Double-stranded Ribonucleic Acid Research Articles

Lipid Nanoparticles as a Platform for miRNA and siRNA Delivery in Hepatocellular Carcinoma.

Liver cancer is the sixth most common cancer and the fourth leading cause of death worldwide. Hepatocellular carcinoma (HCC) comprises 75-80% of liver cancer cases. Therapeutic strategies for HCC are available and have been shown to prolong survival but not treat HCC. Gene expression and regulation are responsible for the pathogenesis and progression of HCC. Altering these genetic networks can impact cellular behaviors and in turn cure HCC. Single-stranded and double-stranded non-coding ribonucleic acid known as microRNA and small interfering RNA, respectively have been investigated as possible therapeutic options. Currently, efficient delivery systems that ensure cell-specific targeting and efficient transfection into tumor cells are still under investigation. Viral vectors have been studied extensively, but immunogenicity hinders their use as delivery systems. Non-viral vectors which include inorganic, lipid, or polymeric nanoparticles are promising delivery systems. However, there are a lot of challenges during the formulation of such systems to ensure efficient and specific delivery. In vitro and in vivo studies have investigated different LNPs to deliver miRNA or siRNA. In this review, we highlight the role of LNPs as a delivery system for miRNA and siRNA in HCC in addition to the latest results achieved using this approach.

Melanoma differentiation-associated protein 5 prevents cardiac hypertrophy via apoptosis signal-regulating kinase 1–c-Jun N-terminal kinase/p38 signaling

Pathological cardiac hypertrophy (CH) is driven by maladaptive changes in myocardial cells in response to pressure overload or other stimuli. CH has been identified as a significant risk factor for the development of various cardiovascular diseases, ultimately resulting in heart failure. Melanoma differentiation-associated protein 5 (MDA5), encoded by interferon-induced with helicase C domain 1 (IFIH1), is a cytoplasmic sensor that primarily functions as a detector of double-stranded ribonucleic acid (dsRNA) viruses in innate immune responses; however, its role in CH pathogenesis remains unclear. Thus, the aim of this study was to examine the relationship between MDA5 and CH using cellular and animal models generated by stimulating neonatal rat cardiomyocytes with phenylephrine and by performing transverse aortic constriction on mice, respectively. MDA5 expression was upregulated in all models. MDA5 deficiency exacerbated myocardial pachynsis, fibrosis, and inflammation in vivo, whereas its overexpression hindered CH development in vitro. In terms of the underlying molecular mechanism, MDA5 inhibited CH development by promoting apoptosis signal-regulating kinase 1 (ASK1) phosphorylation, thereby suppressing c-Jun N-terminal kinase/p38 signaling pathway activation. Rescue experiments using an ASK1 activation inhibitor confirmed that ASK1 phosphorylation was essential for MDA5-mediated cell death. Thus, MDA5 protects against CH and is a potential therapeutic target.

Antiviral Activity of Double-Stranded Ribonucleic Acid and Interferon Alpha Composition in the Model of Experimental Influenza Infection of Mice

