Orthosiphon aristatus (Blume) Miq. 1858 is a Lamiaceae plant. It is mainly found in southern China. It is an excellent medicinal plant. The complete chloroplast genome of O. aristatus is 152,155 bp in length, with an average depth of 287×, and the GC content was 37.86%, a large single-copy (LSC) region of 83,098 bp, a small single-copy (SSC) region of 17,665 bp, and an inverted repeats (IRs) region of 25,696 bp make up the genome's typical tetragonal shape. In addition, the genome consisted of 128 genes, including 85 protein-coding genes, 35 transfer RNA (tRNA), and eight ribosomal RNA (rRNA) genes. A monophyletic group was established by O. aristatus and 13 plants from five genera of Lamiaceae, according to the phylogenetic tree. In contrast, an isolated monophyletic group was formed by the alien plant Cinnamomum aromaticum. The ML tree bootstrap value was relatively high, and O. aristatus was most closely related to Ocimum tenuiflorum and Ocimum basilicum. This study can help with species identification and phylogenetic analysis within O. aristatus and Lamiaceae species.
Primulina hedyotidea (Woon Young Chun) Yin Zheng Wang 2011 is an important medicinal plant that has a long history of medicinal use in China. In this experiment, the whole chloroplast genome of P. hedyotidea was determined by next-generation sequencing technology. The total base length of P. hedyotidea was 153,297 bp, the GC content was 37.62%, the inverted repeat (IR) region length was 25,494 bp, the large single copy (LSC) region was 84,158 bp and the small single copy (SSC) region was 18,151 bp. In addition, the genome consisted of 80 protein-coding genes, 4 rRNA genes, and 28 tRNA genes, for a total of 112 genes. A phylogenetic tree was constructed to explore the evolutionary relationship between P. hedyotidea and other species. The findings of phylogenetic tree analysis show that Primulina huaijiensis and P. hedyotidea have a close relationship, and this study can help with species identification and phylogenetic analysis within Primulina and Gesneriaceae species.
Endometrial cancer (EC) is one of the most common cancers of the female reproductive system. Multi-epitope vaccine may be a promising and effective strategy against EC. In this study, we designed a novel multi-epitope vaccine based on the antigenic proteins PRAME and TMPRSS4 using immunoinformatics and bioinformatics approaches. After a rigorous selection process, 14 cytotoxic T lymphocyte (CTL) epitopes, 6 helper T lymphocyte (HTL) epitopes, and 8 B cell epitopes (BCEs) were finally selected for vaccine construction. To enhance the immunogenicity of the vaccine candidate, the pan HLA DR-binding epitope was included in the vaccine design as an adjuvant. The final vaccine construct had 455 amino acids and a molecular weight of 49.8 kDa, and was predicted to cover 95.03% of the total world population. Docking analysis showed that there were 10 hydrogen bonds and 19 hydrogen bonds in the vaccine-HLA-A*02:01 and vaccine-HLA-DRB1*01:01 complexes, respectively, indicating that the vaccine has a good affinity to MHC molecules. This was further supported by molecular dynamics (MD) simulation. Immune simulation showed that the designed vaccine was able to induce higher levels of immune cell activity, with the secretion of numerous cytokines. The codon adaptation index (CAI) value and GC content of the optimised codon sequences of the vaccine were 0.986 and 54.43%, respectively, indicating that the vaccine has the potential to be highly expressed. The in silico analysis suggested that the designed vaccine may provide a novel therapeutic option for the individualised treatment of EC patients in the future.Communicated by Ramaswamy H. Sarma.
