Kalydeco and Class IV Mutations

[JustaCFmom]

<div class="FTQUOTE"><begin quote><i>Originally posted by: <b>marcob</b></i> Hi, There are also splicing mutations and frameshift mutations
Thanks so much for the great explanation. My kids have W1282X the meaning of which I somehow managed to figure out (partly because it isn't so hard to understand ). Can you explain the splicing mutation (in my case it's
<span style="font-size: small;">3849+10kb C->T) I figured out that the "C" is replaced with a "T", but more than that got too complicated for my poor little brain!
<span style="font-size: small;">Thanks!

 

[CyrilCrodius]

Thank you! This is great! Joining right now.

Great post.....thank you for this!There is another person in the Ataluren facebook group who has DF508 & 621+1G>T, she improved 11% (FEV1) and went down 30 points with the sweat chloride. I'm not sure if she posts here. So there are at least two people who have improved...

 

[GenH]

<div class="FTQUOTE"><begin quote><em>Originally posted by: <strong>JustaCFmom</strong></em> Can you explain the splicing mutation (in my case it's <span style="font-size: small;">3849+10kb C->T) I figured out that the "C" is replaced with a "T", but more than that got too complicated for my poor little brain! <span style="font-size: small;">Thanks!</end quote> <span class="commentBody" data-jsid="text">The latest mutation categories suggest that splicing mutations can be put into two categories. The first is class 5 splicing, where some functional CFTR is made and gets to the surface. There is no stop codon with these<span>. The second category is splicing that leads to a stop codon, class 1. Generally it is thought that little CFTR makes it to the surface with these mutations. A simplified explanation of what normally happens: The CFTR gene is made up of DNA. This DNA is copied/transcribed and RNA is formed. The entire length of the RNA is not all needed to make the protein, so some parts are removed, forming mRNA (this is splicing). In order to make normal CFTR proteins there are particular parts of RNA that are needed, so splicing normally occurs in the same way each time. After splicing the mRNA is used to make the protein, by a ribosome. When a stop codon is reached, the ribosome stops. Normally the ribosome stops at the correct point and a functional CFTR protein is made. In CF Splicing Mutations: If the mutation in the DNA affects the splicing, the code/parts that are in the mRNA and are translated will be different to normal. In class 5 splicing mutations, sometimes splicing occurs normally, so the mRNA is normal, and the correct CFTR is made. Sometimes it does not splice correctly, so the mRNA is not normal, and a non functional CFTR protein can be made. Class 1 splicing mutations are not supposed to have much correct splicing, so a lower level of correct CFTR is made. With class 1 the incorrect splicing leads to abnormal mRNA, leading to a stop codon being present that should not be there. Ataluren can help the ribosome to continue to the proper stop codon (ie ignoring the premature stop codon). This means the mRNA is fully translated, so the CFTR protein is hopefully made properly and makes it to the surface. Clinical trials so far have been held with nonsense mutations (class 1, ends in X, has a stop codon), not class 1 splicing mutations, so it has not been determined if Ataluren can help class 1 splicing mutations.<img src="http://www.uncommondescent.com/wp-content/uploads/2011/10/alternative-splicing.gif" alt="" width="387" height="221" /><img src="http://www.nature.com/scitable/content/ne0000/ne0000/ne0000/ne0000/14711098/U2CP3-1_SynthesisDegredati_ksm.jpg" alt="" width="400" height="354" /><img src="http://www.intechopen.com/source/html/26187/media/image4.jpg" alt="" width="500" height="507" /><img src="http://3.bp.blogspot.com/-dxSvb49hqV8/Tyg3yRAvIyI/AAAAAAAAL10/3sh8hNAo9EE/s1600/CFTR%2BMutations.gif" alt="" width="515" height="332" /> I like this one, but it is older as it should have class 6 now.

 

[GenH]

Also, there seems to be conflicting opinions about the 3849+10kbC>T mutation, so I am not sure which type of splicing it is. The images above and the iphone app by vertex say it is class 5, but this suggests in the discussion that it is class 1 http://ajrccm.atsjournals.org/content/182/10/1262.long . The article it refers to (29) is not available for free but I have accessed it through work- it says 3849+10kBC>T is an "Insertional mutation resulting in an elongated messenger RNA, containing an in-frame premature UAA stop codon." In their study they had 1 patient who improved with Ataluren with 3849+10kbC>T / F508del (a short study looking at the chloride changes in the nose).

