Functional investigation of SCN1A deep-intronic variants activating poison exons inclusion.

Dravet syndrome is a devastating epileptic syndrome characterized by intractable epilepsy with an early age of onset, regression of developmental milestones, ataxia, and motor deficits. Loss-of-function pathogenic variants in the SCN1A gene are found in the majority of patients with Dravet syndrome; however, a significant number of patients remain undiagnosed even after comprehensive genetic testing. Previously, it was shown that intronic elements in the SCN1A gene called poison exons can incorporate into SCN1A mRNA, leading to haploinsufficiency and potentially causing Dravet syndrome. Here, we developed a splicing reporter assay for all described poison exons of the SCN1A gene and validated it using previously reported and artificially introduced variants. Overall, we tested 18 deep-intronic single nucleotide variants and one complex allele in the SCN1A gene. Our approach is capable of evaluating the effect of both variants affecting cis-regulatory sequences and splice-site variants, with the potential to functionally annotate every possible variant within these elements. Moreover, using antisense-modified uridine-rich U7 small nuclear RNAs, we were able to block poison exon incorporation in mutant constructs, an approach that could be used as a promising therapeutic intervention in Dravet syndrome patients with deep-intronic variants.

Enhanced magnetic modulation of surface plasmon polaritons on hyperbolic metasurfaces.

In this Letter we demonstrate a fundamentally new, to the best of our knowledge, concept to enhance the magnetic modulation of the surface plasmon polaritons (SPPs) by using hybrid magneto-plasmonic structures consisting of hyperbolic plasmonic metasurfaces and magnetic dielectric substrates. Our results show that the magnetic modulation of SPPs in the proposed structures can be an order of magnitude stronger than in the hybrid metal-ferromagnet multilayer structures conventionally used in active magneto-plasmonics. We believe that this effect will allow for the further miniaturization of magneto-plasmonic devices.

The role of NSD1, NSD2, and NSD3 histone methyltransferases in solid tumors.

NSD1, NSD2, and NSD3 constitute the nuclear receptor-binding SET Domain (NSD) family of histone 3 lysine 36 (H3K36) methyltransferases. These structurally similar enzymes mono- and di-methylate H3K36, which contribute to the maintenance of chromatin integrity and regulate the expression of genes that control cell division, apoptosis, DNA repair, and epithelial-mesenchymal transition (EMT). Aberrant expression or mutation of members of the NSD family is associated with developmental defects and the occurrence of some types of cancer. In this review, we discuss the effect of alterations in NSDs on cancer patient's prognosis and response to treatment. We summarize the current understanding of the biological functions of NSD proteins, focusing on their activities and the role in the formation and progression in solid tumors biology, as well as how it depends on tumor etiologies. This review also discusses ongoing efforts to develop NSD inhibitors as a promising new class of cancer therapeutic agents.

Leigh Syndrome: Spectrum of Molecular Defects and Clinical Features in Russia.

Leigh syndrome (LS), also known as infantile subacute necrotizing encephalopathy, is the most frequent mitochondrial disorder in children. Recently, more than 80 genes have been associated with LS, which greatly complicates the diagnosis. In this article, we present clinical and molecular findings of 219 patients with LS and give the detailed description of three cases with rare findings in nuclear genes MORC2, NARS2 and VPS13D, demonstrating wide genetic heterogeneity of this mitochondrial disease. The most common cause of LS in Russian patients are pathogenic variants in the SURF1 gene (44.3% of patients). The most frequent pathogenic variant is c.845_846delCT (66.0% of mutant alleles; 128/192), which is also widespread in Eastern Europe. Five main LS genes, SURF1, SCO2, MT-ATP6, MT-ND5 and PDHA1, account for 70% of all LS cases in the Russian Federation. Using next generation sequencing (NGS) technique, we were able to detect pathogenic variants in other nuclear genes: NDUFV1, NDUFS2, NDUFS8, NDUFAF5, NDUFAF6, NDUFA10, SUCLG1, GFM2, COX10, PMPCB, NARS2, PDHB and SLC19A3, including two genes previously associated with Leigh-like phenotypes-MORC2 and VPS13D. We found 49 previously undescribed nucleotide variants, including two deep intronic variants which affect splicing.