Chikungunya virus (CHIKV), a type A virus borne by mosquitoes that can cause major clinical manifestations including rash, fever and debilitating arthritis, grown into a reemerging serious public health issue. Currently, there is no licensed therapy or vaccine available for CHIKV, although the most promising form of treatment appears to be immunotherapy. Neutralizing antibodies for CHIKV can provide high protection for all CHIKV strains, as well as other alphaviruses. Development of a protective vaccine may be an effective strategy to prevent the outbreak of CHIKV and provide protection for travelers. In this study, we designed a multi-epitope vaccine with a 543-amino-acid structure based on the E1, E2 and capsid proteins of CHIKV, including 6 CTL epitopes, 6 HTL epitopes, 12 linear B epitopes, along with the adjuvant ß-defensin III. All T-cell epitopes were docked with their corresponding MHC alleles to validate their effect on inducing immune responses, and the vaccine's sequence was proven to have acceptable physicochemical properties. Further, the developed vaccine was docked with TLR3 and TLR8, both of which play an important role in recognizing RNA viruses. Basic analyses of the docked complexes and molecular dynamic simulations revealed that the vaccine interacted strongly with TLRs. Immunological simulations indicated that the vaccine could induce both cellular and humoral immunity. Hopefully, this proposed vaccine structure can serve as a viable candidate against CHIKV infection.Communicated by Ramaswamy H. Sarma.
BACKGROUND: Immunotherapy is effective only in limited patients. It is urgent to discover a novel biomarker to predict immune cells infiltration status and immunotherapy response of different cancers. CLSPN has been reported to play a pivotal role in various biological processes. However, a comprehensive analysis of CLSPN in cancers has not been conducted. METHODS: To show the whole picture of CLSPN in cancers, a pan-cancer analysis was conducted in 9125 tumor samples across 33 cancer types by integrating transcriptomic, epigenomic and pharmacogenomics data. Moreover, the role of CLSPN in cancer was validated by CCK-8, EDU, colony formation and flow cytometry in vitro and tumor cell derived xenograft model in vivo. RESULTS: CLSPN expression was generally upregulated in most cancer types and was significantly associated with prognosis in different tumor samples. Moreover, elevated CLSPN expression was closely correlated with immune cells infiltration, TMB (tumor mutational burden), MSI (microsatellite instability), MMR (mismatch repair), DNA methylation and stemness score across 33 cancer types. Enrichment analysis of functional genes revealed that CLSPN participated in the regulation of numerous signaling pathways involved in cell cycle and inflammatory response. The expression of CLSPN in LUAD patients were further analyzed at the single-cell level. Knockdown CLSPN significantly inhibited cancer cell proliferation and cell cycle related cyclin-dependent kinase (CDK) family and Cyclin family expression in LUAD (lung adenocarcinoma) both in vitro and in vivo experiments. Finally, we conducted structure-based virtual screening by modelling the structure of CHK1 kinase domain and Claspin phosphopeptide complex. The top five hit compounds were screened and validated by molecular docking and Connectivity Map (CMap) analysis. CONCLUSION: Our multi-omics analysis offers a systematic understanding of the roles of CLSPN in pan-cancer and provides a potential target for future cancer treatment.
Background: Nocardia genus, a complex group of species classified to be aerobic actinomycete, can lead to severe concurrent infection as well as disseminated infection, typically in immunocompromised patients. With the expansion of the susceptible population, the incidence of Nocardia has been gradually growing, accompanied by increased resistance of the pathogen to existing therapeutics. However, there is no effective vaccine against this pathogen yet. In this study, a multi-epitope vaccine was designed against the Nocardia infection using reverse vaccinology combined with immunoinformatics approaches. Methods: First, the proteomes of 6 Nocardia subspecies Nocardia subspecies (Nocardia farcinica, Nocardia cyriacigeorgica, Nocardia abscessus, Nocardia otitidiscaviarum, Nocardia brasiliensis and Nocardia nova) were download NCBI (National Center for Biotechnology Information) database on May 1st, 2022 for the target proteins selection. The essential, virulent-associated or resistant-associated, surface-exposed, antigenic, non-toxic, and non-homologous with the human proteome proteins were selected for epitope identification. The shortlisted T-cell and B-cell epitopes were fused with appropriate adjuvants and linkers to construct vaccines. The physicochemical properties of the designed vaccine were predicted using multiple online servers. The Molecular docking and molecular dynamics (MD) simulation were performed to understand the binding pattern and binding stability between the vaccine candidate and Toll-like receptors (TLRs). The immunogenicity of the designed vaccines was evaluated via immune simulation. Results: 3 proteins that are essential, virulent-associated or resistant-associated, surface-exposed, antigenic, non-toxic, and non-homologous with the human proteome were selected from 218 complete proteome sequences of the 6 Nocardia subspecies epitope identification. After screening, only 4 cytotoxic T lymphocyte (CTL) epitopes, 6 helper T lymphocyte (HTL) epitopes, and 8 B cell epitopes that were antigenic, non-allergenic, and non-toxic were included in the final vaccine construct. The results of molecular docking and MD simulation showed that the vaccine candidate has a strong affinity for TLR2 and TLR4 of the host and the vaccine-TLR complexes were dynamically stable in the natural environment. The results of the immune simulation indicated that the designed vaccine had the potential to induce strong protective immune responses in the host. The codon optimization and cloned analysis showed that the vaccine was available for mass production. Conclusion: The designed vaccine has the potential to stimulate long-lasting immunity in the host, but further studies are required to validate its safety and efficacy.
