Genome Editing Potential for Cystic Fibrosis

People always ask what new information from NACFC excites me the most. I've listed my top 3 below, and will go into further detail about one of those--Gene Editing, as the topic of this entry.

Rebecca's Top 3 from the NACFC

1) The sheer number of new correctors and potentiators appearing in clinical research has exploded! There are almost too many of them to even keep track...and they are certainly NOT all coming from Vertex. There is a robust pipeline and a competetive surge to get these compounds on the market.

2) The development of new ways to measure CFTR function and personalized drug response. Small "organoids" can be grown from rectal tissue biopsy, nasal brushings (nasopheres), or bronchial tissue (bronchospheres). Once harvested, these cells can allow researchers to test whether or not an individual might respond to a drug treatment. As the number of new CFTR modulators increases, and as we try to treat patients with rare mutations, these techniques could prove to be extremely valuable. Once the cells are harvested, they can be reproduced indefinitely outside of the body, and drugs can be tested on a person's organoids in the lab as a good predictor of a clinical response in that individual. This kind of testing could streamline early phase clinical trials, and provide the safety of testing drugs in the lab vs. in vivo. 

3) Gene therapy strategies as a potential CURE for ANY mutation of cystic fibrosis. Investigators are examining several different techniques, as seen in the slide below. This entry will focus on CFTR gene editing using the CRISPR/Cas9 system.

  

One method of gene editing utilizes a system call CRISPR Cas9. CRISPR stands for clustered regularly interspaced short palindromic repeats--specific targets on a gene, containing short repetitions of base sequences, followed by short segments of "spacer" DNA. Cas9 is a single DNA targeting enzyme that serves to "code" for proteins related to CRISPRS.  In simpler terms, the CRISPR can be thought of as the specific portion of DNA targeted for alteration (the section where we find the presence of the CF mutation).  Cas9 can be thought of as a tiny pair of scissors, programmed to make a cut in the strand of DNA at precisely the right spot. This is a complicated process, but is explained nicely in this video produced by the CFF and shown during the first Plenary Session. 

Dr. Hao Yin from the Massachusetts Institute of Technology in Cambridge, MA gave a talk on Thursday afternoon entitled: 

In Vivo Genome Editing: From Proof-of-Concept to Therapeutic Delivery. 

Dr Yin's study utilized mice with a hereditary liver disease (tyrosinemia type I)

caused by a genetic mutation. He was able to demonstrate that CRISPR cas9 mediated correction of a genetic mutation in live mammals was truly possible, and has the potential for correction of human genetic diseases like CF.  As seen in the video, gene editing is a complex process. In this study, Dr. Yin combined lipid (fat) nanoparticle mediated delivery of Cas9 mRNA (messenger RNA) with adeno-associated viruses, and a repair template to induce gene repair in living mice. He was able to show that the mice exhibited short-term expression of the Cas9 nuclease by in vivo mRNA delivery, which provided efficienct on-target genome editing, and reduced off-target editing (altering the genome at unintended sites can obviously be problematic!). 

This proof-of-concept study is extremely exciting, but several challenges still remain. Two primary issues that investigators have always struggled with in regard to gene therapy strategies are the precision and specificity of targeting, and the method of delivery inside the nucleus of cells.

One method of getting information through the cell membrane to the inside of the cell is to use a modified virus to sort of "infect" cells with new information.  

It is profound that investigators have shown gene editing techniques may be successfully performed in living mammals, but there is still considerable progress to be made before we see these therapies in humans. At last year's NACFC, I also shared my excitement about development of these new gene therapy techniques. I'm really optimistic that progress will continue to accelerate in the coming year, and more exciting trials will be reported in 2017! 

Slides from the first Plenary Session of NACFC 2016. A Cure for All:Leaving No One Behind

The CFF has already produced a wonderful blog that detailing the first Plenary session. Thank you Katherine Tuggle! Here are the slides that correspond with her narrative. Enjoy <3

NACFC2016--Notes from Day 1

This is my 6^th year attending the NACFC, and I always consider it the absolute most exciting 3 days of the my entire year.  We spent most of yesterday traveling from northern Idaho to Orlando, and celebrated our arrival by connecting with old friends over cocktails.   

The workshop sessions kicked off this morning. I ran as fast as I could (in heels with a bad knee!) between rooms to catch the talks that had piqued my interest most, but spent most of my time in—

Clinical Advances in Cystic Fibrosis Research

Comparison of Lung Clearance Index and Magnetic Resonance Imaging for Assessment of Lung Disease in Infants and Preschool Children with CF.

There are a couple of important points that I hope to drive home from this discussion. 

1)There is a robust body of data showing that lung disease begins early in life in children with CF—often in the first few weeks or months, and that this early progression in the smallest airways often takes place in the complete absence of symptoms.

2) There is a need for a highly sensitive, non-invasive method to examine early structural lung changes. Currently, we don't have a reliable standardized technique to measure lung function for children too young to properly perform spirometry.

This study examined the relationship between a measurement called Lung Clearance Index (LCI), with structural lung changes determined by MRI.  Determining  LCI in children <4 requires sedation and administration of a “tracer gas,” and takes between 30-60 minutes to perform. 

*MBW stands for "Multiple Breath Washout." 

Dr. Mall’s data showed a correlation between LCI and structural abnormalities on MRI. He suggests that LCI may be an effective tool for monitoring early lung disease progression, and may offer opportunities for early intervention. He also suggests that LCI may be a reasonable endpoint when conducting clinical trials. 

