16pdel lipid changes in iPSC-derived neurons and function of FAM57B in lipid metabolism and synaptogenesis

Identification, Clinical Values, and Prospective Pathway Signaling of Lipid Metabolism Genes in Epilepsy and AED Treatment

The dysregulation of lipid metabolism has been associated with the etiology and progression of the neurological pathology. However, the roles of lipid metabolism and the molecular mechanism in epilepsy and the use of antiepileptic drugs (AEDs) are relatively understudied. Gene expression profiles of GSE143272 from blood samples were included for differential analysis, and the lipid metabolism-related differentially expressed genes (DEGs) were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed. The STRING database and Cytoscape software were used to establish and visualize protein-protein interaction (PPI) networks. RT-PCR and western blotting were used to verify the expression levels of lipid metabolism-related DEGs in serum and cerebrospinal fluid (CSF). Eleven lipid metabolism-related DEGs were identified including CXCL8, PTGS2, FOSB, G0S2, HLA-C, CLEC12A, ARG1, ELANE, RSAD2, CTSG, and DEFA1. And among them, five lipid metabolism-related Hub DEGs including CXCL8, PTGS2, ELANE, CTSG, and ARG1 were finally verified in serum samples of epilepsy patients. Moreover, CXCL8 was selected and validated in the epilepsy without AEDs and epilepsy with AEDs. G0S2 was significantly decreased in serum and CSF in epilepsy with AEDs compared to epilepsy without AEDs. Collectively, these findings suggest that lipid metabolism is closely related to epilepsy. This revelation opens up opportunities to further investigate the associated molecular mechanisms and possible therapeutic targets for epilepsy.

A Hypothesis: Metabolic Contributions to 16p11.2 Deletion Syndrome

16p11.2 deletion syndrome is a severe genetic disorder associated with the deletion of 27 genes from a Copy Number Variant region on human chromosome 16. Symptoms associated include cognitive impairment, language and motor delay, epilepsy or seizures, psychiatric disorders, autism spectrum disorder (ASD), changes in head size and body weight, and dysmorphic features, with a crucial need to define genes and mechanisms responsible for symptomatology. In this review, we analyze the clinical associations and biological pathways of 16p11.2 locus genes and identify that a majority of 16p11.2 genes relate to metabolic processes. We present a hypothesis in which changes in the dosage of 16p11.2 metabolic genes contribute to pathology through direct or indirect alterations in pathways that include amino acids or proteins, DNA, RNA, catabolism, lipid, energy (carbohydrate). This hypothesis suggests that research into the specific roles of each metabolic gene will help identify useful therapeutic targets.

Applying newly suggested simultaneous analysis of metabolomics and lipidomics into perfluorooctanesulfonate-derived neurotoxicity mechanism in zebrafish embryos

Developing methodologies for performing multi-omics with one sample has been challenging in zebrafish toxicology; however, related studies are lacking. A new strategy for the simultaneous analysis of metabolomics and lipidomics in zebrafish embryos was proposed and applied to explore the neurotoxicity mechanisms of perfluorooctanesulfonate (PFOS). Metabolite and lipid profiled simultaneously with methyl tert-butyl ether (MTBE) were compared with individual results from other extraction solvents. Behavioral alterations were measured after the zebrafish embryos were exposed to 0.1-20 μM PFOS for 5 days. The metabolite-lipid profiles of the MTBE-based strategy analyzed with optimized larval pooling size of 30 were comparable to those of other extraction solvents, indicating the feasibility and efficiency of MTBE-based multi-omics analysis. Many metabolites and lipids, which were enriched more than those previously reported, completed the toxicity pathways involved in energy metabolism and sphingolipids, improving our understanding of PFOS-induced neurotoxicity mechanism manifested by increased movement under dark conditions. Our novel MTBE-based strategy enabled the multi-omics analysis of one sample with minimal use of zebrafish embryos, thereby improving data reliability on changes in multi-layered biomolecules. This study will advance multi-omics technologies that are critical to elucidating the toxicity mechanisms of toxic chemicals including per- and polyfluoroalkyl substances.

Lipid metabolism: Novel approaches for managing idiopathic epilepsy

Epilepsy is a common neurological condition characterized by abnormal neuronal activity, often leading to cellular damage and death. There is evidence to suggest that lipid imbalances resulting in cellular death play a key role in the development of epilepsy, including changes in triglycerides, cholesterol, sphingolipids, phospholipids, lipid droplets, and bile acids (BAs). Disrupted lipid metabolism acts as a crucial pathological mechanism in epilepsy, potentially linked to processes such as cellular ferroptosis, lipophagy, and immune modulation of gut microbiota (thus influencing the gut-brain axis). Understanding these mechanisms could open up new avenues for epilepsy treatment. This study investigates the association between disturbances in lipid metabolism and the onset of epilepsy.

