Imbalance of a rare second messenger – FIG4 mutations in polymicrogyria

Brain malformations. Various brain malformations are thought to have a genetic basis, and several genes have already been identified. Polymicrogyria is a particular form of congenital brain malformation due to an excessive number of small and sometimes malformed gyri. In a recent publication in Neurology, mutations in FIG4 are described in a familial form of polymicrogyria. However, the FIG4 gene is no stranger in the field of neurogenetics.

The study. Baulac and collaborators performed homozygosity mapping with subsequent exome sequencing in a family with temporo-occiopital polymicrogyria and epilepsy. Of the 6 affected sibs in this family, three siblings were available for analysis, and an interval on chromosome 6 had previously been identified in this family. In their current study, the authors performed exome sequencing and focused on this particular region. This is where a homozygous mutation in the FIG4 gene was identified. Baulac and collaborators performed a set of functional studies that demonstrated that the mutated protein was incapable of rescuing the knock-out phenotype. In fact, the knock-out phenotype was very obvious on the cellular level when assessing fibroblasts: in the absence of FIG4, the cell was filled with multiple round vacuoles, highlighting the important role of FIG4 in endosome fusion.

PMG. Polymicrogyria (PMG) refers to the presence of multiple, small malformed gyri in particular parts of the brain. Within the classification of the congenital disorders of brain malformation, PMG is a disorder that occurs relatively late within neuronal development, a process referred to as cortical organization. Polymicrogyric areas of the brain may give rise to epileptic seizures. While a broad range of insults may result in polymicrogyria, particularly bilateral forms are thought to be genetic. Several genes have been implicated in genetic PMG syndromes including recessive mutations in GPR56, RAB3GAP1, RAB3GAP2 and RAB18 as well as dominant mutations in TUBA1A, TUBB2B, TUBB3, TUBA8 and COL18A1. Most of these genes result in frontal PMG or diffuse PMG. SRPX2 is implicated in rolandic PMG, but the role of this gene is uncertain as some families were subsequently found to have GRIN2A mutations.

Hypothesized structure of the PIKfyve-ArPIKfyve-Sac3 core complex that generates and cleaves PtdIns3,5P2. This phosphoinositide is a rare and very short lived second messenger whose effector proteins are still largely unknown. Disrupting the physiology of PtdIns3,5P2 metabolism severe disrupts endosome trafficking. Mutations in FIG4, the phosphatase within this complex, result in Yunis-Varon syndrome, a skeletal malformation syndrome with severe neurological impairment, and in Charcot-Marie-Tooth disease type 4J. In their recent publication, Baulac and collaborators identify recessive mutations in FIG4 in a Moroccan family with polymicrogyria and epilepsy. (Figure adapted from http://www.biochemj.org/csb/002/csb002.pdf)

Hypothesized structure of the PIKfyve-ArPIKfyve-Sac3 core complex that generates and cleaves PtdIns3,5P2. This phosphoinositide is a rare and very short lived second messenger whose effector proteins are still largely unknown. Disrupting the physiology of PtdIns3,5P2 metabolism severe disrupts endosome trafficking. Mutations in FIG4, the phosphatase within this complex, result in Yunis-Varon syndrome, a skeletal malformation syndrome with severe neurological impairment, and in Charcot-Marie-Tooth disease type 4J. In their recent publication, Baulac and collaborators identify recessive mutations in FIG4 in a Moroccan family with polymicrogyria and epilepsy. (Figure adapted from http://www.biochemj.org/csb/002/csb002.pdf)

Phosphatitdyl inositol. Trying to understand what exactly FIG4 does cost me the better part of an afternoon. I’ll try to summarize it as follows: FIG4 is a phosphatase, i.e. it cleaves phosphate residues off molecules. The molecule that FIG4 acts on is called Phosphatidylinositol 3,5-bisphosphate (PtdIns3,5P2). Phosphatidylinositol (PtdIns) or phosphoinositide is a membrane-bound molecule that consists of a glycerol anchor, which is coupled to an inositol molecule through a phosphate residue. As the phosphate and the inositol are hydrophilic, the PtdIns molecule sticks out of the membrane with its carbohydrate residue, the inositol. This inositol is target for various kinases that attach additional phosphate residues. These modified phosphoinositols act as second messengers in a variety of cellular events. PtdIns3,5P2 is the rarest amongst the seven different PtdIns’s and is only present on the outside of endosomes. It is generated by a single molecule named PIKfyve, the Phosphoinositide kinase with a FYVE domain. As the counteracting phosphatase Sac3/FIG4 is present in the same molecular complex as the kinase, the resulting PtdIns3,5P2 is very short-lived. This complex is referred to as the PIKfyve-ArPIKfyve-Sac3 core complex (Figure). Nevertheless, this short time span is sufficient to act on various events relating to endosome formation. If this mechanism is disrupted, the endosome formation is severely disrupted. Baulac and collaborators identify a homozygous missense mutation in FIG4 in a family with polymicrogyria.

Related syndromes. Mutations in FIG4 were previously found in Yunis-Varon syndrome (YVS), a skeletal malformation syndrome with severe neurological impairment, and in Charcot-Marie-Tooth disease type 4J (CMT4J), a disease of the peripheral nerves. These conditions have very little in common with the polymicrogyria syndrome identified by Baulac and collaborators. This raises the question how mutations in the very same gene may result in such diverse phenotypes. The authors suggest that YVS may represent the most extreme FIG4-related phenotype, while PMG and CTM4J might be milder phenotypes with deficits of different functional segments of the protein. Nevertheless, it is uncommon to see an otherwise non-syndromal brain malformation as a hypomorphic phenotype of a complex genetic syndrome.

Lessons learned. Exome sequencing in single families can be extremely useful to discover candidate genes that would not have been considered normally. In the case of the family described by Baulac and collaborators, the FIG4 mutations are likely to be causal given the genetic and functional evidence, but this would not have been a candidate to start with, not even on an extended gene panel. We will probably learn about the phenotypic spectrum of quite a number of genes this way.

One thought on “Imbalance of a rare second messenger – FIG4 mutations in polymicrogyria

  1. Pingback: The many faces of PIGA – from paroxysmal nocturnal hemoglobinuria to epileptic encephalopathy | Beyond the Ion Channel

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