Cold atmospheric plasma (CAP) treatment increased reactive oxygen and nitrogen species (RONS) levels in tumor samples obtained from patients with low-grade glioma.

Low-grade gliomas (LGGs) are a heterogeneous group of tumors with an average 10-year survival rate of 40%-55%. Current treatment options include chemotherapy, radiotherapy, and gross total resection (GTR) of the tumor. The extent of resection (EOR) plays an important role in improving surgical outcomes. However, the major obstacle in treating low-grade gliomas is their diffused nature and the presence of residual cancer cells at the tumor margins post resection. Cold Atmospheric Plasma (CAP) has shown to be effective in targeted killing of tumor cells in various glioma cell lines without affecting non-tumor cells through Reactive Oxygen and Nitrogen Species (RONS). However, no study on the effectiveness of CAP has been carried out in LGG tissues till date. In this study, we applied helium-based CAP on tumor tissues resected from LGG patients. Our results show that CAP is effective in promoting RONS accumulation in LGG tissues when CAP jet parameters are set at 4 kV voltage, 5 min treatment time and 3 lpm gas flow rate. We also observed that CAP jet is more effective in thinner slice preparations of tumor as compared to thick tumor samples. Our results indicate that CAP could prove to be an effective adjunct therapy in glioma surgery to target residual cancer cells to improve surgical outcome of patients with low-grade glioma.

RNA Sequencing of Intraoperative Peritumoral Tissues Reveals Potential Pathways Involved in Glioma-Related Seizures.

Tumor-induced changes in the peritumoral neocortex play a crucial role in generation of seizures. This study aimed to investigate the molecular mechanisms potentially involved in peritumoral epilepsy in low-grade gliomas (LGGs). Intraoperative peritumoral brain tissues resected from LGG patients with seizures (pGRS) or without seizures (pGNS) were used for RNA sequencing (RNA-seq). Comparative transcriptomics was performed to identify differentially expressed genes (DEGs) in pGRS compared to pGNS using deseq2 and edgeR packages (R). Gene set enrichment analysis (GSEA) using Gene Ontology terms and Kyoto Encyclopedia of Genes & Genomes (KEGG) pathways was performed using the clusterProfiler package (R). The expression of key genes was validated at the transcript and protein levels in the peritumoral region using real-time PCR and immunohistochemistry, respectively. A total of 1073 DEGs were identified in pGRS compared to pGNS, of which 559 genes were upregulated and 514 genes were downregulated (log2 fold-change ≥ 2, padj < 0.001). The DEGs in pGRS were highly enriched in the "Glutamatergic Synapse" and "Spliceosome" pathways, with increased expression of GRIN2A (NR2A), GRIN2B (NR2B), GRIA1 (GLUR1), GRIA3 (GLUR3), GRM5, CACNA1C, CACNA1A, and ITPR2. Moreover, increased immunoreactivity was observed for NR2A, NR2B, and GLUR1 proteins in the peritumoral tissues of GRS. These findings suggest that altered glutamatergic signaling and perturbed Ca2+ homeostasis may be potential causes of peritumoral epilepsy in gliomas. This explorative study identifies important genes/pathways that merit further characterization for their potential involvement in glioma-related seizures.

Epigenetics of neurological diseases.

Higher-order DNA structure and gene expression are governed by epigenetic processes like DNA methylation and histone modifications. Abnormal epigenetic mechanisms are known to contribute to the emergence of numerous diseases, including cancer. Historically, the chromatin abnormalities were only considered to be limited to discrete DNA sequences and were thought to be associated with rare genetic syndrome however, recent discoveries have pointed to genome-wide level changes in the epigenetic machinery which has contributed to a better knowledge of the mechanisms underlying developmental and degenerative neuronal problems associated with diseases such as Parkinson's disease, Huntington's disease, Epilepsy, Multiple sclerosis, etc. In the given chapter we describe the epigenetic alterations seen in various neurological disorders and further discuss the influence of these epigenetic changes on developing novel therapies.