The pleiotropic spectrum of proximal 16p11.2 CNVs

Recurrent genomic rearrangements at 16p11.2 BP4-5 represent one of the most common causes of genomic disorders. Originally associated with increased risk for autism spectrum disorder, schizophrenia, and intellectual disability, as well as adiposity and head circumference, these CNVs have since been associated with a plethora of phenotypic alterations, albeit with high variability in expressivity and incomplete penetrance. Here, we comprehensively review the pleiotropy associated with 16p11.2 BP4-5 rearrangements to shine light on its full phenotypic spectrum. Illustrating this phenotypic heterogeneity, we expose many parallels between findings gathered from clinical versus population-based cohorts, which often point to the same physiological systems, and emphasize the role of the CNV beyond neuropsychiatric and anthropometric traits. Revealing the complex and variable clinical manifestations of this CNV is crucial for accurate diagnosis and personalized treatment strategies for carrier individuals. Furthermore, we discuss areas of research that will be key to identifying factors contributing to phenotypic heterogeneity and gaining mechanistic insights into the molecular pathways underlying observed associations, while demonstrating how diversity in affected individuals, cohorts, experimental models, and analytical approaches can catalyze discoveries.

In vitro human cell culture models in a bench-to-bedside approach to epilepsy

Epilepsy is the most common chronic neurological disease, affecting nearly 1%-2% of the world's population. Current pharmacological treatment and regimen adjustments are aimed at controlling seizures; however, they are ineffective in one-third of the patients. Although neuronal hyperexcitability was previously thought to be mainly due to ion channel alterations, current research has revealed other contributing molecular pathways, including processes involved in cellular signaling, energy metabolism, protein synthesis, axon guidance, inflammation, and others. Some forms of drug-resistant epilepsy are caused by genetic defects that constitute potential targets for precision therapy. Although such approaches are increasingly important, they are still in the early stages of development. This review aims to provide a summary of practical aspects of the employment of in vitro human cell culture models in epilepsy diagnosis, treatment, and research. First, we briefly summarize the genetic testing that may result in the detection of candidate pathogenic variants in genes involved in epilepsy pathogenesis. Consequently, we review existing in vitro cell models, including induced pluripotent stem cells and differentiated neuronal cells, providing their specific properties, validity, and employment in research pipelines. We cover two methodological approaches. The first approach involves the utilization of somatic cells directly obtained from individual patients, while the second approach entails the utilization of characterized cell lines. The models are evaluated in terms of their research and clinical benefits, relevance to the in vivo conditions, legal and ethical aspects, time and cost demands, and available published data. Despite the methodological, temporal, and financial demands of the reviewed models they possess high potential to be used as robust systems in routine testing of pathogenicity of detected variants in the near future and provide a solid experimental background for personalized therapy of genetic epilepsies. PLAIN LANGUAGE SUMMARY: Epilepsy affects millions worldwide, but current treatments fail for many patients. Beyond traditional ion channel alterations, various genetic factors contribute to the disorder's complexity. This review explores how in vitro human cell models, either from patients or from cell lines, can aid in understanding epilepsy's genetic roots and developing personalized therapies. While these models require further investigation, they offer hope for improved diagnosis and treatment of genetic forms of epilepsy.

Mysterious sphingolipids: metabolic interrelationships at the center of pathophysiology

Metabolic pathways are complex and intertwined. Deficiencies in one or more enzymes in a given pathway are directly linked with genetic diseases, most of them having devastating manifestations. The metabolic pathways undertaken by sphingolipids are diverse and elaborate with ceramide species serving as the hubs of sphingolipid intermediary metabolism and function. Sphingolipids are bioactive lipids that serve a multitude of cellular functions. Being pleiotropic in function, deficiency or overproduction of certain sphingolipids is associated with many genetic and chronic diseases. In this up-to-date review article, we strive to gather recent scientific evidence about sphingolipid metabolism, its enzymes, and regulation. We shed light on the importance of sphingolipid metabolism in a variety of genetic diseases and in nervous and immune system ailments. This is a comprehensive review of the state of the field of sphingolipid biochemistry.

