Like at least some of you, I've wondered about Dr. Sweeney's comments about exon skipping not helping boys with deletions at exon 44, like my son and that of whoever it was (not me or Cheryl) that asked him the question. There are members of our little sub club here whose kids have multiple deletions that are predicted to be "in frame" according to the on line widgets like the one from the University of Utah ( http://www.genome.utah.edu/DMD/deletion_worksheet/ ) or Robin Sharp's ( http://www.dmdregistry.org/reports/predictor/ ). I'm now wondering if the assumption of a lot of us that our boys will be better off if they have an in frame, truncated dystrophin is really accurate.

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Replies to This Discussion

Hi Paul,

I think that with a deletion of 44 you would need to skip 43 or 45 to make it in-frame. That doesn't guarantee a functional protein though. There are examples of boys with in-frame mutations who do not progress like Becker. It's not clear to me why and none of the scientists I asked did not have a clear answer about this. That is why I think that exon skipping will work only for a subset of the boys, although in theory it should work for most.

Ofelia
Yup. There is still a lot we don't know. My son also has an "in-frame" deletion, but presents with a classic Duchenne phenotype. Apparently about 10% of kids who are in-frame will have the Duchenne phenotype, if my memory serves me correctly (I think I found this on the Leiden database webpage, but I can't be certain).

I can't remember much from high school biology, but the way a protein is folded (which could be impacted by how/where it is truncated) can have a significant impact on its functionality. Even if you are making some dystrophin protein, there is no guarantee on how functional it will be. So, even for boys who are "out-of-frame" and could theoretically benefit from exon skipping, the response or amount of benefit (if any) will probably vary highly from person to person. I don't think this should stop us from pursuing exon skipping by any means...but I guess it speaks to the need to not put all our eggs in one basket.
Ofelia and James,

Thanks for the response. I can't figure out how to read that Leiden data base well enough to determine whether there is any reason to believe that a child with a dystrophin protein made by skipping either 43 and 44 or 44 and 45 would be more like a Becker's than a Duchenne. Being the natural pessimist that I am, I am also worried about the fact that when exon skipping is employed in the mice, bad out of frame dystrophin is still made along with the supposedly better in frame dystrophin.
Hi James,

I was wondering what your son's deletion is?

Hi Paul,

You can look at Linden's database and see how many cases of DMD are reported. For example, my son has a deletion of exon 50, if I look for RNA change r.(ex50ex51del) which should be in-frame I still can find a number of reported DMD cases for this deletion.

http://www.dmd.nl/nmdb/variants.php?select_db=DMD_d&action=sear...

We don't know why these in-frame mutations progress as DMD. For 2 of them you can note the comments: "3' junction fragment", "ex52 junction fragment". These explain why these 2 cases are not BMD, the deletion is not starting/ending "nice" in the introns before 50 and after 51. This is one point Steve Wilton mentioned to me, we need to have the mRNA level diagnosis (which can be done with a simple skin biopsy), not only DNA level to make sure that at the RNA level exons 50 and 51 are the only one missing. If the deletion starts/ends too close to the splicing sites that creates problems.
So unless we know exactly what happens at the RNA level we cannot say why some in-frame mutations are not BMD.

On the other hand, if a muscle biopsy for a case with in-frame mutation shows enough dystrophin then it is clear that the protein is not functional. I would really want to know if any of the kids with in-frame mutations had a muscle biopsy and what were the results.

Ofelia
Hi Ophelia,

My son's deletion is 47-57, confirmed via genetic testing at two different locations. I wonder if the new microarray chip will clarify the whole in-frame/out-of-frame issue.

Anyway, you make a good point and it makes me wonder if they are taking this into account when planning their exon skipping trials...I'm not aware of anyone planning on confirming at the mRNA level.

Maybe this whole topic is something that we can bring up during a panel discussion at the conference.

Best wishes,

James
Hi James,

Thanks for your answer. I think that for the clinical trials they do look at the RNA before they accept a boy. Steve Wilton suggested that to me some time ago.

Ofelia
There's some related pre-clinical stuff going on in Utah, and while the conversation I had with the researchers left me a little mystified, they did take a skin sample from my son, and I understood that the reason for doing so related to his mRNA.
My son has a deletion of 3-23, in frame with a Duchenne phenotype (historically) I guess. Does anyone else have this same mutation. I am thinking about muscle biopsy but wondering what the skin sample will tell you. We see Dr. Flanigan in Utah,
Alex' skin sample was strictly for the research project and not for any diagnositic purposes. In Alex' case, Dr. Flanigan did not think that the clinical information he would get from the muscle biopsy would tell him anything that he would use in connection with Alexander's treatment, and he did not recommend pursuing the biopsy at this time.

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