Mass spectrometry-based lipidomic analysis reveals altered lipid profile in brain tissues resected from patients with focal cortical dysplasia (FCD).

Focal cortical dysplasia (FCD) is a common pathology responsible for drug-resistant epilepsy (DRE). Failure to precisely localize the epileptogenic zones (EZs) is a major reason for poor surgical outcome in FCD. Currently, there are no molecular or cellular biomarkers available which can aid in defining the EZs in FCD. Phospholipid alterations between healthy and malignant tumor tissues are reported and have been used for marking tumor margins. In this study, we utilize liquid chromatography and tandem mass spectrometry to identify altered lipids in resected brain specimens from FCD patients compared to non-epileptic controls. Based on these results, we propose that a similar approach utilizing unique lipid mass spectra can be used for defining the EZs in FCD. The observed distinct lipid mass spectra of cortical tissues from FCD patients could be used for real-time guidance during surgery as well as for ex vivo examination of resected tissues for diagnostic purposes.

Transcriptomic profiling of high- and low-spiking regions reveals novel epileptogenic mechanisms in focal cortical dysplasia type II patients.

Focal cortical dysplasia (FCD) is a malformation of the cerebral cortex with poorly-defined epileptogenic zones (EZs), and poor surgical outcome in FCD is associated with inaccurate localization of the EZ. Hence, identifying novel epileptogenic markers to aid in the localization of EZ in patients with FCD is very much needed. High-throughput gene expression studies of FCD samples have the potential to uncover molecular changes underlying the epileptogenic process and identify novel markers for delineating the EZ. For this purpose, we, for the first time performed RNA sequencing of surgically resected paired tissue samples obtained from electrocorticographically graded high (MAX) and low spiking (MIN) regions of FCD type II patients and autopsy controls. We identified significant changes in the MAX samples of the FCD type II patients when compared to non-epileptic controls, but not in the case of MIN samples. We found significant enrichment for myelination, oligodendrocyte development and differentiation, neuronal and axon ensheathment, phospholipid metabolism, cell adhesion and cytoskeleton, semaphorins, and ion channels in the MAX region. Through the integration of both MAX vs non-epileptic control and MAX vs MIN RNA sequencing (RNA Seq) data, PLP1, PLLP, UGT8, KLK6, SOX10, MOG, MAG, MOBP, ANLN, ERMN, SPP1, CLDN11, TNC, GPR37, SLC12A2, ABCA2, ABCA8, ASPA, P2RX7, CERS2, MAP4K4, TF, CTGF, Semaphorins, Opalin, FGFs, CALB2, and TNC were identified as potential key regulators of multiple pathways related to FCD type II pathology. We have identified novel epileptogenic marker elements that may contribute to epileptogenicity in patients with FCD and could be possible markers for the localization of EZ.

Neuromodulatory effects of SARS-CoV2 infection: Possible therapeutic targets.

INTRODUCTION: Although SARS-CoV-2 primarily manifests in the form of respiratory symptoms, emerging evidence suggests that the disease is associated with numerous neurological complications, such as stroke and Guillain-Barre syndrome. Hence, further research is necessary to seek possible therapeutic targets in the CNS for effective management of these complications. AREAS COVERED: This review examines the neurological complications associated with SARS-CoV-2 infections and the possible routes of infection. It progresses to illuminate the possible therapeutic targets for effective management of these neuromodulatory effects and the repurposing of drugs that could serve this purpose. To this end, literature from the year 1998-2021 was derived from PubMed. EXPERT OPINION: The neurological manifestations associated with COVID-19 may be related to poor prognosis and higher comorbidity. Identification of the key molecular targets in the brain that are potential indicators of the observed neuropathology, such as inflammatory mediators and chromatin modifiers, is key. The repurposing of existing drugs to target potential candidates could reduce the mortality attributed to these associated neurological complications.

Increased levels of α4-containing GABAA receptors in focal cortical dysplasia: A possible cause of benzodiazepine resistance.