Nocardia , Vaccinology , Humans , Molecular Docking Simulation , Vaccinology/methods , Proteome , Vaccines, Subunit , Epitopes, B-Lymphocyte , Epitopes, T-Lymphocyte , Molecular Dynamics Simulation
Staphylococcus aureus is an extraordinarily versatile pathogen, which is currently the most common cause of nosocomial and community infections. Considering that increased antibiotic resistance may hasten the spread of S. aureus, developing an effective vaccine can possibly aid in its control. The RNA vaccine coding immunodominance epitopes from bacteria provide a potential method to induce T and B cell immune responses by translating them into cells. Furthermore, using bioinformatics to create circular RNA vaccines can ensure that the translation of the vaccine is potent and durable. In this study, 7 cytotoxic T lymphocyte (CTL) epitopes, 4 helper T lymphocyte (HTL) epitopes, and 15 B cell epitopes from 6 proteins that are closely associated with the S. aureus virulence and invasion and critical to natural immune responses were mapped. To verify their interactions, all epitopes were docked with the corresponding MHC alleles. The final vaccine was composed of 26 epitopes and the adjuvant ß-defencin, and a disulfide bond was also introduced to improve its stability. After the prediction of structure and characteristics, the developed vaccine was docked with TLR2 and TLR4, which induce immunological responses in S. aureus infection. According to the molecular dynamic simulation, the vaccine might interact strongly with TLRs. Meanwhile, it performed well in immunological simulation and population coverage prediction. Finally, the vaccine was converted into a circular RNA using a series of helper sequences to aid in vaccine circulation translation. Hopefully, this proposed structure will be proven to serve a viable vaccine against S. aureus.Communicated by Ramaswamy H. Sarma.
RNA, Circular , Staphylococcus aureus , Staphylococcus aureus/genetics , RNA, Circular/genetics , Epitopes, T-Lymphocyte , Epitopes, B-Lymphocyte , Molecular Dynamics Simulation , Molecular Docking Simulation , Computational Biology/methods , Vaccines, Subunit
Human metapneumovirus (HMPV) is one of the main pathogens causing severe respiratory infections in children, as a common cause of immunodeficiency-related deaths in children and elderly individuals, the prevalence of HMPV has been showing an increasing trend during the last years. However, no vaccines or effective treatment plans are available currently. In this present, based on candidate proteins highly associated with viral virulence and has promising protective potential, we screened for immunodominant cytotoxic T cells, helper T cells, and Linear B-cell epitopes from the most promising candidate Fusion protein, together with G, SH, M, and M2. All epitopes were predicted to have strong antigenicity by Vaxijen and pose no potential toxicity, allergenicity, or hormonology to human proteins by Toxinpred, Allerpred, and Blast analysis, meanwhile, high conservancy is demanded to cover different subtypes. adjuvants ß-defensin II and Pam2Cys was attached with EAAAK linkers to improve vaccine's efficiency. Then, calculation of physicochemical properties proved the protein vaccine as a product can stably exist in the human body. Besides, we assessed the docking between the vaccine and immune receptors to evaluate its ability to stimulate immune responses, and the dynamic simulation further confirmed that the vaccine can tightly bind with immune receptors, which approved that the construction has the potential to induce strong humoral and cellular immune response. Finally, the vaccine was constructed into a multi-epitope mRNA vaccine, the immune simulations suggest that this is a vaccine candidate for controlling HMPV infection.