High variability of influenza viruses requires the development of agents for nonspecific resistance stimulation, along with the development of new drugs for prevention and treatment. Among the antiviral drugs, interferons and their inducers are known to exhibit a universally wide spectrum of action. The Institute of Medical Biotechnology, a branch of SRC VB «Vector», Rospotrebnadzor, has developed the technology and obtained pharmaceutical compositions containing an interferon inducer — double stranded ribonucleic acid (dsRNA) from the killer strain of Saccharomyces cerevisiae yeast and recombinant human interferon-alpha-2b (IFN- alpha-2b). The specific antiviral activity of the preparations and synergistic effect of the components within the compositions were shown in L-68 and L-929 cell cultures. The aim of this work was to study antiviral activity of intranasal forms of the pharmaceutical compositions containing yeast dsRNA and recombinant human interferon-alpha-2b in a model of lethal influenza infection in mice. The outbred ICR/CD1 mice were intranasally infected with influenza A/Aichi/2/68 (H3N2) virus. The study compositions were intranasally administered 3 hours before infection with influenza virus, as well as 1 and 3 days post infection. The doses of active components in the administered compositions were as follows: for dsRNA — 2.5 mg/kg, for IFN-alpha-2b — 500 IU/kg, 2500 IU/kg, or 5000 IU/kg. The antiviral activity of the drugs was assessed based on the mortality rate and the average life expectancy of mice. It was shown that a three-time intranasal administration of the composition of dsRNA (2.5 mg/kg) and IFN-alpha-2b (2500 IU) into the infected mice according to therapeutic-prophylactic regimen led to an increase in the rates of survival and average life expectancy of animals, which were comparable to the effect of Tamiflu. The comparison preparations — dsRNA and IFN-alpha-2b — administered intranasally at the same doses and regimen exerted no antiviral effect in this mouse model of viral infection. The data obtained confirm the prospects for further development of new dosage forms of dsRNA and interferons for intranasal application as agents for prevention and treatment of influenza.

Adenosine deaminase acting on RNA 1 (ADAR1) as crucial regulators in cardiovascular diseases: structures, pathogenesis, and potential therapeutic approach.

Cardiovascular diseases (CVDs) are a group of diseases that have a major impact on global health and are the leading cause of death. A large number of chemical base modifications in ribonucleic acid (RNA) are associated with cardiovascular diseases. A variety of ribonucleic acid modifications exist in cells, among which adenosine deaminase-dependent modification is one of the most common ribonucleic acid modifications. Adenosine deaminase acting on ribonucleic acid 1 (Adenosine deaminase acting on RNA 1) is a widely expressed double-stranded ribonucleic acid adenosine deaminase that forms inosine (A-to-I) by catalyzing the deamination of adenosine at specific sites of the target ribonucleic acid. In this review, we provide a comprehensive overview of the structure of Adenosine deaminase acting on RNA 1 and summarize the regulatory mechanisms of ADAR1-mediated ribonucleic acid editing in cardiovascular diseases, indicating Adenosine deaminase acting on RNA 1 as a promising therapeutic target in cardiovascular diseases.

Options for the development of colorectal cancer immunotherapy

In colorectal cancer immunotherapy, the use of antibodies against the PD-1/PD-L1 checkpoints showed low efficacy and the development of a number of side effects with damage to the liver, lung, and thyroid gland. For this reason, to stimulate the antitumor immune response, it is necessary to search for other targets, which can be used as retroelements. Epigenetic activation of their expression with inhibitors of histone methyltransferases and deoxyribonucleic acids (DNA) leads to the formation of double-stranded ribonucleic acids (RNA) that stimulate the antiviral response of interferon, which causes apoptosis of tumor cells. This method of viral mimicry shows an objective response in colorectal cancer and other malignant neoplasms. However, activation of retrotransposons is an inducer of carcinogenesis and a necessary condition for clonal evolution and the development of chemoresistance. Therefore, the most rational combination of the method of viral mimicry is with selective inhibition of retroelements involved in the pathogenesis of colorectal cancer. For this purpose, specific miRNAs, that recruit DNA methyltransferases to the loci of the location of retroelements due to the complementarity of nucleotide sequences, which is due to their evolutionary relationship, can be used. An analysis of the scientific literature revealed 28miRNAs derived from transposons and associated with colorectal cancer, some of which exhibit oncosuppressive activity, while others exhibit oncogenic activity. These miRNAs can be used as guides for epigenetic effects on retroelements involved in colorectal cancer carcinogenesis.

Coronavirus disease 2019 vaccines: challenges of using global mass vaccination to achieve herd immunity.

Coronavirus disease 2019 vaccines: challenges of using global mass vaccination to achieve herd immunity.