Benzodiazepines are the first choice of anti-epileptic drugs used to treat seizures. However, it has been seen that their efficacy decreases with time leading to drug insensitivity, plausibly caused by an alteration in the expression of the benzodiazepine biding site on GABAA receptors. This study was designed to investigate if the differential expression of GABAA receptor subunits α1/α4/γ2/δ across the postsynaptic sites could contribute to benzodiazepine resistance in patients with focal cortical dysplasia (FCD), the most common cause of drug resistant epilepsy in pediatric population. Differential gene and cellular expression of GABAA receptor subunits α1, α4, γ2 and δ were evaluated and validated using qPCR and immunohistochemistry. Whole cell patch clamp studies were performed on pyramidal neurons of resected cortical FCD samples to measure the spontaneous GABAA receptor activity. Upregulation of α4-and γ2-subunits containing GABAA receptors were observed at both mRNA and protein level. α1-and δ-subunits containing GABAA receptors did not show any significant changes. Flumazenil treatment did not affect the kinetics of GABAergic events in FCD; however, it significantly reduced the frequency and amplitude of spontaneous GABAergic activity in non-seizure control samples. Our results demonstrate the enhanced expression of α4-containing GABAA receptors and GABAergic activity in pyramidal neurons which in turn may contribute to benzodiazepine resistance in FCD patients.

GABAA Receptor-Mediated Epileptogenicity in Focal Cortical Dysplasia (FCD) Depends on Age at Epilepsy Onset.

Enhanced spontaneous GABAA receptor activity is associated with focal cortical dysplasia (FCD), a developmental malformation of the cerebral cortex. Clinical manifestations in FCD vary with age at epilepsy onset with a more favorable prognosis in patients with late-onset (LO) compared to that in cases with early-onset (EO). This study was designed to test the hypothesis in FCD that spontaneous GABAA receptor-mediated epileptogenicity depends on the age at epilepsy onset and varies between patients with early and late-onset age in FCD. To this end, brain specimens were obtained from the maximal spiking region (MAX) and minimal spiking region (MIN) of the epileptic foci of EO (n = 14, mean age = 10.6 ± 2.9 years) and LO (n = 10, mean age = 27 ± 5.6 years) patients undergoing electrocorticography (ECoG) guided surgery. The whole-cell patch-clamp technique was used to record spontaneous GABAergic currents from normal-looking pyramidal neurons in slice preparations of resected brain samples. We detected higher frequency and amplitude of GABAergic events in MAX samples compared to MIN samples of LO patients, while they were comparable in MIN and MAX samples of EO patients. Further GABAergic activity in the MIN and MAX samples of EO patients was higher than the MIN samples of LO patients. This suggests that in LO patients, GABAA receptor-mediated epileptogenicity is confined only to the high spiking areas, but in EO patients, it affects low spiking regions as well.

Genome-wide DNA Methylation and RNAseq Analyses Identify Aberrant Signalling Pathways in Focal Cortical Dysplasia (FCD) Type II.

Focal cortical dysplasia (FCD) is one of the most common pathologies associated with drug-resistant epilepsy (DRE). The pharmacological targets remain obscured, as the molecular mechanisms underlying FCD are unclear. Implications of epigenetically modulated aberrant gene expression in disease progression are reported in various DRE pathologies except FCD. Here we performed genome-wide CpG-DNA methylation profiling by methylated DNA immunoprecipitation (MeDIP) microarray and RNA sequencing (RNAseq) on cortical tissues resected from FCD type II patients. A total of 19088 sites showed altered DNA methylation in all the CpG islands. Of these, 5725 sites were present in the promoter regions, of which 176 genes showed an inverse correlation between methylation and gene expression. Many of these 176 genes were found to belong to a cohesive network of physically interacting proteins linked to several cellular functions. Pathway analysis revealed significant enrichment of receptor tyrosine kinases (RTK), EGFR, PDGFRA, NTRK3, and mTOR signalling pathways. This is the first study that investigates the epigenetic signature associated with FCD type II pathology. The candidate genes and pathways identified in this study may play a crucial role in the regulation of the pathogenic mechanisms of epileptogenesis associated with FCD type II pathologies.

