In today’s #apaperaday, Prof. Aartsma-Rus reads and comments on the paper titled: Clinical, muscle imaging, and genetic characteristics of dystrophinopathies with deep-intronic DMD variants
Today’s paper is from the journal of Neurology by Xie et al. A comprehensive study of Chinese dystrophinopathy patients with intronic mutations. DOI: 10.1007/s00415-022-11432-0
Duchenne is caused by lack of dystrophin, while Becker and X-linked dilated cardiomyopathy (XLDCM) is caused by mutations that allow production of partially functional dystrophin. Most patients have large deletions or duplications or small exonic mutations.
However, a small proportion of patients have deep intronic mutations, which cause missplicing. These variants are difficult to find. Here authors did a very comprehensive analysis to identify also intronic variants and discovered 31 mutations in 1141 dystrophinopathy patients
Missplicing was confirmed on mRNA analysis from muscle biopsy material for at least one family member (if multiple were affected). For other family members the DNA variant was confirmed. 31 PATIENTS were found with 19 different mutations (correction for previous tweet)
These mutations caused cryptic splicing (inclusion of cryptic exon/pseudoexon), partial intron retention (before or after an exon), partial or complete exon skipping and finally inclusion of other coding sequences of other genes due to insertions or inversions.
The insertion of exons from other genes (CCDC83 and PICALM from chromosome 11 insertion and IL3RA from chromosome X inversion) is something that generally is missed but authors picked it up due to their comprehensive analysis of combining mRNA analysis and long read sequencing.
The cryptic exons and partial intron retentions caused premature truncation of translation because they disrupted the reading frame and/or contained a stop. For Becker and XLDCM patients also some normal transcripts were observed, while this was not the case for Duchenne patients
Authors also performed phenotyping of the patients, using ao MRI – inserting the picture for Hermien Kan. However, even I (not MRI expert) can see that there is a dystrophic pathology and fat infiltration ongoing here
Authors describe that there is variability BETWEEN families with the same mutation. For one mutation, 1 patient had XLCDM with a stroke at age 20, while another patient with the same variant had Becker with muscle symptoms appearing at age 16, without heart involvement.
For another mutation, one family had a Becker patient with symptoms at age 9, who is still walking at age 12.5, while in another family the same mutation resulted in Duchenne with symptoms starting at age 4 and loss of ambulation at age 11.
Also WITHIN families there was variability between patients, e.g. a mutation resulted in severe Becker in 1 family member (symptoms starting at 3.5 years), a family member had symptoms at age 13 yrs & now has moderately severe Becker at 38 yrs, while a 47 yr person had high CK.
Authors discuss the large heterogeneity for the same mutations. They do not discuss a potential cause. I think it is likely that there are differences between how much normal transcripts exist between different patients and perhaps even tissues (heart vs muscles).
It is very difficult to confirm this obviously, but it is known that cryptic splicing levels can vary between patients and tissues so this is a likely explanation. Authors also discuss that intronic mutations are difficult to identify as splicing predictors are far from perfect
All in all I like the paper and appreciate the diligent work the authors did to find these intronic mutations and to do the phenotypic analysis of the different affected persons. In their set of 1141 patients, they found 31 patients with intronic variants –> about 2.5%
I notice that more and more papers appear about deep intronic mutations for Duchenne. Kudos to people doing these efforts. Given the intron sizes I know it is not easy.