Double-stranded RNAs are promising adjuvants for enhancing immunogenicity of vaccines

Background. The most effective way to prevent infectious diseases is vaccination. Adjuvants contribute to the optimization of the immune response of vaccines. Double-stranded ribonucleic acids (dsRNAs) from natural sources are promising, but insufficiently studied adjuvants.
 The aim of the work was to study the adjuvant activity of dsRNA obtained from the killer strain of Saccharomyces cerevisiae using two models of induction of a specific immune response.
 Materials and methods. In the experiments, the substance of the drug Ridostin containing dsRNA, 21.72% (produced by Institute of Medical Biotechnology of the State Research Center of Virology and Biotechnology Vector), was used. A specific immune response was modeled using ovalbumin (OVA) or the substance of the EpiVacCorona vaccine (EVC). The experiments were carried out in 200 female BALB/c mice. Mice of the experimental groups were injected twice with antigen and adjuvant together with a 28-day interval, mice of the comparison group with antigen only. On the 10th day after the second immunization, blood samples were collected to determine the level of specific antibodies using enzyme immunoassay. The results were evaluated by calculation of the average geometric titers of specific antibodies against OVA or EVC.
 Results. OVA or EVC administered twice induced the specific antibodies in mice in dose-dependent titers. The combined administration of antigen and dsRNA increased the strength of the immune response. The highest stimulating effect of dsRNA was observed in the dose of 100 g/mouse administered into mice immunized with OVA (1 g/mouse) or in the dose of 50 g/mouse in mice immunized with EVC substance (0.25 of a human dose per mouse).
 Conclusion. The data obtained indicate that the substance of dsRNA exerts adjuvant properties, which gives reason to consider dsRNA as a promising adjuvant for peptide vaccines.

Study of RNA interference of HSPA1L in Acyrthosiphon pisum

Acyrthosiphon pisum, commonly known as pea aphids, are agricultural pests that cause billions in damage to crops, particularly Febaceae, also known as legumes. The goal of this study is to determine the relationship that exists between the concentration of dsRNA (double-stranded ribonucleic acid) and the survival of A. pisum.

Transport of double-stranded ribonucleic acids (dsRNA) and deoxyribonucleic acids (DNA) in sand and iron oxide-coated sand columns under varying solution chemistries.

Assessing ecological risks associated with the use of genetically modified RNA interference crops demands an understanding of the fate of crop-released insecticidal double-stranded RNA (dsRNA) molecules in soils. We studied the adsorption of one dsRNA and two double-stranded DNA as model nucleic acids (NAs) during transport through sand- and iron oxide-coated sand (IOCS)-filled columns over a range of solution pH and ionic compositions. Consistent with NA-sand electrostatic repulsion, we observed only slight retention of NAs in sand columns. Conversely, pronounced NA retention in IOCS columns is consistent with strong and irreversible NA adsorption involving electrostatic attraction to and inner-sphere complex formation of NAs with iron oxide coatings. Adsorption of NAs to iron oxides revealed a fast and a slow kinetic adsorption regime, possibly caused by the excluded-area effect. Adsorption of NAs to sand and IOCS increased in the presence of dissolved Mg2+ and with increasing ionic strength, reflecting cation-bridging and screening of repulsive electrostatics, respectively. The co-solute phosphate and a pre-adsorbed dissolved organic matter isolate competitively suppressed dsRNA adsorption to IOCS. Similar adsorption characteristics of dsRNA and similarly sized DNA suggest that existing information on DNA adsorption to soil particles helps in predicting adsorption and fate of dsRNA molecules in soils.

Study on Antiviral Activity and Pharmacological Safety of Double-Stranded Ribonucleic Acid for Intranasal Administration

