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Missense variants in genes encoding ion channels are associated with a spectrum of severe diseases. Variant effects on biophysical function correlate with clinical features and can be categorized as gain- or loss-of-function. This information enables a timely diagnosis, facilitates precision therapy, and guides prognosis. Functional characterization presents a bottleneck in translational medicine. Machine learning models may be able to rapidly generate supporting evidence by predicting variant functional effects. Here, we describe a multi-task multi-kernel learning framework capable of harmonizing functional results and structural information with clinical phenotypes. This novel approach extends the human phenotype ontology towards kernel-based supervised machine learning. Our gain- or loss-of-function classifier achieves high performance (mean accuracy 0.853 SD 0.016, mean AU-ROC 0.912 SD 0.025), outperforming both conventional baseline and state-of-the-art methods. Performance is robust across different phenotypic similarity measures and largely insensitive to phenotypic noise or sparsity. Localized multi-kernel learning offered biological insight and interpretability by highlighting channels with implicit genotype-phenotype correlations or latent task similarity for downstream analysis., Competing Interests: The authors declare that they have no competing interests., (Copyright: © 2023 Boßelmann et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Genetic mutations causing dysfunction of both voltage- and ligand-gated ion channels make a major contribution to the cause of many different types of familial epilepsy. Key mechanisms comprise defective Na(+) channels of inhibitory neurons, or GABA(A) receptors affecting pre- or postsynaptic GABAergic inhibition, or a dysfunction of different types of channels at axon initial segments. Many of these ion channel mutations have been modelled in mice, which has largely contributed to the understanding of where and how the ion channel defects lead to neuronal hyperexcitability. Animal models of febrile seizures or mesial temporal epilepsy have shown that dendritic K(+) channels, hyperpolarization-activated cation channels and T-type Ca(2+) channels play important roles in the generation of seizures. For the latter, it has been shown that suppression of their function by pharmacological mechanisms or in knock-out mice can antagonize epileptogenesis. Defects of ion channel function are also associated with forms of acquired epilepsy. Autoantibodies directed against ion channels or associated proteins, such as K(+) channels, LGI1 or NMDA receptors, have been identified in epileptic disorders that can largely be included under the term limbic encephalitis which includes limbic seizures, status epilepticus and psychiatric symptoms. We conclude that ion channels and associated proteins are important players in different types of genetic and acquired epilepsies. Nevertheless, the molecular bases for most common forms of epilepsy are not yet clear, and evidence to be discussed indicates just how much more we need to understand about the complex mechanisms that underlie epileptogenesis.

Ion channelopathies are caused by malfunction or altered regulation of ion channel proteins due to hereditary or acquired protein changes. In neurology, main phenotypes include certain forms of epilepsy, ataxia, migraine, neuropathic pain, myotonia, and muscle weakness including myasthenia and periodic paralyses. The total prevalence of monogenic channelopathies in neurology is about 35:100,000. Susceptibility-related mutations further increase the relevance of channel genes in medicine considerably. As many disease mechanisms have been elucidated by functional characterization on the molecular level, the channelopathies are regarded as model disorders for pathogenesis and treatment of non-monogenic forms of epilepsy and migraine. As more than 35% of marketed drugs target ion channels, there is a high chance to identify compounds that counteract the effects of the mutations.

Idiopathic epilepsies are considered to be genetically determined. The inheritance can be monogenic and the detected mutation considered sufficient to cause the phenotype. In contrast, when the inheritance is complex, the epileptic phenotype is determined by several minor genetic defects that are much more difficult to discover. In recent years, an increasing number of mutations, mainly associated with rare monogenic idiopathic epilepsy syndromes, have been identified in genes encoding subunits of voltage- or ligand-gated ion channels. A few mutations have also been found in the frequent classical forms of idiopathic generalized epilepsies which are thought to follow a complex genetic trait, for example, in absence or juvenile myoclonic epilepsies. Functional studies characterizing the molecular defects of the mutant channels point to an important role of GABAergic synaptic inhibition in the pathophysiology of idiopathic epilepsies. As a result of genetic and functional investigations, not only will the pathophysiology of epilepsy be better understood, but newly discovered genes and pathophysiological pathways may also determine novel targets for pharmacotherapy, as has been shown for the anticonvulsant drug retigabine, which enhances the activity of neuronal KCNQ potassium channels.

Single ion channel currents can be analysed by hidden or aggregated Markov models. A classical result from Fredkin et al. (Proceedings of the Berkeley conference in honor of Jerzy Neyman and Jack Kiefer, vol I, pp 269-289, 1985) states that the maximum number of identifiable parameters is bounded by 2n(o)n(c), where n(o) and n(c) denote the number of open and closed states, respectively. We show that this bound can be overcome when the probabilities of the initial distribution are known and the data consist of several sweeps.

