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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New science: SULT4A1, oxidative stress and mitochondria disorder

A visit with David during the COVID-19 epidemic

It has been known for some time that many people with Phelan McDermid syndrome (PMS) have mitochondrial issues. I discussed this in an earlier post (see Is 22q13 deletion syndrome a mitochondrial disorder?). At the time of that posting there were 17 PMS genes known to impact mitochondria. There is evidence that the PMS gene RABL2B generates a protein to transport mitochondria into synapses. That would be 18 genes. Now, new evidence has emerged that the SULT4A1 gene, a highly important PMS gene (see Which PMS genes are most important?) is critical for protecting the brain from oxidative stress by regulating mitochondria function.

After 20 years the role of SULT4A1 is finally coming to light. SULT enzymes have been known as important enzymes for a while, but SULT4A1 has always been a mystery. The other SULT enzymes have an active region used to regulate critical proteins in the cell, some involved with mitochondria function and the key neurotransmitter, dopamine. But, the SULT4A1 protein lacks the same active enzyme site. The other mystery has been that the SULT4A1 gene is highly specific for brain and brain development. Cathrine Ziats’ scientific paper last year found SULT4A1 to be one of the top 4 PMS genes expressed in the human brain during development (see her paper: Functional genomics analysis of Phelan-McDermid syndrome).

The new evidence paints a picture placing SULT4A1 as a critical regulator of brain metabolism. The thing to understand about the brain is that it sucks up 30% of the total body’s energy supply! This puts a huge load on the mitochondria of the brain. SULT4A1 regulates two other SULT proteins, SULT1A1 and SULT1A3. These enzymes are found on the outside membrane of mitochondria, connected together in pairs. By regulating these enzymes, SULT4A1 is able to crank up the output of the brain’s mitochondria. This reduces the reactive oxygen species, reduces oxidative stress and prevents neuronal damage. (See the two articles on PubMed: Hossain et al 2019 and Idris et al 2020). As SULT4A1 regulates these two other enzymes it can also regulate the effects of dopamine. Dopamine is a key neurotransmitter involved in learning and decision making. Too much dopamine, especially during development, can damage a cell. Too little dopamine is associated with motor and psychiatric disorders, like Parkinson’s disease and major depressive disorder.

Nearly a third of our PMS kids are missing the SULT4A1 gene (deletions larger than 7 Mb). Finding a way to fix the SULT4A1 gene would be a game-changer for these children. Like the other essential brain genes of PMS (e.g., SHANK3), the precise regulation of SULT4A1 is critical to normal development and healthy brain function. There are people with interstitial deletions of 22q13 that impact SULT4A1 without affecting SHANK3, and these people have severe developmental problems indistinguishable from others with PMS. (That some scientists are still arguing over whether or not to keep them in the family of PMS is a travesty, in my opinion as a father. See PMS, IQ and why interstitial deletions matter.)

We need more research on SULT4A1. We need treatments sooner rather than later.

 

arm22q13

 

 

 

What do we know about PMS genes?

Our children trust us to do the best for them

Originally posted 24 January 2018
Updated 20 April 2021
Available in Portuguese http://pmsbrasil.org.br/o-que-nos-sabemos-sobre-os-genes-pms/

Recap

In the previous blog we learned which Phelan McDermid syndrome (PMS) genes are most important. SHANK3 has often been touted as the gene that causes PMS, but SHANK3 rarely operates on its own and in some people has nothing to do with PMS (those with interstitial deletions). We learned that large studies of human populations identify 18 PMS genes that are impacted by “natural selection”. Loss of these genes are highly likely to cause problems, the problems that add up to PMS. The genes are:

SHANK3, MAPK8IP2, PLXNB2, TRABD, PIM3, ZBED4, BRD1, TBC1D22A, GRAMD4,
CELSR1, SMC1B, PHF21B, PRR5, SULT4A1, SCUBE1, TCF20, SREBF2, and XRCC6.

The big question is, what do we know about these genes? That is, how might they be contributing to PMS? This blog is based on a paper that not only identified these genes, but also pulled together what is currently known about each. Although the paper describes each gene’s function in detail (for well-characterized genes), it also classifies genes into groups. Those groups are quite informative and help us understand why PMS has certain characteristics.

Genes that impact brain development

It is now very clear why PMS can occur with or without SHANK3. Of the 18 PMS genes that are likely to have a high impact on PMS, at least 7 impact brain development: SHANK3, MAPK8IP2, PLXNB2, BRD1, CELSR1, SULT4A1, TCF20.

MAPK8IP2 sits almost adjacent to SHANK3 and we have known for years that loss of MAPK8IP2 in mice interferes with brain function (see MAPK8IP2 (IB2) may explain the major problems with walking and hand use).

PLXNB2 regulates the growth of neurons, especially early in development. PMS is a neurodevelopmental disorder, so nothing could be more important than regulating neuron growth.

CELSR1 is also crucial for neurodevelopment. Neurons are exquisitely organized into nuclei in the deep structures of the brain and into very precise layering in the cortex. For example, pyramidal neurons of the cortex are located only in certain layers of the cortex, with the dendrites reaching upwards and the axon pointing down. The axon often winds its way towards the white matter. CELSR1 is important for orchestrating the orientation of neurons to assure proper organization.

BRD1 regulates hundreds of other genes during development. It is highly associated with schizophrenia, as well as PMS. PMS individuals with terminal deletions greater than 1 Mb are missing BRD1 and the loss of BRD1 impacts the entire genome (see https://pubmed.ncbi.nlm.nih.gov/33407854/).

SULT4A1 was recently shown to impact the mitochondria in the brain (see New science: SULT4A1, oxidative stress and mitochondria disorder). Mitochondria convert food into energy for cells. Dysfunction of mitochondria explains why deletions that disrupt SULT4A1 can have a severe impact on neurodevelopment and adult brain function.

TCF20 is a very important gene for brain function. It can cause intellectual disability and other problems on its own. It probably explains why very large deletions in PMS can be more devastating than smaller deletions (see TCF20 may explain why some big deletions are worse than others).

Genes associated with sleep

There are three genes that have close association with sleep or sleep disturbance. SHANK3 impacts sleep in some individuals with PMS, but PIM3 (see this paper) and PRR5 (see this paper) have been identified in studies that explore which genes regulate circadian rhythms (so called, “clock” genes).

Gene associated with lymphedema

CELSR1, the gene important for proper orientation of cells during neurodevelopment, is also associated with inherited lymphedema. Presumably CELSR1 influences cell orientation and the structure in the lymph system during development.

Genes that have unknown function

We must recognize that just because a gene has never been closely studied, that does not mean it is unimportant. In fact, one genomic study makes a convincing argument that genes of unknown function are just as important as the well-characterized genes. PMS has 7 genes likely to be important, yet not well-studied: TRABD, ZBED4, SMC1B, PHF21B, SCUBE1, SREBF2, and XRCC6. The first two genes, TRABD and ZBED4, are of very special concern. One copy of each gene is missing in over 95% of individuals with terminal deletions. It is imperative we find out what these genes are doing and how loss impacts PMS.

Conclusion

This study of PMS genes was a critical step forward in understanding PMS. It provided a short list of culprits. It explains why interstitial deletions cause PMS and it identifies where our research efforts need to be focused. Most importantly, it provides new targets for therapeutics. Unfortunately, a lot of time has gone by without any serious effort to encourage research into the full array of PMS genes. The genes listed above warrant much more study. As a parent of a child with PMS, I strongly feel we should make an effort to encourage the scientists who study these genes. It is hard to understand why so many important genes of PMS are being ignored by the PMS community.

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Previous blogs

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
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

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