Hyperbolic plasmonics with anisotropic gain-loss metasurfaces.

In this Letter, a fundamentally new concept of realization of hyperbolic plasmonic metasurfaces by anisotropic gain-loss competition is proposed, and the possibility of highly directional propagation and amplification of surface plasmon polaritons is predicted. A simple realistic configuration of such a metasurface represents the periodic array of lossy metallic slabs embedded in the gain matrix. Our results may pave the way for numerous applications ranging from integrated and highly directional quantum light emitters to nonlinear-optical frequency converters.

Functional Analysis of the PCCA and PCCB Gene Variants Predicted to Affect Splicing.

It is estimated that up to one-third of all variants causing inherited diseases affect splicing; however, their deleterious effects and roles in disease pathogenesis are often not fully characterized. Given their prevalence and the development of various antisense-based splice-modulating approaches, pathogenic splicing variants have become an important object of genomic medicine. To improve the accuracy of variant interpretation in public mutation repositories, we applied the minigene splicing assay to study the effects of 24 variants that were predicted to affect normal splicing in the genes associated with propionic acidemia (PA)-PCCA and PCCB. As a result, 13 variants (including one missense and two synonymous variants) demonstrated a significant alteration of splicing with the predicted deleterious effect at the protein level and were characterized as spliceogenic loss-of-function variants. The analysis of the available data for the studied variants and application of the American College of Medical Genetics and the Association for Molecular Pathology (ACMG/AMP) guidelines allowed us to precisely classify five of the variants and change the pathogenic status of nine. Using the example of the PA genes, we demonstrated the utility of the minigene splicing assay in the fast and effective assessment of the spliceogenic effect for identified variants and highlight the necessity of their standardized classification.

Complex Transposon Insertion as a Novel Cause of Pompe Disease.

Pompe disease (OMIM#232300) is an autosomal recessive lysosomal storage disorder caused by mutations in the GAA gene. According to public mutation databases, more than 679 pathogenic variants have been described in GAA, none of which are associated with mobile genetic elements. In this article, we report a novel molecular genetic cause of Pompe disease, which could be hardly detected using routine molecular genetic analysis. Whole genome sequencing followed by comprehensive functional analysis allowed us to discover and characterize a complex mobile genetic element insertion deep in the intron 15 of the GAA gene in a patient with infantile onset Pompe disease.

Plasma FGF-21 and GDF-15 are elevated in different inherited metabolic diseases and are not diagnostic for mitochondrial disorders.

Recently, the plasma cytokines FGF-21 and GDF-15 were described as cellular metabolic regulators. They share an endocrine function and are highly expressed in the liver under stress and during starvation. Several studies found that these markers have high sensitivity and specificity for the diagnosis of mitochondrial diseases, especially those with prominent muscular involvement. In our study, we aimed to determine whether these markers could help distinguish mitochondrial diseases from other groups of inherited diseases. We measured plasma FGF-21 and GDF-15 concentrations in 122 patients with genetically confirmed primary mitochondrial disease and 127 patients with non-mitochondrial inherited diseases. Although GDF-15 showed better analytical characteristics (sensitivity = 0.66, specificity = 0.64, area under the curve [AUC] = 0.88) compared to FGF-21 (sensitivity = 0.51, specificity = 0.76, AUC = 0.78) in the pediatric group of mitochondrial diseases, both markers were also elevated in a variety of non-mitochondrial diseases, especially those with liver involvement (Gaucher disease, galactosemia, glycogenosis types 1a, 1b, 9), organic acidurias and some leukodystrophies. Thus, the overall positive and negative predictive values were not acceptable for these measurements to be used as diagnostic tests for mitochondrial diseases (FGF-21 positive predictive value [PPV] = 34%, negative predictive value [NPV] = 73%; GDF-15 PPV = 47%, NPV = 28%). We suggest that FGF-21 and GDF-15 increase in patients with metabolic diseases with metabolic or oxidative stress and inflammation.

Plasmon mediated inverse Faraday effect in a graphene-dielectric-metal structure.