Comparative analysis of cytokine/chemokine regulatory networks in patients with hippocampal sclerosis (HS) and focal cortical dysplasia (FCD).

Experimental and clinical evidence have demonstrated aberrant expression of cytokines/chemokines and their receptors in patients with hippocampal sclerosis (HS) and focal cortical dysplasia (FCD). However, there is limited information regarding the modulation of cytokine/chemokine-regulatory networks, suggesting contribution of miRNAs and downstream transcription factors/receptors in these pathologies. Hence, we studied the levels of multiple inflammatory mediators (IL1ß, IL1Ra, IL6, IL10, CCL3, CCL4, TNFα and VEGF) along with transcriptional changes of nine related miRNAs and mRNA levels of downstream effectors of significantly altered cytokines/chemokines in brain tissues obtained from patients with HS (n = 26) and FCD (n = 26). Up regulation of IL1ß, IL6, CCL3, CCL4, STAT-3, C-JUN and CCR5, and down regulation of IL 10 were observed in both HS and FCD cases (p < 0.05). CCR5 was significantly up regulated in FCD as compared to HS (p < 0.001). Both, HS and FCD presented decreased miR-223-3p, miR-21-5p, miR-204-5p and let-7a-5p and increased miR-155-5p expression (p < 0.05). As compared to HS, miR-204-5p (upstream to CCR5 and IL1ß) and miR-195-5p (upstream to CCL4) were significantly decreased in FCD patients (p < 0.01). Our results suggest differential alteration of cytokine/chemokine regulatory networks in HS and FCD and provide a rationale for developing pathology specific therapy.

Mutations in GABRG2 receptor gene are not a major factor in the pathogenesis of mesial temporal lobe epilepsy in Indian population.

AIM: This study is focused on GABRG2 gene sequence variations in patients with mesial temporal lobe epilepsy (mTLE). The GABAAreceptor is a heteropentameric receptor and alpha-1 beta-2 gamma-2 subunits combination is most abundant and present in almost all regions of the brain. The gamma-2 subunit (GABRG2) gene mutations have been reported in different epilepsy pathologies. In the present study we have looked for GABRG2 gene sequence variations in patients with mTLE. MATERIALS AND METHODS: Twenty patients (12 females and eight males, age 4.6-38 years) with MTLE were recruited for this investigation. Patients were recommended for epilepsy surgery after all clinical investigations as per the epilepsy protocol. Ethnically matched glioma or meningioma patients were considered as nonepileptic controls. During temporal lobectomy of amygdalohippocampectomy, hippocampal brain tissue samples were resected guided by intraoperative electrocorticography (ECoG) activity. All 11 exons of GABRG2 gene with their flanking intronic regions were amplified by polymerase chain reaction (PCR) and screened by DNA sequencing analysis for sequence variations. STATISTICAL ANALYSIS USED: Comparison of allele frequencies between patient and control groups was determined using a c(2) test. RESULTS AND CONCLUSIONS: Total five DNA sequence variations were identified, three in exonic regions (c.643A > G, rs211035), (c.T > A, rs424740), and (c.C > T, rs418210) and two in intronic regions (c.751 + 41A > G, rs211034) and (c.751 + 52G > A, rs 34281163). Allele frequencies of variants identified in this study did not differ between patients and normal controls. Thus, we conclude that GABRG2 gene may not be playing significant role in the development of epilepsy or as a susceptibility gene in patients with MTLE in Indian population.

RNA-seq analysis of hippocampal tissues reveals novel candidate genes for drug refractory epilepsy in patients with MTLE-HS.