Interferon inducers are of interest as the first line of defense against viral infections, including influenza. Double-stranded ribonucleic acid (dsRNA) for intranasal administration has been developed, the excipients and drug components were selected at the Institute of Medical Biotechnology, a branch of the State Research Center of Virology and Biotechnology «Vector». This work presents the results of the study on antiviral activity and pharmacological safety of a new form of dsRNA. The antiviral activity of the preparation was studied in BALB/c mice infected with influenza A/Aichi/2/68 (H3N2) or Bishkek/01/2009 (H1N1pdm09) viruses. A safety study was performed with a single administration of intranasal dsRNA into white outbred ICR mice. The study showed that the administration of therapeutic and prophylactic regimen of intranasal dsRNA at a dose of 2.5 mg/kg increases the survival and average life expectancy of mice infected with the mentioned strains of influenza virus. The protective effect of the preparation in mice infected with a lethal dose of Bishkek/01/2009 virus was comparable to the effect of Tamiflu. The absence of toxic effects of intranasal dsRNA at a pharmacological dose in laboratory mice, the functional state of their physiological systems, as well as main types of metabolism, established in the experiments, lead to a conclusion concerning pharmacological safety of the preparation and the prospects for further work to complete pharmaceutical development of a new antiviral drug.

Studying the effect of double-stranded RNA upon activity of mouse splenocytes using flow cytometry

Ribonucleic acids (RNA), in particular, double-stranded RNAs, due to their ability to modulate innate immune responses, are of undoubted interest in view of their usage as vaccine adjuvants. However, despite the fact that dsRNA preparations have been known for a long time, the issues of cellular interactions and orientation of immune response upon their exposure have not yet been properly studied. The aim of this work was to evaluate the in vitro response of mouse splenocytes to dsRNA exposure in cell cultures, and after drug administration in vivo. The studies were carried out in female Balb/c mice. Activation status of various splenocyte populations after treatment with yeast dsRNA and reference substance (PolyI:PolyC) was assessed by means of flow cytometry by expression of CD69 and CD86 activation markers on CD19+B lymphocytes and CD11c+ dendritic cells (DC). During in vitro studies, the splenocytes were incubated in DMEM medium containing 10% fetal calf serum for 22 hours following addition of the yeast dsRNA preparations, or PolyI:PolyC (2.5 μg/mL) preparation. Single-stranded high-polymer RNA (hpRNA), which is a component of the substance, was used as an additional control at the dose of 16 μg/mL. Our study has shown that the activating effect of dsRNA and PolyI:PolyC on expression of CD86 and CD69 markers upon the cells of the entire pool of splenocytes, B lymphocytes and DC. Highly polymeric RNA increased the total number of CD86+ cells in the population without changing the expression level of these markers upon B lymphocytes and DCs. When performing the in vivo studies, yeast dsRNA substance was administered intravenously into mice at a dose of 2.5 mg/kg, and hpRNA was used at a dose of 16 mg/kg. The number of CD69+ and CD86+ splenocytes was assessed 4 hours after drug administration. The highest stimulating effect of dsRNA was registered with CD69 expression marker: significantly increased numbers of CD69+ cells were registered for B lymphocytes and the entire cell population. The stimulation of CD86 co-receptor expression on B lymphocytes was less pronounced, but statistically significant. The ability of single-stranded and double-stranded RNAs to cause significant increase in CD86+ cell numbers was demonstrated among dendritic cell population. The results of the study made it possible to evaluate the effect of dsRNA on the immune cell function, with respect of their interaction, maturation, and migration. This approach may be useful for developing optimal strategies for selection and screening of new nucleic acid-based adjuvants.

Abstract IA012: Intratumoral activation of double-stranded RNA sensors induces systemic immune response to irradiated sarcoma

