Is “PMS-SHANK3 unrelated” truly unrelated to SHANK3? Maybe not.

David relaxing in the car during a drive through the countryside

Originally posted 10 April 2024

In 2022 a group of scientists associated with the Phelan McDermid Syndrome Foundation (PMSF) published a consensus paper that addressed a controversy around what constitutes Phelan McDermid syndrome (PMS). It was an important step toward defining the disorder, providing guidance to geneticists, and working towards an ICD code for diagnosis and medical reimbursement. Although the consensus opinion was not universal, the clarification was welcome. These experts split PMS into two mutually exclusive classes: “PMS-SHANK3 related” and “PMS-SHANK3 unrelated”. It is a simple, clear dichotomy. But genetics are rarely simple, as we shall see.

The thinking at the time was from the perspective of genetic testing. If the test result includes an abnormality of the SHANK3 “coding region”, then it gets the designation PMS-SHANK3 related. All other test results would be PMS-SHANK3 unrelated.

The people who hammered out this definition (distinction) are all experts. They were fully aware of all the possible ways genes can contribute to a disorder. There are dissenters, also experts, who feel that if SHANK3 is not involved, then the name PMS should not be applied. The consensus paper explains that people with interstitial deletions (PMS-SHANK3 unrelated) do not appear to have a syndrome different from PMS. There is also no transition from PMS to some other syndrome as deletion sizes get larger, whether or not SHANK3 is involved. There is no clear evidence that PMS-SHANK3 unrelated is some other type of disorder. The key concern for dissenters is that genes other than SHANK3 do not contribute to the disorder in the same way that SHANK3 causes PMS.

However, what if we can show that other genes on chromosome 22 contribute to PMS through their impact on SHANK3, or their impact on the molecules that interact with SHANK3? If the genes of 22q13.3 (the site of interstitial deletions) have such direct impact on SHANK3, then perhaps the term “PMS-SHANK3 unrelated” is misleading. If the biology of PMS-SHANK3 unrelated is highly related to SHANK3, then a distinction may not be warranted. The latest evidence suggests there are at least six genes that impact SHANK3 (and partner molecules), and these genes contribute to PMS when deleted. I would call these genes SHANK3 related.

The six genes and the details of how they interact with SHANK3 are discussed in a recent paper. The paper is open source (anyone can read it), but very technical. Full disclosure: I helped write the paper, so this blog post is undeniably biased. People who have read my previous blog posts should know that I have long been a proponent of looking closely at the many genes of PMS. The paper is a review of work done by scientists primarily between 2017 and 2024. Science is a continuous process and during this period enough information came to light to explain the tight relationships between six genes (PLXNB2, BRD1, CELSR1, PHF21B, SULT4A1, TCF20) and SHANK3. The first two genes are physically close to SHANK3 on chromosome 22, and thus are deleted in most deletions that include SHANK3. The remaining four genes are fairly evenly spaced across the last 4 Mb (megabases) of the PMS region of chromosome 22.

I have written blog posts about all of these genes at one time or another. I identified PLXNB2 and PHF21B in Why PMS is worse for people with larger deletions, and PMS Gene PHF21B is critical for normal brain development. I wrote about TCF20, a gene that has long been associated with intellectual disability (TCF20 may explain why some big deletions are worse than others). I have flagged the potential importance of BRD1 in several blogs (e.g., Regression and psychiatric dysfunction in PMS). CELSR1 was highlighted in CELSR1: Do some people with PMS have more fragile brains? SULT4A1 has also been on the radar for some time: New science: SULT4A1, oxidative stress and mitochondria disorder. My message has always been that genes important to PMS will emerge once there was sufficient evidence to critically explain why larger deletions have greater impact. SHANK3 has always been the most important gene and it has been the most intensely studied, but from the beginning of PMS research, it was never the only important gene. By “important” I mean important to families.

All seven genes (including SHANK3) impact brain development and all are involved with the process of inflammation. In this case inflammation includes “cellular stress”, “mitochondrial function”, and “recovery from injury”. These are all related processes, and all known to exacerbate PMS. So, impact on early development and response to stress and injury are features common to all of the genes.

Three of the genes (BRD1, PHF21B and TCF20) regulate what other genes do in the brain. For example, all three regulate the activity at synapses, the part of neurons that SHANK3 regulates. In addition, two more genes (PLXNB2 and SULT4A1) are directly involved in synaptic function. In fact, SULT4A1 not only regulates the same glutamate receptor as SHANK3, but it also regulates breakdown of SHANK3 at the synapse.

At this point it should be clear why PMS-SHANK3 unrelated may not really be unrelated to SHANK3. The six genes listed above join SHANK3 in shaping the development of the brain, the response of the brain to insults, and the operation of the synapses – the most important role of SHANK3 in the brain. It should also be clear why people with interstitial deletions typically have symptoms consistent with other cases of PMS. Likewise, it should also be clear why people with larger and larger deletions tend to have more severe PMS (see: Why PMS is worse for people with larger deletions).

The very close association between SHANK3 and at least six other PMS genes has a number of ramifications. First, while the distinction between SHANK3-related and -unrelated is sensible from the point of view of genetic testing, it may not be a good way to think about PMS as a disorder. Second, treatments that target SHANK3 will likely miss other relevant genes that tightly influence SHANK3, and thus may not produce very satisfying results in patients with chromosomal deletions. One way to think of the problem is that SHANK3 treatment in people with deletions essentially expands the number of PMS patients with interstitial deletions. It may be difficult to distinguish between a treatment that is not effective for SHANK3, and a treatment that is not effective because of other genes. Finally, when we are searching for an effective treatment for SHANK3 haploinsufficiency, maybe we should also look at treatments for one or more of the other genes. We may be missing out on developing additional valuable treatments.

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Why PMS is worse for people with larger deletions

David uses an adaptive switch to compensate for his poor coordination

Originally posted 27 December 2022

It is colder during wintertime

No one in the continental US would say that the autumn is colder than the winter. There are some days during the autumn that are colder than some days during the winter. But, winter is colder than autumn. Phelan-McDermid syndrome (PMS) is much the same. After many years of study, the scientific consensus is clear. Larger deletions come with greater loss of function, even though there are some cases of small deletions having greater impact than some cases of larger ones. The problems with larger deletions come in many forms. In the most recent study, people with very small deletions or only SHANK3 variants had “fewer delayed developmental milestones and higher cognitive ability”. People with larger deletions were “more likely to have a variety of medical features, including renal abnormalities, spine abnormalities, and ataxic gait” [1]. These same larger deletions greatly disrupt the genetics and profile of immune cells in the blood [2]. The whole genetic profile and metabolism of people with deletions greater than 1 Mb is off kilter: “DNA methylation epi-signature showed significantly different metabolomic profiles indicating evidence of two … distinct clinical subtypes of Phelan-McDermid syndrome” [3]. These new studies have only served to validate what was originally shown nearly 10 years ago [4].

What do scientist look for?

While scientists affiliated with the Phelan-McDermid syndrome community have focused largely on the SHANK3 gene, many scientists outside this community have been quietly advancing our understanding of other critical genes of PMS. I have written blogs on some of these important genes, including CELSR1, SULT4A1, TCF20, PHF21B, and others. When it comes to the core symptoms of PMS, which are all associated with brain dysfunction, three aspects of a gene are important to understand. First, what problems are caused by losing the gene in humans and model animals? Second, what biological impact does losing a gene have during early (pre-natal) development? Third, what role does the gene play in the adult human/animal?

Pleiotropy

When the same gene can impact a person in multiple ways, that is called pleiotropy. For example, losing SHANK3 can cause multiple problems, including low muscle tone, slower or less reaction to pain, GI disturbances, psychiatric illness, and regression. SHANK3 is said to be a pleiotropic gene. Multiple problems can arise from a single gene that gets used at different times in different places. When we think about different times we usually think about how a gene is used during prenatal development, a process that occurs only once in life, and how the gene gets used after birth. Prenatal development lays down the architecture of the brain. In humans, development of the brain continues into the 20s, but the most rapid changes occur before birth. Rapid, but slower changes continue during the first 3 years of life. Things like movement and language rapidly develop in the first few years. But, these changes depend upon the framework laid down in the uterus.

SHANK3 is active during prenatal development. It is involved with axon guidance, the process that neurons use to find each other during development [5] and other processes in early development [6-10]. These processes are distinct from how SHANK3 contributes to synaptic function in the adult brain.

What has come to light in the past few years is the pleiotropy of other PMS genes that contribute both during brain development and in the adult brain.

PLXNB2

One gene that is getting a lot of research attention is PLXNB2. From 2007 through 2014 a series of papers describe how Plexin-B2, the protein produced by the Plxnb2 gene as studied in mice, is critical for normal brain development [11-13].  In 2017 it was shown that the same protein is involved in pain sensation [14]. In the past few years the research has been extended. Loss of Plexin-B2 interferes with normal learning and memory in the adult mouse brain [15]. The role of Plexin-B2 parallels and overlaps the role of Shank3. Both are used at excitatory synapses in the brain. Both are involved in pain pathways in the spinal cord. In humans, these two genes are very near each other on chromosome 22, so almost all people who have PMS from a deletion are missing both genes. We can speculate that these genes exacerbate the damaging influence of each other.

What makes Plexin-B2 especially interesting for PMS is that it affects the brain circuit essential for remembering danger. Specifically, loss of Plexin-B2 in mice interferes with “conditioned fear recall”. That is, the mice will learn to recognize a warning tone when the tone signals a brief foot shock, but 2 days later they have forgotten the meaning of the warning tone. The neurons involved fail to form adequate synapses 2 to 3 days after the training period [15]. These are some of the same synapses where Shank3 operates. When I read this I nearly fell off my chair. (You could say I was shocked.) If there is one thing that my son, David does poorly, it is learning about danger. It took years to explain to David what it means when something is (dangerously) hot. It took equally long to warn him about stepping over an obstacle or curb. We often suppose that our children do not have the same sensitivity to pain as most people. That may be true, but we also might be misled by their inability to incorporate painful or fearful experience into memory.

PHF21B

Larger deletions of chromosome 22 can disrupt the PHF21B gene. This blog is about genes that have a role both in development and adult function. I have already written a blog on how PHF21B is critical for normal brain development. Now there is new research showing that PHF21B regulates synapses during “social” learning [16]. Social learning in mice is when a mouse can distinguish between a new mouse and one that has visited the cage before. Not distinguishing between a familiar mouse and a stranger is a serious inability. The Phf21b protein normally triggers parts of the DNA to build a memory after spending time with a new animal. In animals missing about half of their Phf21b protein, the ability to remember a fellow mouse (“conspecific”) is disrupted. The circuitry that is disrupted involves the Shank proteins. Thus, PHF21B is another gene that is important for both development and adult function, and is intimately associated with SHANK3.

CCDC134

Another gene that has received recent attention is CCDC134. To be honest, I did not pay much attention to this gene until recently. The gene is lost only with the very largest deletions (> 9 Mb), so loss of this gene is rare. CCDC134 had long been suspected to be essential for normal brain development, but mice missing CCDC134 died before they were old enough for behavioral studies. This past year a group in China produced a mouse that was missing Ccdc134 protein only in the cerebellum of the brain [17]. The cerebellum is well known as a critical area for motor coordination. Making a custom knockout mouse did the trick. Mice missing only Ccdc134 and only from the cerebellum develop malformation of the cerebellar Purkinje and granule cells. Mice with these deficits had problems with grip strength, motor coordination and motor learning. If you know a PMS child with a very large deletion who has serious difficulties standing and walking, it could be largely because of this gene. Most people with PMS have problems with the cerebellum. There is evidence that loss of Shank3 impacts the cerebellum in mice [9], but that more prominent malformations occur with deletions in people [18]. Now we know the largest deletions likely add substantially to the problem.

It can get very cold in winter

Larger and larger deletions have greater and greater impact on people with PMS. Even people with interstitial deletions that do not disrupt SHANK3 can have PMS. The combined developmental and adult functions of missing PMS genes, and their overlap with the function of SHANK3 at the synapse, conspire to make larger PMS deletions more detrimental in multiple ways. This blog is about recent finding in 3 PMS genes. Previous blogs have discussed other genes that impact PMS. As science advances we will learn more.

My parents never lived in a warm climate. One December my mother came to visit me at school in Atlanta, GA.  It was an unexpected 80 degrees that day. She asked, “Is it always this warm?” I said, “Yes.” The truth was, a year prior Atlanta had been blanketed with an equally rare snowstorm. Everyone in Atlanta knows it is colder in the winter, even though there can be the rare warm day. At this point, it is quite clear that larger [terminal] deletions of 22q13 are more impactful than smaller deletions or SHANK3 variants. PMS is more impactful than many other neurodevelopmental disorders. There will always be exceptions, but we must fully understand the rule before we can explain the exceptions.

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Papers referenced

1.            Levy, T., et al., Strong evidence for genotype-phenotype correlations in Phelan-McDermid syndrome: results from the developmental synaptopathies consortium. Hum Mol Genet, 2022. 31(4): p. 625-637.

2.            Breen, M.S., et al., Large 22q13.3 deletions perturb peripheral transcriptomic and metabolomic profiles in Phelan-McDermid syndrome. HGG Adv, 2023. 4(1): p. 100145.

3.            Schenkel, L.C., et al., DNA methylation epi-signature is associated with two molecularly and phenotypically distinct clinical subtypes of Phelan-McDermid syndrome. Clin Epigenetics, 2021. 13(1): p. 2.

4.            Sarasua, S.M., et al., Clinical and genomic evaluation of 201 patients with Phelan-McDermid syndrome. Hum Genet, 2014. 133(7): p. 847-59.

5.            Halbedl, S., et al., Shank3 is localized in axons and presynaptic specializations of developing hippocampal neurons and involved in the modulation of NMDA receptor levels at axon terminals. J Neurochem, 2016. 137(1): p. 26-32.

6.            Liu, X., et al., SHANK family on stem cell fate and development. Cell Death Dis, 2022. 13(10): p. 880.

7.            Pillerova, M., et al., Neuromotor Development in the Shank3 Mouse Model of Autism Spectrum Disorder. Brain Sci, 2022. 12(7).

8.            Panagiotakos, G. and S.P. Pasca, A matter of space and time: Emerging roles of disease-associated proteins in neural development. Neuron, 2022. 110(2): p. 195-208.

9.            Otazu, G.H., et al., Neurodevelopmental malformations of the cerebellum and neocortex in the Shank3 and Cntnap2 mouse models of autism. Neurosci Lett, 2021. 765: p. 136257.

10.          Mossa, A., et al., Developmental impaired Akt signaling in the Shank1 and Shank3 double knock-out mice. Mol Psychiatry, 2021. 26(6): p. 1928-1944.

11.          Deng, S., et al., Plexin-B2, but not Plexin-B1, critically modulates neuronal migration and patterning of the developing nervous system in vivo. J Neurosci, 2007. 27(23): p. 6333-47.

12.          Vodrazka, P., et al., The semaphorin 4D-plexin-B signalling complex regulates dendritic and axonal complexity in developing neurons via diverse pathways. Eur J Neurosci, 2009. 30(7): p. 1193-208.

13.          Laht, P., et al., B-plexins control microtubule dynamics and dendrite morphology of hippocampal neurons. Exp Cell Res, 2014. 326(1): p. 174-84.

