Discovering conserved epitopes of Monkeypox: Novel immunoinformatic and machine learning approaches.

The Monkeypox virus, an Orthopoxvirus with zoonotic origins, has been responsible for a growing number of human infections reminiscent of smallpox since May 2022, as reported by the World Health Organization. As of now, there are no established medical treatments for managing Monkeypox infections. In this study, we used machine learning to select conserved epitopes. Proteins were determined using Reverse Vaccinology and Gene Ontology subcellular localization, and their epitopes were predicted. NextClade was used to calculate the number of mutations in each amino acid position using 2433 Monkeypox sequences. The Unsupervised Nearest Neighbor machine learning algorithm and ideal matrix [0 0] were used to calculate the conservancy score of epitopes. Six proteins were determined for epitope prediction. Finally, 47 MHC-I epitopes, 5 MHC-II epitopes, and 10 Linear B cell epitopes were discovered. Our method can select epitopes for vaccine design to prevent viruses with accelerated evolution and high mutation rate.

Design of a multi-epitope-based peptide vaccine against the SARS-CoV-2 Omicron variant using bioinformatics approach.

SARS-CoV-2, a member of the coronavirus family, is an RNA virus characterized by a single-stranded genome and is responsible for the development of COVID-19. The emergence of the Omicron variant of SARS-CoV-2 in 2021 marked a significant variation recognized by the World Health Organization. The primary objective of this study is to investigate the spike glycoprotein of the Omicron variant of SARS-CoV-2 and identify potential immunogenic epitopes in order to design multi-epitope vaccine constructs. Among the other major structural proteins of the coronavirus, the spike glycoprotein stands out as the largest. Importantly, individuals who have recovered from SARS-CoV-2 and COVID-19 were found to possess antibodies that target the spike glycoprotein. This article asserts that the vaccine presented in this study has the potential to elicit immune responses against previous variants, including the Omicron variant, as well as future variations. This is attributed to the utilization of a Java-based tool, which facilitated the identification of conserved epitopes with high immunogenicity scores, ensuring their non-toxic and non-allergenic properties. Our analysis provides strong evidence for the conservation of these epitopes across all coronavirus sequences detected in various countries since the beginning of the pandemic. The vaccine was subsequently constructed by integrating the identified conserved epitopes with linkers and adjuvants. The vaccine was subsequently evaluated through computational tests to assess their efficacy and performance.Communicated by Ramaswamy H. Sarma.

Mechanistic Approach for Protective Effect of ARA290, a Specific Ligand for the Erythropoietin/CD131 Heteroreceptor, against Cisplatin-Induced Nephrotoxicity, the Involvement of Apoptosis and Inflammation Pathways.

ARA 290, an 11-amino acid linear nonhematopoietic peptide derived from the three-dimensional structure of helix B of the erythropoietin (EPO), interacts selectively with the innate repair receptor (IRR) that arbitrates tissue protection. The aim of this study was to investigate the protective effects of ARA290 against cisplatin-induced nephrotoxicity. For this purpose, HEK-293 and ACHN cells were treated with ARA290 (50-400 nM) and cisplatin (2.5 µM) in pretreatment condition. Then, cytotoxicity, genotoxicity, oxidative stress parameters (ROS, GPx, SOD, and MDA), and inflammatory markers (TNFα, IL6, and IL1ß) were evaluated. Furthermore, apoptotic cell death was assessed via caspase-3 activity and tunnel assay. To determine the molecular mechanisms of the possible nephroprotective effects of ARA290, gene and protein expressions of TNFα, IL1ß, IL6, Caspase-3, Bax, and Bcl2 were evaluated by real-time PCR and western blot assay, respectively. The findings indicated that ARA290 significantly reduced the DNA damage parameters of comet assay and the frequency of micronuclei induced by cisplatin. Besides, ARA290 improved cisplatin-induced oxidative stress by reducing MDA/ROS levels and enhancing antioxidant enzyme levels. In addition, reduced levels of pro-inflammatory cytokines indicated that cisplatin-induced renal inflammation was mitigated upon the treatment with ARA290. Besides, ARA290 ameliorates cisplatin-induced cell injury by antagonizing apoptosis. Furthermore, the molecular findings indicated that gene and protein levels of TNFα, IL1ß, IL6, Caspase-3, and Bax were significantly decreased and gene and protein levels of Bcl2 significantly increased in the ARA290 plus cisplatin group compared with the cisplatin group. These findings revealed that ARA290 as a potent chemo-preventive agent exerted a protective effect on cisplatin-induced nephrotoxicity mostly through its anti-apoptotic, anti-inflammatory, and antioxidant potentials and also suggested that ARA290 might be a new therapeutic approach for patients with acute kidney injury.