This Letter shows the features of inverse Faraday effect (IFE) in a graphene-dielectric-metal (GDM) structure. The constants of propagation and attenuation of the surface plasmon-polariton modes are calculated. The effective magnetic field induced by surface plasmon modes in the dielectric due to the IFE is estimated to reach above 1 tesla. The possibility to control the distribution of the magnetic field by chemical potential of graphene is shown. The concept of strain-driven control of the IFE in the structure has been proposed and investigated.

Giant Faraday Rotation of High-Order Plasmonic Modes in Graphene-Covered Nanowires.

Plasmonic Faraday rotation in nanowires manifests itself in the rotation of the spatial intensity distribution of high-order surface plasmon polariton (SPP) modes around the nanowire axis. Here we predict theoretically the giant Faraday rotation for SPPs propagating on graphene-coated magneto-optically active nanowires. Upon the reversal of the external magnetic field pointing along the nanowire axis some high-order plasmonic modes may be rotated by up to ∼100° on the length scale of about 500 nm at mid-infrared frequencies. Tuning the carrier concentration in graphene by chemical doping or gate voltage allows for controlling SPP-properties and notably the rotation angle of high-order azimuthal modes. Our results open the door to novel plasmonic applications ranging from nanowire-based Faraday isolators to the magnetic control in quantum-optical applications.

Plasmonically induced magnetic field in graphene-coated nanowires.

In this Letter, we investigate a magnetic field induced by guiding plasmonic modes in graphene-coated nanowire via an inverse Faraday effect. Magnetic field distribution for different plasmonic modes has been calculated. It has been shown that a magnetic field has a vortex-like distribution for some plasmonic modes. The possibility of producing magnetic field distribution that rotates along the nanowire axis and periodically depends on azimuthal angle has been demonstrated.

Magnetic field control of plasmon polaritons in graphene-covered gyrotropic planar waveguide.

In this Letter, we report about magnetic field switching of plasmon polaritons propagating into a planar gyrotropic waveguide covered by two graphene layers at a deeply subwavelength scale. It is shown that applying an external magnetic field may lead to energy redistribution between two waveguide surfaces. The effect value resonantly depends on the relation between waveguide size and exciting light wavelength. A change in chemical potential of graphene layers may be used for tuning the phase shift between plasmon polaritons at near-resonant wavelengths. Evident effect may be observed at low magnetic fields (less than one tesla) for wavelengths about microns on a scale of tens of nanometers. Such an effect may be used for plasmonics, photonics. and optoelectronics devices, as well as sensing applications.

Influence of graphene coating on speckle-pattern rotation of light in gyrotropic optical fiber.

In the present work, change in speckle-pattern of linearly polarized light passed through graphene-covered optical fiber placed in external magnetic field is investigated. The possibility of magnetic speckle-pattern rotation suppression and inverse speckle-pattern rotation effect is shown. This effect can be controlled by a chemical potential of graphene layer, which can be changed easily by a gate voltage, for example. For quartz optical fiber at wavelength 0.633 µm, core diameter 9 µm, and fiber length 5 cm, an inverse rotation value of 17° is reached at chemical potential of graphene layer about 1 eV and magnetic field strength 30 kOe. Results of the work may be useful for different magneto-optics, opto-electronics, and photonics applications.

NSD1 supports cell growth and regulates autophagy in HPV-negative head and neck squamous cell carcinoma.

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide. Despite advances in therapeutic management and immunotherapy, the 5-year survival rate for head and neck cancer remains at ~66% of all diagnosed cases. A better definition of drivers of HPV-negative HNSCC that are targetable points of tumor vulnerability could lead to significant clinical advances. NSD1 is a histone methyltransferase that catalyzes histone H3 lysine 36 di-methylation (H3K36me2); mutations inactivating NSD1 have been linked to improved outcomes in HNSCC. In this study, we show that NSD1 induces H3K36me2 levels in HNSCC and that the depletion of NSD1 reduces HNSCC of cell growth in vitro and in vivo. We also find that NSD1 strongly promotes activation of the Akt/mTORC1 signaling pathway. NSD1 depletion in HNSCC induces an autophagic gene program activation, causes accumulation of the p62 and LC3B-II proteins, and decreases the autophagic signaling protein ULK1 at both protein and mRNA levels. Reflecting these signaling defects, the knockdown of NSD1 disrupts autophagic flux in HNSCC cells. Taken together, these data identify positive regulation of Akt/mTORC1 signaling and autophagy as novel NSD1 functions in HNSCC, suggesting that NSD1 may be of value as a therapeutic target in this cancer.