14.          Paldy, E., et al., Semaphorin 4C Plexin-B2 signaling in peripheral sensory neurons is pronociceptive in a model of inflammatory pain. Nat Commun, 2017. 8(1): p. 176.

15.          Simonetti, M., et al., The impact of Semaphorin 4C/Plexin-B2 signaling on fear memory via remodeling of neuronal and synaptic morphology. Mol Psychiatry, 2021. 26(4): p. 1376-1398.

16.          Chin, E.W., et al., The epigenetic reader PHF21B modulates murine social memory and synaptic plasticity-related genes. JCI Insight, 2022. 7(14).

17.          Yin, S., et al., Ccdc134 deficiency impairs cerebellar development and motor coordination. Genes Brain Behav, 2021. 20(7): p. e12763.

18.          Aldinger, K.A., et al., Cerebellar and posterior fossa malformations in patients with autism-associated chromosome 22q13 terminal deletion. Am J Med Genet A, 2013. 161A(1): p. 131-6.

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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The four types of Phelan McDermid syndrome

David has PMS Type 1

Originally created 12 September 2020
Updated 31 January 2022

I am going to describe four types of Phelan-McDermid syndrome (PMS). By type, I mean four different genetic arrangements that can result in PMS. These are technically called “genotypes”. The four genotypes do not address the mechanisms that create each genotype. For example, my son, David, has Type 1 (Genotype 1) from an unbalanced translocation, but others have PMS Type 1 from de novo deletions or ring chromosomes. The types can be used by parents as a very simple short-hand to share information about their child.

Phelan McDermid syndrome Type 1, terminal microdeletion

This is the original 22q13.3 microdeletion syndrome described by Katy Phelan and Heather McDermid. It is also the most common type among people identified with PMS.

A microdeletion occurs when multiple genes on a chromosome are removed. Most microdeletions are too small to see under a microscope, but Katy Phelan has described some microdeletions that are large enough to be visible. Deletion sizes range from about 0.2 Mb to 9.3 Mb, with an average of 4.5 Mb. Nearly all of the microdeletions observed are terminal deletions (continue to the end of the chromosome). Terminal deletions much smaller than 0.2 Mb do not include SHANK3 and do not produce a syndrome.

Phelan McDermid syndrome Type 2, interstitial microdeletion

An interstitial microdeletion is a deletion that removes multiple genes, but does not extend to the end of the chromosome. For PMS Type 2, the deletion does not reach SHANK3, which is near the end of the chromosome.

Interstitial deletions that produce PMS, but do not disrupt SHANK3 are relatively rare. Some scientist have argued against including them in the definition of PMS. However, a recent scientific consensus paper (https://ojrd.biomedcentral.com/articles/10.1186/s13023-022-02180-5) justifies the strong reasoning for including Type 2 in the definition of PMS.

Phelan McDermid syndrome Type 3, single SHANK3 rare variant

A rare variant is an atypical version of a single gene. PMS caused by a rare variant of SHANK3 is called Type 3. Sometimes this has been called a “mutation” of SHANK3. That terminology is not always technically correct, so “variant” is preferred.

Type 3 is currently the second-most common example of PMS. However, rare variants of SHANK3 have been found in large collections of DNA from people with autism spectrum disorder (ASD). Although only 1 to 2% of people with ASD might have a rare variant of SHANK3, this still a potentially large population of people who might have PMS Type 3. More research is needed.

Phelan McDermid syndrome Type 4, heterozygous deleterious variants

You child does not have PMS Type 4. PMS Type 4 is included here for completeness. Individuals can inherit two copies of unusual variants of SHANK3, one from each parent. This can produce PMS as a recessive disorder. There may be cases of Type 4, but they would be very rare, indeed.

Comments

The consensus paper (see the link, above) has provided a clear statement about how the PMS diagnosis should be applied. This is the classification that geneticists and scientist should use.

1. PMS-SHANK3 related      (Types 1, 3, 4)
2. PMS-SHANK3 unrelated   (Type 2)

Note that most cases of PMS fit one of the four PMS types. However, the reality of genetics is that some cases can be very messy. The four genotypes of PMS are not always clearly segregated in any given individual. An individual can have an interstitial deletion, yet also have a pathological variant of SHANK3. This could be described as both PMS Type 2 and PMS Type 3. The classification system from the consensus group, PMS-SHANK3 related versus PMS-SHANK3 unrelated,covers all possible cases without any overlap.

Sometimes two different genotypes are actually very similar

Most PMS Type 1 and PMS Type 3 cases are very different from each other. An individual with a large terminal deletion is likely to have problems not shared by an individual with a SHANK3 variant. With Type 1 there are many important genes involved, some known to produce profound effects. In Type 2, any effect would only result from disturbing SHANK3. Yet, someone with a small terminal deletion (PMS Type 1) might be very similar to someone else with PMS Type 3. Although in different categories, they could end up being very similar.

PMS is a syndrome

PMS is defined by its genetics. However, central to all syndromes is that the individual must have a phenotype reflecting the syndrome. There are some individuals with interstitial deletions and other individuals with with SHANK3 variants who simply do not have significant features of Phelan-McDermid syndrome. These are very interesting cases, but they cannot be called PMS.

This simple system of PMS Types 1 to 4 can help parents quickly share the basic genetics of their children. PMS Types 1 and 2 have a deletion size associated with them. PMS Type 3 does not. Some manifestations of PMS, like lymphedema are not seen with Type 3. Sharing your child’s PMS Type can be an ice breaker during introductions and help a parent share key information without having to be a genetics expert.

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Earlier posts related to this one:

Understanding deletion size

Gene deletion versus mutation: sometimes missing a gene is better.

PMS, IQ and why interstitial deletions matter

How can the same deletion have such different consequences?

We need to study interstitial deletions to cure PMS

Defining Phelan McDermid syndrome

Regression and psychiatric dysfunction in PMS

David has not experienced a major regression.

Originally posted 30 December 2019
Updated 4 March 2022

Regression is one of the scariest words among the Phelan McDermid syndrome (PMS) community. It is not clear how common regression is in PMS. Recent and ongoing studies are addressing the problem. Regardless, regression does occur, can be unpredictable, and it can sometimes be devastating. After years of hard work helping your child navigate a world that is well beyond his or her comprehension, you then lose some or all of the gains to an invisible and unforgiving demon. In the PMS world, you either loath regression or fear its occurrence.

Three papers recently looked at regression in PMS, each taking a somewhat different approach. Reierson et al 2017 used scores from the Autism Diagnostic Interview-Revised (ADI-R) based on 50 patients seen in their clinical study. Verhoeven et al 2019 studied 24 adult PMS patients with psychiatric presentations and followed them over years. Kolevzon et al 2019 did a detailed literature review of PMS and SHANK3 mutations (de novo deleterious variants). This blog will be mostly a technical overview of the Kolevzon paper, with some additional notes from the Verhoeven study, both aimed at patients over 12 years of age and who present with psychiatric issues or sudden loss of function.

All of the authors have struggled to define “regression” and identify trends in occurrence and treatment methods. I am told there are important differences between “regression” and psychiatric decompensation. I’m not a psychiatrist so I won’t untangle the technical differences. But from what I read, either type of event can be a setback. Psychiatric decompensation seems to bring with it the likelihood of recovery and can repeat (episodes).

If you don’t want to read my full post, here some of the take-home messages.

1) There is yet no clear measure of how often regression or psychological decompensation occurs with PMS.
2) Relying on previous papers is difficult because not all descriptions in the literature provide sufficient detail about each patient.
3) Diagnosis of psychiatric illness is more difficult in people with low intellectual function and absent of functional language.
4) People with SHANK3 variants (“mutations”) and tiny chromosome deletions are a small minority of identified PMS cases. In general, they are more functional than others with PMS (higher intellectual function, better language and better motor skills). This minority are the patients who most often present with psychiatric problems. The great majority of patients with deletions greater than one or two Mb (more common PMS patients), show psychiatric problems far less often, at least given the limited research done so far.
5) When looking at the psychopathology overlap between SHANK3 variants and typical PMS patients, the common feature seems to be bipolar disorder.
6) In spite of the difficulties studying psychiatric problems in PMS, following best practices of psychiatric care used in the general population can be helpful for people with PMS.
7) Over-medication and certain medication choices can harm, rather than help.
8) Proper personal and social care of the adult with PMS is important for the successful management of regression and psychiatric problems.
9) These early studies provide a first, and perhaps hopeful picture, but much more work needs to be done to understand the natural history of PMS and the risks we face as parents.

Kolevzon and his co-authors specifically excluded individuals with interstitial deletions (called PMS-SHANK3 unrelated, explained here). That is, they chose to only study the category of PMS called PMS-SHANK3 related. The Kolevzon paper could have included interstitial deletions to look more closely at the causes of PMS regression. It is an unfortunate omission that I have warned against in the past (see: PMS, IQ and why interstitial deletions matter and We need to study interstitial deletions to cure PMS).

Most of the important information from the Kolevzon paper is in their Table 1, which is the result of an in-depth search for papers on PMS patients. Table 1 provides an excellent resource to the PMS research community despite ignoring interstitial deletions. I spent a few hours hunting down the original articles listed on the table and studying them. PMS science benefits greatly from this work. The table itself has a flaw that readers should be aware of. The reference numbers of the table are messed up. The following reference numbers are wrong (4-6, 8-12, 15-19, 22-25, 30, 32, 35-42). The author names and dates are correct, so there is no problem if you simply ignore the reference number and do a text search for the author name.

As noted above, it is difficult to define regression and the authors did not clearly describe the difference between regression and psychological decompensation. Presumably, experts in the field recognize the distinction. Regardless, the Kolevzon study required some rule set to execute a literature review. These authors chose: “Sudden change in the psychopathological presentation”. They focused on patients older than 12 years. The literature search looked for: 1) psychiatric decompensation, 2) loss of skill, 3) sudden behavioral change.

They found 56 cases, including 15 cases of ring chromosome, referred to as r(22). While it is laudable to dig deep into older medical literature and pull out r(22) cases, most of these predate the time when deletion size was easy to measure. There is another problem with evaluating r(22). Just as interstitial deletions can cause PMS without disrupting SHANK3, r(22) can cause developmental delays without disrupting SHANK3. In fact r(22) can cause developmental delays without disrupting any gene (see: Guilherme et al 2014). Also, as the Kolevzon paper points out, r(22) can lead to Neurofibromatosis 2 (NF2) disorder, which can be degenerative. The authors are careful to identify which results are dominated by r(22) cases. I think only the most recent cases (cases 19, 35 and 51) are helpful to the study. The earlier cases date from 1985 to 2007. One other case, 32, does not seem to provide much information.

By removing cases of PMS deletions that lack deletion size information, we can explore the impact of deletion size. What we discover is that psychopathology is almost exclusively diagnosed in patients with small deletions. The plot below uses the Kolevzon data from Table 1. It shows the frequency of diagnosis (number of cases) as a function of deletion size. SHANK3 variants are not included.

Psychiatric problems show up mostly with small deletions, which are uncommon.

To understand these results, remember that 95% of people identified with PMS have deletions greater than 1 Mb (see: Understanding deletion size). The cases found by Kolevzon are heavily weighted towards small and very small deletion. That is, most cases of psychopathology in the literature come from deletions that represent about only 5% of the PMS population.

If we merge the data from SHANK3 variants with the smallest deletions (size 0 to .9 Mb), the first bar more than doubles in size. We can conclude that psychopathology shows up almost exclusively when chromosome 22 is disrupted near the terminal end. That is, it shows up in the atypical cases where damage is limited to primarily SHANK3 disruption. Is this generally true for PMS or just for the sample of papers found during the literature search? We don’t know. For the moment, it is the best data available.

The authors suggest that because people with SHANK3 variants and tiny deletions are higher functioning, psychopathological changes might be easier to observe. Indeed, in their sample the cases of SHANK3 mutation and small deletions had both significantly higher intellectual function and motor skills. I suggest another possibility. It may be that loss of genes in the 2 – 4 Mb region of the chromosome help stabilize brain function. The most likely candidates in this region of the chromosome are BRD1, TBC1D22A, GRAMD4, CELSR1. I have discussed some of these genes in detail, in my other blogs (see 22q13: a hotbed for autism and intellectual disability genes?, and CELSR1: Do some people with PMS have more fragile brains?) Whether these genes seriously impact brain function, stabilize the brain, or both, there is no doubt that these genes greatly influence the outcomes of patients with PMS. The importance of these genes have come up in other studies, as well. These genes likely also contribute to the impact of PMS from interstitial deletions (see: Which PMS genes are most important?).

These initial results are concerning to families dealing with very small deletions or SHANK3 variants (limited primarily to SHANK3 disruptions). On the other hand, most of the Kolevzon study has less relevance to 95% of families. Still, there are 8 of the 56 patients that represent typical size deletions: P20, P21, P23, P24, P28, P33, P47 and P50. It is valuable to look specifically at these typical cases of PMS to see what might be more generally relevant to PMS families. For example, none of these 8 patients were diagnosed with psychosis and only one had tremor. Thus, psychosis and tremor might not be very relevant to most families. On the other hand, only typical PMS patients lost the ability to walk. Catatonia was seen in only one typical PMS patient (P50).

One feature in common between typical PMS patients and the uncommon cases of SHANK3 disruption is the incidence of bipolar disorder. Half of the typical PMS patients were diagnosed with bipolar disorder, as were many of the patients with SHANK3 disruption. This observation suggests a common mechanism, likely the SHANK3 gene. Do PMS patients with interstitial deletions have bipolar disorder? That would be an extremely valuable question to explore. Reviewing cases of interstitial deletions may support or refute the specific role of SHANK3 in bipolar disorder.

Verhoeven et al observed a similar overlap between typical PMS and cases of SHANK3 disruption. They state: “Based on actual psychiatric classification, in 18 patients, a diagnosis of atypical bipolar disorder was established of which symptoms typically started from late adolescence onward. In most patients, treatment with mood stabilizing agents in combination with individually designed contextual measures, and if indicated with the addition of an atypical antipsychotic, resulted in gradual stabilization of mood and behaviour.” Note the phrase “with individually designed contextual measures”. Proper social treatment of the person with PMS appears to be important for “recovery” (not a technical term).

Kolevzon et al discuss which treatments were more or less effective for both the SHANK3 disruptions and typical PMS patients. The overlap with Verhoeven is very encouraging. Together, the agreement between recent studies on regression and psychopathology provide improved guidance for the medical caregivers who may encounter bipolar disorder in PMS patients. The work of Kolevzon is especially valuable for cases of SHANK3 disruption (variants and very small chromosomal deletions). The number of cases where the PMS adult was stabilized was encouraging in both studies, which provides hope for families facing adult psychopathology.

It will take more studies to make strong statements about regression and psychological decompensation in Phelan McDermid syndrome. These early studies hint at the type of problems that do occur in PMS, the types of remediation that have been beneficial and the differences that appear to be associated with deletion size.

My son, David started life with some rather major problems. He was 6 years-old before he could walk and 9 years-old before he could eat by mouth. He never developed speech. His developmental trajectory has been slowly upward. At age 34, he has not had a regression or anything that could be called psychological decompensation. (His mom is qualified to recognize decompensation.) His deletion size is unknown, but I would wager it is not a small deletion. Does his stability come from missing certain genes?

When we moved David to a new group home two years ago, his mom and I were vigilant about managing the changes and constantly gauging his comfort. We were, frankly, scared that he would decompensate or regress. The transition was successful and David feels at home. But, what will be the next challenge and how will David respond? We don’t know.

