PMS Gene PHF21B is critical for normal brain development

In spite of his poor motor function, David loves walking in the woods.

Originally posted 11 December 2021
Updated 14 June 2022

Multiple studies of Phelan-McDermid syndrome (PMS) have demonstrated worse intellectual outcomes with larger chromosome deletions. Genetic studies on large populations of people with intellectual disabilities show that the measure called “pLI” is useful for predicting IQ as a function of deletion size (see PMS, IQ and why interstitial deletions matter). The high pLI PMS genes are the most import genes of 22q13.3, the chromosome site of PMS problems (see Which PMS genes are most important?). In the past I have written about which PMS genes might cause the structural abnormalities in brain MRIs of PMS patients (see Which genes cause brain abnormalities in Phelan McDermid syndrome?). But, just this past year, scientists have discovered that a high pLI PMS gene is vital to the proper microstructure of the brain. Based on a series of very careful studies in mouse embryos, this group of researchers uncovered the special role of PMS gene, Phf21b. The high pLI of Phf21b (0.987 out of a possible 1.00) already tells us that it is an important PMS gene. The scientific team now tells us why it is so important in their 20+ page scientific paper (Phf21b imprints the spatiotemporal epigenetic switch essential for neural stem cell differentiation.) They solved the mystery of Phf21b and the whole PMS community benefits from their work. The paper is difficult reading, but open to the public.

To understand the new research we need to take a moment to review how our brains develop in the uterus. PMS is a neurodevelopmental disorder. That is, it is a disorder of brain development. Our brains assemble into complex structures with even more complex synaptic connections as they grow. The higher centers for thought, precise movement and proper interpretation of our senses are located in the cortex. The cortex is the part of the brain that we can see in photographs of the human brain. It is the most developed and expanded part of the brain that humans have.

Part of Figure 8
Amitava Basu et al. Genes Dev. 2020;34:1190-1209
© 2020 Basu et al.; Published by Cold Spring Harbor Laboratory Press

I have borrowed part of figure 8C from the paper on Phf21b to show the developing cortex in a mouse. It shows that neurons (the specialized brain cells responsible for thinking and acting) arise as general purpose cells from the ventricular zone (VZ, magenta color) and subventricular zone (SVZ, green color). Together, these are called progenitor cells. They are especially good at reproducing at a high rate to fill the areas above the SVZ. The rapidly growing and reproducing cells actually climb their way into final position. I found this video on the Internet that shows the process (Neurogenesis Animation). The rapid growth is shown 2:39 (min:sec) into the animation. This process creates about 100,000 cells per mm3 in the developing mouse. The process is driven by a large group of specialized genes that fuel the rapid growth and reproduction. These genes are collectively called, cell cycle genes. At a certain very crucial moment in the life of a progenitor cell, the cell stops growing and reproducing. The cell switches from being a progenitor to a neuron, and then spends the rest of its life as a neuron. Phf21b is the gene that tells the progenitor cells when to switch.

How does one gene stop the frenetic activity of progenitor cells? How does it switch off the many cell cycle genes involved in rapid growth and reproduction? The scientists spent some time figuring this out. Phf21b protein is not produced much in progenitor cells until the proper moment. Then, Phf21b protein production suddenly increases. It goes into the nucleus and searches out the precise spot in the DNA that regulates each cell cycle gene of the cortex. Phf21b is an epigenetic switch. It wraps around the regulatory site of each growth gene, and assembles a toolkit of proteins to shut that gene off.

Right side of Figure 8C. See credits (above)

Here is the right half of figure 8C from the paper. The magenta neural progenitor (NPC) cell on the left gets transformed into a neuron (blue cell on the right) by the action of Phf21b (green molecule in the middle). Through several steps involving other molecules (Rcor1, Hdac2, and Lsd1), Phf21b acts as a precision switch. It turns off just the cell cycle genes that promote rapid cortical growth. Phf21b literally hits the brakes on growth to trigger the creation of neurons in the cortex of mammals.

The experiments used by the authors to figure out this exquisite mechanism were complicated and, in some cases, exceedingly delicate. The team of nine researchers represented six institutes in three different countries. Among the many experiments undertaken, they showed the impact of disrupting this mechanism. With insufficient Phf21b, the normal pattern of neurons in the cortex is disrupted.

It has recently been shown that improper regulation of proliferation, both too little or too much, is associated with autism.

In spite of the groundbreaking work, certain questions remain. First, what aspects of the PMS disorder (what phenotypic characteristics) are driven by loss of PHF21B in humans? One hint comes from a paper published in 2014 by Disciglio and colleagues. It describes nine patients with interstitial deletions of 22q13. Although these authors argued that they discovered a new syndrome, the phenotype readily overlaps with PMS, with intellectual disability and speech delay being the two central traits. Many people (including myself) see these simply as cases of PMS (see The four types of Phelan McDermid syndrome). Regardless, of the nine patients in the study, eight are missing PHF21B and the exception (called patient #4) had a deletion that was very near PHF21B (within 84 Kb). That patient was arguably the least affected individual, as well. Thus, PHF21B may have been a major driver of the manifestations (symptoms) seen in these patients. More cases of PMS with interstitial deletions (PMS type 2) are needed to confirm this observation. What would be especially useful would be to find patients with pathological variants of PHF21B. As more genetic testing is done in newborns, especially whole exome or whole genome sequencing, there will be more cases. Why should we expect a growth in cases? We already know the two critical characteristics: 1) loss of one functional copy of PHF21B is pathological (the pLI is greater than 0.9) and 2) loss of one functional copy of PHF21B is compatible with life (there are patients with PMS type 1 that have deletions that include PHF21B because their deletions are greater than 5.81 Mb). About 40% of all identified individuals with PMS are missing this gene (see Understanding deletion size). So, we know these patients are common in PMS.

The second unanswered question is what, exactly, does the loss of PHF21B do to the human cortex once development is complete. The human primate cortex is far more complex than the rodent cortex (see Mashiko et al 2012, Chen et al 2016, Preuss and Wise 2022). Still, the mouse cortex can provide insights into the dysplasia likely to occur in humans. One research direction would be to compare the histology of rodent cortex in a Phf21b knockout mouse with post-mortem or resected brain tissue from a PMS patient with a terminal deletion greater than 5.81 Mb. Perhaps the answer can come from simply comparing cortex samples from patients with terminal deletions smaller than 5.81 Mb and larger. Brain donations to brain banks by patients with rare diseases are a rare and important resource for this type of work.

The third unanswered question is how can loss of a PHF21B gene be rectified? I will not speculate on what approaches might be used to compensate for the loss of a gene so crucial to neurodevelopment. How to fix the loss of neurodevelopment genes is a central problem for all neurodevelopmental disorders. You can try to fix the gene or you can try to compensate for its absence. Perhaps this topic will be the subject of a future blog.