very different mutation spectrum.

Figure 4

Mutations distribution in DMD and BMD patients from Italy compared to literature data. Overview of genotype data of our cohort in comparison to previously reported other nationwide studies. Tuffery-Giraud et al. (2009). Hum. Mutat. 30, 934-45; Bladen et al. (2015). Hum. Mutat. 36, 395-402.