RUNX1 and Gene Therapy

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We are amid a gene therapy revolution thanks to the development of a new generation of gene editing tools, which have led to game-changing therapies for patients with genetic blood diseases like sickle cell anemia and beta thalassemia.

The very first tools you may have heard of in the news are called CRISPR for short. Today, many different gene editing tools have expanded based on the original CRISPR technology. One can think of these gene editing tools as tiny, molecular scissors, that first cut specific sequences of DNA and then paste a new sequence of DNA directly inside a living cell.

Why is this important for heritable genetic diseases? Well, a heritable genetic disease is caused by an error, a misspelling, in an individual’s DNA at birth. With tools like CRISPR, scientists now have the capability to correct those misspellings. Let’s zoom in on genetic diseases affecting the blood system.

Imagine that the human blood system is a harmonious symphony orchestra. Every musician in this orchestra represents a different blood cell type, and the sheet music they read from is the specific instructions (DNA) guiding them on how to play. In some rare diseases, there is a misprint in the sheet music (a gene variant in an important blood gene, like RUNX1) causing the musicians to play off-key, disrupting the harmony of the entire orchestra. In a heritable genetic disease like RUNX1-FPD, the musicians have been playing slightly off-key, and are unaware since the sheet music (DNA; genetic instructions) provided from the beginning was incorrect.

In this analogy, gene therapy can be likened to correcting the flawed sheet music to enable a harmonious symphony orchestra performance.

How Does This Apply To RUNX1-FPD?

At the heart of our orchestra, there's a master conductor who guides and influences all of the musicians, setting the tone and pace for the entire performance. This is much like the hematopoietic stem cells (HSCs) in the bone marrow, which are responsible for forming different types of mature blood cells throughout life. One key point is that there are many (10-100 thousand) HSCs in the bone marrow, meaning many, many symphonies going on at once. 

In RUNX1-FPD, the conductor's sheet music (DNA) has a misprint (gene variant in RUNX1) which can lead to a discordant symphony (platelet issues and in some cases blood cancer). Here is how gene therapy could come into play to help fix this.

Gene Therapy: Correcting The Notes

The first and most advanced approach, used in the case of sickle cell anemia and beta thalassemia therapies, is to take out all of the HSCs from the bone marrow in a patient through a process called stem cell harvesting. Then the HSCs are placed into laboratory dishes to which the gene editing tools are added to correct the genetic variant. The corrected HSCs are then infused back into the patient. 

The second approach, which is still in animal testing, is to place the gene editing tools inside a special case called a “nanoparticle” which can then be infused into the bloodstream. The nanoparticle then travels to the bone marrow, finds the HSCs and corrects the RUNX1 variant inside a patient’s body. This approach would eliminate the stem cell harvesting step and eliminate conditioning therapy (described below). 

Both sound like a good plan, right? So, if RUNX1-FPD is a genetic disease, caused by variants in RUNX1, then why can’t researchers use the same gene editing tools to correct RUNX1 variants in a patient’s blood cells? 

Gene Therapy: A Masterpiece In Progress

These gene editing tools have only been around for a decade, and there are several challenges to overcome before they can be successfully used for RUNX1-FPD:

• Off-target effects: These tools are designed to make a site-specific cut in the DNA. But it isn’t perfect yet – it still might accidentally cut and edit parts of the DNA it wasn't supposed to. In the case of RUNX1-FPD, scientists are concerned that the gene editing tool could accidentally cut the one healthy copy of RUNX1, leading to a new RUNX1 variant. This new variant could lead to blood cancer, a disastrous side effect.

• Limited Editing Efficiency: It is difficult to get the gene editing tools inside of every single HSC even when the HSCs are harvested and treated in the lab. HSCs are naturally designed to protect themselves from foreign substances. Editing efficiencies are improving, but for RUNX1-FPD patients the goal is to edit as close to 100% of HSCs as possible since it is the HSC with a RUNX1 variant that can develop into blood cancer. That is a high bar.

• Delivery Issues: In the approach where nanoparticles containing the gene editing tools are infused directly into the bloodstream, it remains extremely challenging to get the nanoparticles to the correct cells in the body. Some cells are just harder to reach and fix than others, including HSCs. Many scientists are working to solve this problem.

All three of the challenges above are not major concerns for diseases like sickle cell anemia and beta thalassemia. That’s because one only needs to correct ~20% of the HSCs to treat those diseases. Unfortunately, a RUNX1-FPD gene therapy would need to correct as close to 100% of HSCs as possible to treat the disease successfully.

Other challenges that will need to be addressed before a safe and effective gene therapy can be realized for RUNX1-FPD are as follows:

• Safety Concerns in the Preparation for a Gene Therapy Transplant: As we mentioned above, gene therapies today rely on harvesting HSCs from patients and then correcting HSCs in the laboratory. Once the HSCs have been corrected, they are then put back into the patient.
  
  But when the corrected HSCs are put back into the patient they need to find a home in the bone marrow and they need space to multiply. This means there can’t be any remaining RUNX1-FPD HSCs left in the bone marrow because they will outcompete the new corrected HSCs. To eliminate any remaining RUNX1-FPD HSCs, patients would need to receive high doses of chemotherapy to wipe out all of the HSCs before the new, corrected HSCs are put back in. This process is called conditioning therapy, which basically means preparing the bone marrow for the transplantation of the new cells.
  
  Unfortunately, chemotherapies, even if only given for several days, can increase the risk of new cancer-causing variants. Scientists are especially concerned for RUNX1-FPD patients, because having a RUNX1 variant already increases the risk of cancer-causing variants so exposing RUNX1-FPD patients to chemotherapy may further elevate that risk.
  
  There are many researchers working on discovering new medicines that could eliminate the remaining RUNX1-FPD HSCs without increasing the risk of cancer-causing variants. RRP is watching these developments closely.  

• Number of Different RUNX1 Variants: Individuals and families in our patient community are diverse in every way, even down to their RUNX1 variant. There are over 100 RUNX1 variants identified that cause RUNX1-FPD, and that number continues to grow each year. 
  
  The gene editing tools we have today can only correct a handful of variants at a time, meaning only a few families will benefit per gene therapy. Developing a gene therapy for every patient would cost billions and take several decades if we started with the tools we have today. 

• Identifying High-Risk Patients - Balancing Benefits and Risks: A treatment decision is always influenced by the severity of a disease in an individual patient and whether the potential benefit of a treatment outweighs any potential risks. Today, we still don’t have a clear understanding of who is at greatest risk for blood cancer since at least half of RUNX1-FPD patients may never develop blood cancer.
  
  Being able to identify who is at greatest risk is critical not only for patients and physicians in their shared treatment decision-making discussions but also for regulatory agencies like the FDA who decide on whether a new therapy should be developed. Until many of the potential risks discussed above can be mitigated or even eliminated, the risks of a gene therapy for RUNX1-FPD outweigh the potential benefit. 
  

In summary, the exciting developments in the gene therapy field are real. But for RUNX1-FPD to benefit from a gene therapy there are several significant challenges to overcome. The good news is that RRP and the scientific community have identified the challenges and have a strategy that will position RRP to jump in when the time is right. 

For now, RRP is sponsoring a stem cell harvesting and banking study that will allow patients to collect and store their HSCs today for potential gene therapies in the future.