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:
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. 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, often winding its way towards the white matter. CELSR1 is important for orchestrating the orientation of individual neurons.
BRD1 regulates hundreds of other genes during development. It is highly associated with schizophrenia, as well as PMS.
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 and PRR5 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 has provided a convincing argument that genes of unknown function are 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 why their loss might be highly impactful in PMS.
This new study of PMS genes has breathed new life into PMS research. It has 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, we have new targets for therapeutics. New targets mean new hope.
Unfortunately, a lot of time has gone by without any serious effort to encourage research into the full array of PMS genes. We have not taken any advantage of 17 opportunities to make PMS children better. As a parent of a child with PMS, I strongly feel there should be greater respect for parents’ hopes. These hopes deserves every effort to search for treatment options.
If you ask me what is wrong with David, I don’t think I can answer the question without making a laundry list of problems, deficits and other issues. He has 22q13 deletion syndrome – that is what’s wrong. Some of his problems almost killed him. Someday, that risk may return. In the meanwhile, his biggest problem is learning new knowledge and skills. Can we make learning more efficient for our children? To investigate this question, we need to understand more about how individual and groups of genes can affect the brain.
I have written blog posts on specific issues (cancer, ulcerative colitis, hypotonia) and other issues in the context of individual genes. Individual genes can impact many parts of the body. A single gene may have multiple functions, an effect called “pleiotropy” (plahy-o-truh-pee). We are often concerned with the primary impact of a gene more so than the secondary issues. For example, CTFR is a cystic fibrosis gene. Its impact on the lungs is very damaging, but it also impacts other parts of the body.
Many 22q13 deletion syndrome genes are pleiotropic. We must look carefully at all the potential effects of a gene. Why? Because, so many genes are lost in 22q13 deletion syndrome that subtle effects can add up. When I read the scientific papers on a gene, I spend a lot of time comparing the subtle effects of this gene with all the others. I look for cases where multiple genes have subtle effects on the same organ. By definition, 22q13 deletion syndrome is a chromosomal deletion syndrome. It is not a monogenic syndrome as some have suggested. I recommend using the name “Phelan-McDermid syndrome” if you want to combine SHANK3 mutation syndrome with 22q13 deletion syndrome. See: Introduction to 22q13 deletion syndrome and How to fix SHANK3.
Pleiotropic effects come in two flavors. Either the gene has one function, but in different parts of the body, or the gene can do more than one function. CTFR, is not a 22q13 deletion syndrome gene, but it provides a useful example. It is the most common cystic fibrosis gene. CTFR is involved in making secretions (fluids used in the body). CTFR mutations are most important in the lungs, but the gene also causes faulty secretions in the digestive tract, and elsewhere.
CELSR1 is a 22q13 deletion syndrome gene. Over 40% of our children are missing this gene. Like CTFR, one function affects many different parts of the body. If one copy of CELSR1 is mutated, the most serious result is a neural tube closure defect (e.g., spina bifida or other spinal cord problems). Mouse studies of Celsr1 show that it participates in helping cells organize into physical patterns so that cells can operate as a group. Celsr1 is involved in early development by organizing certain cells into functioning tissues (Feng et al, 2012). However, the central role of CELSR1 in adult brain function was only discovered last year (Schafer et al, 2015).
During development, Celsr1 mutations can interfere with the organization of many different cells (Boutin et al, 2014). For example, ventricles are nourishing fluid lakes inside the brain. Cilia, cells with tiny hairs, line the ventricles of the brain and stir the cerebrospinal fluid (CSF) along its path through the ventricles. Stagnation of the CSF fluid is dangerous. Disordered cilia from Celsr1 mutations cause inefficient motion. In humans, stagnant CSF may have accumulating impact over years.
Very different cells with cilia are used in the ear to hear sounds. CELSR1 mutations disrupt the orientation of “outer hair cells,” responsible for hearing at low sound levels. Cilia are responsible for other body functions, as well, like keeping the airways clear and digesting food. Given its impact on different organs, CELSR1 is pleiotropic.
When someone asks me what is wrong with David, one of the first things I say is he struggles to learn. David is aware and interested in his environment, but he knows trying to learn anything new is difficult. My last blog discussed SHANK3 and its impact on learning that involves the ventral striatum in the brain. Mutations in CELSR1 disrupt a different kind of learning, learning that is unique to the hippocampus of the brain. Only two areas of the brain are able to grow new neurons. One of these areas feeds the new neurons into the dentate gyrus of the hippocampus and has a subtle, but critical effect on learning . Mutation of rodent Celsr1 disrupts the orientation of these new neurons in the hippocampus. This disruption interferes with building proper connections (Schafer et al, 2015). Thus, children with deletions greater than 6 Mbase are likely have problems with “pattern separation,” the very subtle learning process that prevents new learning from interfering with old knowledge (Johnston et al, 2015). The concept of pattern separation has arisen through complex mathematical learning models.