Abstract Background: Undifferentiated pleomorphic sarcoma (UPS) is a common aggressive sarcoma subtype for which existing therapies are ineffective. Immune checkpoint blockade (ICB) is effective in a minority of patients. Most UPS tumors have a predominantly myeloid infiltrate, a highly plastic cellular population with the potential to serve as a substrate for immunotherapy. Radiotherapy (RT), a standard therapy for UPS, can also drive myeloid cells into the tumor. Based on abundant expression of pattern recognition receptors (PRRs) by myeloid cells, we hypothesized that intratumoral injection of a PRR agonist would leverage pre-existing and RT-associated myeloid cells by redirecting them to prime adaptive anti-tumor immunity. Methods: We used BO-112, a nanoplexed double-stranded ribonucleic acid that activates PRRs, most of which are not typically activated by RT. We used an ICB-resistant mouse model, in which tumor cells derived from a KrasG12D/−P53−/− model of UPS are used to establish large tumors in flanks of C57BL/6J mice. Tumor-bearing mice were treated with RT (8 Gy x 3 fractions daily) ± BO-112 (30 ug/dose). Tumor volume and survival between groups were compared by ANOVA and log-rank test, respectively. To test the role of lymphocytes, the study was repeated in RAG−/−gc−/− mice. Kinetic analysis of myeloid and T cells was performed in the tumors and lymph nodes (LN) on days 15, 21, 26 using high-dimensional flow cytometry. To evaluate the fate of monocytes, LysM-eGFP monocytes were intratumorally transferred following treatment, with subsequent analysis of tumors and LNs on days 16, 18, 21. Results: We detected significantly improved tumor control starting from day 16 with mean tumor volume of 240 mm3 in the combination group compared to 490 mm3 in BO112, 790 mm3 in RT, and 875mm3 in mock groups (p<0.0001) which translated into a maximal survival advantage in the combination group (p<0.005), which was associated with both local and systemic increase in IFNg+ CD8 T cells. In RAG−/−gc−/− mice, the benefit of combination therapy was completely negated. Despite the lymphocyte-dependent effect, myeloid cells were preferentially targeted by BO-112. In the combination therapy group (compared to mock), we observed an early reduction in Ly6ChiMHCII+ cells (p<0.05) within the tumor followed by a progressive increase of the same population in the draining LN over time (p=0.01). In parallel, we observed trafficking of adoptively transferred intratumoral eGFP+ monocytes from the tumor to dLNs in response to BO-112 and RT. Conclusions: Local-only therapy of BO-112 and RT yields a lymphocyte-dependent anti-tumor immune response in an immunotherapy-resistant model of UPS. Longitudinal analysis of locoregional immune responses and adoptive transfer experiments indicate that combination BO-112 and RT induces tumor-to-dLN myeloid trafficking that may bridge an adaptive response and confer therapeutic effect. An ongoing phase 1 dose escalation study testing the combination of RT, BO-112 and nivolumab is currently accruing. Citation Format: Anusha Kalbasi. Intratumoral activation of double-stranded RNA sensors induces systemic immune response to irradiated sarcoma [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr IA012.

Abstract 3446: Radiation and intratumoral activation of double-stranded RNA sensors redirects myeloid cells and primes adaptive immunity

