The future of genetic treatments for PMS

David is missing many genes.

The Phelan McDermid spectrum of disorders

Phelan McDermid syndrome (22q13.3 deletion syndrome, PMS) comes in three flavors. By far, the most common variety of PMS that has been observed is a terminal microdeletion. A terminal deletion occurs when from three to 108 genes are chopped off the end of chromosome 22. There is a growing group of identified patients who have structural changes restricted to the SHANK3 gene, a gene very near the end of the chromosome. These changes can be minimal (e.g. single nucleotide polymorphism (SNP)) or substantial, with large parts of the gene duplicated or missing. The least studied form of PMS is found among those deletions that damage the same general region of chromosome 22 without affecting the very end of the chromosome where SHANK3 resides. These are often called interstitial deletions.

Genes of PMS

The SHANK3 gene is an elephant. It is a large, complicated gene and its disruption often (but not always) has severe consequences for its owner (the person harboring the mutation). Numerous studies show that the many genes of 22q13.3 contribute to intellectual disability, muscle tone and movement disorders, hearing problems, lymphedema, autism, schizophrenia and other problems. But, the penetrance of SHANK3 mutations, that is the likelihood that a pathological variant of the gene affects the owner, is high. So, it garners a lot of attention. Especially for people with the second flavor of PMS, fixing SHANK3 could ameliorate many of the symptoms associated with its disruption. For terminal deletions, the most common form of PMS, fixing SHANK3 should have at least a very helpful impact.

There are at least 18 genes that may need repair to fully restore normal function in a child with a large terminal deletion. Average size deletions (about 4.5 Mbase) would benefit from the repair of 10 genes. This blog discusses what we hope will be the future of PMS treatment: genetic repair. While regular medical treatments have been helpful for some problems, no experimental drugs have had an impact any better than physical therapy, speech therapy, ABA or other standard treatments for children with developmental disabilities. Although drug companies are sponsoring testing on children with PMS, these have traditionally been drugs looking for an application rather than targeted treatment for PMS.

We are in the early days

Excitement over gene editing, especially in stem cells (cells typical of a very early embryo) has led to giant research efforts and early attempts to fix diseases by editing. The same excitement has led to the promotion of unproven and occasionally dangerous therapies by entrepreneurs who provide services like stem cell infusion. So, let’s be clear. Gene therapy for PMS is well off into the future. There are many reasons for the delay. Some will be discussed below.

Obviously, we are at the earliest stages of gene therapy. Research and initial attempts at gene therapy target diseases that are the safest and most likely to work. This means that the disease most likely to be cured first may be a rather obscure one. It may also be a lethal disease, since the risks of side effects are no worse than letting the disease take its course.

One relatively safe way to test gene therapy is to modify blood products and then infuse them back into the body. This has safety advantages in a few different ways. First, the genetic modification occurs outside the body. The target cells can be modified without risking other cells of the body. Second, the target cells can be tested and evaluated for successful gene targeting (editing the right spot and not accidentally damaging another gene) outside the body. Third, the product can be infused a little at a time to test the benefits/impact gradually. Fourth, blood products usually have a limited lifetime in the body, so if the test begins having problems, the problems will likely go away with time. Thus, gene editing for diseases of the blood are good early candidates.

Another target for early genetics testing is the eye. It is a squeamish thought, but making injections into the eye are relatively easy. (I have had eye injections, so no need to educate me on the downsides.) The inner parts of the eye are well isolated from the rest of the body, which affords safety. Also, only very small injections are needed to bathe the retina. There is little likelihood of impacting the rest of the body. The amazing thing about eye therapy is that modern cameras and computers can take images of the eye with spectacular resolution. These images can track changes. Combined with vision testing, any progress associated with the therapy is easy to assess. As gross as it sounds, if something goes wrong with gene editing of the eye, the eye can be removed. Gene therapy for the eye would be to save vision. If vision will be lost with no intervention, the risks of trying a new therapy may be acceptable. Thus, genetic defects of the retina are high on the list of early therapeutic trials.

The human brain is not well isolated from the rest of the body and is not easily observed from the outside. There is a barrier between the bloodstream and the brain. The so called blood-brain-barrier can make treatment more difficult. Drugs injected into the bloodstream (systemic injections) may or may not reach the brain. Direct brain injection of genetic altering “vectors” may be an approach used in the future, but it is not ideal. Systemic injections would be a simpler way to reach all parts of the brain and to allow repeat injections to gradually reach the desired effect while watching for side effects. So, genetic editing in the brain is not going to be as simple as other targets.