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References
Verhoeven et al 2019
https://www.ncbi.nlm.nih.gov/pubmed/31465867

Kolevzen et al 2019
https://www.ncbi.nlm.nih.gov/pubmed/31879555

Reierson et al 2017
https://www.ncbi.nlm.nih.gov/pubmed/?term=28346892

Guilherme et al 2014
https://www.ncbi.nlm.nih.gov/pubmed/24700634

Some selected earlier blogs

22q13: a hotbed for autism and intellectual disability genes?
PMS for Dummies
Which genes cause brain abnormalities in Phelan McDermid syndrome?
PMS, IQ and why interstitial deletions matter
MAPK8IP2 (IB2) may explain the major problems with walking and hand use
TCF20 may explain why some big deletions are worse than others
Current trends in SHANK3 research
Which PMS genes are most associated with Autism?
Does SHANK3 cause Autism?
We need to study interstitial deletions to cure PMS
What do we know about PMS genes?
Which PMS genes are most important?
Are children with Phelan McDermid syndrome insensitive to pain?
Looking for Opportunities
Splitting, Lumping and Clustering
Defining Phelan McDermid syndrome
Why don’t we have better drugs for 22q13 deletion syndrome?
Educating children with 22q13 deletion syndrome
How to fix SHANK3
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 translocations in 22q13 deletion syndrome: genetics and evolution
Understanding deletion size
22q13 deletion syndrome – an introduction

22q13: a hotbed for autism and intellectual disability genes?

David has both intellectual disability and some features of autism spectrum disorder.

Introduction

While SHANK3 has been identified as a major contributor to intellectual disability and autism spectrum disorder, there has always been a lingering question of why people with Phelan McDermid syndrome (PMS) have very similar symptoms (phenotype) whether or not SHANK3 is impacted. That is, people with terminal deletions that remove SHANK3 are not very different from people with so-called “interstitial deletions”. This observation is the main reason why the current definition of PMS says that SHANK3 is usually, but not always, impacted (see The 22q13.3 Deletion Syndrome).

I have written several blogs that cover the evidence, so far, why intellectual disability and autism are not limited to one gene of 22q13 (see PMS for Dummies, Which PMS genes are most associated with Autism? Which PMS genes are most important?).  In this blog we look at new data indicating that 22q13 has more autism-associated genes than we previously knew.

What we knew before

Genes with a high “pLI” (genes that are very rarely mutated in the general population) are associated with intellectual disability. For 22q13 they are: SHANK3, MAPK8IP2, PLXNB2, TRABD, PIM3, ZBED4, BRD1, TBC1D22A, GRAMD4, CELSR1, SMC1B, PHF21B, PRR5, SULT4A1, SCUBE1, TCF20, SREBF2, and XRCC6. Most, if not all of these genes contribute to intellectual disability, although some are more certain. While 18 genes may seem like a lot of genes, remember that PMS can delete up to 108 genes. Still, it is impressive that nearly 17% of the genes of 22q13 potentially contribute to intellectual disability. The high number of these high pLI genes explains why intellectual disability is generally more severe with larger deletions, and it explains why interstitial deletions can also produce moderate to severe intellectual disability. But, what about autism spectrum disorder (ASD)? The frequency of ASD in PMS is an area of debate, various studies report anywhere from under 30% to over 70% incidence of ASD. The natural history study of PMS should narrow this range. Regardless, ASD is a component of the PMS population.

So far, three genes of 22q13 have been clearly associated with ASD: SHANK3, MAPK8IP2 and SULT4A1. It is probably no accident that these three genes also show up as high pLI genes.

What is new

Two new lines of research have identified new candidate ASD genes on 22q13.  One candidate gene has arisen from studies of epigenetics, the regulation of genes. Genes occupy only about 1% of the DNA. Much of the remaining DNA is dedicated to controlling when and how often a specific gene is put to work. Gene regulation is essential for successful development of the brain (and all other body parts) and for responding to changes in the environment. By environment we can refer to the external environment (e.g., adapting to colder weather) or we can be concerned with the internal environment of the body (e.g., building muscle with increased exercise). There is earlier data suggesting a weak contribution of the gene BRD1 to ASD (see Which genes cause brain abnormalities in Phelan McDermid syndrome?). However, epigenetic studies have reinforced the connection between BRD1 and ASD (see Next-gen sequencing identifies non-coding variation disrupting miRNA-binding sites in neurological disorders). So, BRD1 can be considered an autism-associated gene.

Perhaps more exciting is the latest work on “second hits”.  Second hits are when one gene is lost or damaged, and then the remaining copy of the gene is also affected. Second hits matter because some genes can operate just fine with only one copy. We have two copies of most genes in our DNA, one from each parent. When a person has a chromosomal deletion, which is what happens in over 95% of the cases of PMS, that leaves the person with only one copy of those genes. A second hit is when the remaining copy has a mutation, or even just an dysfunctional variant inherited from one parent. What do we know about second hits? A new paper has identified up to 4 genes of 22q13 that may contribute to ASD, given a second hit (see Recessive gene disruptions in autism spectrum disorder). One PMS gene stands out, KIAA0930 and three others are additional candidates, CHKB, ARFGAP3, and ZBED4.

This rounds-out the current full list of 8 ASD-associated genes: SHANK3, MAPK8IP2, CHKB, ZBED4, BRD1, KIAA0930, SULT4A1, and ARFGAP3.

Reveiw

PMS is most often a terminal deletion of 22q13. A deletion of the chromosome that includes SHANK3 is the most common deletion, but sometimes a deletion does not disrupt that gene. Interstitial deletions can disrupt up to 17 other genes likely to contribute to the moderate to severe intellectual disability that characterizes PMS. Infrequently, a second hit on one or more of 7 genes in the interstitial region of 22q13 may also contribute to autism spectrum disorder. In the overwhelming cases of PMS (called terminal deletions), many genes contribute to intellectual disability and, if autism spectrum disorder is part of the clinical picture, SHANK3 and one or two other genes may also be contributing to that aspect of the disorder.

 

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Some selected earlier blogs

PMS for Dummies
Which genes cause brain abnormalities in Phelan McDermid syndrome?
PMS, IQ and why interstitial deletions matter
MAPK8IP2 (IB2) may explain the major problems with walking and hand use
TCF20 may explain why some big deletions are worse than others
Current trends in SHANK3 research
Which PMS genes are most associated with Autism?
Does SHANK3 cause Autism?
We need to study interstitial deletions to cure PMS
What do we know about PMS genes?
Which PMS genes are most important?
Are children with Phelan McDermid syndrome insensitive to pain?
Looking for Opportunities
Splitting, Lumping and Clustering
Defining Phelan McDermid syndrome
Why don’t we have better drugs for 22q13 deletion syndrome?
Educating children with 22q13 deletion syndrome
How to fix SHANK3
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
Is 22q13 deletion syndrome a ciliopathy?
Understanding translocations in 22q13 deletion syndrome: genetics and evolution
Understanding deletion size
22q13 deletion syndrome – an introduction

Which genes cause brain abnormalities in Phelan McDermid syndrome?

David has has many of the features of Phelan McDermid syndrome

Originally posted 31 December 2018
Updated 4 June 2021
Available in Portuguese http://pmsbrasil.org.br/quais-genes-causam-anormalidades-no-cerebro-na-sindrome-de-phelan-mcdermid/

Brain structure and functional abnormalities have been reported in Phelan McDermid syndrome (PMS) by a number of different investigators, including a a recent study associated with the Developmental Synaptopathies Consortium natural history study of PMS (Srivastava et al 2019). Prior studies have found abnormal formation of the cerebellum (Aldinger et al 2013), abnormal function of the cortex and amygdala (Philippe et al 2008), micropolygyria (Kurtas et al 2018), as well as commonly observed thinning of the corpus callosum and the presence of arachnoid cysts.

Brain abnormalities can provide important clues to understanding what goes wrong in PMS. They also could serve as “biomarkers”, biological measurements for early indicators of severity or evidence for treatment effectiveness. Readers of my blog will recognize that I spend a lot of time identifying which genes are most important in PMS. You need to know which genes are causing what problems to have any hope of finding effective treatments. My son, David (see picture), is waiting for new treatments. 

So, what do the brain structural studies tell us?

SHANK3 variants can impact the proper development of white matter, but have minimal impact on the gray matter of the brain (Jesse et al 2020). Gray matter is where the neurons and their synapses reside. White matter is made up of the long, thin “axons” that travel together connecting one region of the brain with another region. 

Aldinger and colleagues (Aldinger et al 2013) studied 10 subjects with PMS using x-ray images. Eight of the 10 subjects showed abnormality of the cerebellum (mostly gray matter) in addition to thinning of the corpus callosum (white matter) and enlargement of the cerebral ventricles (fluid space of the brain). Although there was no clear effect of deletion size, mutation of SHANK3 was not sufficient to cause cerebellar problems. They identified MAPK8IP2 and PLXNB2 as the more likely candidates for cerebellar malformation based on preclinical mouse studies.

The study by Philippe (Philippe et al 2008) had similar results from 8 PMS subjects. Three of the 4 subjects with small deletions (150 Kb or less) had no cerebellar or other major magnetic resonance imaging (MRI) results. The 4th subject with a small deletion had the least impressive positive finding. Thus, using MRI, there was a clear effect of deletion size, with small deletions have little or no effect. Four deletions of 1 to 9.3 Mb in size had stronger effects. Like the Aldinger study, SHANK3 did not seem to be a good candidate for most of their findings. In addition to cerebellar malformation, the group studied brain function using positron emission tomography (PET). They showed a group effect of amygdala dysfunction. Importantly, they used children with intellectual disability as their control group, a much stricter standard than other PMS studies.

The Srivastava study (Srivastava et al 2019) showed reduced size of the dorsal striatum, which is the opposite effect that loss of SHANK3 has in mouse models of PMS. Together, the results suggest that genes other than SHANK3 are driving brain malformation. SHANK3 can contribute to thinning of white matter, but is not the cause of other brain malformations.

Which genes might be driving the observed effects? Is there a smoking gun? To be a smoking gun, a gene that drives malformation should meet most, or all, of these criteria:

1. is commonly missing in PMS
2. has a high pLI value (see my blog Which PMS genes are most important?)
3. is expressed in the cerebellum
4. is strongly associated with a human neuropsychiatric or neurodevelopmental condition
5. causes reduced brain size in the striatum
6. impacts the amygdala

There are 6 genes on chromosome 22 that meet criteria 1 and 2. They have a high pLI score and are very frequently lost in PMS. They are located within 1 Mb of the chromosome terminus, which accounts for 95% of patients with a 22q13.3 deletion (see my blog Understanding deletion size). Those genes are: MAPK8IP2, PLXNB2, TRABD, PIM3, ZBED4 and BRD1. Of these, 4 genes meet criterion 3, being highly expressed in the cerebellum: MAPK8IP2, PLXNB2, ZBED4 and BRD1. Of these, 3 genes are associated with neuropsychiatric disorders. BRD1 is strongly associated with and schizophrenia. MAPK8IP2 is weakly associated with ASD (see my blog Which PMS genes are most associated with Autism?), and ZBED4 is weakly associated with schizophrenia. This leaves BRD1 as the strongest candidate gene for brain abnormalities/malformation in PMS.

Animal studies of BRD1 agree with the results from PMS imaging studies. Per Qvist and his colleagues in Denmark have been studying the BRD1 gene for some time. They have shown that loss of one copy of Brd1 in mice is sufficient to reduce cerebellum size, reduce striatum size and reduce the size of the amygdala (Qvist et al 2018). BRD1 is by far the strongest candidate gene for causing altered brain development, especially in gray matter.  

The importance of BRD1 in PMS goes much further than structural brain anomalies. It has been known for some time that BRD1 impacts 100s of other genes through gene regulation (epigenetics), and the role of BRD1 shifts from development in utero (fetus) to a different role after birth (Dyrvig et al 2017). Now, a new epigenetics study of people with PMS Type 1 (terminal deletions) confirms that loss of BRD1 produces widespread changes in the human genome. BRD1 is a crucial gene lost in people with deletions greater than 1 Mb.

There is little doubt at this point that BRD1 plays a crucial role in PMS. 

PMS is a contiguous chromosomal deletion syndrome, meaning that larger deletions interrupt more genes of importance. BRD1 is a critical gene for brain development. If we want to understand PMS, we need detailed studies that explore more genes like BRD1. One great way to study the impact of different genes is to look more deeply at the phenotypes and genotypes of people with interstitial deletions (PMS Type 2). A treasure trove of new information awaits these studies. Not exploring these candidate genes of PMS is a waste precious time. My son, David, and so many others, are waiting for these studies. We need to do the best possible science if we are ever going to find effective treatments.

 

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Some selected earlier blogs

PMS, IQ and why interstitial deletions matter
MAPK8IP2 (IB2) may explain the major problems with walking and hand use
TCF20 may explain why some big deletions are worse than others
Current trends in SHANK3 research
Which PMS genes are most associated with Autism?
Does SHANK3 cause Autism?
We need to study interstitial deletions to cure PMS
What do we know about PMS genes?
Which PMS genes are most important?
Are children with Phelan McDermid syndrome insensitive to pain?
Looking for Opportunities
Splitting, Lumping and Clustering
Defining Phelan McDermid syndrome
Why don’t we have better drugs for 22q13 deletion syndrome?
Educating children with 22q13 deletion syndrome
How to fix SHANK3
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 translocations in 22q13 deletion syndrome: genetics and evolution
Understanding deletion size
22q13 deletion syndrome – an introduction

TCF20 may explain why some big deletions are worse than others

David is quite the fan of Jimi Hendrix

I don’t know how big David’s deletion is, but he has all the hallmarks of a PMS individual with a large deletion. His developmental delays were substantial: walking took 6 years and full oral feeding required 3 more years. He is nonverbal and even as an adult it is difficult to estimate his receptive language.

Deletion size explains some of the differences between individuals, but any given individual may be far from the “average” for a given deletion size. Is deletion size unimportant? TCF20 is a PMS gene that can help explain some of the mystery.

I have started cataloging all the different factors that influence phenotype (the features of people with a disorder). The number of factors and how the different factors interplay is rather staggering. It has been known for over a 100 years that even a relatively small number of genetic factors can produce a rather wide spectrum of phenotype characteristics. “Phenotype variability” is the term used to describe the diversity. As I progress on the cataloging of what causes phenotype variability in PMS, I will blog on various aspects and examples.

This blog is on TCF20, an important PMS gene that is lost in large (over 8.6 Mb) terminal deletions and some interstitial deletions. I mentioned that TCF20 is an important brain development gene in an earlier blog (What do we know about PMS genes?). TCF20 has all the characteristics of an important gene based on several different studies. At the time I wrote that blog I did not notice a paper (Prevalence and architecture of de novo mutations in developmental disorders) in Nature, a top scientific journal. In that study, the authors were able to affirm TCF20‘s role in genetic disorders. The cases they studied were not PMS, with large deletions. These cases were de novo mutations. Their results show that loss of TCF20 function can, on its own, cause a developmental disorder. It is yet another reminder that a number of PMS genes can cause disorders on their own, without any involvement of SHANK3.

This blog is about phenotype variability. TCF20 provides not one, but two examples of variability. These two factors operate together to explain why some kids with large deletions are more impacted by deletion size than other PMS kids.