How can we take this information on CELSR1 and translate it into treatments? There are several paths. First, we would like someone to study a mouse missing one complete copy of Celsr1 (heterozygous knockout mouse) to make sure the effects seen in the current mice are not simply mutation effects (see Gene deletion versus mutation). There is a scientist in Belgium, Fadel Tissir, who has a “null” mouse (no copies of the gene), but has not reported any studies with a heterozygous knockout mouse yet. Second, we need to find out about outer hair cell loss and its potential impact on hearing. Perhaps someday we can arrange for a medical histologist to examine the cochlea (hearing organ) from a 22q13 deletion syndrome organ donor. Third, we need genetic testing (sequencing is best) on all patients missing CELSR1 to identify cases where the remaining CELSR1 gene is mutated. A mutation on the remaining CELSR1 gene could unmask recessive traits in a way that may be very informative.
Finally, if we really want to understand our children’s learning problems, we need to: 1) engage people involved in computational models of learning, and 2) study patients with interstitial deletions. Interstitial deletions will allow us to study genes in better isolation. These patients may be higher functioning, which is ideal for careful testing (see How to fix SHANK3). As the new studies start to bear fruit, we can then use the results to target our teaching methods. Right now parents, teachers and our children are frustrated with how poorly our children learn. Imagine how much better it will be when we know how to maximize learning for each child based on their genetic report. I dream of seeing the next generation of children with 22q13 deletion syndrome having all the benefits we never had for David. Let’s take lesson planning into the 21st century!
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.
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.
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.
Although he is a bit unsteady at times, David loves to walk. When he first started his day program, the aid assigned to him nearly gave up. Keeping up with David’s constant motion — walking — forced her to become an athlete. She looks back at the experience now in an appreciative way. David brought fitness into her life and the two of them have a deep affection for each other. They have enriched each other’s lives in very deep ways.
Having very low muscle tone interferes with normal growth and development in many ways. Muscle tone is important for breathing in newborns (Lopes et al., 1981). David was born prematurely and he was on a ventilator for weeks. Low muscle tone slowed his recovery. Muscle tone is important for normal cognitive development and function (e.g., Jongsma et al., 2015). Gastroesophageal reflux plagues many children with 22q13 deletion syndrome (including David) and is likely caused by low tone in the esophageal sphincter (Hershcovici et al., 2011). The most obvious problem with low muscle tone is delayed or absent walking. Walking requires stable standing, which requires sufficient tone to hold the body erect. Building strength in David’s abdominal, back and leg muscles was years of work.
What is muscle tone and what interferes with normal tone? “Muscle tone refers to the resistance that an examiner perceives when moving someone’s limb in a passive manner” (Mitz and Winstein, in Neuroscience for Rehabilitation, 1993). Normal muscle tone disappears when someone is knocked unconscious, or when the muscle itself is unable to support contractions. Diagnosing the cause of hypotonia in infants can be complex, especially in the presence of a genetic syndrome (Bodensteiner, 2008). In genetic syndromes that include both hypotonia and intellectual disability, the hypotonia is often diagnosed as “central hypotonia”: hypotonia caused by problems with the brain or spinal cord. However, the hypotonia associated with 22q13 deletion syndrome may be from multiple causes. Certainly, it is not caused by any one gene. No single gene deletion or mutation has been identified that always causes hypotonia, and no one gene is essential to cause hypotonia. There is also no doubt that infant hypotonia is far more common in children with somewhat larger deletions (Sarasua et al., 2014, figure S1).
The severe hypotonia so often seen with 22q13 deletion syndrome infants comes from multiple sources. Since finding a way to treat hypotonia could help 100s of our children, understanding all the causes might open the door to improving their lives.
Genes that directly affect synapses
If your child was seen by a pediatrician or pediatric neurologist, it is likely the physician concluded that the hypotonia was of central origin (see, Bodensteiner, 2008). Although the conclusion would be based on accepted clinical practice, it would actually require a battery of tests to rule out other sources. Without other signs of major muscle or metabolic problems, the physician may be wise to avoid additional tests. Right now, such testing is best done as part of a research study.
One obvious source of central hypotonia is a problem with synaptic proteins. Two important proteins coding genes nearly always deleted together are SHANK3 and MAPK8IP2. I have found only one published clear case where MAPK8IP2 is deleted without SHANK3 (Vondráčková et al., 2014). That patient had hypotonia, but another important gene was involved (SCO2, discussed later). There are also very few cases of SHANK3 deletions without impacting MAPK8IP2. I am not considering SHANK3 mutations, since we know mutations can be much more severe than deletions. See my earlier blog: When missing a gene is a good thing. For those who wish to consider SHANK3 mutations, we know that hypotonia with SHANK3 mutations is much less prevalent (33%) than hypotonia in 22q13 deletion syndrome (65% to 75%), whether or not SHANK3 is involved (Vondráčková et al., 2014). Thus, synaptic genes may play a role, but the jury is still out on how important they are to hypotonia.