Metapneumovirus , Respiratory Tract Infections , Child , Humans , Aged , Metapneumovirus/genetics , mRNA Vaccines , Epitopes, B-Lymphocyte/genetics , T-Lymphocytes, Cytotoxic , Epitopes, T-Lymphocyte , Computational Biology , Vaccines, Subunit
Total flavonoids in Premna fulva Craib (TFPFC) are a kind of flavonoid compound synthesized via photosynthesis extracted from Premna fulva Craib, which possess a strong anti-oxidative effect. Cerebral Ischemia-Reperfusion refers to the body's damage mainly caused by oxidative stress. This study aims to investigate the alleviating effect of TFPFC on brain neurological impairment and its influences on Nuclear factor E2-related factor 2 (Nrf2) and heme oxygenase 1 (HO-1) expressions in rats with Ischemia-Reperfusion. The rat model of Ischemia-Reperfusion was established, and rats were treated with TFPFC or normal saline. At 24 h after reperfusion, the neurological score, volume of cerebral infarction and cerebral water content were analyzed in different groups. The influences of TFPFC treatment on the proliferative activity and apoptosis of oxygen and glucose deprivation/reoxygenation (OGD/R) neural stem cells were detected via methyl thiazolyl tetrazolium (MTT) assay and flow cytometry. Moreover, the malondialdehyde (MDA) level and superoxide dismutase (SOD) activity were measured to evaluate the oxidative stress effect. The influences of TFPFC treatment on the protein and messenger ribonucleic acid (mRNA) expressions of Nrf2 and HO-1 were analyzed using reverse transcription-polymerase chain reaction (RT-PCR) and Western blotting. The TFPFC treatment alleviated the neurological impairment in rats after Ischemia-Reperfusion and reduced the volume of cerebral infarction and cerebral edema status in rats with Ischemia-Reperfusion. TFPFC increased the proliferative activity of OGD/R neural stem cells and decreased damage and apoptosis. In addition, the TFPFC treatment reduced the MDA level, improved the SOD activity, and up-regulated the protein and mRNA expressions of Nrf2 and HO-1. The TFPFC treatment may improve oxidative damage and protect the nervous system through the up-regulation of expressions of transcription factors Nrf2 and HO-1.
Lamiaceae , Reperfusion Injury , Animals , Brain/metabolism , Cerebral Infarction , Flavonoids/pharmacology , Flavonoids/therapeutic use , Glucose/pharmacology , Heme Oxygenase-1/genetics , Heme Oxygenase-1/metabolism , Ischemia , Malondialdehyde , NF-E2-Related Factor 2/genetics , NF-E2-Related Factor 2/metabolism , Oxidative Stress , Oxygen , RNA/metabolism , RNA, Messenger/metabolism , Rats , Rats, Sprague-Dawley , Reperfusion , Reperfusion Injury/drug therapy , Reperfusion Injury/metabolism , Saline Solution/pharmacology , Superoxide Dismutase/metabolism , Water/pharmacology
The spinal cord injury is a site of severe central nervous system (CNS) trauma and disease without an effective treatment strategy. Neurovascular injuries occur spontaneously following spinal cord injury (SCI), leading to irreversible loss of motor and sensory function. Bone marrow mesenchymal stem cell (BMSC)-derived exosome-educated macrophages (EEM) have great characteristics as therapeutic candidates for SCI treatment. It remains unknown whether EEM could promote functional healing after SCI. The effect of EEM on neurovascular regeneration after SCI needs to be further explored. We generated M2-like macrophages using exosomes isolated from BMSCs, which were known as EEM, and directly used these EEM for SCI treatment. We aimed to investigate the effects of EEM using a spinal cord contusive injury mouse model in vivo combined with an in vitro cell functional assay and compared the results to those of a normal spinal cord without any biological intervention, or PBS treatment or macrophage alone (MQ). Neurological function measurements and histochemical tests were performed to evaluate the effect of EEM on angiogenesis and axon regrowth. In the current study, we found that treatment with EEM effectively promoted the angiogenic activity of HUVECs and axonal growth in cortical neurons. Furthermore, exogenous administration of EEM directly into the injured spinal cord could promote neurological functional healing by modulating angiogenesis and axon growth. EEM treatment could provide a novel strategy to promote healing after SCI and various other neurovascular injury disorders.