Large deletions that are almost the same size can be very different from each other. An 8.5 Mb deletion does not impact TCF20, whereas a 8.6 Mb does. We can be confused about the impact of deletion size if we do not look closely at the genes. That is the first factor: a small change in deletion size can have a large effect. Note that the opposite can also be true. In some locations on chromosome 22, large changes (500 kb or more) can be unimportant.

The second factor is a bit more subtle. A recent paper has affirmed something else about TCF20.  TCF20 is especially sensitive to “genomic imprinting” (Genome-wide survey of parent-of-origin effects on DNA methylation identifies candidate imprinted loci in humans). Normally, either copy of a gene is used by the cell. Genomic imprinting is when only one copy of a gene is used by the cell. The other copy is permanently turned off, never used. Consider this, if someone has a large deletion, but the deletion removed the copy of TCF20 already turned off, the deletion will have no effect on the production of TCF20 protein (a transcription factor). On the other hand, if the large deletion removed the active copy of TCF20, no TCF20 protein will be produced by the cell. Thus, for TCF20, “genomic imprinting” can determine whether deletions over 8.6 Mb are more devastating than smaller deletions. The two factors, deletion size and genomic imprinting, operate together. We cannot predict the effect of one without understanding the other.

Very few PMS genes are subject to genetic imprinting, but this story serves as an example. We have the scientific tools to explain phenotype variability. There are cases where deletion size seems unimportant, but these cases can be explained. The many factors that influence the future of a baby with PMS are not magical. Many people have overestimated the role of SHANK3 because PMS phenotype variably seems so mysterious. Genetics are complicated, but not mysterious. TCF20 provides a great example of how applying the science carefully can uncloak some of the mystery.

 

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Previous blogs

Current trends in SHANK3 research
Which PMS genes are most associated with Autism?
Does SHANK3 cause Autism?
We need to study interstitial deletions to cure PMS
What do we know about PMS genes?
Which PMS genes are most important?
Are children with Phelan McDermid syndrome insensitive to pain?
Looking for Opportunities
Splitting, Lumping and Clustering
Defining Phelan McDermid syndrome
Why don’t we have better drugs for 22q13 deletion syndrome?
What do parents want to know?
Is 22q13 deletion syndrome a mitochondrial disorder?
Educating children with 22q13 deletion syndrome
How to fix SHANK3
Have you ever met a child like mine?
How do I know which genes are missing?
Mouse modelsScience Leadership
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
Is 22q13 deletion syndrome a ciliopathy?
Understanding translocations in 22q13 deletion syndrome: genetics and evolution
Understanding deletion size
Can 22q13 deletion syndrome cause ulcerative colitis?
Can 22q13 deletion syndrome cause cancer?
22q13 deletion syndrome – an introduction

Current trends in SHANK3 research

David likes to munch on pieces of cereal bar and watch music videos.

David, like most people with Phelan-McDermid syndrome (PMS), is missing one of his two SHANK3 genes. One copy of SHANK3 is gone, the other copy is intact. Some people with PMS have both copies fully intact (often called interstitial deletions) and some people have small or large disruptions of SHANK3 without affecting other genes (often called variants or mutations). For the vast majority of people with PMS, loss of SHANK3 contributes to the problems of PMS. Fixing SHANK3 has been a priority in the PMS world, although fixing SHANK3 won’t necessarily fix PMS (see Which PMS genes are most important?). I am an advocate for studying (and fixing) the other critical genes of PMS (see Looking for opportunities and Why don’t we have better drugs for 22q13 deletion syndrome?). Too much focus on SHANK3 has been an impediment to progress. Regardless, this blog is about SHANK3 research.

Science is slow

The autism world is hot on SHANK3, so research on this gene has moved forward relatively quickly. That sounds like good news, and it is, as long as we recognize that “quickly” is measured in decades. Research on SHANK3 started when my son, David, was 12 years-old. He is now 32. Over the past 20 years there have been many papers heralding the “rescue” of autism-behaviors in SHANK3 mice. Parents need to understand that “rescue” is mouse research jargon for “our genetically modified mouse is different from normal mice, and the drug we tested made them a little more like normal mice”. It does not mean “a treatment is almost here”.

The reality of research progress is less rosy than the headlines. Most research studies are done these days on rodents. A mouse with a modified SHANK3 gene is nothing like a human with PMS. Most mouse models are SHANK3 mutations, not deletions. Most people with PMS have deletions (see Gene deletion versus mutation: sometimes missing a gene is better), and human deletions affect other critical genes (see How do I know which genes are missing? and Which PMS genes are most important?). Most “SHANK3 mice” have mutations in both copies of the gene. Mutation of just one copy often results in no detectable effect. Contrast that with humans, where it is unlikely that humans can even survive without at least one working copy of SHANK3. Further, although this should be obvious, only rodent researchers talk about “autism-like behavior” in rodents. It is a rather strange concept. Measuring autism in PMS patients is difficult and sometimes controversial. There is no measure of autism in rodents, just tests to see if a mouse prefers exploring another mouse over an inanimate object. Why a mouse might do that is anyone’s guess. Certainly, you won’t have much luck asking the mouse.

It is not simply bad luck that multiple drug rescues have been reported in mice without the development of any PMS or even autism drugs that work on the core symptoms in people. The reality is that not enough is understood about the relationship among genes, drugs and behaviors. To date, there are no PMS-specific drugs currently available for testing on people. If you get invited into a drug study, that drug was invented for some other purpose. Most often, it was a drug that failed its original purpose and researchers or drug companies are looking for a different disease group to test it on.

Despite the limitations of mouse research for testing drugs, mouse research does help us learn about the proteins used in the brain and what category of drugs might someday be useful for treatment.

SHANK3 regulation

Twenty years of looking at SHANK3 has laid important groundwork. More recent studies have benefited from these earlier studies and from development of new research tools. Researchers are beginning to address the complexity of SHANK3 regulation. SHANK3, like most genes, is simply a recipe for making its protein, shank3 (note lower case spelling, no italics). The recipe is copied onto a template called mRNA, and then many copies of shank3 are manufactured using the mRNA template. The shank3 protein is then delivered to the synapses that need more. Like any manufactured commodity, you need to manage the supply to meet the demand. The manufacture takes place at the factory of the cell (soma) and shank3 is used in 10,000 to 100,000 or more synaptic sites elsewhere in the cell. Thus, there is an ordering and distribution network throughout the cell. Orders for more shank3 come from thousands of different sites. SHANK3 regulation is the complex process of making sure the right amount of shank3 is available at each synapse at any given time.

Synapses are the communications connection between neurons. Each synapse has a different strength of connection, and together, turn the protoplasm of the brain into an amazing computer-like machine. The machine is constantly adjusting itself to perform the tasks we call learning, memory, skill acquisition, and decision-making. Like a muscle, when a synapse is used more, it tends to get stronger and larger. That is how the computer adjusts itself. The increase and decrease of shank3 is important for these adjustments. Thus, processes like learning and memory rely on having the right amount of shank3 at the synapse. Regulation of shank3 production, distribution and utilization starts with the amount of synaptic activity at each of thousands of synapses. Complex processes connect synaptic activity with every step of shank3 production and distribution.

New research on SHANK3 regulation

There are two new papers on SHANK3 regulation that represent the next steps in understanding how the cell manages the amount of shank3 protein at each synapse. One paper forces us to rethink about what a shank3 deficiency really means.

Campbell and Sheng just published a paper on DUB enzymes and the regulation of shank3 at the synapse (USP8 Deubiquitinates SHANK3 to Control Synapse Density and SHANK3 Activity-dependent Protein Levels). DUB enzymes prevent the destruction of a protein. Normally, shank3 is destroyed after use by the USP system. These authors have identified an enzyme “USP8”. When the synapse gets very active, USP8 finds shank3 (and shank1) molecules already tagged for destruction by the USP system, and untags them. It is part of the cell’s natural system to retain extra shank3 in anticipation of needing to build up the synapse for future increases in activity. The authors point out that drugs might someday be found to mimic USP8 and help increase the amount of shank3 at the synapse of those people who have insufficient shank3 production.

In the other recent study, work by Yan and her colleagues has teased-apart some of the communications between the synapse and the nucleus used to regulate shank3 production (Social deficits in Shank3-deficient mouse models of autism are rescued by histone deacetylase (HDAC) inhibition). They show that too little shank3 at the synapse can trigger movement of β-catenin to the nucleus. The surprising part is that when β-catenin reaches the nucleus, it triggers a series of genetic effects that lead to unusual mouse social behavior. The unusual behaviors can be turned on and off independently of shank3. Thus, the strange social behaviors of these mice are not caused by shank3 levels directly. Rather, the reduced shank3 simply releases β-catenin. It is a case of synapse regulation system gone awry. These results suggest that shank3 is not the most important protein for poor social behavior. Rather, the reduced level of shank3 triggers a series of events that improperly regulate other brain genes. Curiously, this agrees with another recent study of proteins in humans with autism (see Which PMS genes are most associated with Autism?).

This is the end of the blog except for a few final thoughts, below. For those who wish to dig a little deeper into the science, I have provided additional background material on genes, proteins and regulation called “A primer on the lifespan of a protein“.

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A primer on the lifespan of a protein

This is a primer about the lifespan of proteins. Shank3 is a protein (note lower case spelling for the protein). Like nearly all proteins, it is born, gets called-upon to work, does its job, then is dissolved and discarded. The most important point is, the amount of shank3 in the cell is highly regulated. At any given moment, there are complicated processes deciding how much is needed and where it is needed. Usually, some parts of a cell may be building up shank3 supplies and incorporating them into synapses, while other parts of the cell are breaking down shank scaffolding (structures built from shank molecules). I sometimes think of shank3 as a construction material, like plywood. Lots of wood scaffolding may be used to frame a concrete pillar. After the pillar is in place, the wood may be torn down and discarded. Some wood may be discarded at the same time other is being nailed in place for the next pillar, wall or sidewalk. You always want a supply of wood around, but that supply should never be more than the anticipated need. Construction management involves reading blueprints, anticipating needs, ordering the manufacture of materials, and delivering what is needed, on time. Timely and organized manufacture, distribution, utilization and disposal of shank3 very important for the cell.

SHANK3 manufacturing

The SHANK3 gene is simply a blueprint for shank3 protein. The blueprint is converted into a template for stamping out the protein (call mRNA). Gene regulation (via “promoters”) control how many copies of mRNA are created. Each mRNA is degraded and discarded after a certain number of copies of shank3 have been made. While functioning, mRNA is used to stamp out copies of shank3. Shank3 is then transported and collected in a pool of proteins near the synapse. The synapse is a very active site, like the beehive of activity at a busy construction site. Shank3 molecules near the synapse gets incorporated into the “post-synaptic density” as needed. The buzz of activity includes constantly building up and breaking down of shank3 molecules. Old shank3, whether it be after a piece of scaffolding is no longer needed, or if the molecule has been sitting around unused, is degraded and discarded.

Breakdown and disposal of shank3 protein

Shank3 is tagged and trashed by the USP system (ubiquitin-proteasome system). Ubiquitin tags it and the proteasome dissolves it. That is the last step in the life cycle. There is a way of untagging, with a deubiquitinating enzyme (DUB), which I would never even mention except that a recent study looks at untagging as a way to increase shank3 levels at the synapse.

Regulation of shank3 occurs at every step

Many different processes regulate transcription (making the mRNA template), synthesis (stamping out shank3 molecules), incorporation (using the shank3), and degradation (USP system). Each of these processes is a potential therapeutic target for increasing shank3 protein in people who have only one working copy of the SHANK3 gene.

Early work on shank proteins (shank1, shank2 and shank3) focused on how each protein is used at the synapse. Increases in shanks are associated with establishing and maintaining strong synaptic connections, whereas decreases can inhibit the formation of new connections. Too much or too little shank3 affects the sizes or number of synapses. Synapse size is related to information transmission in the brain. Too much information from the wrong channel creates noise. Too little information interferes with learning, memory, skill acquisition or other function. Thus, the early research looked closely at shank3 levels at the synapse.

Shank3 production is largely regulated in the cell nucleus where DNA is found. Each brain cell has only one nucleus, yet it regulates shank3 production for thousands to over 100,000 synapses in that cell. So, the signal to increase and decrease Shank3 production comes from a potentially huge number of synapses and converges at the one and only nucleus. Transcription (making the mRNA template) is regulated by many mechanisms. Most mechanisms influence the “promoter” region of a gene. That is the region where the hardware for reading DNA and making the mRNA template is assembled to do that task. A dizzying array of molecules influence the promoter region. To complicate things even more, shank3 has not one, but 7 total promoter regions that regulate not only when to transcribe, but also which of the 20 to 100 various versions of Shank3 to produce. Yes, there are at minimum 20 versions (isoforms) of shank3 produced during a person’s lifetime. “Turning on and off” a gene is another way of saying the gene is set to transcribe or not. In actuality, neurons that use shank3 don’t turn the genes on or off. Rather, they increase and decrease transcription rate of one, two, up to 20 isoforms of shank3. If it sounds complex, it is. Most papers focus on one or two isoforms. They overlook the rest to make the research manageable. For the moment, it is enough that we recognize that transcription of the SHANK3 gene for making mRNA and many copies of the shank3 protein is regulated at each step. The gene is regulated largely at the promoters, controlling how many mRNA molecules are created for which isoforms. Recent studies have looked for ways to modify the regulation of transcription to compensate for a missing copy of the SHANK3 gene.

Shank3 mRNA is used to synthesize shank3 protein. How rapidly shank3 protein is produced is, like the other steps, under careful regulation. For example, each mRNA does not last forever. At some point it is disassembled (degraded) and can no longer produce protein. Its regulation is yet another possible way to manage shank3 protein production.

As mentioned earlier, shank3 protein is used (or just sits around waiting), and is then broken down by the USP system. Unlike signaling in the nucleus, the USP system is operating at or near the synapse. It can influence shank3 availability on a fine grained scale.

Increasing or decreasing shank3 with blunt instruments

Each step along the life cycle of shank3 is an opportunity to increase the amount of shank3 in the cell. One might be eager to try one or many of the steps on mice or people. This eagerness should be tempered by the potential pitfalls of circumventing the normal regulatory process of the cell. Let’s remember why shank3 is so highly regulated. Shank3 levels must be adjusted at each synapse on an individual basis. Large cells can have up to 200,000 synapses. If we choose to increase shank3 transcription in the nucleus, we may start to force some, perhaps too many, synapses to overproduce shank3. The cell needs to remove unnecessary and unwanted synapses (called “pruning”). Pruning is one of the most important processes in brain development. Another related process is called synaptic homeostasis. One theory about why sleep is important is that it gives the brain a chance to readjust all the synapses to consolidate learning and properly reset the brain for new learning the following day. Both pruning and homeostasis are likely affected by changes in overall shank3 levels.

A drug that simply increases the shank3 in a cell could be beneficial, but we must be wary of blunt instruments. We must be concerned that increasing shank3 by short-cutting the built-in regulation of shank3 may worsen PMS, or perhaps replacing one problem with a new one. This is why a potential drug treatment requires thorough testing in animals to develop a deep understanding of the mechanism of action. Improving one behavior in a mouse is not enough. At a minimum, we need to carefully explore what other behaviors might be affected in the model animal. In this blog, I have not discussed that SHANK3 is used in different ways in different parts of the brain, and regulation is likely to vary for each brain region. Methods to deliver different amounts of a drug to different brain regions are complex and experimental.