Tissue- and cell-type-specific molecular and functional signatures of 16p11.2 reciprocal genomic disorder across mouse brain and human neuronal models

Chromosome 16p11.2 reciprocal genomic disorder, resulting from recurrent copy-number variants (CNVs), involves intellectual disability, autism spectrum disorder (ASD), and schizophrenia, but the responsible mechanisms are not known. To systemically dissect molecular effects, we performed transcriptome profiling of 350 libraries from six tissues (cortex, cerebellum, striatum, liver, brown fat, and white fat) in mouse models harboring CNVs of the syntenic 7qF3 region, as well as cellular, transcriptional, and single-cell analyses in 54 isogenic neural stem cell, induced neuron, and cerebral organoid models of CRISPR-engineered 16p11.2 CNVs. Transcriptome-wide differentially expressed genes were largely tissue-, cell-type-, and dosage-specific, although more effects were shared between deletion and duplication and across tissue than expected by chance. The broadest effects were observed in the cerebellum (2,163 differentially expressed genes), and the greatest enrichments were associated with synaptic pathways in mouse cerebellum and human induced neurons. Pathway and co-expression analyses identified energy and RNA metabolism as shared processes and enrichment for ASD-associated, loss-of-function constraint, and fragile X messenger ribonucleoprotein target gene sets. Intriguingly, reciprocal 16p11.2 dosage changes resulted in consistent decrements in neurite and electrophysiological features, and single-cell profiling of organoids showed reciprocal alterations to the proportions of excitatory and inhibitory GABAergic neurons. Changes both in neuronal ratios and in gene expression in our organoid analyses point most directly to calretinin GABAergic inhibitory neurons and the excitatory/inhibitory balance as targets of disruption that might contribute to changes in neurodevelopmental and cognitive function in 16p11.2 carriers. Collectively, our data indicate the genomic disorder involves disruption of multiple contributing biological processes and that this disruption has relative impacts that are context specific.

Noninvasive Electrophysiology: Emerging Prospects in Aquatic Neurotoxicity Testing

The significance of neurotoxicological risks associated with anthropogenic pollution is gaining increasing recognition worldwide. In this regard, perturbations in behavioral traits upon exposure to environmentally relevant concentrations of neurotoxic and neuro-modulating contaminants have been linked to diminished ecological fitness of many aquatic species. Despite an increasing interest in behavioral testing in aquatic ecotoxicology there is, however, a notable gap in understanding of the neurophysiological foundations responsible for the altered behavioral phenotypes. One of the canonical approaches to explain the mechanisms of neuro-behavioral changes is functional analysis of neuronal transmission. In aquatic animals it requires, however, invasive, complex, and time-consuming electrophysiology techniques. In this perspective, we highlight emerging prospects of noninvasive, in situ electrophysiology based on multielectrode arrays (MEAs). This technology has only recently been pioneered for the detection and analysis of transient electrical signals in the central nervous system of small model organisms such as zebrafish. The analysis resembles electroencephalography (EEG) applications and provides an appealing strategy for mechanistic explorative studies as well as routine neurotoxicity risk assessment. We outline the prospective future applications and existing challenges of this emerging analytical strategy that is poised to bring new vistas for aquatic ecotoxicology such as greater mechanistic understanding of eco-neurotoxicity and thus more robust risk assessment protocols.

Fatty acid transport protein 2 interacts with ceramide synthase 2 to promote ceramide synthesis

Dihydroceramide is a lipid molecule generated via the action of (dihydro)ceramide synthases (CerSs), which use two substrates, namely sphinganine and fatty acyl-CoAs. Sphinganine is generated via the sequential activity of two integral membrane proteins located in the endoplasmic reticulum. Less is known about the source of the fatty acyl-CoAs, although a number of cytosolic proteins in the pathways of acyl-CoA generation modulate ceramide synthesis via direct or indirect interaction with the CerSs. In this study, we demonstrate, by proteomic analysis of immunoprecipitated proteins, that fatty acid transporter protein 2 (FATP2) (also known as very long-chain acyl-CoA synthetase) directly interacts with CerS2 in mouse liver. Studies in cultured cells demonstrated that other members of the FATP family can also interact with CerS2, with the interaction dependent on both proteins being catalytically active. In addition, transfection of cells with FATP1, FATP2, or FATP4 increased ceramide levels although only FATP2 and 4 increased dihydroceramide levels, consistent with their known intracellular locations. Finally, we show that lipofermata, an FATP2 inhibitor which is believed to directly impact tumor cell growth via modulation of FATP2, decreased de novo dihydroceramide synthesis, suggesting that some of the proposed therapeutic effects of lipofermata may be mediated via (dihydro)ceramide rather than directly via acyl-CoA generation. In summary, our study reinforces the idea that manipulating the pathway of fatty acyl-CoA generation will impact a wide variety of down-stream lipids, not least the sphingolipids, which utilize two acyl-CoA moieties in the initial steps of their synthesis.