How to fix SHANK3

David snacking on some cereal bar bits

Human – Mouse Partnership

Originally posted 16 June 2016
Updated 19 August 2022

Anyone who has read the majority of my blog pages knows that my goal is to help parents, scientists and other members of the Phelan-McDermid syndrome (PMS) community understand how the genetic landscape of chromosome 22 must shape our thinking if we are going to realistically pursue treatments. At least one company has proposed to tackle the challenging task of a genetic intervention. While very exciting, we also must be humble about the difficulty of making it work. This blog looks at the limitations of this approach.

If you have not read the earlier blogs, much of this one may seem foreign. This blog is based heavily on prior ones. Because of the overlap, I will omit most scientific references and simply recommend reviewing prior posts for supporting evidence.

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There are a remarkable number of optimistic-sounding mouse model papers on the SHANK3 gene. The number of model mice has passed one dozen. People who work on SHANK3 mice often describe their rodents’ behaviors as mouse analogs to human behaviors. When an unusual mouse behavior is “rescued” with a chemical compound, the implicit (sometimes explicit) suggestion is that mouse research is on a path to curing autism, PMS, or maybe even schizophrenia. Some researchers like to define PMS as a disturbance of SHANK3, which guarantees that any SHANK3 fix will fix PMS. This is not consistent with research that looks at the complete genetic landscape of PMS. Rodent research papers are often rather optimistic. Perhaps writing papers this way promotes optimism in the patient community. Optimistic papers help to keep financial donors excited. These are probably good things, but we need to recognize the limitations of the research.

From a practical standpoint, we need a strategy for fixing SHANK3 problems in humans that accurately reflect the science. We need a plan that has more to do with the human disorder than the rodent one, and more to do with  therapeutic benefit than a detectable statistical change. The plan needs to be based on what we know more than what we speculate. The plan needs to be about the patients, not the scientists, funding agencies or charity organizations.

One critical clinical concern is the relationship between SHANK3 deletions and SHANK3 sequence variants (sometimes referred to as SHANK3 mutations). Nearly all rodent studies are studies of SHANK3 mutations. The reason for so many rodent models is largely because different laboratories study different mutations. This is not such a bad idea because many of these mutations are designed to duplicate human SHANK3 gene variants. The mouse studies are virtually always described as studies of SHANK3 deletion. However, they are rarely complete removal of the SHANK3 gene (or removal of both SHANK3 genes). Among the many different SHANK3 mutations studied in mice, the behavioral, molecular, electrophysiological and drug effects differ widely. Importantly, a study that looked at total removal of SHANK3 protein from a mouse found less impact on the mouse behavior than many of the other SHANK3 mutation studies. The important message here: in rodents some mutations have a greater impact than complete SHANK3 deletion.

What about humans? Are SHANK3 variants different from SHANK3 deletion? That is, do people with SHANK3 variants have the same problem as people with 22q13 terminal deletions (complete deletion of SHANK3). In 2022 there was a paper that hints at the answer. After carefully looking at patients with small terminal deletions (under 0.25 Mb) and comparing them to patients with SHANK3 variants, they observed:

Although individuals with small deletions and SHANK3 variants showed similar findings in most of the categorical variables (Table 5), a remarkable difference was observed in “the ability to make sentences” between the two groups, with 30/65 (46.2%, Supplementary Table S3) of individuals with deletions below 0.25 Mb able to make sentences compared with 5/18 (27.7%, Table 1a) among those with SHANK3 variants.
Nevado et al 2022 Variability in Phelan-McDermid syndrome in a cohort of 210 individuals, Frontiers in Genetics

Significantly more people with complete deletions of SHANK3 were able to speak in sentences compared to people with SHANK3 variants. This and previous studies have shown that different human SHANK3 variants can produce very different impacts. Clearly, some of these variants interfere with the normal operation of SHANK3 in ways that are worse than just reducing the amount of available protein.

This effect is not difficult to explain. Some SHANK3 variants can produce improper SHANK3 proteins that wreck havoc with the assembly of the synapse. As an analogy, think about placing a bunch of defective nuts and bolts into the manufacturing process for a car or airplane. The production line may be better off omitting some hardware (or producing fewer products) than installing defective parts. The somewhat surprising conclusion is that we might want to to treat some SHANK3 variants by shutting down a defective SHANK3 gene.