PIP4K2B Protein Regulation by NSD1 in HPV-Negative Head and Neck Squamous Cell Carcinoma.

Head and neck squamous cell carcinoma (HNSCC) ranks among the most prevalent global cancers. Despite advancements in treatments, the five-year survival rate remains at approximately 66%. The histone methyltransferase NSD1, known for its role in catalyzing histone H3 lysine 36 di-methylation (H3K36me2), emerges as a potential oncogenic factor in HNSCC. Our study, employing Reverse Phase Protein Array (RPPA) analysis and subsequent validation, reveals that PIP4K2B is a key downstream target of NSD1. Notably, PIP4K2B depletion in HNSCC induces downregulation of the mTOR pathway, resulting in diminished cell growth in vitro. Our investigation highlights a direct, positive regulatory role of NSD1 on PIP4K2B gene transcription through an H3K36me2-dependent mechanism. Importantly, the impact of PIP4K2B appears to be context-dependent, with overexpression rescuing cell growth in laryngeal HNSCC cells but not in tongue/hypopharynx cells. In conclusion, our findings implicate PIP4K2B as a novel NSD1-dependent protein in HNSCC, suggesting its potential significance for laryngeal cancer cell survival. This insight contributes to our understanding of the molecular landscape in HNSCC and establishes PIP4KB as a promising target for drug development.

Musashi-2 (MSI2) regulation of DNA damage response in lung cancer.

Lung cancer is one of the most common types of cancer worldwide. Non-small cell lung cancer (NSCLC), typically caused by KRAS and TP53 driver mutations, represents the majority of all new lung cancer diagnoses. Overexpression of the RNA-binding protein (RBP) Musashi-2 (MSI2) has been associated with NSCLC progression. To investigate the role of MSI2 in NSCLC development, we compared the tumorigenesis in mice with lung-specific Kras-activating mutation and Trp53 deletion, with and without Msi2 deletion (KPM2 versus KP mice). KPM2 mice showed decreased lung tumorigenesis in comparison with KP mice. In addition, KPM2 lung tumors showed evidence of decreased proliferation, but increased DNA damage, marked by increased levels of phH2AX (S139) and phCHK1 (S345), but decreased total and activated ATM. Using cell lines from KP and KPM2 tumors, and human NSCLC cell lines, we found that MSI2 directly binds ATM mRNA and regulates its translation. MSI2 depletion impaired DNA damage response (DDR) signaling and sensitized human and murine NSCLC cells to treatment with PARP inhibitors in vitro and in vivo. Taken together, we conclude that MSI2 supports NSCLC tumorigenesis, in part, by supporting repair of DNA damage by controlling expression of DDR proteins. These results suggest that targeting MSI2 may be a promising strategy for lung cancers treated with DNA-damaging agents.

Magnetic Properties of 2D Nanowire Arrays: Computer Simulations.

The paper considers a nanowires 2D array located in the nodes of a square lattice. Computer simulations use the Heisenberg model and Metropolis algorithm. The array consists of small nanowires that are monodomain. The exchange interaction orders the spins within a single nanowire. Dipole-dipole forces act between neighboring nanowires. The shape of an individual nanowire affects its magnetic anisotropy. Computer simulations examine the phase transition temperature and magnetization behavior of the system. The type of magnetic moments ordering in the array of nanowires depends on the orientation of their long axis. We consider two types of systems. The nanowires' long axes are oriented perpendicular to the plane of their location in the first case. A dipole-dipole interaction results in first-type superantiferromagnetic ordering of the nanowires' magnetic moments for such orientation. The nanowires' long axes are oriented in the plane of the system in the second case. Dipole-dipole interaction results in second-type superantiferromagnetic ordering in such systems. The dependence of the phase transition temperature on the dipole-dipole interaction intensity is investigated.