Once we start thinking about genetic manipulations in the body, we need to remember that nearly every cell in the body has the same 20,000 genes. Given that all cells in the body could be the same, what makes heart and lungs different from kidney and brain? The answer is gene expression. Heart cells know they are heart cells because only heart cell genes are turned on, making the proper heart cell proteins in the proper proportions. We hope that injecting a vector into the body will improve brain function, but we must worry about what else may change. We worry in two ways. First, we could modify our target gene in such a way that the brain improves, but the heart (or some other organ) suffers. Second, we could accidentally modify other genes (so called, off target effects) that have no adverse impact on brain cells, but might be bad for the heart. I used the heart as an example, but there are so many different tissues in the body we cannot know which might be adversely affected.

One more consideration is important in choosing a target for the early tests of genetic therapy. The complexity of the organ and the importance of early development in creating its detailed structure influence the age at which therapy may be effective. The brain is complex almost beyond comprehension and its early patterning during development is critical to adult function. Repair of a gene after early development may have limited benefit, and except for the most deadly of disorders, we dare not test interventions on fetuses or babies until we are confident of our methodology. Additionally, the complexity of the brain poses another risk. Increasing the production of a gene may be beneficial for one part of the brain, but could be detrimental elsewhere in the brain.

The challenges of PMS

The opening of this blog hinted at some of the challenges of PMS. Together with the subsequent discussion, we can now list the major challenges of applying early genetic methods to PMS: 1) the overwhelming majority of people diagnosed with PMS are missing many genes and modern methods are still struggling for success with single genes, 2) the gene of greatest interest is large and complex, neither of which is good for gene editing, 3) the brain is a challenging target for genetic manipulation, and 4) PMS is a developmental disorder and we have insufficient information on whether treatment in older children or adults will be beneficial.

Given the many hurdles, it may be a very long time before a comprehensive treatment for PMS emerges. To be sure, there are people working on strategies to manage the disadvantages. One approach is to target only one gene in the hopes that at least some subset of patients might benefit. Likewise, there are model (rodent) experiments that suggest some of the deficits of PMS can be mitigated by treating adults. Genetic treatments for other diseases are addressing the problem of reaching the brain without adversely impacting other organs. Both animal and early clinical trials are creating improved toolboxes for genetic therapies. We hope these technologies converge on better opportunities for PMS.

Progress in the field

Techniques like CRISPR/Cas9 grew out of studies in bacteria and other science far afield from human clinical work. Recent work in E. Coli and other bacteria, as well as work on yeasts and viruses have moved genetic editing towards more precise targeting, the possibility of replacing whole deleted sections of chromosome, and the ability to enhance the activity of the remaining gene after one has been deleted. There are new methods of turning on and off a newly inserted gene, so the proper dose of a gene can be safely titrated to avoid overdose. This blog has not addressed the different methods of gene editing and which ones might apply to PMS. Rather, it provides a framework to understand why one approach or another might be more suitable. Perhaps a future blog will cover the different tools and which ones are likely to provide the first clinical tests.

A strategy for PMS

After reading the scientific literature and talking with scientists, I have a policy suggestion for how we should approach PMS. Currently, the only genetic intervention being pursued for PMS is targeted at the SHANK3 gene. There are historical and logical reasons for targeting this gene. It is highly associated with several developmental disorders. That work should continue, but from a technical perspective, SHANK3 is not an easy gene to treat. The SHANK3 gene can produce from 20 to 100 isoforms (versions) of the shank3 protein, up to 1731 amino acids in size. (By comparison, the UBE3A gene associated with Angelman syndrome produces a maximum of 12 ube3a isoforms, with 875 amino acids being the largest. The MECP2 gene associated with Rett Syndrome, has two isoforms, with 486 amino acids being the largest.) Manipulating a large, complex gene like SHANK3 has consequences, at least some of which will likely be negative consequences. Like all early genetic clinical studies, initial trials will be on a few hand-picked cases. Unfortunately, even among people with SHANK3 mutations, there are many flavors and early treatment methods might not generalize to many patients.

If we are serious about a long-term solution for PMS we need to work on a smaller and more simple gene. Solving problems caused by SHANK3 is going to be a very slow process. We should choose a gene much easier to fix, and yet still has a serious impact in our children with PMS. The idea is to bring relief sooner, and to begin the important task of treating the full spectrum of PMS. There are 17 possible genes, three or four of which are among the best candidates. One possible target is BRD1. This is a regulatory gene that has been very well characterized. It is smaller than SHANK3 and one copy is missing in about 90% of the PMS population. Evidence so far supports the importance of missing only one copy of BRD1.

Titrating expectations, but not hope

There is always a balance between the enthusiasm for research into effective treatments and maintaining a realistic view of scientific progress. Young parents have so many compromises to make in their hope for the future when they receive a diagnosis of PMS. Placing the disorder into perspective takes years. We grow into a life consumed by a child with a major developmental disability. Hope requires embracing the possibilities, maintaining enthusiasm about the future, yet titrating our expectations to match today’s realities. We are a long way off. Our own children will likely be adults, perhaps old ones, before effective genetic treatments are ready for widespread application. We need to be realistic about our expectations without diminishing our hopes. Indeed, this is what raising a child with PMS is all about.

 

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