Mice are handy experimental animals, but their brain function is not at all like human brain function. In mice, you can remove 100% of all shank3 protein and the mice, although behaviorally unusual, are able to eat, drink, run, play and procreate much like normal mice. Humans missing both copies of SHANK3 are unheard of, most likely because they don’t survive in the womb.

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Final thoughts

The take-home messages from the new research are simple enough. First, there is much hype in the online press reports and magazines about scientific progress. The fact is, science is slow and we have a long way to go. The details are sometimes complicated, but the basic principles are not. Second, studies of shank3 have not reached the point where we truly understand the relationship between SHANK3 gene loss and the many problems that result. Progress is being made, but, as often happens in science, the latest results tell us what we thought we understood was not exactly correct.

arm22q13

Previous blogs

Does SHANK3 cause Autism?
We need to study interstitial deletions to cure PMS
What do we know about PMS genes?
Which PMS genes are most important?
Are children with Phelan McDermid syndrome insensitive to pain?
Looking for Opportunities
Splitting, Lumping and Clustering
Defining Phelan McDermid syndrome
Why don’t we have better drugs for 22q13 deletion syndrome?
What do parents want to know?
Is 22q13 deletion syndrome a mitochondrial disorder?
Educating children with 22q13 deletion syndrome
How to fix SHANK3
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 translocations in 22q13 deletion syndrome: genetics and evolution
Understanding deletion size
Can 22q13 deletion syndrome cause ulcerative colitis?
Can 22q13 deletion syndrome cause cancer?
22q13 deletion syndrome – an introduction

Which PMS genes are most important?

David hanging out on a Saturday morning

Originally posted 23 August 2017
Updated 4 June 2021
Available in Portuguese http://pmsbrasil.org.br/quais-genes-pms-sao-mais-importantes/

What makes a gene important?

If you ask someone familiar with 22q13 deletion syndrome (Phelan McDermid Syndrome, PMS), “which genes are most important?”, they will start with SHANK3. Even though some people with PMS have no problem with SHANK3, it is still the most important gene for two reasons. First, deletions of SHANK3 and many uncommon variants of SHANK3 can have a strong negative impact on individuals. Second, a large percentage of the PMS population are missing SHANK3. Thus, SHANK3 meets the criteria of 1) potentially large impact on an individual and 2) a large percentage of the population is missing SHANK3. This blog is a closer look at all the genes that meet these two criteria.

In a recent study, a group of researchers looked at genes that are highly likely to contribute to PMS and are missing in most people with PMS (Identification of 22q13 genes most likely to contribute to Phelan McDermid syndrome [full disclosure: this blog was written by an author on the paper]). That is, genes that appear to meet the two criteria listed above. What makes this study important is that it does not differentiate between genes that have been carefully studied and genes that have never been studied. From my perspective as a parent of a child with PMS, we parents are not interested in gene popularity contests. We are interested in learning what is making our children sick.

I read that SHANK3 was the only important gene

Until recently, nearly all PMS research was focused on one well-known gene, SHANK3. Some scientists have promoted the false narrative that only the SHANK3 matters. But, PMS is a polygenetic disorder. That is, many genes are involved. For individuals who have a pathogenic variant of SHANK3 and no other genetic issues (PMS Type 3), it is true that only SHANK3 matters. But, the vast majority of people identified with PMS have chromosomal deletions (PMS Type 1). Some 97% of people identified with PMS are missing up to 108 genes! (See Understanding deletion size and How do I know which genes are missing?). Consider, as well, that some people have PMS even with intact SHANK3 (PMS Type 2). SHANK3 is clearly not the only important gene. One major goal of PMS research it to identify which genes are most important.

How can we find out which genes are most important?

There are 108 PMS genes and only 44 have been well studied. If there was no independent way to identify the important genes, we would be in serious trouble. Fortunately, there is a way to predict the importance of a gene without knowing what the gene does. A large group of scientist compiled a database of over 140,000 genomes including those of “normal” individuals (Genome Aggregation Database). Normal in this case means no developmental or neurological disorder. This huge database lets you predict which genes can cause trouble. Let me explain.

There is a trick to finding a likely troublemaker gene. Pick a gene. Look at all the copies of that gene in the database. (Each human has 2 copies of each gene.) The same genes in different people are not always the same. Different people can have slightly different versions, called “variants”. It is possible to estimate (with biology and statistics) how many different variants you would expect to occur by chance in a population. For example, for a given size gene you might expect to discover 40 different variants among 60,000 people. What if you find only 5 variants? Something’s fishy if you find only 5. The best explanation is — here is the trick — that the other 35 possible variants of that gene cause serious problems. For one reason or another, those 35 variants remove a person from the category of “normal individuals”. There is a name for this: natural selection. It is a principle discovered by Darwin and it works for genes.

Those missing 35 variants are pathogenic. The variation causes a loss of normal function, and the body cannot operate normally without the gene. Genes that are highly sensitive to variation are called “loss-of-function (LoF) intolerant”.  Genes that are LoF intolerant in this way are the ones most likely to cause major health problems. Only a minority of genes are LoF intolerant. Most genes tolerate all kinds of variation. Either they are less important genes, or the body has found ways to work around variations.

Wow! Which genes are most important?

So, which PMS genes are very LoF intolerant? That is an easy question to answer. You can go to the gnomAD browser and look up any gene. Look for the row with pLoF and get the “pLI” value. A value between 0.9 and 1.0 is a bad news gene. SHANK3 is 1.0 — no surprise there, but what about other genes? Let me save you some time. Below is a list of PMS genes that have a pLI value above 0.9.

Genes in this list are in the order of their position on the chromosome. The ones at the top of the list are more frequently lost in the population. If your child has a terminal deletion, look at all the genes with a Kb value smaller than your child’s deletion size. Those are the genes that most likely contribute to his/her disorder.

   Gene       Minimum deletion size (Kb) 
   SHANK3          85 
   MAPK8IP2       207 
   PLXNB2         540 
   TRABD          619 
   PIM3           854 
   ZBED4          928 
   BRD1           995 
   TBC1D22A     3,643 
   GRAMD4       4,181 
   CELSR1       4,281 
   SMC1B        5,405 
   PHF21B       5,809 
   PRR5         6,081 
   SULT4A1      6,956 
   SCUBE1       7,475 
   TCF20        8,603 
   SREBF2       8,911 
   XRCC6        9,154

The first thing to notice is that what started out as 108 genes is now reduced to 18 genes. There are a few other genes with pLI below 0.9, but not far below 0.9. These may also be important. Regardless, the number of PMS genes has gone from intractable (108) to something much more manageable (18 or maybe 20). If your child has an average size deletion (around 4,500 kb), then there are 10 relevant genes. Note that some children are missing only SHANK3. We will not forget them. But, in the meantime we need a major push to fully understand the other important genes of PMS.

In future blogs I will discuss what some of these genes do and how they might impact your child.

arm22q13

Some previous blogs

Are children with Phelan McDermid syndrome insensitive to pain?
Looking for Opportunities
Splitting, Lumping and Clustering
Defining Phelan McDermid syndrome
Why don’t we have better drugs for 22q13 deletion syndrome?
What do parents want to know?
Is 22q13 deletion syndrome a mitochondrial disorder?
How to fix SHANK3
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 translocations in 22q13 deletion syndrome: genetics and evolution
Understanding deletion size
22q13 deletion syndrome – an introduction

Looking for opportunities

Six years to learn walking, 9 years before eating by mouth. This picture seems so ordinary, but his parents see more than meets the eye.

Originally posted 10 March 2017
Updated 16 January 2022
Available in Portuguese  https://pmsbrasil.org.br/procurando-oportunidades/

Success is very much about seizing opportunities. With all of David’s early issues caused by his Phelan-McDermid syndrome (PMS), we could not address everything at once. That said, we always looked for opportunities. For example, when he started climbing in the refrigerator we encouraged him to climb (under watchful eyes). See the picture here: Gene deletion versus mutation.

Like raising a child with a serious genetic disorder, science is about hard work and seizing opportunities. The discovery of penicillin is a classic example.  Alexander Fleming made his discovery in a moldy petri dish. The open dish left sitting in the sink was contaminated by a mold that killed bacteria in the dish. The mold in the dish was accidental, but Fleming’s observation was not. He was a scientist looking for ways to kill bacteria. A few years after the initial discovery, penicillin saved its first life: a child. We need to keep our eyes open for opportunities and we need to make the most of these opportunities. So how can we do that with PMS?

In March of 2017 a group of parents took on a challenge. I asked them to identify other children with PMS who were most like their own child. The goal was to find ways to “cluster” the characteristics of children with PMS, as described in my blog: Splitting, Lumping and Clustering. It was a lot of fun and, just as I suspected, there are groups of kids that are very similar to each other. The exercise on Facebook was an example of crowdsourcing. There are people who are experts at crowdsourcing studies. I would recommend someone expand this exercise into a real study. There is a lot to learn. Parents have insights into their children that medical researchers cannot. Categorizing how groups of children are alike and different could accelerate research, should someone want to take the opportunity

This blog is about untapped opportunities to look at categories of PMS (also called 22q13 deletion syndrome). There are special cases we should not overlook.

Matched deletions

I hear people say that no two deletions are exactly alike. That is not true. There are special cases where the deletions are exactly the same: 1) twins (yes, there are twins in our community), 2) unbalanced translocations (my son’s deletion and my niece’s deletion are exactly the same, as are several other children and adults in our extended family), and 3) germline deletions. I do not know any PMS family with multiple children from germline deletions, but I suspect they exist. In addition to exact matches, there are deletions in regions of the chromosome that have few genes, or few genes that affect the central nervous system. In these cases, nearby deletions may be equivalent in terms of genetic loss (see Understanding Deletion Size).

I have heard some physicians and scientists say “no two deletions are alike” even though they should know better. We need to exploit these cases to find out what matched deletions have in common and how they differ from each other. Those observations will hint at which aspects are purely due to the genes deleted and which are due to more complex interactions between genes and the environment. We need a more nuanced understanding of PMS.

Interstitial math

Most known cases of PMS are associated with terminal deletions of chromosome 22. “Interstitial deletions” (I call PMS Type 2) are far less common. What if we take each person with an interstitial deletion and compare them directly with those who have terminal deletions that start at the same spot on the chromosome? In such comparisons, both people would be missing the same interstitial genes, but not the remainder of the genes. What can we learn? It is a kind of A minus B experiment. It might or might not be very informative, but we won’t know until we take the opportunity. The data are already available in the PMS DataHub.

Pure SHANK3 deletions

If one copy of the SHANK3 gene is missing altogether and no other genes are affected, that specific case can examine the impact of loosing just the SHANK3 gene. But this specific circumstance (a pure SHANK3 deletion) is very rare and not systematically studied. I feel someone should take the opportunity to study these cases systematically. So far, there are studies of larger deletions with attempts to compare different deletion sizes. That is a helpful approach, but not quite the same. There are also scientists who argue strongly that pathogenic SHANK3 variants (sometimes called SHANK3 “mutations”) act simply by reducing the amount of SHANK3 protein. The theory predicts that pathogenic SHANK3 variants are the same as losing one copy of the SHANK3 gene, and nothing else. But the theory has not held up to scientific testing.

Various studies show that pathogenic variants of SHANK3 likely disrupt special “isoforms” of SHANK3 during fetal development, or may disrupt the normal operation of SHANK3 protein in the adult. The difference between having insufficient SHANK3 protein and having an errant (interfering) version of the SHANK3 protein, is important. Oversimplifying the effects of pathogenic variants may lead us down the wrong path when seeking ways to treat people with PMS.

There are opportunities to study the difference between deletions and variants. I describe this in my blog Gene deletion versus mutation. We need a study that specifically compares these two groups: people with SHANK3 mutations and people with complete (or nearly complete) SHANK3 deletions that are specific  enough to leave other, nearby genes, alone.  Once again, we parents seed these opportunities with family data in the PMS DataHub.

Where next?

I believe parents can be major contributors just by our ability to see similarities and differences in our children. The scientists and clinicians studying our children have all kinds of ideas, but frankly they can use a little guidance. I am not a fan of drug studies that mix kids with different pathogenic variants and different deletion sizes without first making the comparisons I have listed. There are more opportunities. We need to encourage greater discussion on the potential role of each important gene of PMS (see Which PMS Genes are Most Important).

Not every parent is interested in the detailed science. But, I encourage parents who take an interest to learn about the genes I discuss in my blogs. I also encourage scientists to think more critically about PMS. It is not a disorder of just one gene, and even in the cases of pathogenic variants of SHANK3, PMS may be a far more nuanced disorder than one of haploinsufficiency. We should always be looking for opportunities to address central questions, and we should always be cautious about our assumptions.

arm22q13

Some previous blogs

Splitting, Lumping and Clustering
Defining Phelan McDermid syndrome
Why don’t we have better drugs for 22q13 deletion syndrome?
What do parents want to know?
Is 22q13 deletion syndrome a mitochondrial disorder?
Educating children with 22q13 deletion syndrome
How to fix SHANK3
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.
Is 22q13 deletion syndrome a ciliopathy?
Understanding translocations in 22q13 deletion syndrome: genetics and evolution
Understanding deletion size
22q13 deletion syndrome – an introduction

 

Defining Phelan McDermid syndrome

It is all a matter of how you look at the problem.

Originally posted 4 March 2017
Updated 10 April 2024

It is very hard to talk about and explore, much less cure, a syndrome if you don’t define it first. While 22q13 deletion syndrome seems like it should be straightforward — a deletion of 22q13 — life is rarely that simple. In 2012 I was offered a chance to bring people together to address the question of how to define Phelan McDermid syndrome (PMS). I took the role and opportunity seriously. I decided to make a slide presentation that would set the stage for parents, scientists and clinicians to discuss a definition for the syndrome. As it turned out, the offer was rescinded. Without any modification, I present the final slide from my talk (see figure).  There has been a more recent effort to establish a simple classification (see this blog). However, there remains poor agreement in the field and the catagories, thus far, contribute more to diagnostic criteria than a structure to understand the disorder.

The color coding is important. Things in green are PMS. Things in rust red are not PMS. Dashed lines are just to make it easier to see. The scheme covers nearly every circumstance, including pathology of regulatory sites. The only unaddressed issue is what might be considered phenotypic. It seems to me now that any intellectual disability that is not syndromic in some other way (e.g., metachromatic leukodystrophy caused by the deficiency of arylsulfatase A, OMIM #250100), should be considered the core phenotypic trait of PMS. Regardless, the slide represents the only detailed framework I have ever seen for a definition of PMS.

There is a great interest in SHANK3 and its relationship with 22q13 deletion syndrome. Using the scheme, above, and other information that we know about SHANK3 and 22q13 chromosomal deletions, I recently put together this chart:

In this case, the dashed line indicates that autism spectrum disorder may accompany intellectual disability and still be part of PMS. The chart shows that many SHANK3 mutations are not PMS. They are either nothing (have no phenotype) or some other neuropsychiatric disorder. When 22q13 deletions include SHANK3 (even just a part of SHANK3), they can be PMS. In fact, they are rarely not PMS. Some SHANK3 mutations (pathogenic variants) lead to the phenotypic traits of PMS. Mutations of SHANK3 that confer a different primary phenotype (e.g., schizophrenia or autism spectrum) should not be lumped into the PMS category.