Idiopathic epilepsies are genetically determined diseases of the central nervous system characterized by typical epileptic seizures and EEG abnormalities but not associated with structural brain lesions. In recent years, an increasing number of mutations associated with idiopathic epilepsy syndromes were identified in genes encoding subunits of voltage- or ligand-gated ion channels. These encouraging results provide a plausible pathophysiological concept, since ion channels form the basis for neuronal excitability and are the major targets for anticonvulsive pharmacotherapy. The first epilepsy genes were identified for rare autosomal dominant syndromes within large pedigrees. Recently, a few mutations were also found for the frequent classical forms of idiopathic generalized epilepsies (IGE), for example absence or juvenile myoclonic epilepsy. The mutations can affect ion channels which on one hand have been known since several decades to be crucial for neuronal function, such as the voltage-gated sodium channel or the GABA(A) receptor, or on the other hand were newly identified within the last decade as KCNQ potassium channels or the ClC-2 chloride channel. Functional studies characterizing the molecular defects of the mutant channels point to a central role of GABAergic synaptic inhibition in the pathophysiology of IGE. Furthermore, newly discovered genes may be suitable as novel targets for pharmacotherapy such as KCNQ channels for the anticonvulsant drug retigabine. Altogether, these genetic and pathophysiological investigations will enhance our knowledge about the understanding of epileptogenesis and can help to improve anticonvulsive therapy.

Ion channelopathies have common clinical features, recurrent patterns of mutations, and almost predictable mechanisms of pathogenesis. In skeletal muscle, disorders are associated with mutations in voltage-gated Na(+), K(+), Ca(2+), and Cl(-) channels leading to hypoexcitability, causing periodic paralysis and to hyperexcitabilty, resulting in myotonia or susceptibility to malignant hyperthermia.

Predicting ion channel variant phenotypes: Ion channel variants have been associated with disease, predominantly neurological. Heyne et al. developed a tool to predict the functional effects of variants in disease-associated voltage-gated sodium and calcium ion channels using machine learning–based statistical models. Loss of function versus gain of function (LOF or GOF) was predicted separately from neutrality versus pathogenicity. Their model was trained to classify variant effects using protein sequences and structures containing missense variants with known or highly probable effects and validated against experimentally tested variants and in cohorts including individuals with epilepsy and autism. This work could have implications for ion channel and clinical genetics research. Malfunctions of voltage-gated sodium and calcium channels (encoded by SCNxA and CACNA1x family genes, respectively) have been associated with severe neurologic, psychiatric, cardiac, and other diseases. Altered channel activity is frequently grouped into gain or loss of ion channel function (GOF or LOF, respectively) that often corresponds not only to clinical disease manifestations but also to differences in drug response. Experimental studies of channel function are therefore important, but laborious and usually focus only on a few variants at a time. On the basis of known gene-disease mechanisms of 19 different diseases, we inferred LOF (n = 518) and GOF (n = 309) likely pathogenic variants from the disease phenotypes of variant carriers. By training a machine learning model on sequence- and structure-based features, we predicted LOF or GOF effects [area under the receiver operating characteristics curve (ROC) = 0.85] of likely pathogenic missense variants. Our LOF versus GOF prediction corresponded to molecular LOF versus GOF effects for 87 functionally tested variants in SCN1/2/8A and CACNA1I (ROC = 0.73) and was validated in exome-wide data from 21,703 cases and 128,957 controls. We showed respective regional clustering of inferred LOF and GOF nucleotide variants across the alignment of the entire gene family, suggesting shared pathomechanisms in the SCNxA/CACNA1x family genes. [ABSTRACT FROM AUTHOR]

Next-generation sequencing has enhanced discovery of many disease-associated genes in previously unexplained epilepsies, mainly in developmental and epileptic encephalopathies and familial epilepsies. We now classify these disorders according to the underlying molecular pathways, which encompass a diverse array of cellular and sub-cellular compartments/signalling processes including voltage-gated ion-channel defects. With the aim to develop and increase the use of precision medicine therapies, understanding the pathogenic mechanisms and consequences of disease-causing variants has gained major relevance in clinical care. The super-family of voltage-gated potassium channels is the largest and most diverse family among the ion channels, encompassing approximately 80 genes. Key potassium channelopathies include those affecting the K V , K Ca and K ir families, a significant proportion of which have been implicated in neurological disease. As for other ion channel disorders, different pathogenic variants within any individual voltage-gated potassium channel gene tend to affect channel protein function differently, causing heterogeneous clinical phenotypes. The focus of this review is to summarise recent clinical developments regarding the key voltage-gated potassium (K V) family-related epilepsies, which now encompasses approximately 12 established disease-associated genes, from the KCNA -, KCNB -, KCNC -, KCND -, KCNV -, KCNQ - and KCNH -subfamilies. [ABSTRACT FROM AUTHOR]