Array-based profiling studies have shown implication of aberrant gene expression patterns in epileptogenesis. We have performed transcriptome analysis of hippocampal tissues resected from patients with MTLE-HS using RNAseq approach. Healthy tissues from tumour margins obtained during tumour surgeries were used as non-epileptic controls. RNA sequencing was performed using standard protocols on Illumina HiSeq 2500 platform. Differential gene expression analysis of the RNAseq data revealed 56 significantly regulated genes in MTLE patients. Gene cluster analysis identified 3 important hubs of genes mostly linked to, neuroinflammation and innate immunity, synaptic transmission and neuronal network modulation which are supportive of intrinsic severity hypothesis of pharmacoresistance. This study identified various genes like FN1 which is central in our analysis, NEUROD6, RELN, TGFßR2, NLRP1, SCRT1, CSNK2B, SCN1B, CABP1, KIF5A and antisense RNAs like AQP4-AS1 and KIRREL3-AS2 providing important insight into the understanding of the pathophysiology or genomic basis of drug refractory epilepsy due to MTS.

Role of inflammation and its miRNA based regulation in epilepsy: Implications for therapy.

There is a need to develop innovative therapeutic strategies to counteract epilepsy, a common disabling neurological disorder. Despite the recent advent of additional antiepileptic drugs and respective surgery, the treatment of epilepsy remains a major challenge. The available therapies are largely based on symptoms, and these approaches do not affect the underlying disease processes and are also associated frequently with severe side effects. This is mainly because of the lack of well-defined targets in epilepsy. The discovery that inflammatory mediators significantly contribute to the onset and recurrence of seizures in experimental seizure models, as well as the presence of inflammatory molecules in human epileptogenic tissue, highlights the possibility of targeting specific inflammation related pathways to control seizures that are otherwise resistant to the available AEDs. Emerging studies suggest that miRNAs have a significant role in regulating inflammatory pathways shown to be involved in epilepsy. These miRNAs can possibly be used as novel therapeutic targets in the treatment of epilepsy as well as serve as diagnostic biomarkers of epileptogenesis. This review highlights the immunological features underlying the pathogenesis of epileptic seizures and the possible miRNA mediated approaches for drug resistant epilepsies that modulate the immune-mediated pathogenesis.

Molecular biomarkers in drug-resistant epilepsy: Facts & possibilities.

Despite great advances in our understanding of the process of epileptogenesis we are yet to develop reliable biomarkers that have the potential to accurately localize the epileptogenic zone (EZ), and to resolve the issue of heterogeneity in epilepsy surgery outcome. Inability to precisely localize the epileptogenic foci is one of the reason why more than 30% of these DRE patients are not benefited. Molecular and cellular biomarkers in combination with imaging and electrical investigations will provide a more specific platform for defining epileptogenic zone. Potential molecular biomarkers of epileptogenesis including markers of inflammation, synaptic alterations and neurodegeneration may also have the potential for localizing EZ. At molecular level components derived from epileptogenic tissues, such as metabolites, proteins, mRNAs and miRNAs that are significantly altered can serve as biomarkers and can be clubbed with existing techniques to preoperatively localize the EZ. Neurosurgeons across the world face problems while defining the margins of the epileptogenic tissues to be resected during surgery. In this review we discuss molecular biomarkers reported so far in the context of epileptogenesis and some of the unexplored markers which may have the potential to localize EZ during surgery. We also discuss "Intelligent knife" technique that couples electrosurgery and mass spectrometry allowing near-real-time characterization of human tissue and may prove to be instrumental in defining the margins of the epileptogenic zone during surgery.

Presurgical epileptogenic network analysis: A way to enhance epilepsy surgery outcome.

Accurate localization of the "epileptogenic zone (EZ)" is an important issue in epilepsy surgery. The EZ is not discrete and focal; in fact, the epileptogenic networks can spread ictal activity to different regions of the brain. Changes in network characteristics and functional connectivity are shown to be associated with epilepsy. Seizures are thought to represent a hyper-synchronous state and presumable changes in synchronization between different brain regions underlie the mechanisms of seizure spread. Although presurgical evaluation of the epileptogenic network analysis can be carried out using existing investigative techniques like electroencephalogram (EEG), video-EEG, magnetic resonance imaging, single-photon emission computed tomography, and magnetoencephalography, advanced imaging techniques such as optical intrinsic spectroscopy, auto-fluorescence imaging, voltage sensitive dye imaging, and calcium imaging have the advantage of better spatiotemporal resolution over a large area of cortex. Understanding the wide-scale dynamic networks by analyzing the changes in the synchronization patterns using advanced imaging techniques will be instrumental in the presurgical analysis of the epileptogenic network and better localization of the EZs in the future.