There are other ways to define a disorder, but the worse thing we can do is not define it at all. Developing any classification system is tricky. It is always political. The politics impacts both the science and the families. Even after 12 years, the politics have not been resolved. Perhaps the answer is to have multiple definitions, and identify the definition being used when writing or speaking about the disorder. The definition of this disorder remains in disarray.

arm22q13

Previous blogs

Why don’t we have better drugs for 22q13 deletion syndrome?
What do parents want to know?
Is 22q13 deletion syndrome a mitochondrial disorder?
Educating children with 22q13 deletion syndrome
How to fix SHANK3
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

Why don’t we have better drugs for 22q13 deletion syndrome?

Originally posted 27 February 2017
Updated 10 April 2024

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This blog was originally posted in 2017. Read later blog posts to see the advances in medicine since that time. The information here is still quite valuable in understanding why treatments for 22q13 deletion syndrome (Phelan McDermid syndrome, PMS) are so difficult to develop.

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David does not talk, although I am certain he would like to. He has poor hand control. He can just barely manage a spoon or glass of water with great effort. Although he walks a lot, he is always at risk of falling. There are so many things that are difficult for David. It would be nice if we had a medication to make his life easier.

After years of drug testing on children with 22q13 deletion syndrome we are probably no closer to a treatment now than when it started. This problem is not unique to 22q13 deletion syndrome; it is true for many, if not most neuropsychiatric disorders (see: Hope for autism treatment dims as more drug trials fail).  Recently, Rachel Zamzow wrote a very readable review about why autism clinical trials have failed (Why don’t we have better drugs for autism?).  Her review is in Spectrum, the on-line magazine affiliated with the Simons Foundation Autism Research Initiative (SFARI). Rachel identifies three problems that plague clinical trials: 1) bad design, 2) wrong measures and 3) too broad a range of participants. While problems 1 and 2 are important, problem 3 is a major stumbling block for 22q13 deletion syndrome that I would like to address.

Clinical trials for 22q13 deletion syndrome are intended to treat defects or loss of SHANK3 (Kolevzon et al., 2014). The problem with finding a treatment for SHANK3 is just as Rachel – and many others – have described. If the subjects you are testing are too diverse, you will never see a clear impact of the drug you are testing. The subjects recruited for these studies have either SHANK3 mutations or have 22q13 deletion syndrome with terminal deletions of different sizes. This group is more diverse than many, perhaps all, of the other autism-related clinical studies that have failed. Going on past experience in the field, this clinical group may not provide useable results. Here are the reasons why.

SHANK3 mutations are complicated

Early on, there was hopeful enthusiasm about hunting for a cure for people with 22q13 deletion syndrome. At that time, SHANK3 mutations were lumped together with chromosomal deletions.  Importantly, SHANK3 mutations were thought of as simply a loss of SHANK3 function. As it turns out, SHANK3 mutations are tremendously complicated. Different SHANK3 mutations can have very different effects on the gene, on the proteins it produces, on the neural development of the brain, and on the net effect in both people and experimental animals. The most recent and most thorough review of Shank proteins (Monteiro and Feng, 2017) says it clearly: “Indeed, the idea that isoform-specific disruptions [different mutations] will result in different phenotypic consequences (and even result in different disorders) has recently gained momentum.”  I can say with some pride that the momentum includes my June 2016 blog How to fix SHANK3, which makes that very same point.  You probably cannot lump together people with different SHANK3 mutations and expect to get a single clear result.

Too few patients have the same SHANK3 mutation

To date, no one has been able to find enough people with the same SHANK3 mutation to do a drug study. You can find SHANK3 mutations in large autism databases, but these are not like a registry where you can call the patient up and ask them to participate. There is no doubt that medical researchers would pull together a SHANK3 drug study population, if they could. Finding a large enough group of people with one (or two) SHANK3 mutations to study drugs may never happen.

Individuals with 22q13 deletions are too diverse

Another approach might be to use 22q13 deletion syndrome patients with terminal deletions that remove SHANK3 altogether.  Every one of these patients would have exactly the same SHANK3 loss.  Further, there is a registry for 22q13 deletion syndrome patients that might help with recruitment (PMSIR).  While this seems appealing, it has its own limitations. Just as the SHANK3 mutation population is likely to have other autism and intellectual disability genes complicating the picture, chromosome 22 is full of genes that likely contribute to autism, intellectual disability, hypotonia and other phenotypic traits associated with SHANK3. Anyone who has read my other blogs has seen numerous examples of those genes (see Mouse models and How do we know which genes are important?).  Because of the densely packed genes near SHANK3 (see Understanding deletion size), it is difficult to develop a big enough group of people with SHANK3 deletions that don’t involve other important genes on 22q13.

Solutions

In her article, Rachel Zamzow discusses the N-of-1 Trials approach. We parents do this all the time. We experiment with different medicines on our one child. N-of-1 design simply has the clinical researcher follow the child during the test. I’m not a big fan of N-of-1. I prefer a mixed experimental approach where research animal testing is done in tandem with human testing (see Have you ever met a child like mine?). But, I leave decisions like these up to the experts.

In their detailed review of Shank proteins and autism, Monteiro and Feng recommended that “..careful genotype-phenotype patient stratification is required before individual testing of specific pharmacological agents.”  That is, don’t test drugs until you understand the impact of the genes that have been lost. If you have been reading my blogs, that should sound very familiar.

Two things must change before we can expect drug testing to bring meaningful results. First, we need to organize Phelan McDermid syndrome, SHANK3 mutation syndrome(s), and chromosome 22q13 deletion syndrome into a meaningful “genotype-phenotype patient stratification”. That is, we need to define different types and subtypes of the syndrome that was once called 22q13 deletion syndrome.  I proposed running an interactive session with parents and researchers in 2012, and for the session I put together a Power Point presentation called: “Defining PMS across Genotypes Phenotypes and Molecular Pathology.”  I was asked not to present my ideas.  Perhaps I will be given a chance, someday. Since then, some progress has been made at subtypes (see this blog post).

Second,  we must spend the time to characterize the genes that are near SHANK3 on chromosome 22 and understand (in experimental animals) how they might contribute to 22q13 deletion syndrome.  We need to study people with interstitial deletions, so we can isolate the effects of these genes. Efforts to explore the contributions of 22q13 genes has been lacking, yet they are a major impediment to the search for effective drug treatments.

22q13 deletion syndrome has left David completely dependent upon others for his day-to-day living. Both David and I have come to accept that fact. What we cannot do for David is know where it hurts when he is sick or injured. If I had one wish for a new medicine, that medication would let David point to where it hurts. That medicine, or any useful medication, is not going to happen until someone takes the needed steps to remove the impediments that interfere with productive drug testing. It is clear where we need to go. It will take time to get there.

arm22q13

Some previous blogs

What do parents want to know?
Is 22q13 deletion syndrome a mitochondrial disorder?
Educating children with 22q13 deletion syndrome
How to fix SHANK3
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

What do parents want to know?

David dressed up in his birthday best

One nice thing about writing a blog is getting feedback.  While I embrace and benefit from all kinds of feedback, I admit being partial to positive feedback.  I get some nice comments from friend on my Facebook page.  I love the encouraging comments that get posted here.  There is another kind of feedback that is neither positive nor negative, but very informative.  It is the kind of feedback that we should all pay attention to.  Visitors vote with their mouse (or touchscreen).  Every time someone clicks on a blog link, WordPress adds one to a blog page counter.   Now that it is 2017, let’s see what the numbers recorded in 2016 tell us.

Frequency of access for all English Language pages of this blog in 2016

The most requested page is at the bottom of the graph: How do I know which genes are missing?  That is the number one question on parents’ minds.  It makes sense.  If your car breaks down, you want to know what caused it, even if you don’t know much about cars.  At the very least, you have some idea of what needs fixing.

Three more questions are virtually tied for 2nd place. Have you ever met a child like mine? and How to fix SHANK3 are discussions of SHANK3 and its relationship to the other genes of 22q13 deletion syndrome.  Together, with the most requested blog page, over one-third (35%) of mouse clicks on this blog are from people who want to understand how all the genes of 22q13 deletion syndrome operate together to produce the disorder.  The other blog page that is tied for 2nd place addresses the same topic from the opposite direction: How can the same deletion have such different consequences?

Taken together, nearly half (46%) of the information people want from this blog is to understand what genes are missing and why those genes matter.

Most visitors in 2016 already knew about 22q13 deletion syndrome.  Only about 4% of all clicks went to 22q13 deletion syndrome – an introduction. Fewer clicks went to learning about the author. (I can live with that!)  But, I think there are a other links that deserve attention.  Here is a suggestion for the new year:

Gene deletion versus mutation: sometimes missing a gene is better.
SHANK3 is not the only gene of 22q13 that can have serious consequences when mutated (modified, but not lost altogether).  Much is said about SHANK3 mutations, but 98% of people with 22q13 deletion syndrome are missing SHANK3 altogether. Understanding the difference may be crucial to finding cures.

I have dedicated the past few months to formal writing about 22q13 genes aimed at the scientific community.  That work has taken me away from this blog, but, hopefully, taken us all closer to effective treatments for our children.   That work is done for the moment and I hope to get back to this blog on a more regular basis.

arm22q13

Previous blogs

Is 22q13 deletion syndrome a mitochondrial disorder?
Educating children with 22q13 deletion syndrome
How to fix SHANK3Have 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

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

Have you ever met a child like mine?

Sometimes, David likes to be held.

Jannine Cody, the parent/scientist who studies 18q deletions, says that since every deletion is different, every child with a deletion is different.  At the PMS family conferences we met other children with 22q13 deletion syndrome who, at the time, had striking similarities with David.  These children had chromosome 22 deletions of various sizes, and similar children did not always seem to have the same size deletions.  We know now that genes are not distributed equally along 22q13, so children with small deletions can be quite different from each other, and children with large deletions can be quite similar (see Understanding deletion size).  We also know there are good scientific reasons to expect differences (see How can the same deletion have such different consequences?).  Some things are pretty obvious after a while.  The kids who could not walk or talk generally had larger deletions.  Those with larger deletions also had many more medical problems.  Obviously, more genes lost means more problems.  Regular readers of this blog have seen evidence of why it is very important to know which genes are missing (see How do I know which genes are missing?).

Some people feel that research on 22q13 genes should be done one gene at a time, starting with SHANK3.  I am not a big proponent of this approach, since it ignores a lot of research already done on ARSA, MAPK8IP2, CHKB, CPT1B,  PANX2, ALG12, BRD1, SULT4A1 and other genes known to cause disorders in humans, mice or both.  The one gene-at-a-time approach also slows research by making one gene sound much more important than others.  It seems to me if we spend 5 to 10 years on each gene, we are doomed to spending 500 to 1,000 years. If that sounds pretty absurd, well, it is.  Maybe it will only take 200 years to do it this way.  That still seems too long to me.  That is why I recommend the scientific program be managed by someone with a deep understanding of science leadership (see 22q13 deletion syndrome and science leadership).  The “SHANK3 or bust” research program has succeed in some ways.  Recently, after about a dozen mouse models of Shank3, there is a new mouse with the first complete deletion of the gene. All the other mice were various examples of gene mutation.  As we know, the effects of mutation (or removing part of the gene) can be very different from deletion (see Gene deletion versus mutation: sometimes missing a gene is better). This is critically important! The main reason for supporting Shank3 mouse research is the argument that most (not all) patients are missing the SHANK3 gene entirely.  Thus, it is SHANK3 deletions that make the research important to our families. (Note that mouse Shank3 mutation research has a very separate goal: understanding how mutations might contribute to general forms of autism.)

So, we now have a real Shank3 deletion mouse and everyone is very excited about it (Mouse Model of Autism Offers Insights to Human Patients, Potential Drug Targets).  Of course, be skeptical of what the university PR team says (see Mouse models).  Let’s take a look at this first-ever complete Shank3 knockout mouse. First off, the major finding is that this mouse is different from the many mutation mouse models.  No one should be surprised.  What is surprising is that you have to completely wipe out 100% of Shank3 to see a measurable difference between these mice and normal mice. Even more shocking is that these mice are walking around, playing with other mice, eating, talking mice talk (ultrasonic sounds) with no shank3 whatsoever in their bodies!  The mice missing 100% of Shank3 are different from other mice, but mice missing 50% are not different in any measurable way. Note that humans with 22q13 deletion syndrome are missing only one of the two genes and best evidence is that they have lost only about 25% of their shank3 protein (See this research paper).

So, is there something wrong with the mouse study?  Are mice just way different from humans, or is there another explanation?  Maybe it all makes sense.  Have you ever met a human missing all of SHANK3 and only SHANK3?  The complete knockout Shank3 mouse is best compared with a person like that, someone who is not missing any other genes and has no known mutations.  It is not good enough to have someone with a “small deletion”, since there is strong evidence that adjacent genes impact brain function.  This mouse models SHANK3 deletion.  I have met only one person who seems to fit this description.

Phelan McDermid syndrome is characterized by developmental delays, moderate to severe intellectual disability, little or no expressive language, and infant hypotonia (floppy baby syndrome).  Some people argue that the syndrome is also characterized by a high incidence of autism spectrum disorder, although some top scientists disagree.  The person I met was probably never a floppy baby, has practically normal speech, and that person has no evidence of autism.  Rather, the person I met has some problems with coordination, has a great difficulty learning and is socially a wonderful person to meet and engage with, perhaps to a fault.  Tragically, like all of our children, that person will never navigate the world well enough to live an independent life.

In summary, when I read the scientific paper on the complete Shank3 knockout mouse, what struck me was how many tests the complete, 100% knockout mouse passed without demonstrable evidence of a problem. Mice missing one copy are normal in almost every test.  Mice missing both copies are not “normal”,  but clearly, even these mice are nothing like my son.

How important is SHANK3?  It is impossible to make that judgement based on only one clinical case.  The person I met has lost all independence for that person’s entire life. That is very important.  Moreover, it is tragic.  But for 95% of families, 22q13 deletion syndrome comes with the full set of core features of 22q13 deletion syndrome.  David cannot tell me when he feels sick, where it hurts, or if he was mistreated in his group home. It took him 6 years to overcome his floppy baby syndrome enough to walk and three more years before he could eat by mouth.  His autism-like features interfere with social contact.

As of now, the most parsimonious explanation of what we know is that SHANK3, alone, does not produce the core features of 22q13 deletion syndrome.  It is a contributor in most, but not all, cases.

 

arm22q13

 

Previous blogs

How do I know which genes are missing?
Mouse models
Science Leadership
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.
Is 22q13 deletion syndrome a ciliopathy?
Understanding translocations in 22q13 deletion syndrome: genetics and evolution
Understanding deletion size
Can 22q13 deletion syndrome cause ulcerative colitis?
Can 22q13 deletion syndrome cause cancer?
22q13 deletion syndrome – an introduction

 

Mouse models

DRW51015. Model of SR-71A Blackbird by Dragon Models ( http://www.dragon-models.com.cn )

There have been a number of press releases and feel-good articles circulating among my 22q13 deletion syndrome Facebook friends celebrating the advancement of mouse models of “Phelan McDermid syndrome”.  I am all for enthusiasm! However, cheering is more fun if you know how the game is played and what to cheer for.  With that in mind, I would like to look carefully at models.  What is a good model and what might it tell us?