Other genes that affect normal function of the brain
Hypotonia of central origin can be caused by other genes important to brain function. We sometimes forget that the brain must have lot of things working properly for synapses to operate. For example, the brain is about 2% of our total body weight, but it uses up 20% of the oxygen we breathe (Rolfe and Brown, 1997). So, the blood flow from the heart, nutrition from the gut and oxygen from the lungs are of critical importance to human brain function. Any missing gene that might affect the brain’s ability to burn energy will likely impact synaptic function. Note, this raises an important limitation of studies that use rats and mice. Rats have very small brains and only use 3% of the oxygen they breathe for the brain. They are not nearly as sensitive to the “energetics” of brain function.
SCO2 and TYMP are genes that are important in making full use of nutrients, oxygen and blood flow to maintain healthy synaptic operation. One copy of these genes is missing from nearly everyone with a terminal deletion. You may recall that humans and other animals normally have 2 copies of every gene. People missing just one copy of SCO2 or TYMP seem to do fine (Pronicka et al., 2013). I found a paper that investigates the role of SCO2 and TYMP in patients with an interstitial deletion of 22q13 (Vondráčková et al., 2014). The authors describe two children who are not only missing these genes from the deletion, but, tragically, the remaining gene (on the other chromosome) is mutated. That is, both copies of the gene are affected. One child has a mutation of his remaining SCO2 gene. The other child has a mutation of the TYMP gene. One child died before age 2. The other is 12 years old and is going downhill. Over 95% of children with terminal deletions of 22q13 are missing one copy of SCO2 and one copy of TYMP. We do not know how much these genes contribute to infant hypotonia in 22q13 deletion syndrome, but if a child has a life-threatening failure to thrive, he or she should be tested for SCO2 and TYMP mutations. There are potential treatments (Casarin et al., 2012; Viscomi et al., 2011).
Unfortunately, there are many genes deleted in 22q13 deletion syndrome that might impact normal brain function. My earlier blog pointed out that 95% of people with 22q13 terminal deletions (including ring 22) are missing at least 10 genes that operate in the brain (Understanding deletion size). ALG12 is a gene critical for allowing cells to recognize each other. Loss of both copies of ALG12 produces a severe disorder (CDG-Ig) that can include hypotonia, as well as moderate to severe intellectual disabilities and seizures. Loss of one copy by itself is not pathological, but loss of ALG12 along with other genes could have a big contribution to hypotonia. CELSR1 is an example of a gene that could worsen the impact of ALG12. We know that larger deletions are more likely to cause serious hypotonia (Sarasua et al., 2014, figure S1). CELSR1 is associated with deletions larger than 4.5 Mbase. CELSR1 along with ALG12 is a one-two punch to the development of normal synaptic pathways. Both are important for the intricate organization of brain cells during early development. What about a 1-2-3 punch? I have already discussed RABL2B (Is 22q13 deletion syndrome a ciliopathy?). RABL2B is used in primary cilia, which are also responsible for guiding neuronal organization during early brain development.
There are other genes deleted in 22q13 deletion syndrome that are important to maintain healthy brains. I will cover some of these in future blog postings. However, I would like to look now at genes that might act outside the brain to cause or exacerbate hypotonia.
Genes that affect the muscles
It is probably no surprise that hypotonia can come from problems with the muscles. Muscle cells share a lot in common with the neurons of the brain. They rely on electrical activity, they have a junction with the nerve that is very much like a synapse and they require lots of blood flow and energy. Sitting very near the synaptic genes and missing in over 95% of children with 22q13 deletion syndrome, is a gene that is crucial to the energy supply of muscles, CPT1B. CPT1B is like the shovel for an old coal-burning steam engine. It grabs the coal and throws it into the steam-engine’s firebox. Technically, it helps transport fatty acids into the mitochondria for the generation of ATP. ATP interacts with muscle actin and myosin to power muscle contraction.
Genes that affect the nerve fibers leading to the muscles
SBF1 is one of about 70 genes associated with Charcot-Marie-Tooth (CMT) disease. (CMT has nothing to do with teeth. It is named, in part, after Howard Henry Tooth.) CMT is a demyelinating disease (Baets et al., 2014). Myelin is a fatty tissue that wraps around the nerves. It is the insulator that makes sure electrical signals traveling down the nerve fibers reach the muscles quickly. Demyelination, the loss of myelin, leads to weakness and muscle dysfunction. CMT is a degenerative disease. It usually appears in the 20s and starts with leg weakness. How the loss of SBF1 might interact with other genes lost with 22q13 deletion syndrome is not known. SBF1 may not contribute to infant hypotonia, but it is something to consider if weakness starts to occur early in adulthood. Like many of the genes described here, SBF1 is missing in over 95% of patients with 22q13 terminal deletions.
I have provided just a few examples of genes that are known to be involved in hypotonia. In my own review of the genes of 22q13 deletion syndrome, I have only looked closely at 34 of the approximately 200 genes that can be deleted. I have focused on the distal-most genes, those that affect the overwhelming majority of our children. Even looking at just this small selection, we begin to see the complexity of a chromosomal deletion. Focusing on just one or two genes may seem like a way to simplify the problem, but it steals the opportunity to understand what is happening to our children. The more we get to know 22q13 deletion syndrome, the more we can find opportunities to make things better.