An in-silico approach for discovery of microRNA-TF regulation of DISC1 interactome mediating neuronal migration

SARS-CoV-2 proteins show great binding affinity to resin composite monomers and polymerized chains

BACKGROUND

Due to saliva and salivary glands are reservoir to severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), aerosols and saliva droplets are primary sources of cross-infection and are responsible for the high human-human transmission of SARS-CoV-2. However, there is no evidence about how SARS-CoV-2 interacts with oral structures, particularly resin composites.

AIM

To evaluate the interaction of SARS-CoV-2 proteins with monomers present in resin composites using in silico analysis.

METHODS

Four SARS-CoV-2 proteins [i.e. main protease, 3C-like protease, papain-like protease (PLpro), and glycoprotein spike] were selected along with salivary amylase as the positive control, and their binding affinity with bisphenol-A glycol dimethacrylate, bisphenol-A ethoxylated dimethacrylate, triethylene glycol dimethacrylate, and urethane dimethacrylate was evaluated. Molecular docking was performed using AutoDock Vina and visualised in Chimera UCSF 1.14. The best ligand-protein model was identified based on the binding energy (ΔG-kcal/moL).

RESULTS

Values for the binding energies ranged from -3.6 kcal/moL to -7.3 kcal/moL. The 3-monomer chain had the lowest binding energy (i.e. highest affinity) to PLpro and the glycoprotein spike. Non-polymerised monomers and polymerised chains interacted with SARS-CoV-2 proteins via hydrogen bonds and hydrophobic interactions. Those findings suggest an interaction between SARS-CoV-2 proteins and resin composites.

CONCLUSION

SARS-CoV-2 proteins show affinity to non-polymerised and polymerised resin composite chains.

Adaptation responses to salt stress in the gut of Poecilia reticulata

Osmoregulation is essential for the survival of aquatic organisms, particularly teleost fish facing osmotic challenges in environments characterized by variable salinity. While the gills are known for ion exchange, the intestine's role in water and salt absorption is gaining attention. Here, we investigated the adaptive responses of the intestine to salinity stress in guppies (Poecilia reticulata), observing significant morphological and transcriptomic alterations. Guppies showed superior salt tolerance compared to zebrafish (Danio rerio). Increasing salinity reduced villus length and intestinal diameter in guppies, while zebrafish exhibited damage to villus structure and loss of goblet cells. Transcriptomic analysis identified key genes involved in osmoregulation, tissue remodeling, and immune modulation. Upregulated genes included the solute carrier transporters slc2al and slc3al, which facilitate ion and water transport, as well as a transcription factor AP-1 subunit and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta, both of which participate in tissue repair and growth responses. In contrast, many genes related to the innate immune system (such as Tnfaip6) were downregulated, suggesting a shift toward the prioritization of osmoregulatory functions over immune responses. Interestingly, the differential expression of adaptation genes was linked to variations in epigenetic modifications and transcription factor activity. Transcription factors crucial for adapting to salt stress, such as bhlhe40, cebpd, and gata6, were progressively upregulated in guppies but remained downregulated in zebrafish. Our findings highlight the intricate mechanisms of adaptation to salinity stress in P. reticulata, providing insights into osmoregulatory mechanisms involving the intestine in aquatic organisms.

A rare cause of epileptic encephalopathy: case report of a novel patient with PEHO-like phenotype and CCDC88A gene pathogenic variants

BACKGROUND

The Coiled-Coil Domain-Containing Protein 88 A (CCDC88A) gene encodes the actin-binding protein Girdin, which plays important roles in maintaining the actin cytoskeleton and in cell migration and was recently associated with a specific form of epileptic encephalopathy. Biallelic protein-truncating variants of CCDC88A have been considered responsible for progressive encephalopathy with edema, hypsarrhythmia, and optic atrophy (PEHO)-like syndrome. To date, only three consanguineous families with loss-of-function homozygous variants in the CCDC88A gene have been reported. The described patients share many clinical features, such as microcephaly, neonatal hypotonia, seizures, profound developmental delay, face and limb edema, and dysmorphic features, with a similar appearance of the eyes, nose, mouth, and fingers.