Missense mutations in SCN2A, encoding the brain sodium channel NaV1.2, have been described in benign familial neonatal-infantile seizures ( BFNIS), a self-limiting disorder, whereas several SCN2A de novo nonsense mutations have been found in patients with more severe phenotypes including epileptic encephalopathy. We report a family with BFNIS originating from Madagascar. Onset extended from 3 to 9 months of age. Interictal EEGs were normal. In two patients, ictal electroencephalography ( EEG) studies showed partial seizure patterns with secondary generalization in one. Seizures remitted before 18 months of age, with or without medication. Intellectual development was normal. A novel missense mutation of SCN2A, c.4766A>G/p.Tyr1589Cys, was found in a highly conserved region of NaV1.2 (D4/S2-S3). Functional studies using heterologous expression in tsA201 cells and whole-cell patch clamping revealed a depolarizing shift of steady-state inactivation, increased persistent Na+ current, a slowing of fast inactivation and an acceleration of its recovery, thus a gain-of-function. Using an action potential waveform in a voltage-clamp experiment we indicated an increased inward Na+ current at subthreshold voltages, which can explain a neuronal hyperexcitability. Our results suggest that this mutation induces neuronal hyperexcitability, resulting in infantile epilepsy with favorable outcome. [ABSTRACT FROM AUTHOR]

KV7 voltage-gated potassium channels, encoded by the KCNQ gene family, have caught increasing interest of the scientific community for their important physiological roles, which are emphasized by the fact that four of the five so far identified members are related to different hereditary diseases. Furthermore, these channels prove to be attractive pharmacological targets for treating diseases characterized by membrane hyperexcitability. KV7 channels are expressed in brain, heart, thyroid gland, pancreas, inner ear, muscle, stomach, and intestines. They give rise to functionally important potassium currents, reduction of which results in pathologies such as long QT syndrome, diabetes, neonatal epilepsy, neuromyotonia, or progressive deafness. Here, we summarize some key traits of KV7 channels and review how their molecular deficiencies could explain diverse disease phenotypes. We also assess the therapeutic potential of KV7 channels; in particular, how the activation of KV7 channels by the compounds retigabine and R-L3 may be useful for treatment of epilepsy or cardiac arrhythmia. [ABSTRACT FROM AUTHOR]

The article comments on a study about ion channel dysfunctions in idiopathic epilepsies. It is claimed that epilepsy is more frequent during childhood. Epilepsy as a medical condition is characterized. The causes of sporadic or recurrent seizures is identified. Details of the first ion channel gene defects found in rare monogenic idiopathic epilepsy, is discussed.

The formation of disulfide bridges is a classical approach used to study the mobility, proximity and distances of residues in a variety of proteins, including ligand- and voltage-gated ion channels. We performed patch-clamp studies to investigate the interaction of a pair of cysteines introduced into the human skeletal muscle voltage-gated Na+ channel (hNav1.4) using the oxidation catalyst, Cu2+(1,10-phenanthroline)3 (CuPhen).Our experiments resulted in a surprising finding, a reversible current inhibition of the mutant I1160C/L1482C containing two cysteines in the D3/and D4/S4–S5 loops, subjected to oxidative cross-linking in the presence of CuPhen.We report here that CuPhen is an open channel blocker of both mutant and wild-type (WT) hNav1.4 channels, however, for WT channels a more than 10-fold higher concentration was needed to induce the same effect. Moreover, 1,10-phenanthroline was capable of blocking Na+ channels in the absence of Cu2+ ions. Our results indicate a use- and voltage-dependent binding and unbinding of CuPhen, reminiscent of the lidocaine quaternary derivative QX-314 and the neurotoxin batrachotoxin.Care should be taken when using CuPhen as an oxidizing reagent in cross-linking experiments, since it may directly affect channel activity. Our results identify CuPhen (and phenantroline) as a novel use-dependent inhibitor of Na+ channels, a mechanism that is shared by drugs widely used in the treatment of epilepsy, neuropathic pain, cardiac arrhythmia and myotonia. We hypothesize that I1160C in D3/S4–S5 and the corresponding L1482C mutation in D4/S4–S5 could allosterically affect a binding site located in the inner pore region of the channel.British Journal of Pharmacology (2006) 147, 808–814. doi:10.1038/sj.bjp.0706667; published online 23 January 2006 [ABSTRACT FROM AUTHOR]

Abstract Transitions between distinct kinetic states of an ion channel are described by a Markov process. Hidden Markov models (HMM) have been successfully applied in the analysis of single ion channel recordings with a small signal-to-noise ratio. However, we have recently shown that the anti-aliasing low-pass filter misleads parameter estimation. Here, we show for the case of a Na[sup +] channel recording that the standard HMM do neither allow parameter estimation nor a correct identification of the gating scheme. In particular, the number of closed and open states is determined incorrectly, whereas a modified HMM considering the anti-aliasing filter (moving-average filtered HMM) is able to reproduce the characteristic properties of the time series and to perform gating scheme identification. [ABSTRACT FROM AUTHOR]