 

[MAC512]

I've also found conflicting information for my daughter's mutation (R1066H). Of the four papers I've found 3 list it as class 4 and 1 listed it as class 2 and the Vertex app also has it as a class 2. GenH I love your posts...I find them very informative. Thanks!

 

[MAC512]

If one of the combo drug therapies for DF508 were approved at least it would open up the use of Kalydeco to more CF people. Since right now its only approved for G551D it seems a lot of us would be able to get it and get insurance to pay for it since most of us have F508. Hopefully they can get through the last hurdles next year and get the ball rolling. I also saw an article that Kalydeco may be tested for COPD hopefully with more users (there's a bunch of people suffering from COPD) the price can come down...well and hopefully help those people as well. <img src="i/expressions/face-icon-small-smile.gif" border="0"> I'm really hoping the Kalydeco will be the "golden ticket" to help my daughter (DF508/R1066H)

 

[CyrilCrodius]

GenH, what is it that determines where a strand of RNA will be spliced? Is there a particular sequence?

 

[GenH]

Yes there is a particular sequence at the start and end of the area that is taken out (spliced). I would imagine the CF splicing mutation is present in one of these sites, or creates a new site in a place where there isnt normally one.

 

[GenH]

JustaCFmom- I just relooked at the presentation by vertex and it mentions that they think 3849 (I'm abbreviating it from now on!!) may benefit from Kalydeco (page 31). Also mentions 2789, A455E, R117H, G551D, Gating + other folding and residual. On page 32 they also mention splicing mutations (4%) population. If I add up the % it means they think 20% may benefit (5% gating + 15% residual phenotype- this means mild).

http://iom.edu/~/media/Files/Activity%20Files/Research/GenomicBasedResearch/2012-MAR-21/3%20-%20Peter%20Mueller.pdf

 

[GenH]

To get back to the original question by pjammer65- I'm under the impression that conductance mutations (class 4) are generally classified as being mild (has some residual function) & vertex said in the presentation that they believe the 15% with a residual function phenotype may benefit. Pancreatic sufficiency would be an indicator of a residual function phenotype.

Have you been able to get Kalydeco? Having a class 4 mutation should be sufficient evidence... (possible that class 3, 4, 5 and 6 may benefit)

 

[pjammer65]

Hi All.
Fred Van Goor gave a presentation at ECFS in Dublin in June entitled "<span>Ivacaftor Potentiates Mutant CFTR Forms Associated with Residual CFTR Function." For those that have read my previous post would know that my CF team said that Van Goor was soon going to publish a paper discussing evidence of the effects that Ivacaftor had on non-gating mutations (specifically how R347p did not respond to treatment). So following the presentation I searched daily for the slides on the web hoping that someone would post them. Then one day I found them. Luckily I saved them because the day after I did the file became private and now it is gone completely.
<span>Unfortunately the information does not help my case as it does suggest that kalydeco does not potentiate the R347p mutation, but I am sure it can help others and maybe shed some light on the direction vertex is headed with Kalydeco as a monotherapy.
<span>The slides can be found here
http://www.flickr.com/photos/66477137@N05/sets/72157630806828898/
The original post was here
http://www.scribd.com/niallvv/98284198-Ivacaftor-Potentiates-Mutant-CFTR-Forms-Associated-With-Residual-CFTR-Function

 

[GenH]

Thanks pjammer65 for saving the images, very interesting.

 

[mom2JD]

Thanks for sharing. As my son has the same muation as you I am also very disappointed. All the best for you, anyway.

 

[JENNYC]

Yes pjammer65, thank you so much for sharing!! And GenH you are so very informative as well!! Love your posts!! <img src="i/expressions/face-icon-small-smile.gif" border="0">

 

[JustaCFmom]

WOW!! Thanks so much! This has been incredibly helpful. I hope you don't mind, I shared a lot of this info with the Israeli forum. They are starving for information since most of the members don't really know English. The doctors just gave a whole presentation for the parents about Ataluren last week. Unfortunately, Tobi seems to nullify the drugs influence, but they seemed optimistic, overall.

 

[GenH]

Hi all, I am new to the site but look forward to being a part of the cf community that has formed here. I am a 34 year old male with the DF508 and R347P and currently in the early stages of transplant evaluation. I have been trying to get my center to prescribe Kalydeco but have been unsuccessful. At my last visit they said they spoke to a vertex rep that said that Van Goor is soon to publish a paper outlining the effects of Kalydeco on different classes of mutations. She also said that Van Goor stated that kalydeco had no effect on my specific mutation, R347P.
This is obviously upsetting to me as I thought that 770 potentiated all CFTR (as per previous Van Goor comments). I also was hoping since R347P is a conductance mutation, the probability that 770 would be effective was high. So maybe it potentiated but was not clinically effective?
Has anyone heard about this publication or having any information from it?
Are there any R347P'ers out there?
Has anyone found any info on class IV mutations and 770? (beyond the presentation slides Vertex distributed recently)
Thanks!

