SHANK3 Haploinsufficiency and Gene Therapy

Image of a bridge borrowed from Wikipedia page on rivets

Originally posted 20 September 2022
Updated 21 September 2022

Haploinsufficiency is a genetics term that gets used frequently. The definition of haploinsufficiency is rather simple but understanding when to use the word can be complicated. Often, describing something as haploinsufficient is an incomplete description. Sometimes, it is misleading or even wrong.

Unpacking the word

Humans and other mammals (e.g., cats, dogs) are diploid animals. That is, we have two copies of the major 22 chromosomes (autosomes). That means, we have two copies of nearly every gene in our DNA. Why two copies? We evolved that way. Apparently, having two copies worked out well given that most animals are diploid. Haploid means one set of chromosomes, not two. It also implies one copy of a gene rather than the normal two copies.

Insufficiency means “not enough”. Thus, the word haploinsufficiency suggests having only one copy of a gene is not sufficient for normal body (or brain) function.

Molecular biology

Haploinsufficiency is a word from the field of molecular biology. Molecular biology includes the study of how a gene is used to make proteins. Typically, a gene is the recipe for making proteins. The cell decides when and how much of a protein is needed. Given two copies of a gene, the cell can summons production from both copies to meet its needs. Haploinsufficiency (or haploinsufficient) means that having only one copy of a gene restricts the production of its protein to the point of causing a major problem.

Understanding problems associated with protein production

I like analogies, so please consider this story about a bridge that uses rivets. A construction company needs 1,500 rivets to build a bridge. (Rivets are like permanent screws used to hold metal part together. See the bridge photograph, above.) There are two suppliers of rivets, each able to supply up to 1,000 rivets. The contractor orders 1,000 rivets from each company to make sure she will have extras in case some extras are needed. Let us review some of the things that might go wrong with the orders.

• One company is unable to deliver any rivets.
• Neither company is able to deliver rivets.
• One company can deliver some rivets, but not the full 1,000.

Other, more pernicious (damaging), things can go wrong.

• Some or all the rivets from one company look like rivets but are too weak or otherwise unable to hold metal parts together.
• Some or all of the rivets will damage the equipment that handles the rivets (e.g., wrong size or shape) or will damage the bridge (e.g., premature rusting).

This scenario is designed to mimic some aspects of protein production by two genes. With genes, similar things can go wrong.

• Two genes can produce enough protein, but one gene cannot. This would be haploinsufficiency (one copy of the gene is not enough).
• One gene can produce enough protein on its own. This is called haplosufficiency (one copy of the gene is sufficient). Haplosufficiency implies that you need to have at least once good copy of the gene, otherwise there is a problem

Like rivets, the product of a gene may be defective.

• A gene can produce a product that looks like the needed protein, but not act like the protein. The defective protein may get used by the cell even when there is sufficient good protein around. I will call this “defective protein“, which is not really a technical term.
• A gene can produce a protein that interferes with the machinery that assembles, transports, or maintains normal cell function. This is called “gain-of-function“. While gain-of-function sounds like a good thing, in this case the “function” is damaging.

What is and is not haploinsufficiency

Now we know that haploinsufficiency is the simple case of not having enough protein after one gene is lost. However, when a gene is abnormal, the resulting protein from that gene might be missing, defective, or have a gain-of-function. In other words, when a person has an unusual and disruptive version of a gene (called a pathogenic variant), that person may suffer from multiple things that can go wrong.

SHANK3 and haploinsufficiency

People who have intellectual disability, autism, or other aspects of the syndrome due to a deletion of the q13.3 region of chromosome 22 have Phelan-McDermid syndrome (PMS). Most of those people have PMS-SHANK3 related, meaning that the SHANK3 gene has been disrupted. In most cases of PMS the SHANK3 gene is missing altogether along with many other genes. In these people PMS results from the combination of genes deleted. Some of these genes, including SHANK3, are haploinsufficient. That is, a problem is created because having only one copy of the gene leads to not producing sufficient protein for normal function. In rare cases, the 22q13.3 deletion precisely deletes the SHANK3 gene without impacting any other haploinsufficient genes. These rare cases have pure SHANK3 haploinsufficiency.

There is another group of PMS patients with pure SHANK3 haploinsufficiency. These individuals have a SHANK3 variant that does not cause the production of any disruptive proteins. There are no proteins produced that have gain-of-function and no defective proteins that might compete with the normal protein for incorporation into the cell. Unfortunately, available molecular testing cannot provide sufficient information to be sure which patients with SHANK3 variants fall into this category. For most patients we do not know what combination of haploinsufficiency, defective protein, or gain-of-function protein a person has.

The messy reality of SHANK3 variants

There is strong evidence that SHANK3 variants include all three types of problems. For example, in general, people with PMS from SHANK3 variants are higher functioning than people with moderate or large deletions of 22q13.3. Yet, among this group with SHANK3 vaiants are some low functioning individuals, suggesting these patients have a substantial contribution from a defective protein or gain-of-function protein. Experiments in rodents where the Shank3 gene is mutated to imitate human cases of SHANK3 variants show that different mutations can have distinctly different impacts on brain development, synapse formation and behavior. This rodent work is further evidence for contributions from defective or gain-of-function proteins.

What does this mean for gene therapy?

Current work on gene therapy for PMS is focused on “gene replacement therapy”. The goal is to supplement the amount of Shank3 protein in the brain to compensate for haploinsufficiency by introducing an additional copy of a gene similar to SHANK3. This is an exciting and cutting-edge approach to seeking an effective treatment for PMS. It is currently in the animal experiment (“pre-clinical”) phase. If this approach leads to drug testing, we need to understand its limitation. While most of PMS involves SHANK3 haploinsufficiency, rarely is that the only problem. People with deletions of 22q13.3 can have many (up to 18) impacted haploinsufficient genes, and many people with SHANK3 pathogenic variants are likely to have contributions from defective or gain-of-function proteins. There is at least one known gain-of-function mutation tested in mice that effectively wipes out any attempt by the cell to produce SHANK3. So, even if the gene therapy helps some people, there are likely those people who would need an alternative therapy to benefit.

The current work on gene replacement therapy may or may not produce a product safe enough to try on human beings. Even if things go well, it may be 10 to 15 or more years before a product becomes available to families with PMS. Even if this happens, we are still faced with the messy reality of PMS: on one hand, people with chromosomal deletions that include SHANK3 are almost always missing other important genes, and, on the other hand, people with SHANK3 variants may be suffering from more than haploinsufficiency. I would like to offer three take-home messages:

• While SHANK3 haploinsufficiency is an important aspect of Phelan-McDermid syndrome (SHANK3-related), we honestly do not know if it is 30%, 50% or 75% to blame in any given individual.
• Because PMS is not just haploinsufficiency of SHANK3, any success with this first-generation gene replacement therapy (if there is any success) will be mixed at best. The first patient might do really well or have no response at all.
• Likewise, we should not be too discouraged if early clinical trials are unimpressive. There are many possible reasons for a weak effect early in testing. There is a long road ahead.

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