If we are considering SHANK3 deletion as a treatment for SHANK3 mutation, then we better be prepared to treat SHANK3 deletion. Results from the first Shank3 complete knockout mouse provides a hint at how to treating human SHANK3 deletion. The most abiding and measurable effect of complete Shank3 deletion in the mouse is failure to engage and benefit from an operant conditioning task (lever pressing for a reward). This effect appears to be associated with abnormal ventral striatal function, which is consistent with many previous studies of the ventral striatum. Failure to explore and learn would be indicative of intellectual disability in humans, so it is of great interest to understand the exact relationship between the learning deficits in humans with pure SHANK3 deletions and mice with pure (complete) Shank3 deletions. Such an undertaking would require a very modern and somewhat novel strategy in the world of pre-clinical neuropsychiatric research.

The precise nature of the mouse learning deficit is not yet understood. Learning is a complex process and many aspects are very subtle. Even the reported rescue of learning in the Shank3 knockout mouse creates more questions than answers. These questions go to the heart of how SHANK3 loss might contribute to intellectual disability in humans. How can the details of learning deficits caused by SHANK3 deletion be dissected out? I do not believe it can be done in mice, but it is difficult to find humans missing the entire SHANK3 gene, but little else (pure SHANK3 deletion). Given the rarity of pure SHANK3 deletion, I propose that scientists could do an in depth study of one or two human volunteers with very small deletions. This research could be modeled after behavioral research methods from studies of nonhuman primates. These are studies where behavior from just one or two animals is studied in great detail.

The studies with the PMS volunteers would combine behavioral testing and advanced computational modeling. The results of each new test leads to a modification of the model, and the results of each new model identifies new things to test. These state-of-the-art computationally-based scientific learning studies are designed to incorporate variables that can be directly tied to equations describing an underlying theoretical framework of the learning process. Animal researchers are adept at designing learning tasks in ways that do not require verbal instruction. They are equally practiced at inferring the results without the need for verbal reports. Still, with the participation of a fluent verbal subject, researchers can work with the subject to help design tasks (games) that are interesting and engaging. Why not let the subject have fun?

As these learning tasks  begin to characterize the nature of the deficit seen in the subject/participant, they are then re-designed for testing in animal models. Current rodent models could be used with simple tasks, but more demanding tasks may require nonhuman primates. These studies could include fMRI and electrophysiological investigations. The technology of gene editing, common in mice, has reached farm animals and at least two species of nonhuman primates. As these methods become more mainstream, complete SHANK3 deletion could be a practical research option, especially in old world monkeys, species that shares important common features with human cortical evolution.

The goal of this scientist/participant research partnership is to develop a sensitive cross-species measure of learning ability that parametrizes the impact of SHANK3 dosage. Such a measure provides two invaluable assets to the development of treatments. First, animal models can be validated (or not) based on exquisite computational approaches that may be able to distinguish species differences from the influence of SHANK3 dosage. Second, interventions, either learning-based or pharmaceutical, could be tested using measures sufficiently sensitive to reflect the identified nature of the deficit. What can this human research/animal research partnership hope to produce? The first successes may be refinements to educational methodologies. The learning models could point the way to improvements in teaching strategies for our kids with PMS. Later, dare we hope, new pharmaceutical treatments could emerge.

We all hope that initial human trials of gene replacement therapy will provide a critical new treatment for our kids with PMS. Those trials may take many years to materialize. In the meantime, we need to better understand what we can expect from gene replacement, and the exact nature of learning deficits that arise from loss of SHANK3.

arm22q13

Previous blogs

Have you ever met a child like mine?
How do I know which genes are missing?
Mouse models
How can the same deletion have such different consequences?
22q13 and the hope of precision medicine
22q13 Deletion Syndrome: hypotonia
Understanding gene size
Gene deletions versus mutations: sometimes missing a gene is better.
Understanding deletion size
22q13 deletion syndrome – an introduction