I was just reading the EMA report about Kalydeco and I noticed R347P was mentioned:

The increase of chloride transport by ivacaftor was most pronounced in cells expressing CFTR gating mutations when compared to other types of CFTR mutations. This group included, G551D, G178R, S549N, S549R, G551S, G970R, G1244E, S1251N, S1255P and G1349D. The fold increase in chloride transport for all 10 studied gating mutation proteins was greater than 10.

Ivacaftor also potentiated chloride transport, of cells carrying CFTR mutations that are associated with residual CFTR function, although to a lesser extent than that observed for CFTR gating mutations, including CFTR conductance mutations (R117H, D110H, R117C, R347H and R352Q), mild CFTR processing mutations (E56K, P67L, L206W, A455E, D579G, S945L, R1070W and F1074L) and CFTR mutations with uncharacterized defects in the CFTR protein (D110E, D1152H, S1235R and D1270N).

Finally, ivacaftor showed minimal effects in vitro on mutant CFTR forms that were associated with minimal chloride transport, including severe CFTR conductance mutations (R334W, T338I, R347P and L927P), severe CFTR processing mutations (F508del, A46D, G85E, E92K, S492F, I507del, V520F, A559T, R560T, R560S, A561E, H1054D, G1061R, L1065P, L1065P, R1066C, R1066H, R1066M, L1077P, H1085R, M1101K and N1303K) and CFTR synthesis mutations (G542X, W1282X, 2184InsA
and 2789+5G->A).

Page 20: http://www.ema.europa.eu/docs/en_GB...ssessment_report/human/002494/WC500130766.pdf

 

[kyeev]

The slides can be found here
http://www.flickr.com/photos/66477137@N05/sets/72157630806828898/

PJammer, you legend, this is the most useful post I've seen in years.
Loads of info on the most common mutations.

Unfortunately for me, it proves Kalydeco monotherapy has no effect my V520F mutation (DF508/V520F).
But hey, now i don't feel so bad, not being able to get on the drug!

In fact, looking at the pathetic mRNA expression and miserly mature CFTR generated by these two mutations, I'm amazed I'm still going at all!

 

[triples15]

Thanks to everyone for the great info! I have a residual function mutation and I have found the slides and power point posted here to be very interesting. However I am FAR from a researcher/doctor and am not 100% clear on how to interpret the info.

GenH (or any other resident expert!), if you ever have some spare time is there any way you would take a look at the Vertex slides and tell me what it is saying about how 770 works specifically with S945L? I would appreciate it SO much!!! I have tried to convince my doc to prescribe it off label but as yet have been unsuccessful. From what I can tell it looks like Kalydeco alone had a decent effect with this mutation but I could be reading it wrong. I am also trying to get into a study in Denver which includes my mutation but that is looking unlikely. I'm trying to decide if I should continue pushing my doc to prescribe it or not.....

Thanks a bunch!!

Autumn

 

[GenH]

Thanks to everyone for the great info! I have a residual function mutation and I have found the slides and power point posted here to be very interesting. However I am FAR from a researcher/doctor and am not 100% clear on how to interpret the info.

GenH (or any other resident expert!), if you ever have some spare time is there any way you would take a look at the Vertex slides and tell me what it is saying about how 770 works specifically with S945L? I would appreciate it SO much!!! I have tried to convince my doc to prescribe it off label but as yet have been unsuccessful. From what I can tell it looks like Kalydeco alone had a decent effect with this mutation but I could be reading it wrong. I am also trying to get into a study in Denver which includes my mutation but that is looking unlikely. I'm trying to decide if I should continue pushing my doc to prescribe it or not.....

Thanks a bunch!!

Autumn

Looks like S945L has 5-10% function without any medications. Was your sweat test a little lower than most CFs? You are right, Kalydeco potentiates your mutation significantly. It looks like it restores about 75% of normal CFTR function. This is one of the best relative % responses on the graph. To put this in perspective, G551D gets to 50%. I would use this data asap to convince your doctor! Also the fact that vertex are studying it in a trial with Kalydeco monotherapy means that vertex believe it may be helped.

 

[kyeev]

Yep, Triples15, looks like you're cured!
You just won the Kalydeco lottery. Lucky sod!