I started out in engineering, where modeling is very important. Let’s imagine modeling an airplane.  The first issue of modeling is, what aspects of the plane are motivating us to build a model? In this case we might want to learn about how the airplane will perform if the tail is damaged in flight.  We can construct a scaled-down miniature with wings, tail, etc. and omit the inside furnishing (cockpit, storage compartments, etc.).  If the miniature has the exact same shape and moving wing/tail parts as the real airplane, we would say our model has construct validity. That is, it is constructed in a way that reflects the original plane.  The next step is to put our model into a wind tunnel and see if it flies. The model is held on a wire.  We can adjust the wing flaps and other control surfaces.  If the model tries to rise at the same wind speed as the real plane, and tries to bank left or right with the same amount of wing flap adjustment as the real plane, we can say this model has face validity.  That is, with regard to what we are testing, the model behaves much like the real plane.  We are finally ready to benefit from all our work.  Let’s take the model for a test flight and then poke a hole in the tail.  What settings of the flaps and other control surfaces allow us to keep control of the plane?  We may struggle with this for weeks or months hoping we can learn to control our crippled model plane. If we find a solution, maybe we have found a way for pilots to rescue their plane in the event of a similar emergency.  If this scheme works, our model has predictive validity.  Thus, we measure a model’s worth by:

• does it model what we want?
• is it constructed in a way that tests what is important to us? (construct validity)
• does it perform in a way that mimics what we already know? (face validity)
• will model manipulations tell us how the real thing will respond? (predictive validity)

I hope you are getting a picture of what an animal model should do.  Let’s look at a mouse model of “Phelan McDermid syndrome” or “PMS”.  I use quotes because different scientists have different definitions of “PMS”.  See Introduction.   For this blog, I will omit the quotes, but remember that there are numerous definitions floating around.

The definition of PMS is important for modeling.  The definition of PMS tells us what people claim to be modeling.  Some scientists define PMS as a deletion or mutation on chromosome 22 that involves SHANK3.  That is fine with me, but that omits the rest of 22q13 deletion syndrome, since there are numerous cases of “interstitial deletions” that don’t affect SHANK3.  So, SHANK3 might not be a good choice of model for many families.  It depends on the deletion and it depends on what is causing your child the greatest difficulties.   There are currently mouse models for 11 different PMS genes for deletions of 1 Mbase or larger.  Every gene on this list is relevant to 95% of patients (See Understanding deletion size.)  The 11 genes are BRD1, CHKB, CPT1B, MAPK8IP2, MAPK11, MAPK12, NCAPH2, PANX2, PIM3, SHANK3, TYMP.  Most of these mouse models are very well studied.  If you go further up the chromosome you find other well studied genes with mouse models, like ATXN10.  So, the choice of gene is all about what aspect of a disease or syndrome you wish to study.

SHANK3 is popular not because of PMS.  It is popular because is has been associated with autism.  There are under 1,000 identified people in the USA with PMS, but there are an estimated 36,500 children born each year in the USA with autism.  Parents of 22q13 deletion syndrome children should appreciate that researchers who study Shank3 mice are tapping into the national (and world) autism crisis. Our children are a convenient source of subjects, which is why the big national study officially excludes PMS families with interstitial deletions that do not affect SHANK3.  Children with SHANK3 mutations are of greatest interest even though they technically do not have 22q13 deletion syndrome (that is why the name PMS was created).  Note that only 1/3 of children with PMS have autism, so patients with SHANK3 mutation and autism are the most valuable research subjects.

Although SHANK3 is of great current interest, autism is caused by hundreds of genes.  Most parents don’t realize that many 22q13 genes are autism-related or suspected to contribute to autism.  Some of the autism genes on chromosome 22 are BRD1, CELSR1, CHKB,  MAPK12, PANX2, BRD1.  Further up the chromosome (associated with somewhat larger deletions) you can find  CELSR1, WNT7B, TCF20, EP300 and others.

Now we understand that Shank3 mice need to be models of something.  From the above lists of genes, it is pretty clear that a mouse missing only one gene is not a universal models of either 22q13 deletion syndrome or autism. Both conditions involve a large number of genes.  The Shank3 mice are single gene models.  The mice are fashioned after super-rare cases of people with specific SHANK3 mutations.  Let’s see how these models stack up in terms of construct, face and predictive validities.

All of the published papers so far describe Shank3 mutations and microdeletions, not deletion. I am not going to cite the specific papers here. I have written brief reviews on most of these papers. Contact me if you would like specifics.  Some of the mouse Shank3 models use deletions that reflect mutations found in actual patients.  For those specific patients (often just one or two), the genetic manipulations have construct validity.  That is, the mouse gene has been changed in a way very similar to the human gene.  As for the rest of us PMS parents, 95% of our children are missing the SHANK3 gene altogether, along with 30 to 100 more genes.  So, these mice do not have very strong construct validity for our children.  It is well known that mutations can be very different from deletions. (see Gene deletion versus mutation.) Of course, mutating a single gene may not be very helpful to understanding your child when so many other important genes may be involved. (see How do we know which genes are important?)  There is also the problem of using a mouse to model a human. The gene is mutated in an animal that lacks brain areas that are crucial to human behavior, like the granular prefrontal cortex.  If these brain areas are important to autism, then the construct validity is weaker.

To be fair, a lot of work goes into to creating a knockout mouse.  I don’t have first-hand experience, but I work down the hall from a colleague who is an expert.  He works hard and I can read the frustration in his brow on tough days.  Just making a mouse is not good enough, you have to prove you have modified the right gene in the right place without messing up the rest of the genome. Then you cross-breed, back breed and then do more validations. My hat is off to those people who make a living this way.  When done, the mouse has construct validity in that the targeted gene has been modified.

Face validity is a huge problem with mouse models. Our model airplane ascends and descends, banks and aerodynamically behaves much like its real-life big brother.  We know the flight behaviors that are important and we can directly (although not perfectly) compare our model plane to the real thing. How do we compare our model disease to the real disease?  Generally, the first step is to compare normal mice to our genetically modified mouse.  We note what is different between the two.  Then, we compare normal human subjects (“developmentally typical”) to those with the syndrome or disorder. The question then becomes, do the mouse differences seem to reflect the human differences?   Mouse models of kidney function and cancer have been very successful with face validity.  Urine output and tumor size are easier to measure than social behavior and eye contact in mice.  Biopsies of human kidney and many tumors are also much easier than brain biopsies.  It is no surprise, then, that mouse models of neuropsychiatric disorders are hard to validate.

The differences between normal and mutated mice can be observed in brain structure, chemical signatures, cellular changes and gene expression.  For the most part, there is very little human data for comparison. There are studies with human post mortem tissue that can be helpful, but most of that tissue is from normal human brain. As you might guess, screening for gene expression and other changes in a donated brain from a PMS patient will have issues.  Most patients have too many genes involved.  One helpful approach is induced pluripotential stem cells (iPScs), grown from skin samples or hair follicles. One might even be fortunate enough to find a donor who’s genetic mutation matches the mouse (or vise versa).  However, iPScs do not undergo normal development, so developmental studies are impossible at the moment. They also don’t produce circuits like an intact brain. These are all limitations that impact face validity.

The one common feature you can examine between mice and humans is behavior.  There are two extreme viewpoints in this regard.  At one extreme, some scientists argue that any behavioral difference between the normal mouse and the genetically modified mouse is “autism-associated” because of the construct validity.  At the other extreme, a few scientists argue that the mouse behavioral difference should reflect the standard manual that defines neuropsychiatric disease (DSM-5).   The remaining scientists are in the middle until it comes to publishing a paper.  Then, they make the argument that their animals’ behavior somehow reflects the behavior of a person with autism. It is my observation that the more popular or prestigious the journal, the more their mouse sounds like a miniature human.

A major problem with Shank3 mice is that, almost universally, they don’t have a significant aberrant behavior.  How can you study behavior when it seems normal?  There are two solutions, but both have problems.  With one approach, researchers find a mutation spot on the gene that is extra good at producing a pathological behavior (e.g., ignoring other mice, not learning, rubbing its fur until the skin is damaged).   Another approach is to mutate both copies of the gene.  Each of these solutions creates a new problem.  In the first case, we are no longer modeling PMS or autism, because this behavior only shows up in very specific mutations. In the second case, we have lost construct validity.  We were never trying to model mutation or loss of both copies of SHANK3. That would likely be a different syndrome (just as mutation is different from deletion).

In the end, current models of SHANK3 mutation (autism and SHANK3 mutation aspect of PMS) provide information about molecules and neurons, but are very limited models of the human diseases.  They don’t necessarily say much about 22q13 deletion syndrome in general.   It is interesting to note that mouse models of other genes of 22q13 deletion syndrome may be more promising.  Several mouse models have clear consequences with only one gene mutated or deleted. For example, the  Cpt1b mouse model is used to study cold tolerance and insulin sensitivity, and the autism and schizophrenia-associated gene, BRD1, is under intense research right now by a group in Denmark. In both cases the behavioral effects are clear when only one copy of the gene is affected.

We are not done yet, because the most important and most difficult type of validity is predictive validity.  That is, does your mouse model tell you what will happen in your human subjects?  Given all the problems with making a mouse model of a neuropsychiatric disorder, it is no surprise that the models have not lead to translational (treatment) gains. (See Hope for autism treatment dims as more drug trials fail).

I have heard many people in the research field try to sound hopeful to parents. I believe that hope, when anchored in reality, is very helpful and important.  But, too many people have alternative reasons for fanning the flames of hope by knowingly or unknowingly misrepresenting the size of strides in research.  My recent blog (How can the same deletion have such different consequences?) touches on why so many parents are mislead by researchers, writers and support organizations. The subsequent blog (22q13 deletion syndrome and science leadership) explains that it does not have to be this way if we bite the bullet and hire qualified leaders.

As a parent, my heartstrings feel the tug of hope every day.  The urge to follow those feelings is managed by having a deeper understanding of the research world, and remembering that too many people are eager to give those strings an extra tug.

arm22q13

Previous posts:

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 translocations in 22q13 deletion syndrome: genetics and evolution
Understanding deletion size
22q13 deletion syndrome – an introduction

Comment la même suppression peut-elle avoir une telle variété de conséquences ?

[English version]

L’auteur, Andy, et sa cousine ont la même chromosome hybride 22 qui provoque le syndrome de la suppression 22q13.

Leurs enfants ont la même suppression mais un des enfants d’Andy est mort et l’autre, David, a failli mourir. La cousine n’a pas eu cette expérience et sa fille, contrairement à David, n’a pas pris 6 ans à apprendre à marcher, 9 ans à manger oralement et elle peut parler avec les phrases courtes. C’est la question la plus posée par les parents d’enfants atteints.

Si SHANK3 n’est pas la cause de la suppression 22q13, pourquoi y a-t-il un enfant avec uniquement la mutation SHANK3 qui ne sait ni parler ni marcher ? Et il y en a d’autres qui savent très bien marcher et parler. Si vous acceptez la dilemme que des suppressions similaires peuvent provoquer des résultats très différents, il n’y a plus l’argument du gène favori (SHANK3 aujourd’hui, demain autre chose probablement.)

Pour expliquer ces différences il y a plusieurs réponses :

1. Perte de l’hétérozygotie : Des petites erreurs génétiques ont lieu tout le temps pendant le développement et dans la vie adulte. Facteurs environnementaux – radiation, infections, coups de soleil, toxines. Le fait d’avoir les paires de gènes de deux parents différents nous protège des erreurs génétiques graves. Lorsqu’il manque des gènes à cause d’un syndrome de suppression, on n’a qu’une copie d’un gène alors il y a l’occasion parfaite pour des erreurs non-corrigées. Si ce gène est endommagé par la suite, les conséquences peuvent être graves. L’erreur peut être globale (corps entiers et détectable avec les tests génétiques) ou local (limité à une partie du corps ou du cerveau.) Quand l’erreur est locale elle n’est pas détectable et devient une différence inexpliquée.

2. Impression (ou empreinte ?) : Quand un des gènes est éteint comme le syndrome d’Angelman. Si la seule copie qui reste du gène s’éteint ça va provoquer des problèmes qui ne seront pas expliquées.

3. Impact de la mutation du gène : Souvent un gène qui est supprimé a moins d’impact qu’un gène qui a subi une mutation. Comme dans le cas des cellules de cancer ; on préfère qu’elles meurent au lieu de pousser avec des gènes modifiés. Si une suppression chromosomique ne frappe qu’une partie du gène, le gène peut commencer à créer des protéines qui empêchent le fonctionnement normal de la cellule et la petite suppression provoque des grands problèmes.

4. Les combinaisons de gènes : Quand il y a plusieurs suppressions et mutations on cumule les erreurs génétiques et chacune fait sa contribution. On a parfois des gènes qui, seuls, n’ont pas d’impact lors de leur suppression/mutation mais avec certains autres peuvent avoir des conséquences beaucoup plus importantes. On ne comprend pas encore ces combinaisons alors on utilise des termes comme ‘antécédents génétiques’ en attendant. La différence génétique principale entre David et la fille de la cousine d’Andy vient de la femme d’Andy et du mari de sa cousine ; des différences dans leurs antécédents génétiques.

5. Mosaïcisme et mutations somatiques : Pendant le développement les erreurs génétiques peuvent avoir lieu dans une petite partie du cerveau. Ces erreurs peuvent expliquer les variations comme les difficultés d’apprentissage. Ces mutations inaperçues peuvent avoir des incidences plus lourdes lorsqu’elles interagissent avec les 30 à 100 gènes manquants. L’impact de SHANK3 peut être amplifié par ces gènes modifiés ou perdus dans des parties spécifiques du cerveau.

6. Les régulateurs génétiques: Le projet génétique ENCODE tente de trouver tous les morceaux régulateurs des gènes de l’ADN. La plupart de l’ADN est composée de régulateurs de gènes. C’est plus facile à comprendre quand vous vous rendez compte que les cellules de foie, de peau, des intestins, du cerveau, ont toutes les mêmes gènes. Ce qui change est les gènes qui sont actifs ou inactifs. Les cellules de peau savent qu’elles sont cellules de peau et n’utilisent que les gènes de cellules de peau. L’ADN est réglé dans chaque tissu à associer la signature génétique nécessaire à fabriquer le tissu. Les suppressions chromosomiques 22 suppriment également les régulateurs de gènes. Les régulateurs sont très difficiles à repérer et pourraient être la cause de ces différences inexpliquées.

Compte tenu de la complexité et de nombreuses possibilités de variation inexpliquée , nous pouvons commencer à apprécier que la connaissance de la taille de suppression d’un individu ne fournit pas toutes les réponses. Cependant, grâce à des outils modernes, il existe des moyens pour étudier les effets de la taille de la suppression même avec une telle variabilité. Ces outils peuvent être utilisés pour démêler les gènes qui contribuent à chaque problème médical. Cela exige un engagement sérieux des parents à pousser les chercheurs et le personnel médical vers ces recherches, tirant pleinement parti des rapports génétiques. Trop l’accent sur un gène préféré entrave le progrès scientifique et médical. Ceux qui travaillent sur un autre chromosome, syndrome de délétion (suppression 18q syndrome) ont étudié leur syndrome à bon escient au cours des 50 dernières années. Ils se tournent vers la médecine scientifique pour les symptomes de 18q (Voir Création d’ anomalies chromosomiques). Les personnes 18q ont développé une feuille de route, que les gens atteints du syndrome de délétion 22q13 peuvent facilement suivre (Voir Conséquences du chromosome 18q suppression). J ai travaillé durement dans mes dernières recherches pour faire ce point , mais rien est plus convaincant que de voir d’autres prendre les devants avec une telle clarté et tel engagement. Pourquoi n en avons-nous pas profité ? La seule explication que je peux trouver est que la communauté du syndrome de délétion 22q13 manque de personnes qualifiées, dirigeant scientifique impartiale. Il y a un problème assez évident, avec des conséquences très tristes. Il n’y a pas plus de traitements pour David aujourd’hui qu’il ya 30 ans. Nous savons quels gènes sont portés disparus et pour beaucoup d’entre eux, nous savons ce qu’ils font (Voir Comment savons-nous quels sont les gènes 22q13 suppression: l’espoir de la médecine de précision). Ce que nous ne semblons pas savoir est comment rendre le travail de la science meilleur pour le bien de nos familles.