Viral nanoparticle-encapsidated enzyme and restructured DNA for cell delivery and gene expression.

Packaging specific exogenous active proteins and DNAs together within a single viral-nanocontainer is challenging. The bacteriophage T4 capsid (100 × 70 nm) is well suited for this purpose, because it can hold a single long DNA or multiple short pieces of DNA up to 170 kb packed together with more than 1,000 protein molecules. Any linear DNA can be packaged in vitro into purified procapsids. The capsid-targeting sequence (CTS) directs virtually any protein into the procapsid. Procapsids are assembled with specific CTS-directed exogenous proteins that are encapsidated before the DNA. The capsid also can display on its surface high-affinity eukaryotic cell-binding peptides or proteins that are in fusion with small outer capsid and head outer capsid surface-decoration proteins that can be added in vivo or in vitro. In this study, we demonstrate that the site-specific recombinase cyclic recombination (Cre) targeted into the procapsid is enzymatically active within the procapsid and recircularizes linear plasmid DNA containing two terminal loxP recognition sites when packaged in vitro. mCherry expression driven by a cytomegalovirus promoter in the capsid containing Cre-circularized DNA is enhanced over linear DNA, as shown in recipient eukaryotic cells. The efficient and specific packaging into capsids and the unpackaging of both DNA and protein with release of the enzymatically altered protein-DNA complexes from the nanoparticles into cells have potential in numerous downstream drug and gene therapeutic applications.

The C-terminal domain of the bacteriophage T4 terminase docks on the prohead portal clip region during DNA packaging.

Bacteriophage ATP-based packaging motors translocate DNA into a pre-formed prohead through a dodecameric portal ring channel to high density. We investigated portal-terminase docking interactions at specifically localized residues within a terminase-interaction region (aa279-316) in the phage T4 portal protein gp20 equated to the clip domain of the SPP1 portal crystal structure by 3D modeling. Within this region, three residues allowed A to C mutations whereas three others did not, consistent with informatics analyses showing the tolerated residues are not strongly conserved evolutionarily. About 7.5nm was calculated by FCS-FRET studies employing maleimide Alexa488 dye labeled A316C proheads and gp17 CT-ReAsH supporting previous work docking the C-terminal end of the T4 terminase (gp17) closer to the N-terminal GFP-labeled portal (gp20) than the N-terminal end of the terminase. Such a terminase-portal orientation fits better to a proposed "DNA crunching" compression packaging motor and to portal determined DNA headful cutting.

Compression of the DNA substrate by a viral packaging motor is supported by removal of intercalating dye during translocation.

Viral genome packaging into capsids is powered by high-force-generating motor proteins. In the presence of all packaging components, ATP-powered translocation in vitro expels all detectable tightly bound YOYO-1 dye from packaged short dsDNA substrates and removes all aminoacridine dye from packaged genomic DNA in vivo. In contrast, in the absence of packaging, the purified T4 packaging ATPase alone can only remove up to ∼1/3 of DNA-bound intercalating YOYO-1 dye molecules in the presence of ATP or ATP-γ-S. In sufficient concentration, intercalating dyes arrest packaging, but rare terminase mutations confer resistance. These distant mutations are highly interdependent in acquiring function and resistance and likely mark motor contact points with the translocating DNA. In stalled Y-DNAs, FRET has shown a decrease in distance from the phage T4 terminase C terminus to portal consistent with a linear motor, and in the Y-stem DNA compression between closely positioned dye pairs. Taken together with prior FRET studies of conformational changes in stalled Y-DNAs, removal of intercalating compounds by the packaging motor demonstrates conformational change in DNA during normal translocation at low packaging resistance and supports a proposed linear "DNA crunching" or torsional compression motor mechanism involving a transient grip-and-release structural change in B form DNA.