Abstract Background: Undifferentiated pleomorphic sarcoma (UPS) is a common aggressive sarcoma subtype for which existing therapies are ineffective. Immune checkpoint blockade (ICB) is effective in a minority of patients whose tumors harbor a pre-existing lymphocytic response. However, most UPS tumors have a myeloid infiltrate, a highly plastic cellular population with the potential to serve as a substrate for immunotherapy. Radiotherapy (RT), a standard therapy for UPS, can also drive myeloid cells into the tumor. Based on abundant expression of pattern recognition receptors (PRRs) by myeloid cells, we hypothesized that intratumoral injection of a PRR agonist would leverage pre-existing and RT-associated myeloid cells by redirecting them to prime adaptive anti-tumor immunity. Methods: We used BO-112, a nanoplexed double-stranded ribonucleic acid that activates PRRs, most of which are not typically activated by RT. We used an ICB-resistant mouse model, in which tumor cells derived from a KrasG12D/-P53-/- model of UPS are used to establish large tumors in flanks of C57BL/6J mice. Tumor-bearing mice were treated with RT (8 Gy x 3 fractions daily) starting on day 8 ± BO-112 (30 ug/dose) on days 8 and 10. Tumor growth and survival between groups were compared by ANOVA and log-rank test, respectively. To test the role of lymphocytes, the study was repeated in RAG-/-gc-/- mice. Kinetic analysis of myeloid and T cells was performed in the tumors and lymph nodes (LN) on days 15, 21, 26 using high-dimensional flow cytometry. To evaluate the fate of monocytes, LysM-eGFP monocytes were intratumorally transferred following treatment, with subsequent analysis of tumors and LNs on days 16, 18, 21. Results: Tumor control was significantly improved in the combination group starting from day 16 with mean tumor volume of 240 mm3 in the combination group compared to 490 mm3 in BO112, 790 mm3 in RT, and 875mm3 in mock groups (p<0.0001) which translated into a maximal survival advantage in the combination group (p<0.005). However, in RAG-/-gc-/- mice, this benefit of combination therapy was completely negated. This therapeutic combination appeared to drive an early reduction in Ly6ChiMHCII+ cells (p<0.05) within the tumor followed by a progressive increase of the same population in the draining LN over time (p=0.01). In parallel, we observed trafficking of adoptively transferred intratumoral eGFP+ monocytes from the tumor to dLNs in response to BO-112 and RT. Conclusions: Local-only therapy of BO-112 and RT yields a lymphocyte-dependent anti-tumor immune response in an immunotherapy-resistant model of UPS. Longitudinal analysis of locoregional immune responses and adoptive transfer experiments indicate that combination BO-112 and RT induces tumor-to-dLN myeloid trafficking that may bridge an adaptive response and confer therapeutic effect. Citation Format: Jie Deng, Scott C. Chin, Mito Tariveranmoshabad, Danielle S. Graham, Hailey R. Lee, Marisol Quintero, Dorthe Schaue, Anusha Kalbasi. Radiation and intratumoral activation of double-stranded RNA sensors redirects myeloid cells and primes adaptive immunity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3446.

Spotlight on Givosiran as a Treatment Option for Adults with Acute Hepatic Porphyria: Design, Development, and Place in Therapy.

Small interfering ribonucleic acids [siRNAs] are short ribonucleic acid (RNA) fragments cleaved from double-stranded RNA molecules that target and bind to specific sequences on messenger RNA (mRNA), leading to their destruction. Therefore, the siRNA down-regulates the formation of selected mRNAs and their protein products. Givosiran is one such siRNA that uses this mechanism to treat acute hepatic porphyrias. Acute hepatic porphyrias are a group of rare, inherited metabolic disorders, characterized by acute potentially life-threatening attacks as well as chronic symptoms with a negative impact on quality of life. It has four types, each associated with distinct enzyme defects in the heme biosynthesis pathway in the liver. By targeting the expression of hepatic 5-aminolevulinic acid [ALA] synthase-1 [ALAS1], givosiran can down-regulate levels of toxic metabolites, leading to biochemical and clinical improvement. Givosiran selectively targets hepatocytes due to its linkage to N-acetylgalactosamine (GalNac) leading to its selective uptake via asialoglycoprotein receptors (ASGPR). We provide an up-to-date literature review regarding givosiran in the context of a clinical overview of the porphyrias, an overview of siRNAs for therapy of human disorders, the design and development of givosiran, key clinical trial results of givosiran for prevention of acute porphyric attacks, emerging concerns regarding chronic use of givosiran, and the overall management of acute hepatic porphyrias. These insights are important not only for the management of acute hepatic porphyrias but also for the emerging field of siRNAs and their role in novel therapies for various diseases.

Application of Clustered Regularly Interspaced Short Palindromic Repeat—Cas12a System in Cancer Research and its Structural Basis

The clustered regularly interspaced short palindromic repeat-Cas12a (CRISPR-Cas12a) system is a new type of CRISPR-Cas system. As a unitary effector protein in this system, Cas12a recognizes 5’-TTTN-3’ protospacer-adjacent motif and exhibits cleavage activity of double-stranded deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), supplementing the toolbox of CRISPR system. Compared to CRISPR-Cas9 system, CRISPR-Cas12a system has the advantage of high specificity, which is a promising tool for genetic manipulation in the basic cancer research and clinical cancer therapy. To date, three Cas12a proteins including Acidaminococcus sp. Cas12a (AsCas12a), Francisella novicida Cas12a (FnCas12a), and Lachnospiraceae bacterium Cas12a (LpCas12a) have been applied in transcriptional regulation or genome editing through CRISPR RNAs complementary to target DNA or RNA in cancer cells or immune cells. This review summarizes the latest applications of CRISPR-Cas12a system in cancer research and its structural basis.