To be honest, this discussion wasn't the most exciting talk on my schedule today. LCI is a technique that I've learned about in previous years, but hasn't arrived in clinical practice as a standard of care. The data on early progression of lung disease in the absence of symptoms is not new information either (AREST CF study). I think it is important to understand that structural changes in the lungs begin very early in CF--"in the first few weeks or months of life" and can be measured. Also notable is that these changes in the very smallest airways can occur in the complete absence of respiratory symptoms. By the time an individual has become symptomatic, damage has already occured. Cystic fibrosis progresses silently in our youngest patients, and finding ways to measure those changes might offer potential opportunities for intervention. Furthermore, as we discover more new therapies to treat CF, it is essential that we have reliable methods to test their effectiveness in our youngest patients. 

My opinion is that preserving structural lung health in pediatric patients with or without symptoms is extremely important, and finding a way to accurately measure the progression of disease in these youngest patients will allow researchers to ultimately find better ways to treat and PREVENT structural lung damage with early intervention strategies. 

Next up:

Long-Term Safety and Efficacy of Ivacaftor in Pediatric Patients Aged 2-5 Years with CF and a CFTR Gating Mutation.

Ok…It felt like this talk was being given directly to ME. For the record, my son Brady began treatment with Kalydeco almost immediately after it was approved in January 2012. The drug was initially approved for children 6+, and Brady was only 4 at the time. We (my husband, I, and Brady’s care team) decided it was in Brady’s best interest to start taking the drug immediately, to halt the cycle of disease progression and PREVENT as much lung damage as possible. We fought for coverage, and were able to start treatment on Feb. 10^th, 2012. Brady has been taking Kalydeco for over 4 1/2 years, and during that time, the FDA extended the approved usage to children as young as 2.  We know that we have seen huge benefits in Brady's health, but it was really nice to see some data on usage in this age group.    

The KLIMB study followed children taking Kalydeco though 84 weeks of treatment.

Data from the KLIMB study showed that the benefits seen immediately after initiation of Ivacaftor treatment were statistically sustained through the 84 week extenstion period. Changes in fecal elastase (a measure of pancreatic function) were also observed in some of the youngest patients, indicating potential for improved or some restored pancreatic function.

The changes in fecal elastase (first reported in the KIWI study) came as a surprise--as restoring any pancreatic function for CF patients was previouly thought to be impossible... Additionally,  no new safety concerns were reported.

It is exciting to imagine what we might be able to achieve as CFTR modulators reach younger and younger patients. Personally, I am reassured beyond doubt that we made the right decision by fighting for early access to Kalydeco. According to CFF President and CEO Dr. Preston Campbell--initiating a CFTR modulator like Kalydeco early in life may REMOVE the traditional life expectancy limits associated with CF and allow individuals to thrive into their '70s and '80s. I truly believe that the length and quality of Brady's life will not be regulated exclusively by cystic fibrosis. When I see the data like this I wonder what types of changes we might be able to see if we started in newborns? Could there be a future where we are even able to treat a fetus with CF in utero??

The last talk I'll summarize in this entry was entitled:

Relations between Potentiator response in Organoids in vivo. Outcome Parameters in Patients with CFTR Gating Mutations.

One theme that I heard woven through many of today's discussions was the desperate need to develop novel methods of determining which patients will respond to which CF modulator therapies. Organoids can be thought of as "mini organs." These organoids live in our digestive tract and can be harvested by rectal biopsy.  

Organoid swelling is correlated with CFTR function (much better correlation than CFTR function with sweat chloride levels, for example). This enables researchers to test drugs on organoids and predict whether people with specific mutations will respond to a particular compound.  

The organoids on the left show normal swelling associated with functional CFTR. The middle panel shows diminished swelling in F508del homozygotes. The organoids on the right exhibit the increase in CFTR function when F508del homozygotes were treated with Orkambi.

For the purposes of this study, organoids with the S1251N mutation were utilized.

Finding new ways to measure CFTR function is extremely important if we want to achieve our mission of reaching 100% of patients with a CFTR modulator therapy. Many mutations of CF are extremely rare, and this technique is being used to help researchers determine if those individuals might respond to existing therapies like Kalydeco or Orkambi. In the future, organoids could allow scientists to test which combination of correctors and potentiators will have the most profound effect on that individual's CFTR function (because we will have multiple potentiators and correctors to choose from in the future), and mixing that cocktail can be tricky business! Another advantage of this technique is that once the tissue biopsy is obtained, endless organoids can be obtained or "grown" from this initial sample for subsequent study--"biobanked." 

My work in advocacy has taught me the importance of developing new ways to accurately test CFTR function and drug response. The goal is to be able to treat every individual with CF with small molecules (potentiators, correctors, and various combos of both). The discovery of which drugs work for which mutations is a first step. Furthermore, to obtain FDA approval and vital insurance coverage, there is a need for some cold hard DATA.  My opinion is that organoid studies will enable researchers to streamline early drug discovery for rare mutations, and also support evolution of the FDA's drug approval process. Organoid studies may not sound very glamorous, but developing endpoints that accurately correlate with CFTR function is a crucial step in helping new drugs reach the individuals that will benefit. 

This entry represents just a few of the talks I attended earlier today. Lots more to come tomorrow!