CASE PRESENTATION

We report on a child from a nonconsanguineous family who presented with profound global developmental delay, severe epilepsy, and brain malformations, including subcortical band heterotopia. The patient harbored two heterozygous pathogenic variants in the trans configuration in the CCDC88A gene, which affected the coiled-coil and C-terminal domains.

CONCLUSIONS

We detail the clinical and cerebral imaging data of our patient in the context of previously reported patients with disease-causing variants in the CCDC88A gene, emphasizing the common phenotypes, including cortical malformations, that warrant screening for sequence variants in this gene.

FEZ1 participates in human embryonic brain development by modulating neuronal progenitor subpopulation specification and migrations

Mutations in the human fasciculation and elongation protein zeta 1 (FEZ1) gene are found in schizophrenia and Jacobsen syndrome patients. Here, using human cerebral organoids (hCOs), we show that FEZ1 expression is turned on early during brain development and is detectable in both neuroprogenitor subtypes and immature neurons. FEZ1 deletion disrupts expression of neuronal and synaptic development genes. Using single-cell RNA sequencing, we detected abnormal expansion of homeodomain-only protein homeobox (HOPX)- outer radial glia (oRG), concurrent with a reduction of HOPX+ oRG, in FEZ1-null hCOs. HOPX- oRGs show higher cell mobility as compared to HOPX+ oRGs. Ectopic localization of neuroprogenitors to the outer layer is seen in FEZ1-null hCOs. Anomalous encroachment of TBR2+ intermediate progenitors into CTIP2+ deep layer neurons further indicated abnormalities in cortical layer formation these hCOs. Collectively, our findings highlight the involvement of FEZ1 in early cortical brain development and how it contributes to neurodevelopmental disorders.

circARL15 Plays a Critical Role in Intervertebral Disc Degeneration by Modulating miR-431-5p/DISC1

Background

Intervertebral disk degeneration (IDD) is a serious public health problem associated with genetic and environmental factors. However, the pathogenic factors involved and the pathological mechanism of this disease still remain enigmatic.

Methods

The associated microarray was downloaded and further analyzed using statistical software R. The competing endogenous RNA (ceRNA) co-expression network was constructed to measure the meaningful correlated expression of differentially expressed genes. We further measured the expression of circARL15/miR-431-5p/DISC1 in IDD tissues. Cell proliferation and apoptosis were detected in NP cells transfected with a circARL15 overexpression plasmid and miR-431-5p mimics. The expression of DISC1 was detected by immunohistochemistry and Western blot analysis.

Results

Within the ceRNA network, circARL15 is the most differentially expressed circular RNA. circARL15 was down-regulated in IDD and was negatively correlated with miR-431-5p and positively associated with DISC1. miR-431-5p was found to bind directly to circARL15 and DISC1. circARL15 inhibited nucleus pulposus cell apoptosis but promoted nucleus pulposus cell proliferation by targeting the miR-431-5p/DISC1 signaling pathway.

Conclusion

circARL15/miR-431-5p/DISC1 is involved in the pathogenesis of IDD, which might be helpful in determining the diagnostic biomarkers and providing potential therapeutic targets for patients with IDD.

Dental workers in front-line of COVID-19: an in silico evaluation targeting their prevention

OBJECTIVE

SARS-CoV-2 has high human-human transmission rate. The aerosols and saliva droplets are the main contamination source. Thus, it is crucial to point out that dental practitioners become a high-risk group of contagion by SARS-CoV-2. Based on this, protocols have been recommended to avoid cross-contamination during dental care; however, appropriate evidence has not yet been established. Our study sought to make a screening, by in silico analysis, of the potential of mouth rinses used in dental practices to prevent the dental workers' contamination by SARS-CoV-2.