ZBP1 is a significant pyroptosis regulator for systemic lupus erythematosus.

BackgroundSystemic lupus erythematosus (SLE) is a common autoimmune disease that affects all organs. Recently, several studies have shown that pyroptosis playsa significant process in the occurrence and progression of SLE. However, no study has investigated the association between pyroptosis genes and SLE. We conducted this study to examine this association.MethodsThe GSE11090, GSE20864, and GSE112087 gene microarrays of normal and SLE patient samples were downloaded from the Gene Expression Omnibus database. A differentially expressed gene (DEG) analysis was performed using the LIMMA package in R software. Log2 fold change |logFC| >0.5 and a false discovery rate (FDR) <0.05 setting for DEGs’ screening value. We also performed an enrichment function analysis of the DEGs. To explore the role of pyroptosis genes in SLE, we selected pyroptosis genes that intersected with the DEGs for further analysis, we also examined the expression levels of the selected genes, their association with immune cell infiltration, and conducted western blotting and polymerase chain reaction analyses to confirm the selected genes expression levels in the SLE and normal samples.ResultsA total of 3,398 identical genes were obtained from 3 datasets for the differential analysis. 84 upregulated genes and 52 downregulated genes were identified in SLE. The enrichment function analysis revealed that DEGs act as key regulators of nicotinamide adenine dinucleotide (NADH) dehydrogenase activity, phospholipid scramblase activity, double-stranded ribonucleic acid (RNA) binding, and the interferon signaling pathway. We identified the SLE-related pyroptosis gene, Z-DNA binding protein 1 (ZBP1), by intersecting the DEGs of SLE and 40 pyroptosis genes. The differential analysis indicated that ZBP1 was more highly expressed in SLE patients compared to normal samples (P<0.001). Additionally, the expression of ZBP1 was higher in females than males (P=0.008). The SLE samples had different immune cell infiltration than the normal samples, and ZBP1 was significantly correlated with immune cell infiltration in the SLE samples. Finally, the validation experiments results showed that ZBP1 expression levels were significantly more highly expressed in female and SLE patients, than male and normal patients.ConclusionsZBP1 may indicate that females have a high incidence rate of SLE, and it plays a significant role in the occurrence and progression of SLE.

Analysis of avian Usutu virus infections in Germany from 2011 to 2018 with focus on dsRNA detection to demonstrate viral infections

Usutu virus (USUV) is a zoonotic arbovirus causing avian mass mortalities. The first outbreak in North-Western Germany occurred in 2018. This retrospective analysis focused on combining virological and pathological findings in birds and immunohistochemistry. 25 common blackbirds, one great grey owl, and one kingfisher collected from 2011 to 2018 and positive for USUV by qRT-PCR were investigated. Macroscopically, most USUV infected birds showed splenomegaly and hepatomegaly. Histopathological lesions included necrosis and lymphohistiocytic inflammation within spleen, Bursa fabricii, liver, heart, brain, lung and intestine. Immunohistochemistry revealed USUV antigen positive cells in heart, spleen, pancreas, lung, brain, proventriculus/gizzard, Bursa fabricii, kidney, intestine, skeletal muscle, and liver. Analysis of viral genome allocated the virus to Europe 3 or Africa 2 lineage. This study investigated whether immunohistochemical detection of double-stranded ribonucleic acid (dsRNA) serves as an alternative tool to detect viral intermediates. Tissue samples of six animals with confirmed USUV infection by qRT-PCR but lacking viral antigen in liver and spleen, were further examined immunohistochemically. Two animals exhibited a positive signal for dsRNA. This could indicate either an early state of infection without sufficient formation of virus translation products, occurrence of another concurrent virus infection or endogenous dsRNA not related to infectious pathogens and should be investigated in more detail in future studies.