 

[My thanks to Betty Sepré for doing this translation.  That said, I take responsibility for any errors in typing, translation or content. Feel free to contact me with corrections. –  arm22q13]

22q13 deletion syndrome: the hope of precision medicine

Although non-verbal, David is clearly in charge of this trip.

David does not talk, but he does know how to express himself. In this photograph we are taking a ride to his brother’s apartment.  As soon as I arrived at David’s house, he grabbed my hand and walked me back to the car.  He pulled on the door leading to the back seat.  “Take me for a ride!  The usual place, of course!” He communicates very well considering all his disabilities, but I would love to have a medication to help him talk, or walk better, or toilet easier, or not overheat in the summer.  In fact, what I really want is a custom pill made for David.  Different patients with different size deletions have different needs. Although intellectual disability affects 100% of our kids and ASD affects up to 30%, the reality is that our children can have many different problems.  Except for a few confusing cases, kids with larger deletions have more problems and often more severe problems.

If you read my earlier blog on deletion size (Understanding deletion size), you will know that over 95% of patients with 22q13 deletion syndrome are missing from 10 to over 100 genes.  The genes near the end of the chromosome are the first ones to be deleted by a terminal deletion (the most common type).  These genes are tightly packed together.  In this region, you cannot simply say “a small deletion”.  You must know the exact deletion size to know how many genes are affected.

Precision medicine

According to the National Institutes of Health, “precision medicine” is “… an emerging approach for disease treatment and prevention that takes into account individual variability in genes, environment, and lifestyle for each person” (from: NIH Precision Medicine Initiative).  The promise of precision medicine has not reached most people because the average patient does not know which genes are most important to his/her health. For patients with 22q13 deletion syndrome, however, the genes that cause the syndrome are obviously the genes of greatest clinical importance.  The primary goal of 22q13 deletion syndrome research should be to maximize the benefit of knowing the exact genes involved on a patient-by-patient basis.  Think: “I want a pill optimized for my child”.   Of course, it is an oversimplification to think about a custom pill, but the NIH definition of precision medicine helps guide us toward more practical thinking.

In my last blog (How do we know which genes are important?) I listed the genes that are likely to contribute to hypotonia.  Categorizing the genes into  clinically meaningful categories provided us with insight into treatment.  Each gene in the list has a known effect on the brain and rest of the body.  Some genes interfere with normal brain function.  Other genes can affect peripheral myelin, a insulator that is needed to transmit information back and forth between the spinal cord and the muscles.  Still other genes can disrupt a muscle’s ability to tolerate sustained work.  Each of these categories provide important information to the physical therapist.  A child with poor sensory feedback from the muscles might be handled differently from a child with poor muscle stamina.  Precision medicine is in its infancy, used mostly in cancer treatment. However, precision medicine for 22q13 deletion syndrome could start today.  Physicians and therapists could readily benefit from a report for each person that brings together an individual’s genetics with the known functions of the missing 22q13 genes.

One might wonder how far this precision medicine idea can be taken.  Well, for next year the White House reports a 215 million dollar initiative for government supported research and promotion of precision medicine (White House Fact Sheet).  Businesses have already invested billions of dollars into electronic health records, the backbone of precision medicine. There is no question that precision medicine will bring major changes to medical practice and patient choices.

Clearing up some misconceptions

It is amusing at times to hear well-meaning parents talk about the barriers to using genetic information to guide treatment. One common misconception is that too little is known about the genes.  Actually, many of the genes have been studied for decades and the research has obvious clinical implications.  For example, at the Society for Neurosciences meeting earlier this month I talked to a young researcher from California who was working on CELSR1 (missing in about 50% of our kids).  He showed that neurons in the hippocampus essential for learning new relationships between events and places (e.g., learning to navigate a new school building or deal with a change in classroom schedule) are disrupted when CELSR1 is deleted.  What he told me next was even bigger news. A researcher in Belgium has been studying mice lacking CELSR1 for years.  It took only one email to that scientist to net a trove of information about CELSR1.  Apparently, CELSR1 is not only important for brain wiring, but also the flow of cerebrospinal fluid (CSF) in the brain. Read that: enlarged ventricles.  A radiologist who evaluates the MRI of a 22q13 deletion syndrome child will someday associate his/her findings with deletion size based on studies like these. After enough MRI reports are collected from enough patients, the association of CELSR1 with ventricle size can be confirmed.  The beauty of precision medicine is that you collect new data for the next generation each time you treat patients in this generation.  Taking your child to the doctor actually helps other patients with 22q13 deletion syndrome. Is that great, or what? For people with 22q13 deletion syndrome, it is knowing the detailed genetic information that will make it work.

Another misconception is that there is no clear relationship between deletion size and the severity of 22q13 deletion syndrome.  Actually, even if there was no clear relationship, it would still be of great value to use our knowledge of which genes are involved in each person.  But, we are sometimes faced with the confusing observation that a few kids with big deletions are more functional than others with smaller deletions.  These apparent exceptions to the rule are examples of how genetics can fool us.  Let’s use two examples to show how important knowing the basics can be.  Reading the scientific literature you can find one or two kids with tiny SHANK3 mutations/microdeletions who are more affected than one or two other kids missing a whole group of genes.  As I discussed in my earlier blog (Sometimes missing a gene is better) a gene mutation is often more damaging than deleting that gene.  Such is the case for specific mutations of SHANK3, ATXN10, CELSR1 and other genes on 22q13.  That is part of the reason I use the term “22q13 deletion syndrome”, which distinguishes deletions from mutations.  The second example is the clumping of important genes on the distal part of the chromosome. Because the genes are not evenly distributed on the chromosome, someone with a 1.5 Mbase deletion and someone with a 2.5 Mbase are actually missing the same genes.  Deletion size is not a measure of gene loss.  It simply provides a map to the list of genes that are deleted.  Comparisons have to be made after making a list of genes.

There are other reasons for a conflict between deletion size and severity of 22q13 deletion syndrome.  One recent study has shown that de novo chromosomal deletions (the most common type) often include mutations and other deletions elsewhere on the chromosome or on other chromosomes.  This more widespread occurrence of genetic errors does not tend to show up in the parents or siblings of a child with a de novo deletion.  That is, a diagnosis is 22q13 deletion syndrome raises the possibility that there are more genetic errors elsewhere in the DNA.  Precision medicine will someday not only include the deletion size, but a list of other genes that show potential issues.  There are other reasons for the unusual cases that I won’t go into, but larger deletions affect more genes and generally cause more problems. Of course, individual differences do matter.  That is why it is called precision medicine.

The future is now

My posting on hypotonia landed me an opportunity to give a guest lecture to a graduate physical therapy class.  The lecture was on the genetics of infant hypotonia.  I ended the lecture with a “hopeful warning” that all of medicine is about to change.  It was a warning, because all clinical practitioners will need to understand the implications of genetics in their practice, and it was hopeful because the lives of patients are about to get better.  It may be a while before we can go to an apothecary for a customized pill, but we can reap benefits today.  Your physicians, nurses and therapists could begin receiving guidance curated from the currently available literature on genes.  Of course, someone has to compile the information.  Perhaps we need to convene a conference that brings together experts on each gene with medical practitioners who would use the information. I have seen a number of conferences for 22q13 deletion syndrome, but none like that.

I should probably get a detailed genetic report for David and combine that with my own readings on his genes so that he can benefit from the promise of precision medicine. I am torn by a moral dilemma. I don’t want to be biased in my pursuit of 22q13 genetics. Whether we like it or not, we are always biased by what our own child needs. Not knowing David’s details is, in a way, liberating. I am hanging out with David as I write this. We are watching the Graceland video with Paul Simon.  If you know the history behind that video, it is a reminder that everyone matters, regardless of their skin color, which is to say, regardless of their genetics.

arm

Previous posts:

How do we know which genes are important
22q13 Deletion Syndrome: hypotonia
Understanding gene size
Gene deletions versus mutations: sometimes missing a gene is better.

Understanding translocations in 22q13 deletion syndrome: genetics and evolution
Understanding deletion size

22q13 deletion syndrome – an introduction

22q13 deletion syndrome: How do we know which genes are important?

When I get on Facebook I look for pictures of our 22q13 deletion syndrome kids.  Every time I see one I give it a “thumbs up”.  It warms my heart to see other parents share their pride in their children, even if our children are peculiar in some way.  Our snapshot may capture a funny posture or gait.  David is almost always looking away from the camera.  Some 22q13 kids are captured chewing on “non food items”.  We post photos to show our pride in accomplishments that would have been easy for most other kids.  Our children are usually not very photogenic, except to families and, of course, other parents of kids with 22q13 deletion syndrome.

There are some pictures that we don’t put on Facebook in deference to families that could not appreciate them.  There are pictures of feces on the sofa, self-inflicted injuries, frightening hospital scenes, and even pictures after an early death. The reality of 22q13 deletion syndrome is often not pretty.  However, our goal is not to provoke a reaction. We simply want to share joy or commiserate with our community, like all parents.

David, like the overwhelming majority of children with 22q13 deletion syndrome, has many things wrong.  He is missing more than one or two genes and the impact is pretty obvious.  Ninety-seven percent of children with terminal deletions are missing from about 30 to 200 genes (see Understanding deletion size).  Science can help us find ways to help our children.  The first step is to find out which gene causes which problem.  Fortunately for our children, science has a bunch of relatively new tools to help create this “genotype-phenotype map“.

First things first.  Let’s have a look at the list of genes that are lost with a 22q13 terminal deletion (the most common type of deletion).

This is a list of genes organized by deletion size.  The deletion size on the left corresponds to the list of missing genes of the same color on the right.  A 1 Mb deletion will delete all genes in dark brown, starting from RABL2B and ending with ALG12 (33 genes).  The next group (reddish brown) are missing if your child has terminal deletions of 5 Mb or more (16 more genes, giving a total of 49 genes).  That covers about half of all common terminal deletions.  Terminal deletions have been observed for sizes up to about 9 or 10 Mb.  The genes above that are usually missing only with certain interstitial deletions.

Ok, so now we have our list.  The crucial question is, which genes do what?  In the past few years scientists have built some rather clever and remarkable tools for figuring this out.  Here are some tools and some examples of how they can be used.

Comparing 22q13 genes with known genetic syndromes

Online Mendelian Inheritance in Man (OMIM) is a database of genes and the problems associated with them.  By choosing a trait like poor body temperature control (poor thermoregulation) or low muscle tone (hypotonia), you can find out what genetic disorders have that feature.  From that information, you can identify which genes are involved.  Sound complicated?  Not at all. If you go to the Human Phenotype Ontology web site and type in “abnormal muscle tone” it does the entire cross-reference in a few seconds.  Click the tab for “genes” and you get a list.  I did just that.  I found which genes match the list of 22q13 genes and highlighted them here.

What is interesting about this list is that only two genes are directly involved with the synapses of the brain (SHANK3 and MAPK8IP2).  Other genes linked to hypotonia have other important functions. One gene is important for the synthesis of neurotransmitters (SULT4A1). Some genes affect white matter and peripheral nerves (ARSA and SBF1).  Another gene affects the muscles directly (CHKB).  Some genes affect many organs (ALG12 and NAGA).  As I see it, each gene is an opportunity to find a treatment for our children.  If one gene is complicated and hard to study, there are other genes that might lead more quickly to important benefits, like new treatments.

Comparing 22q13 genes with genes that work specifically in the brain

If we are interested in behavioral problems and intellectual disability we can benefit from a recent scientific study that has created a list of genes that are specialized for the brain (Pandey et al., 2014).  Using a “gene expression atlas,” these researchers identified genes that are either used (expressed) at a very high level in the brain, or used much more in the brain than anywhere else.  The logic is simple, if the brain treats these genes as important, then they must be important.  

Only 4 genes show up.  These are obviously 4 genes that deserve careful research to help people with 22q13 deletion syndrome.  Two of these genes, MAPK8IP2 and SULT4A1 also appeared in the hypotonia gene search.

Comparing 22q13 genes with genes that evolved for a specific purpose

One of the most interesting new methods for understanding the role of genes comes from the study of how humans evolved.  I have already written about the value of this approach (see Is 22q13 deletion syndrome a ciliopathy ?).  There is an interesting website that automates the process of studying evolution. This approach, called “forward genomics” is more difficult to use than the previous two examples, but this method may solve some important problems.  I am very interested why David gets too hot in the sun and too cold after a bath.  That is, why does he have problems regulating his body temperature.  By studying the scientific literature on which animals are good at body temperature regulation and which animals are not, this web site will tell me which genes are involved.  My job is to read textbooks and papers to find out how well each of 27 species of animals regulate their temperature.  Once I do that, I can ask the website to scan the genomes of these species and identify which genes are associated with the emergence (or loss) of the ability to regulate body temperature. It is a fascinating approach and I am very eager to learn the results. The results may open the door to lowering the risk of febrile seizures.

Other methods

There are other methods for finding genes that affect our children in specific ways.  For example, gastroesophageal reflux was such a serious problem for David that he required major abdominal surgery (Nissen fundoplication).  A comparison of reflux with known genetic conditions (similar to the hypotonia example) provided no new information about 22q13 deletion syndrome genes.  However,  the search did produce a list of 48 reflux genes. How can we use the reflux gene list to learn more about 22q13 genes?  First, there is an analysis method called “guilt-by-association“.  This analysis will indicate which 22q13 deletion syndrome genes naturally operate in concert with the reflux genes.  A even more complex analysis tool for protein-protein interaction can identify which 22q13 genes have chemical interactions with reflux genes. I expect one or more 22q13 deletion syndrome genes will be associated with reflux after these analyses.

Tremendous progress has been made in the understanding of how genes contribute to disorders.  The best way science can help our children is by identifying the many different genes that cause the many different problems.  That is Step One and modern methods make that step much easier and more informative that the old methods of the past.  Step Two is to find treatments.  Many of these genes have been studied in great detail.  Some have related treatments either already in use or suggested by researchers.  As a parent, I want to see new treatments found for David.  As a researcher, I don’t understand why we are not taking these potentially fast tracks to treatment.

 

arm

Previous posts:
22q13 Deletion Syndrome: hypotonia
Understanding gene size
Gene deletions versus mutations: sometimes missing a gene is better.
Is 22q13 deletion syndrome a ciliopathy?
Understanding translocations in 22q13 deletion syndrome: genetics and evolution
Understanding deletion size
Can 22q13 deletion syndrome cause ulcerative colitis?
Can 22q13 deletion syndrome cause cancer?
22q13 deletion syndrome – an introduction