OBJECTIVE: To compare the efficacy and compliance of up-to-date disease modifying therapies (DMTs) in patients with remitting-relapsing MS (RRMS). METHODS: We searched PubMed, EMBASE and Cochrane Library for eligible studies. Annualized relapse rate, discontinuation due to adverse events (AEs) were assessed as primary outcomes. Sensitivity analysis and inconsistency detection were performed to evaluated whether exclusion of high-risk studies affected the validity. Risk of bias was assessed using Cochrane's Risk-of-Bias Tool 2. Surface under the cumulative ranking curve (SUCRA) was used to estimate the rankings among different DMTs. RESULTS: 21 studies were included for main report. Seven studies were evaluated as "high risk" and were therefore excluded. Exclusion of high-risk studies did not affect the validity of evidence. The risk of relapses for most DMTs except Betaseron 50 µg was significantly lower comparing to placebo. Incompliance in patients treated with DMTs was not significantly increased comparing to placebo. Dimethyl fumarate and ocrelizumab had superiority in improving MRI outcomes. Ocrelizumab and ofatumumab had the largest reduction of risk in disability progression at 3 months. Referring to SUCRA, ofatumumab, alemtuzumab and natalizumab showed the best efficacy and compliance. CONCLUSION: The present study demonstrated the hierarchy of DMTs treating RRMS. Ofatumumab, alemtuzumab and natalizumab have superiority with respect to effectiveness and compliance. More studies are required to explore the long-term effect of DMTs. Our findings could provide helpful information and contribute to clinical treatment decision-making.
Multiple Sclerosis, Relapsing-Remitting , Multiple Sclerosis , Humans , Immunologic Factors , Immunosuppressive Agents/therapeutic use , Multiple Sclerosis, Relapsing-Remitting/drug therapy , Natalizumab , Network Meta-Analysis
Spinal cord injury (SCI) is a catastrophic event mainly involving neuronal apoptosis and axonal disruption, and it causes severe motor and sensory deficits. Due to the complicated pathological process of SCI, there is currently still a lack of effective treatment for SCI. Microglia, a type of immune cell residing in the central nervous system (CNS), need to respond to various stimuli to protect neuronal cells from death. It was also reported that microRNAs (miRNAs) had been identified in microglia-derived exosomes that can be taken up by neurons. However, the kinds of miRNAs in exosome cargo derived from microglia and the underlying mechanisms by which they contribute to neuroprotection after SCI remain unknown. In the present study, a contusive SCI mouse model and in vitro experiments were applied to explore the therapeutic effects of microglia-derived exosomes on neuronal apoptosis, axonal regrowth, and functional recovery after SCI. Then, miRNA analysis, rescue experiments, and luciferase activity assays for target genes were performed to confirm the role and underlying mechanism of microglia-derived exosomal miRNAs in SCI. We revealed that microglia-derived exosomes could promote neurological functional recovery by suppressing neuronal apoptosis and promoting axonal regrowth both in vivo and in vitro. MicroRNA-151-3p is abundant in microglia-derived exosomes and is necessary for mediating the neuroprotective effect of microglia-derived exosomes for SCI repair. Luciferase activity assays reported that P53 was the target gene for miR-151-3p and that p53/p21/CDK1 signaling cascades may be involved in the modulation of neuronal apoptosis and axonal regrowth by microglia-derived exosomal microRNA-151-3p. In conclusion, our data demonstrated that microglia-derived exosomes (microglia-Exos) might be a promising, cell-free approach for the treatment of SCI. MicroRNA-151-3p is the key molecule in microglia-derived exosomes that mediates the neuroprotective effects of SCI treatments.