Parameter Optimization of dsRNA Splicing Evolutionary Algorithm Based Fixed-Time Obstacle-Avoidance Trajectory Planning for Space Robot

This paper addresses a smoother fixed-time obstacle-avoidance trajectory planning based on double-stranded ribonucleic acid (dsRNA) splicing evolutionary algorithm for a dual-arm free-floating space robot, the smoothness of large joint angular velocity is improved by 15.61% on average compared with the current trajectory planning strategy based on pose feedback, and the convergence performance is improved by 76.44% compared with the existing optimal trajectory planning strategy without pose feedback. Firstly, according to the idea of pose feedback, a novel trajectory planning strategy with low joint angular velocity input is proposed to make the pose errors of the end-effector and base converge asymptotically within fixed time. Secondly, a novel evolutionary algorithm based on the gene splicing idea of dsRNA virus is proposed to optimize the parameter of the fixed-time error response function and obstacle-avoidance algorithm, which can make joint angular velocity trajectory is planned smooth. In the end, the optimized trajectory planning strategy is applied into the dual-arm space robot system so that the robotic arm can smoothly, fast and accurately complete the tracking task. The proposed novel algorithm achieved 7.56–30.40% comprehensive performance improvement over the benchmark methods, experiment and simulation verify the effectiveness of the proposed method.

Development and Modification of Pre-miRNAs with a FRET Dye Pair for the Intracellular Visualization of Processing Intermediates That Are Generated in Cells.

microRNAs (miRNAs) are small non-coding ribonucleic acids (RNAs), which regulate gene expression via the RNA interference (RNAi) system. miRNAs have attracted enormous interest because of their biological significance and disease relationship. In cell systems, the generation of miRNA is regulated by multiple steps: the transfer of primary miRNA from the nucleus to the cytosol, the generation of the precursor-miRNA (pre-miRNA), the production of double-stranded RNA from pre-miRNA by the Dicer, the interaction with protein argonaute-2 (AGO2), and the subsequent release of one strand to form miRISC with AGO2. In this study, we attempt to visualize the intermediates that were generated in the miRNA-maturation step in the cells to acquire a detailed understanding of the maturation process of miRNA. To achieve this, we developed pre-miRNAs labeling with a Dicer- or AGO2-responsible fluorescence resonance energy transfer (FRET) dye pair. We observed that modifications with the dye at suitable positions did not interfere with the biological activities of pre-miRNAs. Further, imaging analyses employing these pre-miRNAs demonstrated that the processing of pre-miRNA promoted the accumulation of miRNA at the specific foci in the cytosol. The FRET-labeled pre-miRNA would further elucidate the mechanisms of the RNAi process and provide the basis for development of nucleic acid drugs working in the RNAi system.

Reaction Coordinate and Thermodynamics of Base Flipping in RNA.

Base flipping is a key biophysical event involved in recognition of various ligands by ribonucleic acid (RNA) molecules. However, the mechanism of base flipping in RNA remains poorly understood, in part due to the lack of atomistic details on complex rearrangements in neighboring bases. In this work, we applied transition path sampling (TPS) methods to study base flipping in a double-stranded RNA (dsRNA) molecule that is known to interact with RNA-editing enzymes through this mechanism. We obtained an ensemble of 1000 transition trajectories to describe the base-flipping process. We used the likelihood maximization method to determine the refined reaction coordinate (RC) consisting of two collective variables (CVs), a distance and a dihedral angle between nucleotides that form stacking interactions with the flipping base. The free energy profile projected along the refined RC revealed three minima, two corresponding to the initial and final states and one for a metastable state. We suggest that the metastable state likely represents a wobbled conformation of nucleobases observed in NMR studies that is often characterized as the flipped state. The analyses of reactive trajectories further revealed that the base flipping is coupled to a global conformational change in a stem-loop of dsRNA.