The Effects of Quercetin on Apoptosis and Antioxidant Activity in a Renal Ischemia/Reperfusion Injury Animal Model.

Renal ischemia-reperfusion injury (IRI) is considered as one of the most prevalent causes of acute kidney injury (AKI), which can happen in various clinical situations including hypovolemic shock, injury, thrombo-embolism, and after a kidney transplant. This paper aims to evaluate the reno-protective effects of Quercetin in induced ischemia/reperfusion injury by regulating apoptosis-related proteins, inflammatory cytokines, MMP-2, MMP-9, and nuclear factor kappa-light-chain-enhancer inactivated B cells (NF-kB) in rats. The male Wistar rats (n=32) were randomly divided into Sham, untreated IR, and Quercetin-treated IR (gavage and intraperitoneal). Quercetin was given orally and intraperitoneally one hour before inducing ischemia-reperfusion injury . After reperfusion, blood samples and kidneys were collected to assess renal function and inflammatory cytokines, apoptotic signaling proteins, and antioxidants. Urea, creatinine, and MDA levels improved in Quercetin-treated groups with different administration methods. In addition, the activities of other antioxidant in Quercetin-treated rats were higher than those in the IR group. Further, Quercetin inhibited NF-kB signaling, apoptosis-associated factors and produced matrix metalloproteinase protein in the kidneys of rats. Based on the findings, the antioxidant, anti-inflammatory, and anti-apoptotic effects of the Quercetin diminished renal ischemia-reperfusion injury in the rats significantly. It is suggested that a single dosage of Quercetin have a reno-protective impact in the case of renal I/R injury.

Recent advancements to engineer mesenchymal stem cells and their extracellular vesicles for targeting and destroying tumors.

Mesenchymal stem cells (MSCs) have the ability to migrate into tumor sites and release growth factors to modulate the tumor microenvironment. MSC therapy have shown a dual role in cancers, promoting or inhibiting. However, MSCs could be used as a carrier of anticancer agents for targeted tumor therapy. Recent technical improvements also allow engineering MSCs to improve tumor-targeting properties, protect anticancer agents, and decrease the cytotoxicity of drugs. While some of MSC functions are mediated through their secretome, MSCs-derived extracellular vesicles (EVs) are also proposed as a possible viechle for cancer therapy. EVs allow efficient loading of anticancer agents and have an intrinsic ability to target tumor cells, making them suitable for targeted therapy of tumors. In addition, the specificity and selectivity of EVs to the tumor sites could be enhanced by surface modification. In this review, we addressed the current approaches used for engineering MSCs and EVs to effectively target tumor sites and deliver anticancer agents.

Circular RNAs in neuroblastoma: Pathogenesis, potential biomarker, and therapeutic target.

Neuroblastoma (NB) is a common cancer in childhood responsible for 15 % of fatalities by pediatric cancers. Epigenetic factors play an important role in the pathogenesis of NB. Recently, it has been demonstrated that circular RNAs (circRNAs, ciRNAs), a newly identified class of non-coding RNAs, are also dysregulated in NB. CircRNAs mediate their functions by regulating gene expression mainly through microRNA (miRNA) sponging. The dysregulation (abnormal upregulation or downregulation) of circRNAs is involved in tumorigenesis of a variety of tumors including NB. It seems that the expression of some circRNAs is correlated with NB prognosis and clinical features. CircRNAs might be favorable as a diagnostic/prognostic biomarker and therapeutic target. However, due to the lack of studies, it is difficult to make a conclusion regarding the clinical benefits of circRNAs. In this review, we discussed the circRNAs that experimentally have been proved to be dysregulated in NB tissues and cancer cells.