Monte Carlo Computer Simulations of Spin-Transfer Torque.

This article performs computer simulations of the change in magnetization in the ferromagnetic film when polarized electric current passes through it. The model examines multilayer structures from ferromagnetic and nonmagnetic films. A sandwich system comprises two ferromagnetic layers separated by a nonmagnetic gasket. Ferromagnetic films have different magnetic susceptibility. The first ferromagnetic film is magnetically hard and acts as a fixed layer. The second ferromagnetic film is magnetically soft, with a switched direction of magnetization. The current direction is perpendicular to the film plane (CPP geometry). Spin transfer is carried out by electrons that polarize in the first ferromagnetic film and transmit spin to the second ferromagnetic film. We use the Ising model to describe the magnetic properties of the system and the Metropolis algorithm to form the thermodynamic states of the spin system. Simulations are performed at temperatures below the Curie points for both materials. The result of computer simulation is the dependence of magnetization in the magnetically soft film on the current strength in the system. Calculations show that there is a critical value of the current at which the magnetization sign of the controlled film changes. The magnetization versus current plot is stepwise. The change in the magnetization sign is due to an increase in the polarization of the electron gas. The plot of electron gas polarization versus current is also stepwise.

NSD1 supports cell growth and regulates autophagy in HPV-negative head and neck squamous cell carcinoma.

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide. Despite advances in therapeutic management and immunotherapy, the five-year survival rate for head and neck cancer remains at ~66% of all diagnosed cases. A better definition of drivers of HPV-negative HNSCC that are targetable points of tumor vulnerability could lead to significant clinical advances. NSD1 is a histone methyltransferase which catalyzes histone H3 lysine 36 di-methylation (H3K36me2); mutations inactivating NSD1 have been linked to improved outcomes in HNSCC. In this study, we show that NSD1 induces H3K36me2 levels in HNSCC, and that the depletion of NSD1 reduces HNSCC of cell growth in vitro and in vivo. We also find that NSD1 strongly promotes activation of the Akt/mTORC1 signaling pathway. NSD1 depletion in HNSCC induces an autophagic gene program activation, causes accumulation of the p62 and LC3B-II proteins, and decreases the autophagic signaling protein ULK1 at both protein and mRNA levels. Reflecting these signaling defects, knockdown of NSD1 disrupts autophagic flux in HNSCC cells. Taken together, these data identify positive regulation of Akt/mTORC1 signaling and autophagy as novel NSD1 functions in HNSCC, suggesting that NSD1 may be of value as a therapeutic target in this cancer.

Regulation of VEGFR2 and AKT signaling by Musashi-2 in lung cancer.

Lung cancer is the most frequently diagnosed cancer type and the leading cause of cancer-related deaths worldwide. Non-small cell lung cancer (NSCLC) represents most of the lung cancer. Vascular endothelial growth factor receptor-2 (VEGFR2) is a member of the VEGF family of receptor tyrosine kinase proteins, expressed on both endothelial and tumor cells which is one of the key proteins contributing to cancer development and involved in drug resistance. We previously showed that Musashi-2 (MSI2) RNA-binding protein is associated with NSCLC progression by regulating several signaling pathways relevant to NSCLC. In this study, we performed Reverse Protein Phase Array (RPPA) analysis of murine lung cancer which nominated VEGFR2 protein as strongly positively regulated by MSI2. Next, we validated VEGFR2 protein regulation by MSI2 in several human NSCLC cell line models. Additionally, we found that MSI2 affected AKT signaling via negative PTEN mRNA translation regulation. In silico prediction analysis suggested that both VEGFR2 and PTEN mRNAs have predicted binding sites for MSI2. We next performed RNA immunoprecipitation coupled with quantitative PCR which confirmed that MSI2 directly binds to VEGFR2 and PTEN mRNAs, suggesting direct regulation mechanism. Finally, MSI2 expression positively correlated with VEGFR2 and VEGF-A protein levels in human NSCLC samples. We conclude that MSI2/VEGFR2 axis contributes to NSCLC progression and is worth further investigations and therapeutic targeting.