METHODOLOGY

Multiple sequence comparisons and construction of the phylogenetic tree were conducted using the FASTA code. Therefore, molecular docking investigation between SARS-CoV-2 proteins (Main Protease, Spike Glycoprotein, Non-structure Protein, and Papain-like Protease) and molecules used in dental practices (chlorhexidine digluconate, hydrogen peroxide, cetylpyridinium chloride, povidone-iodine, gallic acid, β-cyclodextrin, catechin, and quercetin) was performed using AutoDock Vina. Moreover, 2D interactions of the complex protein-ligand structure were analyzed by Ligplot+.

RESULTS

The obtained results showed a remarkable affinity between SARS-CoV-2 proteins and all tested compounds. The chlorhexidine digluconate, catechin, and quercetin presented a higher affinity with SARS-CoV-2.

CONCLUSIONS

The overall results allowed us to suggest that chlorhexidine is the most suitable active compound in reducing the SARS-CoV-2 salivary load due to its better binding energy. However, in vivo studies should be conducted to confirm their clinical use.

miRNet 2.0: network-based visual analytics for miRNA functional analysis and systems biology

miRNet is an easy-to-use, web-based platform designed to help elucidate microRNA (miRNA) functions by integrating users' data with existing knowledge via network-based visual analytics. Since its first release in 2016, miRNet has been accessed by >20 000 researchers worldwide, with ∼100 users on a daily basis. While version 1.0 was focused primarily on miRNA-target gene interactions, it has become clear that in order to obtain a global view of miRNA functions, it is necessary to bring other important players into the context during analysis. Driven by this concept, in miRNet version 2.0, we have (i) added support for transcription factors (TFs) and single nucleotide polymorphisms (SNPs) that affect miRNAs, miRNA-binding sites or target genes, whilst also greatly increased (>5-fold) the underlying knowledgebases of miRNAs, ncRNAs and disease associations; (ii) implemented new functions to allow creation and visual exploration of multipartite networks, with enhanced support for in situ functional analysis and (iii) revamped the web interface, optimized the workflow, and introduced microservices and web application programming interface (API) to sustain high-performance, real-time data analysis. The underlying R package is also released in tandem with version 2.0 to allow more flexible data analysis for R programmers. The miRNet 2.0 website is freely available at https://www.mirnet.ca.

Durable response of glioblastoma to adjuvant therapy consisting of temozolomide and a weekly dose of AMD3100 (plerixafor), a CXCR4 inhibitor, together with lapatinib, metformin and niacinamide

Glioblastoma multiforme (GBM) is a CNS (central nervous system) malignancy with a low cure rate. Median time to progression after standard treatment is 7 months and median overall survival is 15 months [1]. Post-treatment vasculogenesis promoted by recruitment of bone marrow derived cells (BMDCs, CD11b+ myelomonocytes) is one of main mechanisms of GBM resistance to initial chemoradiotherapy treatment [2]. Local secretion of SDF-1, cognate ligand of BMDCs CXCR4 receptors attracts BMDCs to the post-radiation tumor site.[3]. This SDF-1 hypoxia-dependent effect can be blocked by AMD3100 (plerixafor) [4]. We report a GBM case treated after chemo- radiotherapy with plerixafor and a combination of an mTOR, a Sirt1 and an EGFRvIII inhibitor. After one year temozolomide and the EGFRvIII inhibitor were stopped. Plerixafor, and the MTOR and Sirt-1 inhibitors were continued. He is in clinical and radiologic remission 30 months from the initiation of his adjuvant treatment. To our knowledge, this is the first report of a patient treated for over two years with a CXCR4 inhibitor (plerixafor), as part of his adjuvant treatment. We believe there is sufficient experimental evidence to consider AMD3100 (plerixafor) part of the adjuvant treatment of GBM.