Research Review

KCNQ2 variants causing benign neonatal epilepsy or developmental and epileptic encephalopathy.

INTRODUCTION:
There are several genetic epilepsies in which a mutation in the same gene can cause a wide range of outcomes. This is the case with KCNQ2, which can result in benign neonatal epilepsy (B(F)NE, in which seizures resolve and there is limited long term effect), or KCNQ2 developmental and epileptic encephalopathy (DEE). Scientists previously discovered that DEE occurred when the particular variant of KCNQ2 mutation had a dominant-negative impact on the potassium channel function, meaning, that if any one of the four subunits comprising the channel had the mutation, the channel would not function properly.

The authors of this study used existing databases of known KCNQ2 variants and the associated patient outcomes, alongside genetic data from unaffected individuals, to test various algorithms to predict which variants might be more severe. This analysis identified “hot spots”, in which more severe variants occur and an algorithm to evaluate specific nucleotide substitutions, that could be helpful in evaluating novel variants to determine the severity of outcome.

OBJECTIVE:
The goal of the study was to better understand KCNQ2 variants which lead to severe outcomes in patients by analyzing a large number of variants collected as part of a Japanese study of KCNQ2 cases, the Chinese EpilepsyGene database (led by Dr. JinYu Wu of Wenzhou Medical University), and from the RIKEE database (developed by Dr. Edward Cooper, at Baylor College), and comparing these to data from public datasets of unaffected individuals.

METHOD:
The KCNQ2 variant data from the various sources was aggregated. The data was analyzed using several different prediction algorithms. This process evaluated genetic differences between more severe, DEE KCNQ2 cases, B(F)NE cases, and unaffected individuals. The analysis also took into account whether the variants were missense mutations (a substitution of an incorrect nucleotide into the sequence, deletions (a nucleotide missing from within the sequence), or a truncating variant (a sequence missing nucleotides from the end).

RESULTS:
• Patient characteristics: There were a total of 259 KCNQ2 cases that were used in the evaluation. Of these cases, 148 (57%) were characterized as benign neonatal epilepsy (BFNE, either inherited or de novo) and 111 (43%) as developmental and epileptic encephalopathy (DEE). There were 216 different variants, with 139 B(F)NE and 77 DEE.

The types of variants were seen to impact the outcome. The B(F)NE cases were 59% truncations, 38% missense mutations, 3% deletions. The DEE cases were 98% missense and 2% deletions.

Of the B(F)NE cases, 6% were de novo (not inherited) while 83% of the DEE cases were de novo.

• Location of mutations: The study evaluated whether the mutations occur consistently throughout the KCNQ2 gene sequence, or are located mostly in specific areas. They found that the truncating variants (mostly associated with B(F)NE), appeared evenly distributed. However, the missense mutations (which cause almost all of the DEE cases) seemed to be located in specific regions in the KCNQ2 gene sequence.

Because some missense variants cause B(F)NE and some cause DEE, the investigators analyzed the locations of the missense variants in these two populations, and found that the location of the missense variant impacts the severity of the outcome. They then evaluated different prediction algorithms and found that some could be used to predict the severity of missense mutations based on the location.

• Type of substitution: The investigators further evaluated if the specific substitution (which amino acid took the place of which) affects the severity of the disease. The specific amino acid substitution only appeared to really make a difference in two regions of the gene, while in others it did not appear to have an impact on severity.

CONCLUSIONS:
This study demonstrated that there are particular “hot spots” in the potassium channel. In technical terms, these regions are located at the region starting from S1 to the proximity of helix A and the region from helix B to helix D. The first of these two regions includes all of the membrane-spanning segments, S1-S6. “Specifically, the region from S2 to S3 had more B(F)NE related variants ad the regions to the ion pore to S6 to the proximity of helix A had more DEE related variants.” These are the areas of the KCNQ2 gene sequence that code for the portion of the potassium channel with the most important function, such that these mutations cause more severe outcomes.

However, the algorithms based on the location of the missense mutation alone could not completely predict whether a variant will be severely pathogenic. Depending on the location, a further algorithm, which analyzes the extent to which the specific nucleotide substitution changes the protein product, is able to improve the prediction.

SIGNIFICANCE:
The investigators concluded that an analysis of the type of mutation (missense, deletion, truncation), the location of the missense mutations, and the specific nucleotide substitution, along with the patients EEG findings, could be useful in predicting the severity of the outcome for a patient.

Ayako Goto, Atsushi Ishii, Mami Shibata, Yukiko Ihara, Edward C. Cooper, Shinichi Hirose Characteristics of KCNQ2 variants causing either benign neonatal epilepsy or developmental and epileptic encephalopathy. Epilepsia. 2019 Sep;60(9):1870-1880. doi: 10.1111/epi.16314. Epub 2019 Aug 16.

Overview of Various KCNQ2 Epilepsy Mutation Types and Outcomes

KCNQ2 gene codes for parts of the potassium channel that limits repetitive signaling by the neurons. Mutations in this single gene can lead to very different paths of development and seizure activity.

There are three different categories of outcomes for those affected: 1) Benign Familial Neonatal Convulsions (BFNC), 2) Benign Familial Infantile Convulsions (BFIC), or 3) neonatal epileptic encephalopathy.  For all of these KCNQ2 childhood epilepsies, seizures usually occur within the first week after birth.

Patients with BFNS or BFIC have seizures early on, but they usually spontaneously disappear by one year and development for these children is good.

Most patients with neonatal epileptic encephalopathy present with a specific pattern on their EEG (burst suppression or multiple focal spikes) and generalized tonic, or grand mal, seizures. There are three categories of epileptic activity for these patients: 1) the development of West Syndrome, with epileptic spasms in a small portion of patients, 2) relatively good control with anti-epileptic medications, 3) seizures spontaneously disappear after the patient turns one year old. The MRI in all of these categories is typically relatively normal. However, patients have lasting and significant developmental delays.

Most of the cases of neonatal epileptic encephalopathy are de novo mutations, occurring spontaneously and not inherited from the parents. The KCNQ2 mutation occurs globally, regardless of ethnicity.



Mutations in the KCNQ2 gene are the cause of about 8% of childhood epilepsies not caused by brain trauma. There are over 80 different genotypes or specific variations in the mutation in KCNQ2. The majority of these mutations (69%) are missense mutations, meaning part of the “code” in the gene is replaced with another random sequence. Other mutations are indel 16 (21%), meaning there is an insertion or deletion of nucleotides in the middle of a sequence, or splice-site mutations (10%), meaning there is a mutation at the end of a sequence.

Depending on the specific variant, the mutation can affect a different part of the potassium channel. Which part of the potassium channel is affected appears to be related to the severity of the outcome (seizure severity and degree of disability) for the patient. However, there is not always a direct relationship between the specific variant of the KCNQ2 mutation and the outcome for the patient. For example, there have been cases of a family in which all inherited the same variant, but different members of the family had very different outcomes.  It is not understood exactly why this would happen, but there is a theory that it could be due to an interaction between KCNQ2 and other genes or due to environmental factors beyond the DNA.

Treatment approach of patients suffering from KCNQ2 related epilepsy is not dependent of which variant or severity of outcome the patient has. Most cases can be controlled with phenobarbital, oxcarbazepine, vigabatrin, and valproate. Laboratory studies of retigabine (also known as Potiga or ezogabine) showed that it reversed the functional electrical current changes in cells. Additional studies of this and other treatments are recommended for this severe disease.

Conclusion: The relationship between specific mutations in KCNQ2 and the severity of seizures and disability in patients is still not well understood by experts and additional studies are needed.

Lee, I., Yang, J., and Li, S. (2018) KCNQ2-Associated Epilepsy: A Review of Variable Phenotypes and Neurodevelopmental Outcomes Neuropsychiatry, 8(1): 318-323. doi:10.4172 1000353

Study finds a possible relationship between KCNQ2 and the STXBP1 gene that has been identified as a cause of Ohtahara Syndrome

Background: The potassium channels control the electrical currents sent by the neurons. Mutations of the KCNQ2 gene coding for a component of these potassium channels cause early-onset epileptic encephalopathies. Mutations in the STXBP1 gene, which codes for syntaxin binding protein 1, and causes Ohtahara Syndrome, can cause similar symptoms to those seen in patients with KCNQ2 mutations. The similarities in symptoms caused by these two different gene mutations suggest there is a possible link between STXBP1 and potassium channels.

Potassium channels are known to be modulated by syntaxin-1A, a protein encoded by the STX1A gene, which inhibits the electrical activity of the potassium channels (or M-current). This study evaluated whether the STXBP1 gene, which is a cause of Ohtahara Syndrome and is related to STX1A, prevents syntaxin-1A from limiting the activity of the potassium channel.

Methods: The study examined the electrical signals in cells grown with various mutation combinations to evaluate the interaction between the various proteins expressed by the STXBP1 and STX1A genes.

Results:
The study demonstrated that syntaxin-1A decreased the electrical currents (M currents) of the potassium channel by binding to the channel. The study showed that syntaxin binding protein 1 (encoded by STXBP1) did not directly affect the electrical current of the potassium channel, but it interfered with the binding of syntaxin-1A. In effect, syntaxin binding protein 1 stopped the syntaxin-1A from interfering with the potassium channel activity. When there is a mutation in the STXBP1 gene affecting the production of syntaxin binding protein 1 (as in Ohtahara Syndrome), the syntaxin-1A is able to interfere with potassium channel activity.

Significance:
The results show that there is a link between STXBP1 (a gene found to cause Ohtahara Syndrome) and potassium channels, indirectly, by way of the syntaxin-1A protein. It suggests that defects in the activity of the potassium channel similar to those seen with KCNQ2 mutations could also be caused by certain mutations in STXBP1. The protein syntaxin-1A may be important for regulating potassium channel activity and signaling by the neurons.

Devaux, J., Dhifallah, S., De Maria, M., Stuart-Lopez, G., Becq, H., Milh, M., Molinari, F. and Aniksztejn, L. (2017), A possible link between KCNQ2- and STXBP1-related encephalopathies: STXBP1 reduces the inhibitory impact of syntaxin-1A on M current. Epilepsia, 58: 2073–2084. doi:10.1111/epi.13927